2014-06-12 18:36  pawel

	* sparx/libpy/: applications.py, isac.py: [no log message]

2014-06-12 16:52  jgalaz

	* programs/e2spt_classaverage.py: Negative values allowed on plots
	  now.

2014-06-12 16:36  jgalaz

	* programs/e2spt_hac.py: ranking.txt files produced after each
	  iteration now.

2014-06-12 14:49  scmurray

	* programs/e2version.py: Changed to Beta 3

2014-06-12 14:20  stevel

	* libpyEM/qtgui/emimage3diso.py: Working on color display problem
	  on mac. not fixed

2014-06-12 13:54  pawel

	* sparx/libpy/applications.py: [no log message]

2014-06-12 13:24  pawel

	* sparx/libpy/applications.py: [no log message]

2014-06-12 12:58  stevel

	* programs/: e2ctf.py, e2proc2d.py: outmode warning

2014-06-12 12:01  scmurray

	* programs/e2import.py: Made a fix for importing tilted and
	  untilted boxes

2014-06-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-06-11 18:12  jgalaz

	* examples/e2spt_tomosimjobs.py: Multiple model functionality was
	  broken (meaning that this can generate simulated particles
	  automatically for EACH file within an HDF stack with a single
	  run)

2014-06-11 18:11  jgalaz

	* programs/e2spt_simulation.py: Can't remember what changed.

2014-06-11 18:10  jgalaz

	* programs/e2spt_hac.py: Bug with --maxmergenum fixed.
	  Dendrogram.txt file cleaned up.

2014-06-11 17:40  vern

	* programs/e2proc2d.py: Changed one case missed from earlier today,
	  cleaned up a little.

2014-06-11 16:54  pawel

	* sparx/libpy/: alignment.py, applications.py: [no log message]

2014-06-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-06-11 08:23  vern

	* programs/e2proc2d.py: Added options --outmode and --outnorescale
	  (taken from e2proc3d.py).

2014-06-10 22:34  pawel

	* sparx/libpy/applications.py: more cleanning of nomirror

2014-06-10 22:04  pawel

	* sparx/libpy/isac.py: date updated

2014-06-10 17:58  pawel

	* sparx/libpy/: applications.py, isac.py: Corrected serious mistake
	  in ISAC

2014-06-10 17:03  vern

	* programs/e2ddd_movie.py: Prevented zero divisions by sigma by
	  using 1 instead, gave warnings, cleaned up a little.

2014-06-10 16:00  stevel

	* programs/e2parallel.py: properly disabled dc mode in e2parallel

2014-06-10 12:31  jgalaz

	* programs/e2spt_classaverage.py: [no log message]

2014-06-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-06-09 18:39  jgalaz

	* programs/: e2spt_classaverage.py, e2spt_hac.py: [no log message]

2014-06-09 16:37  vern

	* libEM/mrcio.cpp: Add "minimum" and "maximum" to the file header
	  dictionary, in addition to "MRC.minimum" and "MRC.maximum".

2014-06-09 16:05  pawel

	* libEM/emdata_metadata.cpp: cleaned compilation warnings

2014-06-09 15:51  pawel

	* libEM/sparx/util_sparx.cpp: util_sparx.cpp

2014-06-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-06-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-06-07 13:04  pawel

	* sparx/bin/sxprocess.py: rotpw added

2014-06-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-06-06 14:35  vern

	* libpyEM/qtgui/emimagemx.py: When scaling stack plots in file
	  browser, used 0 for min and max (for defaults) if none found.

2014-06-06 13:24  jgalaz

	* examples/e2melonball.py: Program to scoop melonballs out of 3D
	  maps and orient them to the symmetry axis.

2014-06-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-06-06 03:19  vern

	* libpyEM/qtgui/emimagemx.py: Made a kludgy compensation for
	  MRC/MRCS header missing items named 'minimum' and 'maximum' when
	  scaling stack plots (they use MRC.minimum and MRC.maximum
	  instead).

2014-06-05 21:01  pawel

	* libEM/sparx/util_sparx.cpp, sparx/libpy/alignment.py,
	  sparx/libpy/applications.py, sparx/libpy/multi_shc.py,
	  sparx/libpy/pixel_error.py, sparx/libpy/utilities.py: [no log
	  message]

2014-06-05 18:09  jgalaz

	* programs/e2spt_classaverage.py: Bugs bugs bugs bugs bugs (with
	  formatting of parameters file and parsing of --search and
	  --searchfine and --align and --falign)

2014-06-05 18:02  jgalaz

	* programs/e2spt_hac.py: *Sigh*

2014-06-05 13:58  stevel

	* programs/e2refine_easy.py: Help update

2014-06-05 13:28  stevel

	* programs/e2plotFSC.py: Fix help display

2014-06-05 12:59  stevel

	* programs/e2evalrefine.py: New options in e2evalrefine

2014-06-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-06-05 11:03  stevel

	* programs/e2refine_easy.py: oops

2014-06-05 10:59  stevel

	* programs/e2refine_easy.py: Better options for speed=6 or 7

2014-06-05 10:30  stevel

	* programs/e2refine_easy.py: new option for disabling refine
	  aligner

2014-06-05 10:03  stevel

	* programs/e2refine_easy.py: another little fix

2014-06-05 08:52  stevel

	* libpyEM/qtgui/embrowser.py, programs/e2refine_easy.py: Few more
	  tweaks to gui for beta3

2014-06-05 08:28  stevel

	* programs/: e2initialmodel.py, e2rawdata.py, e2refine_easy.py:
	  trivial fixes to gui

2014-06-05 07:54  stevel

	* programs/e2import.py: crasher in box import

2014-06-04 16:27  stevel

	* programs/e2ctf.py: Fix non-gui mode

2014-06-04 15:02  scmurray

	* programs/e2proc2d.py: Made a change to handle files being labeled
	  as ".mrcs". Before, e2proc2d.py was hardcoded to use only the
	  last 3 characters of the filename but now it checks for .mrcs
	  extensions specifically. In the future, if an extension isnt
	  exactly 3 characters, it will have to be added specifically too.

2014-06-04 14:27  stevel

	* programs/e2import.py: Syntax error fix

2014-06-04 14:25  vern

	* libEM/mrcio.cpp: Stopped checking for image index out of bounds
	  for an MRC stack.

2014-06-04 14:00  vern

	* libEM/emutil.cpp: Make sure image type is set before checking
	  whether image can be written to.

2014-06-04 12:26  scmurray

	* programs/e2emx.py: Made changes to --export_whole_project (added
	  support to export files as .mrcs files)

2014-06-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-06-03 19:57  vern

	* libEM/: emutil.cpp, mrcio.h, mrcio.cpp: Allowed new mrcs (mrc
	  stack) image format (essentially a reinterpretation of the mrc
	  format as an image stack).

2014-06-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-06-03 01:20  jgalaz

	* programs/e2spt_hac.py: Unnecessary imports eliminated.
	  Infrequently used imports relocated to within the function(s)
	  where they are used.

2014-06-03 00:55  jgalaz

	* examples/e2spt_transformdistance.py: It took me (unfortunately)
	  QUITE A WHILE to figure out how to do it: The program can
	  *finally* take into account symmetry related positions to
	  accurately calculate the angular error in alignment for simulated
	  data (before, there was no accounting for the fact that the
	  alignment program could find symmetry-related solutions that made
	  the angular error appear much larger).

2014-06-02 17:26  pawel

	* sparx/libpy/pixel_error.py: [no log message]

2014-06-02 16:58  jgalaz

	* programs/: e2spt_classaverage.py, e2spt_hac.py: [no log message]

2014-06-02 16:00  jgalaz

	* programs/: e2spt_classaverage.py, e2spt_hac.py: Nomeclature bugs
	  and fixes regarding --search and --searchfine overwriting search:
	  provided through the aligners.

2014-06-02 13:33  pawel

	* sparx/libpy/: alignment.py, applications.py: [no log message]

2014-06-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-06-01 23:11  stevel

	* programs/e2make3dpar.py: In thoery this should reduce problems
	  with smearing in 3d reconstruction. Not sure it's quite right
	  yet.

2014-06-01 14:32  stevel

	* programs/e2make3dpar.py: Working on smearing improvement

2014-06-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-31 12:12  pawel

	* sparx/libpy/: pixel_error.py, utilities.py: [no log message]

2014-05-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-31 09:57  pawel

	* sparx/libpy/: multi_shc.py, utilities.py: [no log message]

2014-05-30 15:02  stevel

	* programs/e2refine_easy.py:
	  oops

2014-05-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-30 11:06  stevel

	* programs/e2ctf.py: Error in inverting _hp particles in ctf
	  generate output

2014-05-30 10:25  stevel

	* programs/: e2evalimage.py, e2rawdata.py: oops

2014-05-30 10:19  stevel

	* programs/: e2evalimage.py, e2rawdata.py: Patch to add options for
	  using folder name as part of image filename

2014-05-30 09:56  stevel

	* programs/e2version.py: new version tag

2014-05-30 09:03  stevel

	* programs/e2refine_easy.py: Fix stringent dependency on matplotlib

2014-05-29 23:08  stevel

	* programs/e2evalimage.py: improve import naming ?

2014-05-29 15:12  pawel

	* programs/e2bdb.py: [no log message]

2014-05-29 14:49  scmurray

	* programs/: e2RCTboxer.py, e2tiltvalidate.py: Changed to fix an
	  issue with tilt particle naming

2014-05-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-29 11:37  stevel

	* libEM/: reconstructor.cpp, reconstructor.h: back_projection
	  reconstructor works. Of course it doesn't work well, but at least
	  it doesn't crash.

2014-05-29 11:13  pawel

	* sparx/bin/sxcter.py: [no log message]

2014-05-29 10:06  pawel

	* sparx/bin/sxheader.py: [no log message]

2014-05-29 09:40  pawel

	* sparx/bin/sx_real.py: [no log message]

2014-05-28 22:24  stevel

	* programs/e2_real.py: Hmm... this may be better

2014-05-28 22:19  stevel

	* examples/extracthelp.py, programs/e2_real.py, programs/e2ctf.py,
	  programs/e2initialmodel.py: Fixed problem with e2.py GUI in
	  certain situations.

2014-05-28 18:52  pawel

	* sparx/libpy/multi_shc.py: added increased neighberhood, bsoft =
	  2*nsoft

2014-05-28 18:42  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-05-28 18:35  jgalaz

	* programs/e2spt_hac.py: [no log message]

2014-05-28 18:30  jgalaz

	* programs/e2spt_classaverage.py: Bug fixes regarding --search and
	  --searchfine; better parameter definition too. Fixed --plotccc
	  parameter (which wasn't functional). Other changes probably
	  related to recent changes in e2spt_hac.py since the two are
	  closely related (they use each other's functions).

2014-05-28 18:28  jgalaz

	* programs/e2spt_hac.py: Multiple week-long changes requested by
	  Michele concerning new parameters such as --minscore to disallow
	  mergers that are lower than a certain percentage of the best
	  score so far, and --maxmergenum, to disallow inter-mergers
	  between large classes.  Also corrected nomeclature for
	  simmmx_plot_info.txt files, as well as dendrogram.txt files.

2014-05-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-27 14:07  stevel

	* examples/extracthelp.py, programs/e2version.py: version update

2014-05-27 13:53  pawel

	* sparx/bin/sxprocess.py: [no log message]

2014-05-27 13:47  stevel

	* programs/e2refine_easy.py: Trivial

2014-05-27 13:08  stevel

	* examples/extracthelp.py, programs/e2refine_easy.py: Another tiny
	  doc tweak

2014-05-27 13:07  pawel

	* sparx/bin/sx_real.py: [no log message]

2014-05-27 12:50  pawel

	* programs/e2bdb.py, sparx/bin/sx_real.py, sparx/bin/sxprocess.py,
	  sparx/libpy/utilities.py: [no log message]

2014-05-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-27 11:19  stevel

	* programs/e2_real.py: Improvement to e2.py to automatically
	  disable graphics

2014-05-27 10:24  stevel

	* programs/e2refine_easy.py: More report parameters.

2014-05-26 23:44  stevel

	* programs/e2refine_easy.py: error in resolution computation

2014-05-26 23:39  stevel

	* programs/e2refine_easy.py: A few more verbose comments

2014-05-26 23:30  stevel

	* programs/e2refine_easy.py: tweak display

2014-05-26 23:12  stevel

	* programs/e2refine_easy.py: typo

2014-05-26 23:09  stevel

	* libpyEM/qtgui/emplot2d.py, programs/e2boxer21.py,
	  programs/e2proc3d.py, programs/e2refine_easy.py: Significant
	  improvements to refinement report.

2014-05-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-26 10:36  pawel

	* sparx/bin/sxprocess.py: [no log message]

2014-05-25 20:21  pawel

	* doc/build/install.sh, libEM/sparx/util_sparx.cpp,
	  sparx/bin/sx_real.py, sparx/libpy/global_def.py: sparx startup
	  changes

2014-05-25 13:38  pawel

	* libEM/sparx/util_sparx.cpp: corrected soft

2014-05-25 13:05  pawel

	* libEM/sparx/util_sparx.cpp, sparx/libpy/multi_shc.py: [no log
	  message]

2014-05-25 12:46  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-05-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-24 16:57  pawel

	* sparx/: bin/sxcter.py, bin/sxprocess.py, libpy/morphology.py,
	  libpy/multi_shc.py: start working on cter import

2014-05-24 16:06  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2014-05-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-24 11:48  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-05-24 10:29  pawel

	* sparx/libpy/utilities.py: [no log message]

2014-05-23 17:15  jgalaz

	* programs/e2spt_classaverage.py: Many bug fixes. parameters.txt
	  correctly written now. Program exits if incorrect parameters are
	  supplied using the grid aligner, etc.

2014-05-23 16:20  vern

	* libEM/glutil.cpp: Attempted fix for histogram zooming crash;
	  initialized p to 0 in pixel averaging - was unset but used as an
	  array index, may have picked up garbage and gone out of bounds.

2014-05-23 15:07  vern

	* libEM/glutil.cpp: More debugging for histogram crash.

2014-05-23 14:57  pawel

	* sparx/bin/sx_real.py: [no log message]

2014-05-23 14:50  pawel

	* sparx/bin/sx.py: new sx.py

2014-05-23 14:48  pawel

	* sparx/bin/: sxshiftali.py, sx_real.py: [no log message]

2014-05-23 14:42  vern

	* libEM/glutil.cpp: More debugging for histogram crash.

2014-05-23 14:00  stevel

	* programs/: e2ctf.py, e2make3dpar.py, e2refine_easy.py: Tweaks to
	  make3dpar

2014-05-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-23 10:15  scmurray

	* libpyEM/qtgui/emrctboxergui.py, libpyEM/qtgui/emrctstrategy.py,
	  programs/e2RCTboxer.py: Added some Comments

2014-05-23 10:10  scmurray

	* programs/e2RCTboxer.py: Fixed. Can now box tilt particles. Can
	  also extract particles and box files. All updated to work with
	  EMAN2.1

2014-05-22 17:22  vern

	* libEM/glutil.cpp: More debugging for histogram crash.

2014-05-22 16:47  vern

	* libEM/glutil.cpp: More debugging for histogram crash.

2014-05-22 15:37  scmurray

	* doc/build/install.sh, libpyEM/qtgui/emrctboxergui.py,
	  programs/e2RCTboxer.py: Fixing ipytho issues and updating to
	  EMAN2.1

2014-05-22 14:47  stevel

	* programs/e2make3dpar.py: Tweaking angular sampling again

2014-05-22 13:44  stevel

	* programs/e2make3dpar.py: make3dpar adjustment in fill step

2014-05-22 13:33  stevel

	* libpyEM/EMAN2jsondb.py: Fix setdefault, added getdefault

2014-05-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-21 16:23  scmurray

	* libEM/pmconfig/spr.json, programs/e2RCTboxer.py: Added the
	  RCTBoxer to the workflow and fixed it (mostly). Right now it cant
	  "write boxes" but it can "write ptcls". It boxes just fine now
	  too. Still a work in progress overall so no announcement yet

2014-05-21 12:21  scmurray

	* doc/build/install.sh: Fixed to find new ipython and automatically
	  change its python

2014-05-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-21 11:17  pawel

	* sparx/libpy/: morphology.py, multi_shc.py: [no log message]

2014-05-20 17:52  vern

	* libEM/glutil.cpp: Debug version to help solve Gaussian histogram
	  crash on CentOS Linux.

2014-05-20 16:10  scmurray

	* libEM/pmconfig/spr.json, programs/e2RCTboxer.py,
	  programs/e2rct.py: Fixed e2rct.py to be updated to EMAN2.1 (and
	  some old logic errors...). e2RCTboxer.py is next to be fixed but
	  not fixed yet.

2014-05-20 15:31  stevel

	* programs/e2projectupdate21.py: Projectupdate improvements

2014-05-20 14:26  scmurray

	* libEM/pmconfig/spr.json, programs/e2emx.py,
	  programs/e2tiltvalidate.py: Updated e2tiltvalidate.py to work
	  with EMAN version 2.1 and added more support for emx file
	  passing.

2014-05-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-19 15:10  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-05-19 13:08  pawel

	* sparx/libpy/: multi_shc.py, sparx.py, utilities.py: [no log
	  message]

2014-05-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-18 20:34  stevel

	* programs/e2make3dpar.py: in-between step size, since the smaller
	  size did seem to make some improvement.

2014-05-18 16:37  stevel

	* examples/e2fscallxtal.py, programs/e2make3dpar.py,
	  programs/e2proc3d.py, programs/e2refine_easy.py: Made new
	  e2make3dpar the default. m3dold disables. Fixed serious bug which
	  meant it wasn't actually doing the desired averaging before.

2014-05-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-17 11:45  pawel

	* sparx/: bin/sxisac.py, libpy/isac.py: candidatesexist

2014-05-17 02:14  stevel

	* programs/e2ctf.py: e2ctf work

2014-05-17 00:11  stevel

	* examples/extracthelp.py, programs/e2ctf.py: ctf to permit
	  simulated data

2014-05-16 21:48  jgalaz

	* programs/e2spt_classaverage.py: Nasty bug fixed. --repreprocessed
	  was explicitly needed if --shrink or --shrinkrefine were used,
	  otherwise the alignments were garbage because the reference was
	  NOT being shrunk by default to match the particles if
	  --refpreprocess was not specified.  Normally, this would have
	  made the program crash in the past, but recently EMAN2 took up
	  allowing the computation of CC maps even between two differently
	  sized volumes (this was not true before).

2014-05-16 14:37  stevel

	* programs/e2buildstacks.py: Added buildstacks (corrected)

2014-05-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-15 19:38  stevel

	* programs/e2buildstacks.py: rewrote e2buildstacks.py

2014-05-15 18:28  pawel

	* sparx/libpy/: multi_shc.py, utilities.py: [no log message]

2014-05-15 17:42  pawel

	* libEM/sparx/util_sparx.cpp, libpyEM/libpyUtils2.cpp,
	  sparx/libpy/alignment.py, sparx/libpy/multi_shc.py: [no log
	  message]

2014-05-15 17:01  scmurray

	* programs/e2emx.py: Brand new program that uses the emx (Electron
	  Microscopy Exchange) format that is being developed by Roberto
	  and Jose Maria Corazo in Spain. As of now, it will import box
	  coordinates, particles, and/or ctf information. It will also
	  export the contents of an EMAN2 directort into a folder called
	  emx that contains anything that emx can use as a standard input.
	  Beware that this is all experimental at the moment. It works but
	  its likely to be changed often.

2014-05-15 14:40  pawel

	* libEM/sparx/util_sparx.cpp, sparx/libpy/alignment.py: [no log
	  message]

2014-05-15 13:27  jgalaz

	* examples/e2fixheaderparam.py: "tag_originalfile" is now
	  functional and added to particle headers if --addfilename is
	  supplied.  Also, --input=string*mrc can stack MRC files with a
	  common string into an HDF stack.

2014-05-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-14 23:07  stevel

	* programs/e2markbadparticles.py: starting new program

2014-05-14 12:50  stevel

	* programs/e2classaverage.py: Fixed final alignment problem in
	  class-averaging

2014-05-14 12:28  stevel

	* programs/e2refinemulti.py: Similar orientation fix for
	  e2refinemulti to get to 90 degrees

2014-05-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-14 10:16  stevel

	* programs/e2refine_easy.py: last patch was incomplete

2014-05-14 08:57  stevel

	* programs/e2refine_easy.py: Trivial patch to new normalization
	  scheme.

2014-05-13 23:20  stevel

	* programs/e2project3d.py: Better normalization for e2project3d.py

2014-05-13 18:37  stevel

	* programs/: e2refine_easy.py, e2refinemulti.py: Possible fix for
	  e2refinemulti

2014-05-13 13:48  stevel

	* programs/: e2classaverage.py, e2make3dpar.py, e2refine_easy.py:
	  Working on normalization in new make3dpar processing

2014-05-13 13:29  scmurray

	* libEM/: processor.cpp, processor.h: Added a Radius option to the
	  normalize.circlemean processor

2014-05-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-12 16:22  pawel

	* libEM/sparx/util_sparx.cpp, sparx/libpy/multi_shc.py: [no log
	  message]

2014-05-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-12 10:49  scmurray

	* programs/e2refinetorelion2d.py: Added some normalization to make
	  it happier with Relion

2014-05-12 09:47  stevel

	* programs/: e2import.py, e2make3dpar.py: Oops in e2import

2014-05-11 14:15  stevel

	* programs/e2help.py: trivial

2014-05-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-11 10:53  pawel

	* sparx/libpy/multi_shc.py, libEM/sparx/util_sparx.cpp: [no log
	  message]

2014-05-10 14:04  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-05-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-09 17:28  pawel

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, sparx/libpy/alignment.py,
	  sparx/libpy/multi_shc.py, sparx/libpy/utilities.py: all peaks
	  local

2014-05-09 17:25  vern

	* libpyEM/qtgui/empmtabwidgets.py: Enabled use of file filtering in
	  all variations on the file browser.

2014-05-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-08 13:42  pawel

	* sparx/libpy/reconstruction.py: [no log message]

2014-05-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-07 17:39  pawel

	* libEM/sparx/util_sparx.cpp, sparx/libpy/multi_shc.py,
	  sparx/libpy/projection.py, sparx/libpy/utilities.py: [no log
	  message]

2014-05-07 14:31  vern

	* libpyEM/qtgui/embrowser.py: For the browser filter default items
	  drop down, moved 'help' and 2 other new items to end of list, to
	  prevent help coming up automatically in some instances, as the
	  first item.

2014-05-07 14:06  stevel

	* libpyEM/libpyReconstructor2.cpp, programs/e2make3dpar.py:
	  Threading working in e2make3dpar now

2014-05-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-07 11:42  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2014-05-07 11:08  pawel

	* libEM/sparx/util_sparx.cpp: cleaned util

2014-05-07 10:54  pawel

	* libEM/reconstructor.cpp: mult -> weight

2014-05-07 07:51  stevel

	* examples/mergeproject2.py, libEM/reconstructor.cpp,
	  programs/e2make3dpar.py: Fix minor issue with bad assert in
	  reconstructor

2014-05-06 22:57  stevel

	* libpyEM/libpyReconstructor2.cpp, programs/e2make3dpar.py,
	  programs/e2refine_easy.py: make3dpar seems to be working. Added
	  option to e2refine_easy for testing.

2014-05-06 16:21  pawel

	* libEM/sparx/util_sparx.cpp, sparx/libpy/multi_shc.py,
	  sparx/libpy/reconstruction.py: no message

2014-05-06 16:19  muyuanc

	* programs/e2pathwalker.py: support LKH 2.0.7

2014-05-06 15:12  pawel

	* libEM/sparx/util_sparx.cpp, sparx/libpy/multi_shc.py,
	  sparx/libpy/reconstruction.py, sparx/libpy/user_functions.py: no
	  message

2014-05-06 14:11  pawel

	* sparx/: bin/sxali3d.py, libpy/multi_shc.py: no message

2014-05-06 13:24  vern

	* libpyEM/qtgui/embrowser.py: Replace pop up with print to screen
	  when file filtering is not implemented.

2014-05-06 13:04  pawel

	* sparx/libpy/reconstruction.py: no message

2014-05-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-05 23:20  stevel

	* programs/e2make3dpar.py: almost working :^)

2014-05-05 15:00  pawel

	* programs/e2refine_easy.py, sparx/bin/sxprocess.py: no message

2014-05-05 12:08  scmurray

	* programs/: e2refinetofrealign.py, e2runfrealign.py: Modified to
	  fix some issues

2014-05-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-05 11:38  stevel

	* programs/: e2buildsets.py, e2make3dpar.py: make3dpar work.
	  incomplete

2014-05-04 23:12  stevel

	* programs/e2make3dpar.py: Work in progress (new make3d)

2014-05-04 21:51  stevel

	* programs/: e2mak3dpar.py, e2make3dpar.py: oops. wrong name

2014-05-04 21:49  stevel

	* programs/: e2classaverage.py, e2mak3dpar.py, e2refine_easy.py,
	  e2reliontoeman.py: Fix to deal with images in subdirectories i
	  ne2reliontoeman. first version of e2make3dpar

2014-05-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-02 17:10  pawel

	* sparx/libpy/reconstruction.py: no message

2014-05-02 16:21  pawel

	* sparx/libpy/reconstruction.py: no message

2014-05-02 16:02  pawel

	* libEM/reconstructor.cpp, sparx/libpy/applications.py,
	  sparx/libpy/reconstruction.py: no message

2014-05-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-05-01 11:41  pawel

	* sparx/libpy/: applications.py, reconstruction.py: no message

2014-05-01 10:49  pawel

	* sparx/libpy/applications.py: no message

2014-05-01 10:40  stevel

	* libpyEM/EMAN2jsondb.py, programs/e2ddd_movie.py,
	  programs/e2import.py, programs/e2projectupdate21.py: Fix for
	  importing with blank lines. Issues with unicode in project
	  update. More movie alignment tweaks

2014-05-01 10:16  pawel

	* libEM/reconstructor.cpp, libEM/sparx/util_sparx.cpp,
	  sparx/libpy/reconstruction.py: no message

2014-04-30 12:04  pawel

	* libEM/sparx/emdata_sparx.cpp, sparx/libpy/reconstruction.py: no
	  message

2014-04-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-30 11:24  pawel

	* sparx/bin/sxviper.py: no message

2014-04-30 11:08  pawel

	* sparx/bin/: sxviper.py: no message

2014-04-30 10:20  pawel

	* libEM/cmp.cpp, libEM/reconstructor.cpp,
	  libEM/sparx/emdata_sparx.cpp, libEM/sparx/fundamentals.cpp,
	  sparx/libpy/reconstruction.py: no message

2014-04-30 08:30  stevel

	* programs/e2ddd_movie.py: Changed option naming in ddd_movie

2014-04-30 08:27  stevel

	* programs/e2ddd_movie.py: Will now read MRC stacks.

2014-04-29 17:11  vern

	* libpyEM/qtgui/embrowser.py: Expand any environment variables in a
	  file path.

2014-04-29 17:04  vern

	* libpyEM/qtgui/expand_string.py: Made more efficient and clear by
	  removing some unnecessary variables and a concatenation loop.

2014-04-29 16:37  vern

	* libEM/tifio.cpp: Allowed reading tiff files with multiple images.

2014-04-29 16:35  vern

	* libEM/tifio.h: Added field nimg for number of times and method
	  get_nimg to return it, for processing tiff files with multiple
	  images.

2014-04-29 14:41  stevel

	* programs/e2ddd_movie.py: trivial

2014-04-29 14:24  stevel

	* libEM/xydata.cpp, libEM/xydata.h, libpyEM/libpyCmp2.cpp,
	  programs/e2ddd_movie.py: Better whole-frame ddd alignment

2014-04-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-27 22:57  stevel

	* CMakeLists.txt, programs/e2boxer21.py: Writing a new version of
	  e2boxer. The existing version is responsible for far too many
	  complaints.

2014-04-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-26 15:43  pawel

	* sparx/bin/: sxprocess.py: no message

2014-04-26 15:30  pawel

	* sparx/libpy/reconstruction.py: no message

2014-04-26 14:47  pawel

	* libEM/sparx/emdata_sparx.cpp, sparx/libpy/applications.py,
	  sparx/libpy/reconstruction.py, sparx/libpy/utilities.py: no
	  message

2014-04-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-25 16:47  pawel

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  sparx/bin/sxrecons3d_n.py, sparx/libpy/reconstruction.py: no
	  message

2014-04-25 12:06  stevel

	* libpyEM/EMAN2PAR.py, libpyEM/mpi_eman.py, programs/e2parallel.py,
	  programs/e2project3d.py: New MPI code is working, at least on
	  single nodes

2014-04-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-25 11:01  stevel

	* examples/mpi_test.py, libpyEM/EMAN2PAR.py: Another minor patch

2014-04-25 10:45  stevel

	* examples/mpi_test.py, libpyEM/EMAN2PAR.py, libpyEM/mpi_eman.py:
	  making progress on new mpi

2014-04-25 09:36  stevel

	* libpyEM/: EMAN2.py, EMAN2PAR.py, mpi_eman.py: Simplifying and
	  revamping MPI module. testing...

2014-04-25 06:45  stevel

	* libpyEM/EMAN2PAR.py: oops

2014-04-25 02:38  vern

	* libpyEM/qtgui/embrowser.py: Fixed bug when filtering not allowed,
	  made sure browser path not blank, cleaned up to make more
	  readable.

2014-04-24 22:33  stevel

	* libpyEM/EMAN2PAR.py, programs/e2parallel.py: Work on mpi... still
	  broken

2014-04-24 13:30  pawel

	* libEM/sparx/emdata_sparx.cpp, sparx/bin/sxrecons3d_n.py,
	  sparx/libpy/applications.py: no message

2014-04-24 12:03  stevel

	* libpyEM/EMAN2PAR.py, programs/e2ddd_movie.py: Working on MPI
	  improvements

2014-04-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-24 11:58  pawel

	* sparx/libpy/applications.py: no message

2014-04-24 10:36  pawel

	* sparx/demo/mpi_bdb/run_through_example: [no log message]

2014-04-24 10:34  pawel

	* sparx/demo/mpi_bdb_ctf/run_through_example: no message

2014-04-23 19:17  vern

	* libpyEM/qtgui/expand_string.py: Removed an incorrect comment and
	  an unused constant.

2014-04-23 18:53  vern

	* libpyEM/qtgui/embrowser.py: Fixed glitch in file filtering
	  (needed to strip file name off path when filtering).

2014-04-23 17:55  vern

	* libpyEM/qtgui/embrowser.py: Overwrite last version (a test
	  version loaded by accident when checking in a new file).

2014-04-23 17:07  vern

	* libpyEM/qtgui/: embrowser.py, expand_string.py: New function to
	  return a string with any environment variables in it filled in.

2014-04-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-22 17:30  pawel

	* libEM/sparx/emdata_sparx.cpp: no message

2014-04-22 17:17  pawel

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/fourierfilter.cpp,
	  libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, sparx/bin/sx3dvariability.py,
	  sparx/libpy/applications.py: no message

2014-04-22 13:56  stevel

	* programs/: e2ctf.py, e2ddd_movie.py, e2reliontoeman.py:
	  reliontoeman working. more improvements on ddd_movie

2014-04-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-21 17:54  vern

	* libpyEM/qtgui/matching.py: functions for wildcard pattern
	  matching

2014-04-21 17:52  vern

	* libpyEM/qtgui/embrowser.py: Enhanced file filter in browser to
	  allow wildcard patterns in addition to regular expressions.

2014-04-21 12:26  pawel

	* libEM/sparx/emdata_sparx.cpp: scalecor

2014-04-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-20 20:59  stevel

	* libpyEM/libpyEMData2.cpp: Fixed bug in pawel's new routine

2014-04-20 20:15  pawel

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/libpyEMData2.cpp: broken after I added scale_factors

2014-04-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-19 16:59  pawel

	* sparx/libpy/morphology.py: [no log message]

2014-04-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-18 15:44  pawel

	* sparx/bin/sxfilterlocal.py: [no log message]

2014-04-18 15:27  pawel

	* sparx/bin/sxfilterlocal.py: [no log message]

2014-04-18 15:12  pawel

	* sparx/bin/sxfilterlocal.py: local filter

2014-04-18 14:25  stevel

	* libpyEM/EMAN2star.py, programs/e2reliontoeman.py: Starting on
	  Relion conversion script

2014-04-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-18 10:00  stevel

	* libpyEM/EMAN2star.py: This version of the STAR reader deals with
	  some outliers in specific implementations.

2014-04-17 23:37  stevel

	* libpyEM/EMAN2star.py: STAR reader now seems to read MMCIF files
	  correctly.

2014-04-17 15:57  stevel

	* libpyEM/EMAN2star.py: New STAR file parser. Reading working but
	  poorly tested. Writing not implemented yet.

2014-04-17 13:16  pawel

	* sparx/libpy/utilities.py: [no log message]

2014-04-17 12:17  eman-vm

	* programs/e2version.py: new date stamp

2014-04-17 12:11  eman-vm

	* programs/e2version.py: new date stamp

2014-04-16 18:54  stevel

	* programs/e2reliontoeman.py: New program to convert relion
	  refinements into eman2 refinements

2014-04-16 11:51  stevel

	* libpyEM/mpi_eman.py: again

2014-04-16 11:49  stevel

	* libpyEM/mpi_eman.py: More mpi work

2014-04-16 09:40  stevel

	* examples/mpi_test.py, libpyEM/mpi_eman.py: Working on MPI

2014-04-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-15 10:17  stevel

	* libpyEM/EMAN2PAR.py, programs/e2ddd_movie.py: Quick mpi patch

2014-04-14 14:43  vern

	* libEM/sparx/util_sparx.cpp: Fixed nonstandard usage that broke
	  Windows builds (changed 'not' to '!').

2014-04-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-14 09:57  stevel

	* programs/e2ddd_movie.py: oops. alignment was broken

2014-04-14 09:04  stevel

	* programs/: e2ddd_movie.py, e2projectupdate21.py,
	  e2refine_easy.py: Added --thread option to e2refine_easy to deal
	  with mpi issues when making projections

2014-04-13 22:54  stevel

	* libEM/xydata.cpp, programs/e2ddd_movie.py: ddd_movie working
	  pretty well, but needs more testing

2014-04-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-11 19:55  vern

	* libEM/glutil.cpp: Fixed rotation and translation of 3d image
	  crash on Windows, cleaned up a lot.

2014-04-11 14:56  stevel

	* programs/e2ddd_movie.py: more ddd work

2014-04-11 13:57  stevel

	* libEM/xydata.cpp, libpyEM/EMAN2.py, libpyEM/EMAN2db.py,
	  libpyEM/EMAN2jsondb.py, programs/e2ddd_movie.py,
	  programs/e2display.py, programs/e2speedtest.py: non-gui display()
	  fix. more ddd work

2014-04-10 14:38  stevel

	* libEM/xydata.cpp, libEM/xydata.h, libpyEM/libpyCmp2.cpp: Added
	  some basic interpolation capabilities to XYData. May add splines
	  or somesuch later on.

2014-04-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-09 17:05  pawel

	* sparx/libpy/reconstruction.py: no message

2014-04-09 16:30  pawel

	* libEM/reconstructor.cpp, libEM/sparx/emdata_sparx.cpp,
	  sparx/libpy/applications.py, sparx/libpy/reconstruction.py: no
	  message

2014-04-09 13:58  stevel

	* libpyEM/qtgui/emboxerbase.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emsave.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emtprworkflow.py, programs/e2RCTboxer.py,
	  programs/e2buildstacks.py, programs/e2ctf2eman1.py,
	  programs/e2ddd_movie.py, programs/e2display.py,
	  programs/e2eulerxplor.py, programs/e2history.py,
	  programs/e2resolution.py, programs/e2tomoaverage.py: A few 2.1
	  general fixes, and more playing with DDD

2014-04-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-09 09:54  pawel

	* sparx/libpy/: fundamentals.py, morphology.py, reconstruction.py,
	  utilities.py: no message

2014-04-08 23:12  stevel

	* programs/e2ddd_movie.py: Still working on ddd

2014-04-08 17:08  pawel

	* sparx/libpy/morphology.py: no message

2014-04-08 15:47  vern

	* libpyEM/qtgui/embrowser.py: Seeded the file name field in the
	  Save As dialog box with the current file name.

2014-04-08 14:39  stevel

	* TODO, programs/e2ddd_movie.py: movie work

2014-04-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-07 15:56  pawel

	* sparx/libpy/applications.py: no message

2014-04-07 15:51  pawel

	* sparx/libpy/: applications.py, reconstruction.py: no message

2014-04-07 14:13  pawel

	* libEM/reconstructor.cpp, libEM/sparx/emdata_sparx.cpp,
	  sparx/libpy/reconstruction.py, sparx/libpy/statistics.py: no
	  message

2014-04-07 14:04  stevel

	* programs/: e2.py, e2_real.py: Finally! e2.py now works with
	  (only) more up to date ipython releases

2014-04-07 13:23  pawel

	* libEM/reconstructor.cpp, sparx/libpy/applications.py,
	  sparx/libpy/reconstruction.py, libEM/reconstructor.h,
	  libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h: no
	  message

2014-04-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-06 22:46  stevel

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  programs/e2ddd_movie.py: Reverting some of Pawel's changes which
	  weren't quite working

2014-04-06 16:10  stevel

	* libEM/: reconstructor.cpp, reconstructor.h: another little fix

2014-04-06 13:22  stevel

	* libEM/: reconstructor.cpp, reconstructor.h: Fix broken
	  reconstructor

2014-04-06 12:31  pawel

	* libEM/: reconstructor.cpp, reconstructor.h,
	  sparx/emdata_sparx.cpp, sparx/emdata_sparx.h: HELP I borke it

2014-04-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-05 15:08  pawel

	* libEM/reconstructor.cpp, libEM/sparx/util_sparx.cpp,
	  sparx/libpy/projection.py, sparx/libpy/reconstruction.py: no
	  message

2014-04-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-04 16:09  vern

	* libEM/dm4io.cpp: flipped image read vertically, cleaned up a
	  little

2014-04-04 15:08  vern

	* libEM/dm3io.cpp: flipped image read vertically (apparently been
	  reversed for years), removed fread compiler warnings, generally
	  cleaned up

2014-04-04 14:47  stevel

	* TODO, libEM/processor.h, programs/e2ddd_movie.py,
	  programs/e2proc2d.py, programs/e2symsearch3d.py, pyemtbx/box.py:
	  ddd_movie work. New mode not functional yet, but old modes should
	  be fine still

2014-04-04 12:36  pawel

	* sparx/libpy/morphology.py: no message

2014-04-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-03 16:05  pawel

	* libEM/sparx/util_sparx.cpp, sparx/libpy/applications.py: no
	  message

2014-04-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-03 11:53  pawel

	* sparx/libpy/alignment.py: no message

2014-04-03 11:46  pawel

	* libEM/sparx/util_sparx.cpp: no message

2014-04-03 11:34  pawel

	* libEM/reconstructor.cpp, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h, libpyEM/libpyTransform2.cpp,
	  sparx/libpy/alignment.py, sparx/libpy/applications.py: no message

2014-04-03 10:10  spatel

	* sparx/bin/: sxviper.py, sxwindow.py: Minor changes.

2014-04-02 15:38  pawel

	* libEM/marchingcubes.cpp: =- corrected

2014-04-02 14:20  pawel

	* libEM/: emdata.cpp, emdata.h, emdata_metadata.h,
	  emdata_transform.cpp: annoying warnings removed

2014-04-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-01 19:06  pawel

	* sparx/libpy/: pixel_error.py, utilities.py: no message

2014-04-01 13:21  scmurray

	* doc/build/build.py: Made some changes to get the source upload
	  working

2014-04-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-04-01 10:56  scmurray

	* programs/e2refinetorelion3d.py: test

2014-03-31 14:41  scmurray

	* programs/e2refinetofrealign.py: Little Fix

2014-03-31 14:17  spatel

	* sparx/bin/sxwindow.py: Adding sxwindow.py

2014-03-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-31 10:31  pawel

	* sparx/bin/sxlocal_ali3dm.py: no message

2014-03-31 10:24  pawel

	* libEM/sparx/util_sparx.cpp, sparx/bin/sxmulti_assign.py,
	  sparx/libpy/applications.py: no message

2014-03-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-29 11:54  pawel

	* sparx/libpy/pixel_error.py: [no log message]

2014-03-28 18:21  pawel

	* sparx/libpy/filter.py: no message

2014-03-28 16:08  spatel

	* libpyEM/qtgui/emboxerbase.py: Reverting my changes.

2014-03-28 16:01  spatel

	* programs/e2boxer.py: Reverting my changes.

2014-03-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-27 15:28  pawel

	* sparx/bin/sxprocess.py: no message

2014-03-27 14:30  spatel

	* sparx/demo/mpi_bdb/run_through_example: Fixing
	  run_through_example

2014-03-27 13:51  pawel

	* sparx/libpy/morphology.py: no message

2014-03-27 12:25  pawel

	* sparx/libpy/utilities.py: no message

2014-03-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-27 11:19  pawel

	* sparx/bin/sxali2d.py: no message

2014-03-27 10:55  pawel

	* sparx/: bin/sxplot_projs_distrib.py, libpy/applications.py,
	  libpy/projection.py: no message

2014-03-27 10:35  spatel

	* sparx/bin/sxviper.py: Minor changes to fix checking for number of
	  processes allowed.

2014-03-26 22:19  jgalaz

	* programs/: e2spt_boxer.py, e2spt_classaverage.py,
	  e2spt_simulation.py: [no log message]

2014-03-26 17:28  pawel

	* sparx/libpy/fundamentals.py: no message

2014-03-26 17:08  pawel

	* sparx/libpy/fundamentals.py: no message

2014-03-26 15:37  spatel

	* sparx/bin/: sxcter.py, sxviper.py: 1) Adding checks to number of
	  processes for scviper.py 2) Combining all CTF info into one file.

2014-03-26 14:28  pawel

	* sparx/libpy/multi_shc.py: no message

2014-03-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-26 09:50  pawel

	* sparx/libpy/multi_shc.py: no message

2014-03-26 01:22  jgalaz

	* programs/e2spt_tiltstacker.py: [no log message]

2014-03-25 21:19  jgalaz

	* examples/e2spt_extract_align.py: Program REDONE entirely with
	  EXPANDED capabilities, including generating a .json file from
	  aligned particles, or an average from raw particles iif a .json
	  file is provided. Symmetry can be imposed on the fly. Probably
	  --keep should also be implemented here.

2014-03-25 13:39  pawel

	* sparx/libpy/isac.py: no message

2014-03-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-24 10:33  spatel

	* libpyEM/EMAN2.py, sparx/bin/sxprocess.py: 1) Fixing import errors
	  in sxprocess 2) Make code more readable.

2014-03-24 04:27  irees

	* doc/build/build.py: Require absolute path to build root

2014-03-24 04:23  irees

	* doc/build/build.py: Added SourceTarget for building from source
	  code.

2014-03-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-21 19:29  jgalaz

	* programs/e2spt_classaverage.py: [no log message]

2014-03-21 19:06  vern

	* libpyEM/qtgui/embrowser.py: Called sys.stdout.flush() after
	  printing message to terminal to make sure it shows up
	  immediately.

2014-03-21 19:03  jgalaz

	* programs/e2spt_hac.py: --clipali was broken.

2014-03-21 19:03  jgalaz

	* programs/e2spt_classaverage.py: --clipali was actually broken.
	  Redesigned the preprocessing function ENTIRELY to eliminate
	  redundancies and fix the --clipali bug. (Took more time than
	  expected; and this nasty bugs was responsible for all failed bugs
	  during the past week or so...).

2014-03-21 18:59  vern

	* libEM/glutil.cpp: Tweaked the changes of earlier today to call
	  setbuf(stdout,NULL) to make sure warning messages get printed
	  immediately.

2014-03-21 16:46  vern

	* libEM/glutil.cpp: Added to the changes of earlier today (to
	  prevent Windows rotation crashes), had left out some.

2014-03-21 15:24  pawel

	* sparx/libpy/multi_shc.py: no message

2014-03-21 15:23  vern

	* libEM/glutil.cpp: Prevent crash on Windows if routine
	  glMultTransposeMatrixf to rotate or translate an object is
	  missing.

2014-03-21 15:01  spatel

	* libpyEM/qtgui/emboxerbase.py, programs/e2boxer.py: 1) Remove
	  particle write when Gauss is selected.  2) Remove CTF estimation
	  from boxing tool Gauss.

2014-03-21 14:07  spatel

	* sparx/bin/sxprocess.py: Fixing import error for parsemodopt

2014-03-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-19 15:51  pawel

	* sparx/libpy/utilities.py: [no log message]

2014-03-19 15:14  pawel

	* sparx/libpy/pixel_error.py: [no log message]

2014-03-19 14:52  pawel

	* sparx/libpy/utilities.py: [no log message]

2014-03-19 14:43  pawel

	* sparx/libpy/: pixel_error.py, utilities.py: [no log message]

2014-03-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-18 10:53  pawel

	* sparx/libpy/applications.py: [no log message]

2014-03-17 23:36  jgalaz

	* programs/: e2spt_classaverage.py, e2spt_hac.py: --clipali
	  parameter introduced to make the box used for alignment smaller,
	  while keeping the larger original box for averaging.

2014-03-17 12:36  stevel

	* programs/e2classifyligand.py: Stripped out unnecessary code.
	  Focuses on the one method that actually works. Needs a bit more
	  cleanup still.

2014-03-17 12:27  pawel

	* sparx/demo/: mpi_bdb/run_through_example,
	  mpi_bdb_ctf/run_through_example: [no log message]

2014-03-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-16 22:30  jgalaz

	* programs/e2spt_tiltstacker.py: --unstack was buggy

2014-03-16 17:04  jgalaz

	* programs/e2spt_hac.py: --autocenterpreprocess was buggy

2014-03-16 14:46  jgalaz

	* programs/e2spt_simulation.py: Nasty typo!

2014-03-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-15 17:08  pawel

	* sparx/libpy/utilities.py: [no log message]

2014-03-15 16:51  pawel

	* sparx/bin/: sxmulti_shc.py, sxviper.py: [no log message]

2014-03-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-14 16:44  vern

	* libpyEM/qtgui/embrowser.py: Displayed error messages from saving
	  image files in modal dialog boxes.

2014-03-14 14:19  vern

	* libpyEM/qtgui/embrowser.py: When saving an image file, checked
	  whether it has a valid extension.

2014-03-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-12 17:46  jgalaz

	* programs/e2spt_tiltstacker.py: [no log message]

2014-03-12 17:45  jgalaz

	* programs/e2spt_tiltstacker.py: Latest changes fully debugged
	  (presumably).

2014-03-12 17:16  jgalaz

	* programs/e2spt_tiltstacker.py: [no log message]

2014-03-12 17:06  jgalaz

	* programs/e2spt_tiltstacker.py: [no log message]

2014-03-12 17:02  jgalaz

	* programs/e2spt_tiltstacker.py: New --clip option added.  Also,
	  because EMAN2 messes up the contrast/pixel-values, the program
	  now depends on IMOD's newstack for the actual unstacking and
	  stacking.  So, essentially, this program is useful if you want to
	  fix the apix, if you want to stack individual hdf files into an
	  IMOD .st (3D MRC) stack (HDF is not supported by IMOD), or if you
	  want to clip the images before stacking them.

2014-03-12 16:04  vern

	* libpyEM/qtgui/embrowser.py: Added saving image file error
	  checking, if file name was blank or had extension for
	  non-writeable image file type.

2014-03-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-11 23:18  stevel

	* programs/: e2refine_easy.py, e2refine_postprocess.py: Real space
	  symmetry imposition.

2014-03-11 15:44  stevel

	* libEM/emdata_transform.cpp, libpyEM/qtgui/embrowser.py: Fix set
	  loading/infoname in browser with emimagemx

2014-03-11 14:44  stevel

	* CMakeLists.txt, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emdata_core.h, libEM/emdata_metadata.h,
	  libEM/emdata_transform.cpp: New compile-time optional FFT caching
	  in EMData objects. This may offer a considerable speedup in some
	  cases where FFTs are used repeatedly on static images, at the
	  cost of some RAM.

2014-03-11 12:38  vern

	* libpyEM/qtgui/embrowser.py: Fixed file browser close crashes on
	  Windows by stopping timer before close, for okay, cancel, or X.

2014-03-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-11 10:24  stevel

	* libEM/processor.cpp, libEM/processor.h, libEM/pmconfig/spr.json,
	  programs/e2classifyligand.py, programs/e2ddd_movie.py:
	  Improvement (?) in ddd alignment

2014-03-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-10 07:56  stevel

	* libEM/cmp.cpp, programs/e2classextract.py: Oops

2014-03-10 07:42  stevel

	* programs/e2classextract.py: Classextract eliminates duplicates
	  within one set due to --sep in refinemulti

2014-03-10 07:07  stevel

	* TODO, libpyEM/qtgui/emplot2d.py: slight plot saving tweak

2014-03-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-09 11:44  pawel

	* sparx/bin/sxhelicon_utils.py: [no log message]

2014-03-09 00:13  stevel

	* libpyEM/EMAN2.py: remove debug statement

2014-03-08 21:52  pawel

	* sparx/bin/sxheliconlocal.py: [no log message]

2014-03-08 18:51  pawel

	* sparx/bin/sxheliconlocal.py: [no log message]

2014-03-08 15:58  pawel

	* sparx/libpy/multi_shc.py: corrected

2014-03-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-08 02:27  jgalaz

	* programs/e2spt_tiltstacker.py: [no log message]

2014-03-08 02:07  stevel

	* programs/e2classifyligand.py: Add a couple of options to
	  classifyligand

2014-03-07 17:38  jgalaz

	* programs/e2spt_tiltstacker.py: Pretty much re-did program.
	  Issues ensue with actually stacking the tilt series because of
	  mrc16bit writing issue (e2proc2d.py is called with the
	  '--twod2threed' and '--fixintscaling' and '--mrc16bit' options on
	  when trying to conver an HDF stack of 2D images into a 3D MRC
	  volume).

2014-03-07 16:59  scmurray

	* libpyEM/EMAN2.py, libpyEM/EMAN2jsondb.py,
	  programs/e2refinetofrealign.py: Formatting change in EMAN2.py and
	  EMAN2jsondb.py

	  Massive changes to e2refinetofrealign that alter the way it was
	  doing things. Fixed Euler Angles and logic errors.

2014-03-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-07 10:01  stevel

	* TODO, libEM/processor.cpp, programs/e2classaverage.py,
	  programs/e2ddd_movie.py: Alignment fix in class averager.
	  DDDmovie working again.

2014-03-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-05 17:34  pawel

	* sparx/bin/sxhelical_demo.py: [no log message]

2014-03-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-03-02 11:59  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-03-02 11:15  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-03-02 01:02  jgalaz

	* programs/e2spt_hac.py: [no log message]

2014-03-01 22:30  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-03-01 16:34  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-03-01 12:29  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-03-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-28 14:56  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-02-28 13:31  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-02-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-27 16:41  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-02-27 16:32  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-02-27 15:20  pawel

	* sparx/libpy/multi_shc.py: in progress

2014-02-27 14:06  pawel

	* sparx/libpy/: multi_shc.py, utilities.py: restored even angles
	  for d symmetry

2014-02-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-26 23:52  stevel

	* libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libpyEM/EMAN2jsondb.py, libpyEM/libpyEMData2.cpp: faster
	  compression in json files

2014-02-26 17:09  vern

	* libEM/: dm4io.h, dm4io.cpp: Converted longs to long longs (on
	  Windows a long is 4 bytes, vs. 8 on Linux, Macs).

2014-02-26 14:45  stevel

	* programs/: e2refine_easy.py, e2refinemulti.py:
	  More improvements to angular step selection.

2014-02-26 13:53  pawel

	* sparx/libpy/: multi_shc.py, utilities.py: [no log message]

2014-02-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-26 11:19  stevel

	* programs/: e2refine_easy.py, e2refinemulti.py: breaksym option
	  added

2014-02-26 11:00  stevel

	* TODO, libpyEM/EMAN2.py, libpyEM/EMAN2db.py,
	  programs/e2refine_easy.py, programs/e2refinemulti.py: Better
	  angular step in e2refinemulti. Speed option added.

2014-02-26 10:58  jgalaz

	* programs/e2spt_hac.py: dendRogram

2014-02-26 10:28  jgalaz

	* programs/e2spt_hac.py: Text files to substitue for dendograms now
	  available.  Minor improvement in managing text files
	  corresponding to ranked ccc plots.

2014-02-25 19:34  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-02-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-24 14:02  pawel

	* sparx/libpy/utilities.py: [no log message]

2014-02-24 12:35  pawel

	* sparx/libpy/utilities.py: added d3 symmetry to
	  nearestk_projangles

2014-02-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-23 19:52  pawel

	* sparx/libpy/: multi_shc.py, utilities.py: [no log message]

2014-02-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-21 11:32  pawel

	* sparx/libpy/: applications.py: [no log message]

2014-02-20 14:31  pawel

	* sparx/bin/sxmulti_shc.py: [no log message]

2014-02-20 13:33  stevel

	* programs/e2refine_easy.py: Speed wasn't working perfectly

2014-02-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-20 08:04  stevel

	* TODO, libEM/glutil.cpp, libpyEM/qtgui/emimage.py,
	  programs/e2ddd_movie.py, programs/e2refine_easy.py: New --speed
	  option. command-line e2display of single images should no longer
	  crash.

2014-02-19 14:26  vern

	* libEM/aligner.cpp: Replaced the 2 calls to gsl_vector_ptr with
	  calls to gsl_vector_get, gsl_vector_set, to clean up and fix
	  Windows link error (could not find gsl_vector_ptr).

2014-02-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-19 09:52  pawel

	* sparx/libpy/: applications.py, multi_shc.py: [no log message]

2014-02-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-14 16:58  jgalaz

	* examples/e2spt_autocenter.py: Description entered for
	  e2spt_autoboxer.py was meant for THIS program.

2014-02-14 16:57  jgalaz

	* programs/e2spt_autoboxer.py: MAJOR changes. Main autocentering
	  routine is now based on orthogonal projections rather than on
	  center of mass and spherical averages.

2014-02-14 16:56  jgalaz

	* programs/: e2spt_classaverage.py, e2spt_hac.py: [no log message]

2014-02-14 13:10  stevel

	* programs/e2ddd_movie.py: more alignment tweaks

2014-02-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-14 07:06  stevel

	* libpyEM/qtgui/empmwidgets.py: fixed directory naming related bugs

2014-02-13 18:56  stevel

	* libpyEM/EMAN2.py, libpyEM/EMAN2PAR.py,
	  programs/e2evalparticles.py: Minor bugfixes

2014-02-13 18:30  stevel

	* programs/e2ctf.py, programs/e2ddd_movie.py,
	  programs/e2evalparticles.py, pyemtbx/box.py: remove warning

2014-02-13 15:16  vern

	* libEM/sparx/util_sparx.cpp: Fixed a typo in the previous Windows
	  fixes (removed an extraneous right parenthesis).

2014-02-13 15:06  vern

	* libEM/sparx/util_sparx.cpp: Fixed Windows compile problems: used
	  '&&' instead of 'and'), avoided using std::max.

2014-02-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-13 10:08  stevel

	* programs/e2ddd_movie.py: working on movie mode

2014-02-12 16:28  vern

	* libEM/ctf.cpp: Changed uses of atan2 and pow for Windows so as to
	  know to pick the float versions.

2014-02-12 15:21  vern

	* libEM/emutil.h: To make close_imageio have type void rather than
	  void*, since it returns nothing.

2014-02-12 15:12  vern

	* libEM/analyzer.cpp: Used abs rather than fabs on integer
	  variables (caused Windows C++ error).

2014-02-12 15:06  vern

	* libEM/emutil.cpp: To make close_imageio have type void rather
	  than void*, since it returns nothing.

2014-02-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-10 14:37  pawel

	* sparx/: bin/sxali3d.py, bin/sxmulti_shc.py, libpy/alignment.py,
	  libpy/applications.py, libpy/multi_shc.py, libpy/utilities.py:
	  [no log message]

2014-02-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-10 07:11  stevel

	* programs/e2refine_postprocess.py: Automasking was broken !?!@#

2014-02-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-09 09:18  pawel

	* sparx/libpy/applications.py: [no log message]

2014-02-08 18:55  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-02-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-07 22:08  pawel

	* sparx/libpy/: multi_shc.py, utilities.py: corrected even angles
	  for d symmetry

2014-02-07 18:02  jgalaz

	* programs/e2spt_simulation.py: [no log message]

2014-02-07 17:00  vern

	* libEM/processor.cpp: Fixed a weird Windows problem: used new to
	  allocate an array, then deleted it when done.

2014-02-07 15:02  vern

	* libEM/pointarray.cpp: Fixed mistake from previous version:
	  prefixed Util:: to get_irand call.

2014-02-07 14:44  vern

	* libEM/processor.cpp: Made work on Windows: defined uint for
	  Windows.

2014-02-07 14:40  vern

	* libEM/pointarray.cpp: Made work on Windows: defined uint for
	  Windows, used get_irand rather than random.

2014-02-07 13:18  pawel

	* sparx/libpy/multi_shc.py: GA version of mshc

2014-02-07 12:01  pawel

	* sparx/: bin/sxmulti_shc.py, libpy/multi_shc.py: GA version of
	  mshc

2014-02-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-07 07:15  stevel

	* libpyEM/qtgui/emimagemx.py, programs/e2evalparticles.py,
	  programs/e2refine2d.py: e2evalparticles fixed !

2014-02-06 18:23  pawel

	* sparx/libpy/multi_shc.py: GA version of mshc

2014-02-06 17:49  pawel

	* sparx/libpy/multi_shc.py: GA version of mshc

2014-02-06 17:22  pawel

	* sparx/libpy/multi_shc.py: GA version of mshc

2014-02-06 14:22  pawel

	* sparx/libpy/multi_shc.py: GA version of mshc

2014-02-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-05 15:50  jgalaz

	* programs/e2spt_classaverage.py: [no log message]

2014-02-05 14:13  jgalaz

	* programs/: e2spt_classaverage.py: [no log message]

2014-02-05 14:08  jgalaz

	* programs/e2spt_simulation.py: [no log message]

2014-02-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-05 08:42  stevel

	* examples/ringfit.py, libEM/pointarray.cpp, libEM/pointarray.h,
	  libpyEM/qtgui/emimagemx.py, programs/e2buildsets.py,
	  programs/e2evalparticles.py, programs/e2refine_easy.py: Fix for
	  buildsets GUI layout. projection generation extend to 90 degrees.
	  new pointarray simulation tweaks.

2014-02-04 17:09  pawel

	* sparx/bin/sxprocess.py: [no log message]

2014-02-04 16:58  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-02-04 16:53  pawel

	* sparx/libpy/utilities.py: [no log message]

2014-02-04 15:25  scmurray

	* programs/: e2RCTboxer.py, e2rct.py, e2refinetorelion2d.py,
	  e2refinetorelion3d.py: Relion Programs updated with defocus
	  fixes. RCT programs are being fixed to work with 2.1. They arent
	  quite done...

2014-02-04 13:54  pawel

	* sparx/libpy/multi_shc.py: add reduction of dsym params

2014-02-04 12:54  pawel

	* sparx/: bin/sxmulti_shc.py, libpy/multi_shc.py: removed multipeak
	  shc, added D symmetry

2014-02-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-03 17:31  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-02-03 17:24  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-02-03 15:11  pawel

	* sparx/libpy/utilities.py: [no log message]

2014-02-03 15:09  pawel

	* sparx/libpy/multi_shc.py: added procedure, no major changes

2014-02-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-02 14:42  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-02-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-02-02 10:33  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-02-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-31 12:09  pawel

	* sparx/libpy/multi_shc.py: [no log message]

2014-01-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-25 10:43  pawel

	* sparx/libpy/: multi_shc.py, statistics.py: [no log message]

2014-01-24 15:34  stevel

	* libpyEM/EMAN2PAR.py: Change to logging EMAN2PAR

2014-01-24 15:17  stevel

	* libpyEM/EMAN2PAR.py: debugging tweak

2014-01-24 14:50  stevel

	* libpyEM/EMAN2PAR.py: syntax error

2014-01-24 14:45  stevel

	* libpyEM/EMAN2PAR.py: Debugging support in EMAN2PAR

2014-01-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-23 14:54  stevel

	* programs/: e2buildsets.py, e2ctf.py: Improvements to e2buildsets
	  for programmatic set building. Marginally tested.

2014-01-23 14:35  pawel

	* sparx/: bin/sxmulti_shc.py, libpy/multi_shc.py,
	  libpy/pixel_error.py, libpy/statistics.py: [no log message]

2014-01-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-21 16:58  scmurray

	* programs/e2refinetorelion2d.py: Changed to remove reliance on
	  Relion

2014-01-21 16:40  scmurray

	* programs/: e2refinetorelion2d.py, e2refinetorelion3d.py: Changes
	  to update text and remove reliance on relion for running (for the
	  3d program now. 2d coming shortly)

2014-01-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-21 08:45  stevel

	* libpyEM/qtgui/emplot2d.py: Fixed plotting problem in automatic
	  sym/line selection

2014-01-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-18 20:31  jgalaz

	* programs/e2spt_simulation.py: [no log message]

2014-01-18 19:59  jgalaz

	* programs/e2spt_resolutionplot.py: [no log message]

2014-01-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-17 13:35  stevel

	* examples/ringfit.py, libEM/pointarray.cpp: Simulation with
	  densities is working, but there are still some issues. Lack of a
	  hard-sphere exclusion radius is causing some problems, as is the
	  'Schulten' problem of cramming too much density into space where
	  the map is high.Z

2014-01-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-16 13:49  scmurray

	* programs/e2refinetorelion2d.py: Small change for error checking

2014-01-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-15 23:00  stevel

	* libEM/: pointarray.cpp, pointarray.h, processor.cpp: Added
	  map-based potential to pointarray

2014-01-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-14 14:38  scmurray

	* libEM/processor.cpp: Mac-related Fixes

2014-01-14 14:33  scmurray

	* libEM/: emio.cpp, pointarray.cpp: More fixes

2014-01-14 14:24  scmurray

	* libEM/pointarray.cpp: More Mac-related fixes

2014-01-14 13:39  scmurray

	* libEM/pointarray.cpp: Fixing a bug related to uint on Mac 10.7

2014-01-14 13:08  scmurray

	* libEM/emdata_io.cpp, libEM/emio.cpp, libEM/processor.cpp,
	  libpyEM/EMAN2.py, programs/e2RCTboxer.py, programs/e2proc2d.py:
	  Various changes related to bugfixing and updating

2014-01-14 13:03  scmurray

	* libEM/pmconfig/spr.json: Changed to include the Relion and
	  FreAlign programs

2014-01-14 13:02  scmurray

	* programs/: e2refinefromfrealign.py, e2runfrealign.py: Changed to
	  work with EMAN2.1

2014-01-14 13:02  scmurray

	* programs/e2refinetofrealign.py: Changed to work with EMAN 2.1

2014-01-14 13:02  scmurray

	* programs/e2refinetorelion3d.py: Changed to work with 2.1 Tested
	  well but more testing to come

2014-01-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-13 13:50  vern

	* libEM/: dm4io.h, dm4io.cpp: Removed some warnings, stopped
	  reading all image data to get just one image.

2014-01-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-13 02:04  jgalaz

	* programs/e2spt_hac.py: --precision parameter available in
	  e2spt_classaverage.py MUST exist here too. Added.

2014-01-12 23:31  stevel

	* examples/ringfit.py: Started work combining ring isolation with
	  simulation.

2014-01-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-10 15:40  jgalaz

	* programs/e2spt_resolutionplot.py: Not sure what changed...

2014-01-10 15:40  jgalaz

	* programs/e2spt_refprep.py: No idea what's changed, but apparently
	  my version is different from the one on CVS.

2014-01-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-10 02:06  jgalaz

	* programs/e2spt_classaverage.py: Bug fix.

2014-01-09 13:35  stevel

	* examples/ringsim.py, libEM/pointarray.cpp, libEM/pointarray.h,
	  libpyEM/libpyPointArray2.cpp: Simulations working, but may not be
	  the best energy space (cartesian).

2014-01-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-08 23:42  stevel

	* examples/ringsim.py, libEM/pointarray.cpp, libEM/pointarray.h,
	  libpyEM/libpyPointArray2.cpp: conjugate gradient, but still needs
	  some work

2014-01-08 15:13  stevel

	* examples/ringsim.py, libEM/pointarray.cpp, libEM/pointarray.h,
	  libpyEM/libpyPointArray2.cpp: Simulation work

2014-01-08 15:09  vern

	* libEM/dm4io.cpp: Speeded up and cleaned up read_data routine,
	  fixed a bug in REAL8 case.

2014-01-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-07 23:25  stevel

	* libEM/: pointarray.cpp, pointarray.h: Pointarray simulation work

2014-01-07 18:05  stevel

	* libEM/pointarray.cpp, libEM/pointarray.h, libEM/util.h,
	  libpyEM/libpyUtils2.cpp: Ooops. Broke compilation. Should be
	  fixed.

2014-01-07 14:46  stevel

	* examples/minicircle_stat.py, libEM/analyzer.cpp,
	  libEM/analyzer.h, libEM/pointarray.cpp, libEM/pointarray.h,
	  libEM/util.h, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/emimage.py, libpyEM/qtgui/emplot2d.py: Working on
	  simple loop simulations. Many improvements to file browser for 3D
	  stacks, and better automatic options when doing 2D plots.

2014-01-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-06 23:42  stevel

	* examples/minicircle_stat.py, libpyEM/qtgui/emplot2d.py:
	  Mini-circle analysis working a bit

2014-01-06 22:45  stevel

	* libEM/processor.cpp: Oops. 3d automask was commented out !

2014-01-06 14:44  vern

	* libEM/dm4io.cpp: Removed debugging stuff for Mac error reading
	  too long data, put in a partial fix.

2014-01-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-05 15:35  stevel

	* examples/minicircle_stat.py: New program for analysis of
	  mini-circles

2014-01-05 15:04  stevel

	* libEM/: emdata.h, emdata_core.h, processor.cpp, processor.h: New
	  dust filter working.

2014-01-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-04 19:23  stevel

	* libEM/analyzer.cpp, libEM/analyzer.h, libEM/emdata_core.cpp,
	  libEM/processor.cpp, libEM/processor.h, libpyEM/EMAN2.py: New
	  routines for processing mini-circles.

2014-01-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2014-01-02 02:52  vern

	* libEM/dm4io.cpp: Fixed error in debugging in previous version.

2014-01-02 02:21  vern

	* libEM/dm4io.cpp: Added some debugging stuff for problem reading
	  on Macs.

2014-01-01 13:19  pawel

	* sparx/bin/sxhelicon_utils.py: [no log message]

2014-01-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-31 15:55  vern

	* libEM/dm4io.cpp: Modified invalid tag type error message.

2013-12-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-30 16:23  pawel

	* sparx/demo/mpi_bdb_ctf/run_through_example: [no log message]

2013-12-30 15:10  vern

	* libEM/dm4io.cpp: [no log message]

2013-12-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-22 16:53  pawel

	* sparx/bin/sxhelixboxer.py: [no log message]

2013-12-22 15:15  pawel

	* sparx/bin/sxhelixboxer.py: [no log message]

2013-12-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-22 10:49  pawel

	* sparx/: bin/sxali2d.py, libpy/applications.py: [no log message]

2013-12-22 10:01  pawel

	* sparx/: bin/sxheader.py, bin/sxprocess.py, libpy/applications.py:
	  [no log message]

2013-12-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-20 07:03  stevel

	* programs/e2ddd_movie.py: more improvements to ddd_movie. Frame
	  alignment working properly now as far as I can tell. doign some
	  large tests now.

2013-12-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-19 09:41  stevel

	* libEM/emutil.cpp, libEM/pngio.cpp, libEM/processor.cpp,
	  libEM/processor.h, libpyEM/qtgui/emimage2d.py,
	  programs/e2ddd_movie.py, programs/e2proc2d.py: Added 2-D support
	  to, and fixed 3-D support in xform.applysym.

2013-12-18 16:31  pawel

	* sparx/demo/: mpi_bdb/run_through_example,
	  mpi_bdb_ctf/run_through_example: typo

2013-12-18 14:27  pawel

	* sparx/bin/sxhelixboxer.py: default minseg set to 6

2013-12-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-17 12:52  stevel

	* libEM/emutil.cpp, programs/e2ddd_movie.py,
	  programs/e2refine_postprocess.py, programs/e2refinemulti.py: Fix
	  for refinemulti. work on ddd movie

2013-12-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-17 06:17  pawel

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, sparx/bin/sxlocres.py: set_freq moved to
	  C

2013-12-16 17:44  vern

	* libEM/dm4io.cpp: [no log message]

2013-12-16 16:59  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-12-16 15:00  pawel

	* sparx/bin/sxlocres.py: sxlocres  MPI version

2013-12-16 14:29  pawel

	* sparx/bin/sxlocres.py: sxlocres  MPI version

2013-12-16 13:02  pawel

	* sparx/bin/sxlocres.py: sxlocres  MPI version

2013-12-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-15 10:34  pawel

	* sparx/demo/: mpi_bdb/run_through_example,
	  mpi_bdb_ctf/run_through_example: [no log message]

2013-12-15 10:26  pawel

	* sparx/demo/: mpi_bdb/run_through_example,
	  mpi_bdb_ctf/run_through_example: [no log message]

2013-12-14 14:19  pawel

	* sparx/bin/: sxcter.py, sxlocres.py: [no log message]

2013-12-14 13:19  pawel

	* sparx/bin/sxlocres.py: local resolution

2013-12-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-13 13:00  pawel

	* sparx/demo/: mpi_bdb/run_through_example,
	  mpi_bdb_ctf/run_through_example: [no log message]

2013-12-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-12 22:52  jgalaz

	* programs/e2spt_tiltstacker.py: [no log message]

2013-12-12 20:41  jgalaz

	* programs/e2spt_tiltstacker.py: Now stacks .hdf 2-D images.

2013-12-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-12 09:57  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-12-12 04:13  jgalaz

	* programs/e2spt_simulation.py,
	  examples/e2spt_transformdistance.py: [no log message]

2013-12-11 14:42  stevel

	* libpyEM/qtgui/embrowser.py, programs/e2ddd_movie.py,
	  programs/e2proc3d.py, programs/e2refine_easy.py,
	  programs/e2refine_postprocess.py: Returned default for 3D display
	  to use the same view now that there is a sequencing slider
	  available. More tweaks to the postprocessing infrastructure.

2013-12-11 13:59  vern

	* libEM/dm4io.cpp: [no log message]

2013-12-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-10 19:00  pawel

	* sparx/bin/sxprocess.py: [no log message]

2013-12-10 17:47  jgalaz

	* examples/e2orthoproject.py: Bugs would come up when files had
	  periods/dots (.) in their names.  Now, automatic renaming
	  (splitting, replacing, etc) searches specificallu for ".hdf" as a
	  marker. Therefore, this program only works when fed .hdf files.
	  Might expand it to support .mrc in the future.

2013-12-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-10 05:48  jgalaz

	* programs/e2spt_simulation.py: REFORMED (so that it is easier to
	  get the REFORMED e2spt_tomosimjobs.py working...).  Code is more
	  organized (more compartmentalization in functions of redundant
	  tasks, or simply for organizational purposes).  Output is
	  consistent and no longer the choice of the user. Output files
	  have been standardized: "simptcls.hdf", "simmodel.hdf",
	  "randstack.hdf", "randstack_preproc.hdf", etc.

2013-12-09 22:07  jgalaz

	* programs/e2spt_simulation.py: [no log message]

2013-12-09 18:24  vern

	* libEM/dm4io.cpp: [no log message]

2013-12-09 17:39  jgalaz

	* programs/e2spt_simulation.py: Several bugs were fixed: 1) When
	  providing a previously computed --randstack, particles were not
	  being preprocessed.  2) Particles were being clipped before
	  tomographic reconstruction when --finalboxsize was provided, thus
	  rendering --pad useless.  As a result, simulated subvolumes now
	  look more "realistic" (they were 'weird' before).

	  Preprocessing is handled better now (through a function).

2013-12-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-06 18:25  jgalaz

	* programs/e2spt_classaverage.py: [no log message]

2013-12-06 14:48  pawel

	* sparx/libpy/: multi_shc.py, utilities.py: [no log message]

2013-12-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-06 10:43  stevel

	* programs/e2refine_easy.py: Another postprocess fix

2013-12-06 07:42  stevel

	* libEM/aligner.cpp, programs/e2refine_postprocess.py: Another
	  problem with postprocessing options

2013-12-05 19:19  jgalaz

	* programs/e2spt_simulation.py: Replaced many instances of
	  os.system with subprocess.Popen (which is safer).  Also enabled
	  --finalboxsize to take an 'expansion factor'. So you can either
	  supply the final boxisze (an integer), or you can supply a number
	  to multiply the original boxisze by. For example, if the original
	  boxisze of the model used to simulate subtomograms is 64, and
	  --finalboxsize=1.5x, then the actual finalboxsize will be 96.

2013-12-05 16:10  jgalaz

	* programs/e2spt_simulation.py: Parameter --nosim available to just
	  get a stack of randomly oriented particles if --saverandstack is
	  specified.  Also changed code a bit because when --randstack was
	  supplied (particles already in a random orientation) simulation
	  was inefficiently implemented (it was inside a long loop that is
	  really unecessary when you already have a stack of randomly
	  oriented particles...).

2013-12-05 12:56  pawel

	* sparx/: bin/sxmulti_shc.py, libpy/multi_shc.py: [no log message]

2013-12-05 12:42  pawel

	* sparx/libpy/applications.py: [no log message]

2013-12-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-05 09:02  pawel

	* sparx/bin/sxprocess.py: [no log message]

2013-12-04 13:56  jgalaz

	* programs/e2spt_classaverage.py: Bug fixes: 1) --search and
	  --searchfine handled correctly now when values are 0 (weren't
	  before).  2) --refpreprocess was buggy when --ref was supplied.
	  It should be OFF by default ONLY for the first iteration. After
	  that, the "new reference" will be an average of subtomograms, and
	  thus MUST be preprocessed (it might be ideal to define parameters
	  for preprocessing the references/averages diferent from the
	  particles...).

2013-12-04 13:21  jgalaz

	* programs/e2spt_classaverage.py: Forgot: Changes to --radius too,
	  so it's more conservative. Also, new --precision parameter
	  introduced. You might not want to have a precision of "1 pixel at
	  the edge of the particle" (that is, for the FINE rotation to move
	  the particles by at most one pixel at their edge), because
	  sampling (apix) might be very small, and thus you might be able
	  to afford a coarser sampling based on the attainable resolution
	  (if you're not sampling limited, you might be defocus limited, or
	  particle-number limited, or whateverelse).

2013-12-04 12:48  jgalaz

	* programs/e2spt_classaverage.py: NASTY 'sizing' bug messed up
	  alignments when --shrink or --shrink refine were used and, in
	  particular, when --shrink and --shrinkrefine were not equal.
	  This was linked (kinda' dependent on, or stemming from) a
	  parameter introduced a few months ago, --refpreprocess, which has
	  to be explicitly supplied for EXTERNAL references (--ref) to be
	  preprocessed for the first round of alignment (usually, there's
	  no reason to preprocess a PDB model on iteration 1 of iterative
	  refinement).

2013-12-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-02 14:32  pawel

	* libEM/sparx/fourierfilter.cpp, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h, libpyEM/libpyUtils2.cpp: [no log
	  message]

2013-12-02 13:33  stevel

	* libEM/cmp.h: Warning message.

2013-12-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-12-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-30 16:40  pawel

	* sparx/bin/sx3dvariability.py: [no log message]

2013-11-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-27 17:19  jgalaz

	* programs/e2spt_classaverage.py: Angular parameters automatically
	  calculated based on --radius were inaccurate. Presumably fixed
	  now.

2013-11-27 16:38  jgalaz

	* examples/e2spt_transformdistance.py: Bug fix for latest change.

2013-11-27 16:10  jgalaz

	* examples/e2spt_transformdistance.py: New --angles parameter
	  allows you to calculate the angular distance between any two
	  rotational orientations and prints it out to the screen.

2013-11-27 12:50  stevel

	* programs/e2refine_easy.py: one more tweak so postprocess works

2013-11-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-27 00:19  stevel

	* programs/e2refine_postprocess.py: fixed postprocessing

2013-11-26 19:04  jgalaz

	* examples/e2fixheaderparam.py, programs/e2spt_boxer.py,
	  programs/e2spt_hac.py, programs/e2spt_refinemulti.py: [no log
	  message]

2013-11-26 12:37  stevel

	* examples/focalpairalign.py, programs/e2refine_easy.py,
	  programs/e2refine_postprocess.py: Fixed postprocessing options
	  ... I hope. Not thoroughly tested yet.

2013-11-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-25 13:33  pawel

	* sparx/libpy/: morphology.py, utilities.py: [no log message]

2013-11-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-25 08:04  stevel

	* libpyEM/qtgui/valslider.py: Tweak 3-d animation slider

2013-11-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-22 21:46  stevel

	* libpyEM/qtgui/emscene3d.py: sequence animations in 3D display

2013-11-22 20:19  stevel

	* CMakeLists.txt, TODO: Revamp options for optimization in
	  CMakeList

2013-11-22 18:40  stevel

	* CMakeLists.txt, TODO, libpyEM/qtgui/emscene3d.py: Fix makefile

2013-11-22 12:06  stevel

	* libEM/: processor.cpp, processor.h: Added soft inner/outer mask.

2013-11-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-21 21:21  stevel

	* CMakeLists.txt, libEM/processor.cpp: gsl fix

2013-11-21 18:45  jgalaz

	* programs/e2spt_boxer.py: Messed up coordinates files cause all
	  sorts of issues *sigh* (another bug fixed). Incidentally,
	  --bruteaverage now working.

2013-11-21 18:27  jgalaz

	* programs/e2spt_boxer.py: Bug fixed when coordinates file contains
	  spurious coordinates centered on empty regions, which yield empty
	  boxes.

2013-11-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-20 08:18  stevel

	* libpyEM/qtgui/: embrowser.py, empmtabwidgets.py: sorting issue
	  fixed

2013-11-19 14:22  stevel

	* libpyEM/EMAN2jsondb.py, programs/e2version.py: e2version.py fix

2013-11-19 14:03  pawel

	* sparx/: bin/sxhelicon_utils.py, bin/sxheliconlocal.py,
	  libpy/applications.py: various corrections of helical stuff

2013-11-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-19 07:47  stevel

	* programs/e2filtertool.py: oops

2013-11-19 07:47  stevel

	* libpyEM/EMAN2.py, programs/e2filtertool.py: fix filtertool for
	  parameterless processors

2013-11-18 23:31  jgalaz

	* examples/e2spt_tomosimjobs.py: There was a bug when --comparators
	  had more than one comparator and snr was varied.

2013-11-18 16:18  pawel

	* sparx/bin/sxhelical_demo.py: corrections to make it reproducible
	  and sensible

2013-11-18 15:49  jgalaz

	* programs/e2spt_refprep.py: Typo corrected.

2013-11-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-16 03:29  jgalaz

	* examples/e2spt_tomosimjobs.py: Compatible with latest classmx
	  updates in classaverage.py

2013-11-16 02:52  jgalaz

	* programs/e2spt_classaverage.py: With new classmx functionality,
	  program was broken when no supplying --ref, or when --ref was
	  theere but there was no separation of groups.

2013-11-16 01:19  jgalaz

	* programs/e2spt_classaverage.py: Bug fixes stemming from latest
	  changes.

2013-11-16 00:14  jgalaz

	* programs/e2spt_classaverage.py: classmx files generated now for
	  this program, including for handling the automatic separation of
	  the set into two groups from the start to perform independent
	  refinements on them.

2013-11-15 17:59  pawel

	* sparx/bin/: sxhelical_demo.py, sxhelicon.py: [no log message]

2013-11-15 15:16  pawel

	* sparx/bin/sxhelicon.py: [no log message]

2013-11-15 12:52  pawel

	* sparx/bin/sxprocess.py: added average PW

2013-11-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-14 18:02  jgalaz

	* programs/e2spt_resolutionplot.py: --maskfsc implemented, to mask
	  volumes before fsc computation.  --mask changed to --maskali, for
	  clarity.

2013-11-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-13 16:56  jgalaz

	* programs/e2spt_hac.py: --search and --search fine available (but
	  not functional yet) to prevent crash of functions called from
	  e2spt_classaverage.py

2013-11-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-05 20:57  jgalaz

	* programs/e2spt_classaverage.py: First line was wrong and caused
	  issued on cluster.

2013-11-05 20:40  jgalaz

	* programs/e2spt_hac.py: Can't remember what changed...

2013-11-05 20:40  jgalaz

	* programs/e2spt_refprep.py: Multiple things were wrong.

2013-11-05 20:08  jgalaz

	* programs/e2spt_classaverage.py: --search and --seachfine
	  parameters for when --radius is used and thus defining --align
	  and --ralign is skipped.  Multiple other changes (can't
	  remember).

2013-11-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-05 09:47  piotr

	* sparx/bin/sxair.py: bugfix

2013-11-05 09:09  piotr

	* libEM/sparx/mcqd.h: printouts commented out

2013-11-04 17:12  piotr

	* sparx/libpy/air.py: bugfixes

2013-11-04 17:05  piotr

	* sparx/libpy/air.py: bugfixes

2013-11-04 16:16  piotr

	* sparx/: bin/sxair.py, libpy/air.py, libpy/statistics.py:
	  ab-initio reconstruction - sources moved to sparx - runnable
	  version

2013-11-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-03 21:50  piotr

	* sparx/: bin/sxair.py, bin/sxmulti_shc.py, libpy/air.py: air
	  (ab-initio reconstruction) - temporary version

2013-11-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-03 09:29  stevel

	* libpyEM/EMAN2jsondb.py, libpyEM/qtgui/emboxerbase.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2ctf.py, programs/e2projectmanager.py: Fix to json

2013-11-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-11-01 17:21  piotr

	* sparx/: bin/sxair.py, libpy/air.py: ab-initio reconstruction -
	  sources moved to sparx

2013-11-01 17:06  piotr

	* sparx/libpy/multi_shc.py: bugfix

2013-11-01 16:50  piotr

	* sparx/libpy/multi_shc.py: bugfix

2013-11-01 16:50  piotr

	* sparx/libpy/utilities.py: routine to calculate average
	  configuration

2013-11-01 16:01  piotr

	* sparx/: bin/sxmulti_shc.py, libpy/logger.py, libpy/multi_shc.py:
	  multi_shc - first version

2013-11-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-24 11:14  stevel

	* libEM/: emdata_io.cpp, processor.cpp, sparx/emdata_sparx.cpp: Fix
	  forward problem

2013-10-24 06:28  jgalaz

	* programs/e2spt_simulation.py: Noise not normalized anymore.

2013-10-24 06:28  jgalaz

	* programs/e2spt_refinemulti.py: refrence free mode calling binary
	  tree function debugged.

2013-10-24 06:27  jgalaz

	* programs/e2spt_classaverage.py: [no log message]

2013-10-24 06:24  jgalaz

	* examples/e2spt_tomosimjobs.py: SNR loop was broken.

2013-10-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-23 10:56  piotr

	* libEM/sparx/util_sparx.cpp, sparx/libpy/projection.py: max_clique
	  - bugfix

2013-10-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-18 18:00  jgalaz

	* programs/e2spt_refinemulti.py: Undergoing major rearrangements.

2013-10-18 17:59  jgalaz

	* programs/: e2spt_hac.py, e2spt_classaverage.py: [no log message]

2013-10-18 15:21  jgalaz

	* examples/e2orthoproject.py: The program can now yield the Z, Y or
	  X projections for ALL the particles in stacks as ONE Zprjs, Yprjs
	  or Xprjs stack. (Before, each projection for each particle was
	  output as a separate file since, typically, you want orthogonal
	  projections PER particle to be together in one file).

2013-10-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-18 09:54  piotr

	* libEM/sparx/mcqd.h, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h, libpyEM/libpyUtils2.cpp: add max_clique
	  procedure - it finds max_clique in the undirected graph

2013-10-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-16 14:12  pawel

	* sparx/libpy/: applications.py, morphology.py: normalization of
	  ctf added to cter

2013-10-16 12:21  jgalaz

	* programs/e2spt_simulation.py: --input can now take a comma
	  separated list of stacks.
	  --input=stack1.hdf,stack2.hdf,stack3.hdf... etc.

2013-10-16 12:20  jgalaz

	* programs/e2spt_refprep.py: Most significant changes are that 1)
	  the program is compartmentalized into functions now, 2) several
	  input stacks/files can be provided now
	  --input=stack1.hdf,file2.mrc,vol3.pdb... etc.

2013-10-16 12:19  jgalaz

	* programs/e2spt_hac.py: Same... can't remember what changed.
	  Presumably, updates/improvements/fixes have occured.

2013-10-16 12:18  jgalaz

	* examples/e2fixheaderparam.py: Can't remember what changed, but my
	  version doesn't seem to agree with the one on CVS (and I assume
	  mine would have later changes).

2013-10-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-15 15:12  pawel

	* sparx/libpy/user_functions.py: [no log message]

2013-10-15 15:04  pawel

	* sparx/libpy/user_functions.py: [no log message]

2013-10-15 14:56  piotr

	* sparx/libpy/applications.py, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h, sparx/libpy/alignment.py: add gamma
	  parameter to SHC - improved version

2013-10-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-14 13:48  piotr

	* sparx/libpy/alignment.py: add gamma parameter to SHC

2013-10-14 13:42  pawel

	* sparx/bin/sxali3d.py: [no log message]

2013-10-14 13:23  piotr

	* sparx/libpy/applications.py: bugfix

2013-10-14 13:19  piotr

	* sparx/libpy/applications.py: bugfix

2013-10-14 13:17  piotr

	* sparx/libpy/applications.py: add gamma parameter to SHC

2013-10-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-14 11:32  piotr

	* sparx/bin/sxali3d.py: add gamma parameter to saturn

2013-10-13 12:31  pawel

	* sparx/: bin/sxhelicon_utils.py, libpy/applications.py: [no log
	  message]

2013-10-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-11 17:38  pawel

	* sparx/libpy/applications.py: [no log message]

2013-10-11 17:13  pawel

	* sparx/: bin/sx3dvariability.py, bin/sxhelicon_utils.py,
	  libpy/applications.py, libpy/morphology.py: minor

2013-10-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-11 09:45  piotr

	* libEM/sparx/util_sparx.cpp: SHC - unbiased version (random search
	  for shifts and psi)

2013-10-11 01:16  stevel

	* programs/e2classextract.py: e2classextract.py now works with
	  lists of set numbers

2013-10-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-09 15:56  pawel

	* libEM/sparx/util_sparx.cpp, sparx/bin/sxhelicon.py,
	  sparx/libpy/applications.py: helicon corrected for ywobble

2013-10-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-06 17:14  pawel

	* sparx/: bin/sxhelicon.py, libpy/applications.py: [no log message]

2013-10-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-06 11:02  pawel

	* libEM/sparx/util_sparx.cpp: reworking constrained helix

2013-10-05 20:36  stevel

	* examples/e2ctf2emx.py, programs/e2classvsproj.py: New program to
	  automatically compare class-averages to projections.

2013-10-05 14:30  pawel

	* sparx/libpy/applications.py: [no log message]

2013-10-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-05 11:21  pawel

	* sparx/libpy/applications.py: [no log message]

2013-10-04 12:54  pawel

	* sparx/: bin/sxhelicon.py, libpy/applications.py: [no log message]

2013-10-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-03 20:33  pawel

	* sparx/libpy/applications.py: [no log message]

2013-10-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-03 03:12  stevel

	* examples/e2ctf2emx.py, programs/e2ctf.py: One more tweak

2013-10-03 02:54  stevel

	* programs/e2ctf.py: Bugfix in astigmatism fitting. Had been fixed
	  before, but somehow lost...

2013-10-03 01:51  stevel

	* programs/: e2ctf.py, e2rawdata.py: Additional minor fixes to new
	  CTF scheme. Option for defocus estimation during import now
	  provided.

2013-10-02 20:45  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-10-02 14:16  stevel

	* libpyEM/qtgui/embrowser.py, libpyEM/qtgui/empmtabwidgets.py,
	  programs/e2ctf.py: more CTF improvements targeting close to focus
	  data

2013-10-02 14:04  stevel

	* programs/e2refine_easy.py: fix output generation

2013-10-02 12:45  pawel

	* sparx/: bin/sxheliconlocal.py, libpy/applications.py: [no log
	  message]

2013-10-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-10-01 23:39  stevel

	* programs/: e2ctf.py, e2evalimage.py, e2proc2d.py, e2rawdata.py:
	  Added CTF estimation to image import.

2013-10-01 12:56  pawel

	* sparx/libpy/user_functions.py: [no log message]

2013-10-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-30 23:11  stevel

	* programs/e2ctf.py: New CTF fitting. Seems to work well so far.
	  Need a little final testing on historical data tomorrow.

2013-09-30 22:04  pawel

	* sparx/bin/sxheliconlocal.py: [no log message]

2013-09-30 16:41  pawel

	* sparx/libpy/applications.py: [no log message]

2013-09-30 16:11  pawel

	* sparx/libpy/applications.py: [no log message]

2013-09-30 15:31  piotr

	* sparx/demo/mpi_bdb_ctf/run_through_example: add filter allowing
	  to minimize the CTF influence

2013-09-30 15:29  irees

	* doc/build/build.py: Logging improvements

2013-09-30 14:16  irees

	* doc/build/: build.py, install.sh: Sparx fixes

2013-09-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-30 11:41  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-09-29 23:24  stevel

	* programs/: e2ctf.py, e2evalimage.py: New CTF fitting algorithm.
	  Still testing

2013-09-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-29 10:14  pawel

	* sparx/libpy/applications.py: [no log message]

2013-09-29 09:56  pawel

	* sparx/: bin/sxhelicon_utils.py, libpy/applications.py: [no log
	  message]

2013-09-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-27 09:24  stevel

	* programs/: e2ctf.py, e2evalimage.py: Fix quality factor in
	  e2evalimage

2013-09-27 02:52  irees

	* libpyEM/qtgui/emimagemx.py: Fixed problem with disappearing
	  particles by keeping EMLightWeightParticleCache from having index
	  errors after "refocusing"

2013-09-26 18:54  jgalaz

	* programs/e2spt_refinemulti.py: In transition to being able to
	  start reference-free.

2013-09-26 18:53  jgalaz

	* programs/e2spt_hac.py: --noplot option for when the program is
	  run remotely or on a cluster.

2013-09-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-25 20:24  jgalaz

	* programs/e2spt_resolutionplot.py: Program was borken (not sure
	  why); functional again

2013-09-25 19:52  jgalaz

	* programs/e2spt_hac.py: --savepreprocessed added

2013-09-25 19:43  jgalaz

	* programs/e2spt_classaverage.py: [no log message]

2013-09-25 12:25  jgalaz

	* programs/e2spt_classaverage.py: [no log message]

2013-09-25 12:10  jgalaz

	* examples/e2fixheaderparam.py: [no log message]

2013-09-25 12:10  jgalaz

	* examples/e2fixheaderparam.py: Bug fixed, plus --addparam
	  deprecated. The program now distinguishes automatically between
	  existing parameters to update and new parameters to add

2013-09-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-25 11:17  pawel

	* sparx/bin/: sxhelical_demo.py, sxhelixboxer.py: [no log message]

2013-09-25 10:15  pawel

	* sparx/bin/sxcter.py: [no log message]

2013-09-24 22:26  jgalaz

	* programs/e2spt_resolutionplot.py: Many bugs fixed since 2.1alpha

2013-09-24 22:26  jgalaz

	* programs/: e2spt_classaverage.py, e2spt_hac.py,
	  e2spt_simulation.py: [no log message]

2013-09-24 22:25  jgalaz

	* examples/e2fixheaderparam.py: --params, --addfilename and --stem
	  can ALL be used simultaneously now. --input is no longer
	  overwritten, and if an .mrc file is passed in to add new
	  parameters to its header, it is automatically converted to .hdf
	  so that the task can be accomplished.

2013-09-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-24 10:57  pawel

	* sparx/libpy/fundamentals.py: [no log message]

2013-09-23 18:39  jgalaz

	* examples/e2spt_tomosimjobs.py: Can't remember what changed.

2013-09-23 18:38  jgalaz

	* programs/e2spt_simulation.py: Bug fixed regarding default of
	  --finalboxsize when not provided (defaulted internally in the
	  code)

2013-09-23 18:36  jgalaz

	* programs/e2spt_classaverage.py: Code cleaned a bit.
	  --savepreprocessed fully enabled now, for ptcls and ref. Record
	  of spt_wedge mean, sigma and thresh parameters kept on
	  preprocessed particles, if written.

2013-09-23 15:37  pawel

	* sparx/demo/: demo_user_funcs.py, mpi_bdb_ctf/run_through_example:
	  [no log message]

2013-09-23 13:24  pawel

	* sparx/bin/sxcter.py: [no log message]

2013-09-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-23 11:15  piotr

	* sparx/libpy/: applications.py, statistics.py: bugfix in hist_list
	  - now when all values are the same, the first bin is set to the
	  number of values

2013-09-22 21:30  pawel

	* sparx/: bin/sxcter.py, demo/demo_user_funcs.py: [no log message]

2013-09-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-22 11:25  pawel

	* sparx/demo/: demo_user_funcs.py, mpi_bdb/run_through_example,
	  mpi_bdb_ctf/run_through_example: [no log message]

2013-09-22 10:41  stevel

	* libEM/ctf.cpp, programs/e2ctf.py: CTF astigmatism fitting, and
	  new 2-D astigmatism display in GUI now fully functional (as far
	  as I can tell).

2013-09-21 16:19  stevel

	* libEM/ctf.cpp, libEM/ctf.h, libpyEM/libpyAligner2.cpp: oops

2013-09-21 15:52  pawel

	* sparx/demo/demo_user_funcs.py: [no log message]

2013-09-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-21 10:42  stevel

	* libEM/: ctf.cpp, ctf.h: New zero location routine

2013-09-21 10:01  pawel

	* libEM/sparx/util_sparx.cpp, sparx/libpy/morphology.py: cter
	  sanity check

2013-09-20 20:20  jgalaz

	* programs/e2spt_boxer.py: Z-projections are stored automatically
	  for easy review/evaluation of the dataset.

2013-09-20 15:38  piotr

	* doc/build/build.py: change bin/sparx.py to bin/sx.py

2013-09-20 15:28  piotr

	* doc/build/install.sh, sparx/bin/sparx.py, sparx/bin/sx.py: change
	  bin/sparx.py to bin/sx.py

2013-09-20 13:43  pawel

	* sparx/: demo/mpi_bdb/run_through_example, libpy/morphology.py:
	  [no log message]

2013-09-20 13:26  pawel

	* programs/e2boxer.py, sparx/libpy/morphology.py: [no log message]

2013-09-20 13:22  piotr

	* sparx/bin/CMakeLists.txt: sparx file was replaced by sparx.py
	  file

2013-09-20 12:35  pawel

	* doc/build/install.sh:  added sparx stuff

2013-09-20 12:27  pawel

	* sparx/bin/sparx.py: sparx renamed to sparx.py

2013-09-20 12:27  pawel

	* sparx/bin/sparx: [no log message]

2013-09-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-20 11:10  irees

	* doc/build/install.sh: Fix install.sh for sparx

2013-09-19 23:43  stevel

	* libpyEM/qtgui/emimage2d.py, programs/e2ctf.py: Working on CTF.
	  Still a problem with the zero() function for small defocuses.

2013-09-19 15:06  piotr

	* libEM/sparx/util_sparx.cpp: VERSION update

2013-09-19 14:48  pawel

	* sparx/libpy/morphology.py: [no log message]

2013-09-19 14:34  pawel

	* sparx/: bin/sxali3d.py, bin/sxcter.py, bin/sxhelixboxer.py,
	  bin/sxprocess.py, libpy/applications.py, libpy/global_def.py,
	  libpy/isac.py, libpy/morphology.py: [no log message]

2013-09-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-19 01:51  irees

	* doc/build/build.py: Minor fixes

2013-09-18 17:11  irees

	* doc/build/: README.txt, build.py, order.txt: Updated build system
	  documentation.

2013-09-18 13:30  pawel

	* sparx/: bin/sxhelicon.py, libpy/applications.py: [no log message]

2013-09-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-17 21:50  pawel

	* sparx/bin/sxhelicon.py: ::

2013-09-17 13:07  pawel

	* sparx/: bin/sxcter.py, bin/sxhelixboxer.py,
	  libpy/fundamentals.py: [no log message]

2013-09-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-17 11:06  piotr

	* libEM/sparx/util_sparx.cpp:
	  Util::diff_between_matrix_of_3D_parameters_angles - bugfix

2013-09-17 11:05  piotr

	* sparx/tests/test_Util.py: unittests for
	  Util.diff_between_matrix_of_3D_parameters_angles

2013-09-16 23:32  stevel

	* programs/e2ctf.py: Better background adjustment

2013-09-16 17:43  piotr

	* libEM/reconstructor.h: Bugfix - add new insert_slice method
	  without "weight" parameter to the Reconstructor class and remove
	  default value for the "weight" parameter in the old inserc_slice
	  method. I did it because for some reason the parameters with
	  default values don't work correctly (tested on MAC).

2013-09-16 17:05  pawel

	* sparx/bin/sxhelixboxer.py: [no log message]

2013-09-16 15:51  pawel

	* sparx/libpy/projection.py: [no log message]

2013-09-16 15:38  pawel

	* sparx/libpy/applications.py: [no log message]

2013-09-16 12:06  stevel

	* libpyEM/qtgui/emimagemx.py: Stopgap prevents crash in matrix
	  display, but doesn't fix underlying problem

2013-09-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-16 11:56  stevel

	* libpyEM/EMAN2.py, programs/e2import.py, programs/e2rawdata.py:
	  Fix naming convention issue when importing

2013-09-16 08:54  stevel

	* libEM/ctf.cpp, libEM/util.cpp, libEM/util.h,
	  libpyEM/emdata_wrapitems.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/qtgui/emboxerbase.py, libpyEM/qtgui/emimage2d.py,
	  programs/e2boxer.py, programs/e2ctf.py: Many CTF fitting
	  improvements. Still in testing.

2013-09-15 13:13  pawel

	* libEM/projector.h, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h, libpyEM/libpyUtils2.cpp,
	  sparx/bin/sxhelicon.py, sparx/bin/sxhelixboxer.py,
	  sparx/libpy/applications.py: [no log message]

2013-09-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-14 05:27  pawel

	* sparx/libpy/pixel_error.py: [no log message]

2013-09-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-13 08:44  pawel

	* sparx/libpy/: applications.py, pixel_error.py, utilities.py:
	  get_dist

2013-09-12 22:47  stevel

	* libEM/ctf.h, programs/e2ctf.py: mac compile ?

2013-09-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-12 08:46  stevel

	* libpyEM/EMAN2.py, programs/e2ctf.py, programs/e2import.py,
	  programs/e2rawdata.py: Initial functioning but poorly tested
	  astigmatism fitting. Just a hack for now.

2013-09-11 22:56  stevel

	* libEM/ctf.cpp, libEM/ctf.h, libpyEM/libpyAligner2.cpp,
	  programs/e2ctf.py, programs/e2refine_easy.py,
	  programs/e2refinemulti.py: Ok, this may be a risky commit for
	  normal EMAN2 refinements. Incorporated astigmatism into the
	  interface. Autofitting isn't working yet, but in theory
	  everything else should be ok. In theory...

2013-09-11 18:37  jgalaz

	* programs/e2spt_classaverage.py: [no log message]

2013-09-11 17:30  jgalaz

	* programs/e2spt_classaverage.py: [no log message]

2013-09-11 17:18  jgalaz

	* programs/e2spt_classaverage.py: Copy wedge header values from
	  simage and s2image  to sfixedimage and s2fixedimage rather than
	  having them be arbitrary, when fsc.tomo is used but
	  --refpreprocess is off.

2013-09-11 17:01  jgalaz

	* programs/: e2spt_classaverage.py: [no log message]

2013-09-11 16:43  jgalaz

	* programs/e2spt_hac.py: [no log message]

2013-09-11 16:43  jgalaz

	* programs/e2spt_classaverage.py: --refpreprocess to control
	  whether the reference gets preprocessed like the particles or
	  not. When using a PDB model as a reference, it shouln't be
	  preprocessed (or at least not like the particles). When NOT using
	  a reference, then the program builds one from the raw particles,
	  in which case preprocessing should occur. In particular, for
	  simulations, when the reference is NOT simulated (for control
	  tests), and the fsc.tomo comparator is being used, there's no
	  missing wedge to fit. However, the comparator requires missing
	  wedge statistics values on the reference as well. Dummy values
	  are written in this case.

2013-09-11 14:17  jgalaz

	* examples/e2spt_tomosimjobs.py: x axis plotting should start at 0.

2013-09-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-11 09:37  stevel

	* libEM/: ctf.cpp, ctf.h: More work on astigmatism fitting

2013-09-11 07:55  pawel

	* sparx/demo/SPARX_intro.pdf: [no log message]

2013-09-10 18:47  jgalaz

	* examples/e2spt_tomosimjobs.py: Bug fix when NOT simulating the
	  reference.

2013-09-10 13:02  stevel

	* libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emshape.py,
	  programs/e2ctf.py: Partial integration of astigmatism !

2013-09-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-09 18:29  jgalaz

	* programs/e2spt_classaverage.py: [no log message]

2013-09-09 18:02  jgalaz

	* examples/e2spt_tomosimjobs.py: [no log message]

2013-09-09 16:25  jgalaz

	* programs/e2spt_boxer.py: --path not created by default. Only if
	  specified.

2013-09-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-09 11:09  piotr

	* sparx/libpy/applications.py: bugfix

2013-09-09 10:50  pawel

	* sparx/bin/: sxheliconlocal.py, sxlocalhelicon.py: [no log
	  message]

2013-09-09 09:42  piotr

	* libEM/sparx/util_sparx.cpp: correction of warning

2013-09-08 12:03  pawel

	* sparx/libpy/applications.py: [no log message]

2013-09-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-08 11:37  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-09-08 11:20  pawel

	* sparx/libpy/applications.py: [no log message]

2013-09-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-07 11:06  pawel

	* sparx/libpy/applications.py, libEM/sparx/util_sparx.cpp: [no log
	  message]

2013-09-06 17:52  piotr

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: add function to calculate average of
	  differences between set of configurations (3d parameters)

2013-09-06 16:28  pawel

	* sparx/libpy/applications.py: [no log message]

2013-09-06 14:50  pawel

	* sparx/libpy/: applications.py, pixel_error.py: [no log message]

2013-09-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-06 09:07  stevel

	* libEM/ctf.cpp, libEM/ctf.h, programs/e2ctfsim.py: Astigmatism
	  fixes.

2013-09-06 08:09  stevel

	* examples/ctf_test.py, libEM/ctf.cpp, libEM/ctf.h: Ok, math in CTF
	  should be working again. Prototype of astigmatism support
	  (untested)

2013-09-06 00:04  stevel

	* libpyEM/libpyAligner2.cpp: Fixed now ?

2013-09-05 23:47  stevel

	* libEM/: ctf.cpp, ctf.h: Ok, CTF should compile again.

2013-09-05 23:40  stevel

	* libEM/ctf.h: compile on mac

2013-09-05 23:30  stevel

	* examples/ctf_test.py, libEM/ctf.cpp, libEM/ctf.h,
	  programs/e2speedtest.py: Now that alpha3 has been checked out,
	  I'm committing a risky patch to ctf.	It may break compilation,
	  but I need to check it in for some testing. Will fix it soon if
	  it's really broken.

2013-09-05 21:12  jgalaz

	* programs/e2spt_refinemulti.py, examples/e2spt_tomosimjobs.py,
	  examples/e2spt_transformdistance.py: [no log message]

2013-09-05 14:35  eman

	* doc/build/build.py: Typos

2013-09-05 14:31  eman

	* doc/build/: build.py, install.sh: Typo fixes in build.py; merge
	  pre2-1 in install.sh; remove extlib/site-packages from PYTHONPATH

2013-09-05 14:11  irees

	* doc/build/: build.py, dep.py: Merge pre2-1 back into trunk; Add
	  symlink from site-packages on Linux; Use CVS eman2-installer
	  instead of hard-coded

2013-09-05 13:58  stevel

	* programs/e2version.py: version stamp

2013-09-05 13:52  stevel

	* libEM/pmconfig/spr.json, programs/e2evalparticles.py: Last minute
	  fixes before 2.1alpha2

2013-09-05 12:30  stevel

	* programs/: e2refine.py, e2refine_easy.py, e2refinemulti.py:
	  remove e2refine, fix some display issues for refinemulti

2013-09-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-05 11:51  stevel

	* libpyEM/qtgui/emplot2d.py, programs/e2classaverage.py,
	  programs/e2ctfsim.py, programs/e2refinemulti.py: Big oops on the
	  missing class-average

2013-09-04 17:06  jgalaz

	* examples/e2spt_tomosimjobs.py: [no log message]

2013-09-04 16:59  jgalaz

	* examples/e2spt_transformdistance.py: --nolog option. For
	  simulations, this program is called literally dozens/hundreds of
	  times; if all calls are logged, this floods the log file.

2013-09-04 16:17  jgalaz

	* programs/: e2spt_classaverage.py, e2spt_refprep.py: [no log
	  message]

2013-09-04 12:36  stevel

	* libpyEM/qtgui/emimagemx.py, programs/e2ctfsim.py: New simple ctf
	  simulation program (functional but with bugs)

2013-09-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-03 17:26  jgalaz

	* examples/e2spt_tomosimjobs.py: --normproc available for user to
	  define, instead of defaulted.

2013-09-03 17:16  jgalaz

	* programs/e2spt_hac.py: [no log message]

2013-09-03 14:14  piotr

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  sparx/libpy/reconstruction.py: Add weights to reconstruction
	  algorithm

2013-09-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-03 07:26  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-09-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-09-02 09:57  pawel

	* sparx/: bin/sxhelixboxer.py, libpy/applications.py: corrected
	  faulty gridding windowing

2013-09-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-31 20:43  jgalaz

	* programs/: e2spt_classaverage.py, e2spt_hac.py,
	  e2spt_refinemulti.py: [no log message]

2013-08-31 20:21  jgalaz

	* programs/e2spt_hac.py: parameters.txt file written for this
	  program now too.

2013-08-31 20:21  jgalaz

	* programs/e2spt_refinemulti.py: parameters.txt file now written
	  for this program too.

2013-08-31 20:14  jgalaz

	* programs/e2spt_refinemulti.py: Many changes in this too (can't
	  remember specifically; mostly regarding subtomo_score.json files
	  and such). Compatible with --threshold now too.

2013-08-31 20:14  jgalaz

	* programs/e2spt_hac.py: --threshold option ( last commit to
	  e2spt_classaverage.py was regarding the new --threshold parameter
	  as well ).

2013-08-31 20:12  jgalaz

	* programs/e2spt_classaverage.py: [no log message]

2013-08-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-31 00:32  stevel

	* programs/: e2ctf.py, e2refine_easy.py: New negative background
	  fix

2013-08-30 12:19  piotr

	* libEM/sparx/util_sparx.h, sparx/libpy/applications.py,
	  sparx/libpy/reconstruction.py, libEM/sparx/util_sparx.cpp,
	  libpyEM/libpyUtils2.cpp: 1. Reconstruction can use one projection
	  with several xform.projection: The optional additional
	  xform.projections are saved in a header as [xform.projection1,
	  xform.projection2, ...]

	  2. Reconstruction with weights: Weights are read from the
	  header's parameters: weight, [weight1, weight2, ...].  If not set
	  the value 1.0 is assumed.

	  3. shc_multipeaks - version of shc() routine that can search for
	  several peaks instead of one. It also set weight[,1,2,...]
	  parameters in the header.

2013-08-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-29 12:06  pawel

	* sparx/libpy/applications.py: [no log message]

2013-08-29 12:05  pawel

	* sparx/bin/sxhelixboxer.py: new lines corrected

2013-08-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-28 14:09  piotr

	* libEM/reconstructor.cpp, sparx/bin/sxlocal_ali3d.py,
	  sparx/libpy/pixel_error.py: 2 bugfixes - problems were found
	  during testing mpi_bdb_ctf demo

2013-08-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-28 11:47  piotr

	* sparx/demo/: mpi_bdb/run_through_example,
	  mpi_bdb_ctf/run_through_example: bugfix in demo scripts

2013-08-27 22:33  stevel

	* programs/e2classextract.py: bugfix for empty classes

2013-08-27 12:25  pawel

	* sparx/libpy/pixel_error.py: [no log message]

2013-08-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-27 11:13  pawel

	* sparx/bin/: sxihrsr.py: [no log message]

2013-08-26 16:27  scmurray

	* programs/e2refinetorelion3d.py:
	  Fixed a logic mistake.

2013-08-26 16:03  piotr

	* sparx/: bin/sxali3d.py, libpy/alignment.py,
	  libpy/applications.py: add SHC to the alignment algorithms

2013-08-26 14:17  scmurray

	* programs/e2refinetorelion3d.py: Changed to reflect a change in
	  Relion 1.2

2013-08-26 14:15  pawel

	* sparx/libpy/statistics.py: [no log message]

2013-08-26 13:16  pawel

	* sparx/: bin/sxali2d.py, bin/sxshiftali.py, libpy/alignment.py,
	  libpy/applications.py: [no log message]

2013-08-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-23 17:16  piotr

	* sparx/demo/: mpi_bdb/run_through_example,
	  mpi_bdb_ctf/run_through_example: switch to bdb

2013-08-23 16:25  piotr

	* sparx/demo/: mpi_bdb/run_through_example,
	  mpi_bdb_ctf/run_through_example: bugfix - now sxprocess save
	  ideal projections to bdb:particles

2013-08-23 15:35  piotr

	* sparx/demo/: mpi_bdb/run_through_example,
	  mpi_bdb_ctf/run_through_example: bugfix

2013-08-23 15:17  pawel

	* sparx/libpy/fundamentals.py: corrected center in window2d

2013-08-23 14:51  piotr

	* sparx/: bin/sxprocess.py, demo/mpi_bdb/run_through_example,
	  demo/mpi_bdb_ctf/run_through_example: demo - switch to json files

2013-08-23 13:55  stevel

	* programs/: e2ctf.py, e2refinemulti.py: Rescaling fix (again)

2013-08-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-23 10:15  stevel

	* libpyEM/EMAN2.py: Change info_name() for better behavior with
	  subdirectories

2013-08-22 16:22  stevel

	* libpyEM/qtgui/emimage2d.py: Add coord to probe mode

2013-08-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-22 08:16  stevel

	* programs/e2refinemulti.py: Fixed map rescaling

2013-08-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-20 14:15  stevel

	* programs/e2refinemulti.py: minor bugfixes in e2refinemulti.py

2013-08-20 12:10  pawel

	* sparx/bin/sxhelixboxer.py: Julian's change

2013-08-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-20 11:56  pawel

	* sparx/: bin/sxprocess.py, demo/mpi_bdb/run_through_example,
	  demo/mpi_bdb_ctf/run_through_example: [no log message]

2013-08-20 10:56  stevel

	* libpyEM/qtgui/embrowser.py: fix tiny browser issue

2013-08-20 10:22  pawel

	* libEM/projector.cpp, libEM/sparx/util_sparx.cpp,
	  sparx/libpy/projection.py: general projector

2013-08-19 12:26  pawel

	* sparx/libpy/applications.py: [no log message]

2013-08-19 12:23  pawel

	* libEM/sparx/util_sparx.cpp: non-int rise!

2013-08-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-18 23:39  stevel

	* libEM/processor.cpp: Working on merging mode for watershed
	  segmentation.

2013-08-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-16 16:03  stevel

	* libEM/processor.cpp: working on watershed. Basic method working.
	  Still need to fix segment merging.

2013-08-16 15:29  stevel

	* libEM/processor.cpp: Mac compile problem

2013-08-16 15:09  stevel

	* libEM/processor.cpp: less debugging

2013-08-16 15:06  stevel

	* libEM/: processor.cpp, processor.h: Watershed still slightly
	  broken but will compile.

2013-08-16 14:50  pawel

	* sparx/: bin/sxlocalhelicon.py, libpy/applications.py: rise
	  changes!

2013-08-16 12:26  fjia

	* sparx/bin/: sxhelical_demo.py: [no log message]

2013-08-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-15 23:40  stevel

	* libEM/: processor.cpp, processor.h: Adding functional watershed

2013-08-15 17:45  fjia

	* sparx/bin/sxhelical_demo.py: [no log message]

2013-08-15 17:44  fjia

	* sparx/bin/sxhelical_demo.py: add option for generating run
	  through script for helicon

2013-08-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-15 10:11  stevel

	* programs/e2refinemulti.py: mass fix

2013-08-15 09:06  stevel

	* libpyEM/qtgui/embrowser.py, programs/e2refinemulti.py: Oops. Math
	  error.

2013-08-15 08:04  stevel

	* libEM/pmconfig/spr.json, programs/e2evalimage.py,
	  programs/e2refine_easy.py, programs/e2refinemulti.py: new
	  starting model generation for e2refinemulti

2013-08-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-14 10:44  fjia

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: [no log message]

2013-08-13 23:07  stevel

	* programs/e2refinemulti.py: sigh

2013-08-13 23:05  stevel

	* programs/e2refinemulti.py: trivial

2013-08-13 17:42  fjia

	* sparx/libpy/applications.py: [no log message]

2013-08-13 16:46  cailin

	* libpyEM/qtgui/: embrowser.py, emimagemx.py: dm4 stack

2013-08-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-13 11:43  fjia

	* sparx/bin/sxlocalhelicon.py: import from applications

2013-08-13 11:42  fjia

	* sparx/libpy/applications.py: move localhelicon here

2013-08-12 18:39  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-08-12 17:49  pawel

	* sparx/libpy/alignment.py: [no log message]

2013-08-12 16:53  pawel

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, sparx/libpy/alignment.py: local helicon
	  changes

2013-08-12 16:02  stevel

	* programs/: e2classextract.py, e2refinemulti.py: e2refinemulti is
	  working !  Now automatically splits particle populations for you
	  at end of run.

2013-08-12 15:48  pawel

	* libEM/sparx/util_sparx.cpp, sparx/libpy/alignment.py: [no log
	  message]

2013-08-12 13:24  cailin

	* libEM/: dm4io.cpp, dm4io.h: dm4 stack

2013-08-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-11 02:04  stevel

	* libpyEM/: EMAN2PAR.py, EMAN2db.py: Support for non-standard
	  mpirun command-lines

2013-08-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-09 21:20  stevel

	* install-dependencies.py: another tweak

2013-08-09 18:43  stevel

	* install-dependencies.py: Updated dependencies

2013-08-09 16:23  pawel

	* sparx/libpy/: applications.py, utilities.py: [no log message]

2013-08-09 13:40  stevel

	* programs/e2refinemulti.py: !@#!#$ another fix

2013-08-09 13:26  pawel

	* sparx/: bin/sxhelicon_utils.py, libpy/pixel_error.py: [no log
	  message]

2013-08-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-09 06:37  stevel

	* programs/: e2project3d.py, e2refinemulti.py: adusted model_id so
	  it starts at 1 instead of 0 following the new naming convention

2013-08-09 03:59  jgalaz

	* programs/e2classaveragebysym.py: Multiple bugs fixed in porting
	  this to EMAN2.1 and avoid BDB usage.

2013-08-08 22:44  stevel

	* programs/e2refinemulti.py: Working now ?

2013-08-08 18:36  jgalaz

	* programs/e2spt_refinemulti.py: [no log message]

2013-08-08 17:26  jgalaz

	* programs/e2spt_classaverage.py, programs/e2spt_refprep.py,
	  programs/e2spt_refinemulti.py, examples/e2fixheaderparam.py: [no
	  log message]

2013-08-08 13:52  pawel

	* sparx/bin/sxlocalhelicon.py: [no log message]

2013-08-08 13:41  fjia

	* sparx/bin/sxlocalhelicon.py: [no log message]

2013-08-08 13:33  fjia

	* sparx/bin/sxhelixboxer.py: [no log message]

2013-08-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-08 10:45  fjia

	* sparx/bin/sxhelixboxer.py: [no log message]

2013-08-08 10:40  fjia

	* sparx/bin/sxhelixboxer.py: [no log message]

2013-08-08 10:34  fjia

	* sparx/bin/sxhelixboxer.py: return with error message if twice the
	  particle radius in pixels is larger than boxsize

2013-08-08 10:30  fjia

	* sparx/bin/sxhelixboxer.py: [no log message]

2013-08-08 09:41  stevel

	* programs/: e2refine_postprocess.py, e2refinemulti.py: minor
	  bugfix in refinemulti

2013-08-08 09:35  stevel

	* programs/: e2buildsets.py, e2refinemulti.py: refinemulti may be
	  working (?)

2013-08-08 06:55  stevel

	* programs/e2refinemulti.py: refinemulti bugfix

2013-08-07 19:46  stevel

	* libEM/processor.cpp: Fixed normalize.bymass. It had previously
	  only worked with densities in a relatively narrow range. Now it
	  should work universally.

2013-08-07 15:51  stevel

	* libEM/: processor.cpp, processor.h: Debugging processors

2013-08-07 14:44  fjia

	* sparx/bin/sxhelixboxer.py: add --topdir option for specifying
	  path of directory containing the relevant micrograph directories

2013-08-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-07 11:19  stevel

	* programs/e2refine_easy.py: typo in initial model creation

2013-08-06 22:22  stevel

	* programs/e2refinemulti.py: refinemulti ready for initial testing

2013-08-06 17:30  fjia

	* sparx/bin/sxhelixboxer.py: don't use particle centroid if less
	  than 0.5*boxsize from either helix endpoint

2013-08-06 15:18  stevel

	* programs/: e2proc2d.py, e2refine_easy.py, e2refinemulti.py: More
	  work on refinemulti

2013-08-06 12:11  fjia

	* sparx/bin/sxhelixboxer.py: [no log message]

2013-08-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-05 23:33  stevel

	* programs/: e2refine_easy.py, e2refinemulti.py: Working on
	  refinemulti. not done

2013-08-05 23:01  jgalaz

	* programs/: e2spt_boxer.py, e2spt_classaverage.py,
	  e2spt_refinemulti.py: [no log message]

2013-08-05 23:01  jgalaz

	* programs/e2spt_hac.py: Preprocessing options for fine alignment
	  independent from coarse alignment enabled for e2spt_hac.py now.

2013-08-05 20:20  jgalaz

	* programs/e2symsearch3d.py: --mask is now available. Improved
	  verbosity as well.

2013-08-05 17:43  fjia

	* sparx/bin/sxhelicon_utils.py: [no log message]

2013-08-05 17:15  jgalaz

	* programs/e2spt_classaverage.py: Binary tree function for
	  reference free refinement was broken

2013-08-05 16:36  fjia

	* programs/e2helixboxer.py: reverting back to version 1.83

2013-08-05 16:29  fjia

	* sparx/bin/sxhelixboxer.py: [no log message]

2013-08-05 15:44  fjia

	* sparx/bin/: sxhelixboxer.py: [no log message]

2013-08-05 15:37  pawel

	* sparx/bin/sxhelixboxer.py: [no log message]

2013-08-05 14:56  stevel

	* programs/e2refinemulti.py: Working on new e2refinemulti. Not done
	  yet.

2013-08-05 14:52  pawel

	* sparx/bin/sxlocalhelicon.py: [no log message]

2013-08-05 13:43  fjia

	* sparx/bin/sxhelixboxer.py: helix boxer based on e2helixboxer

2013-08-05 12:51  pawel

	* sparx/: bin/sxhelicon_utils.py, libpy/utilities.py: [no log
	  message]

2013-08-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-05 12:00  piotr

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Change the name of Util::hans to
	  Util::shc

2013-08-05 11:46  pawel

	* sparx/bin/sxhelicon_utils.py: [no log message]

2013-08-05 11:42  pawel

	* sparx/bin/sxhelicon_utils.py: [no log message]

2013-08-05 11:34  fjia

	* sparx/bin/sxlocalhelicon.py: add options for wrapping and
	  boundary segment averaging

2013-08-05 09:44  stevel

	* libpyEM/qtgui/emboxerbase.py, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/emimagemx.py, programs/e2ctf.py,
	  programs/e2ddd_movie.py, programs/e2evalimage.py,
	  programs/e2helixboxer.py, programs/e2import.py: Minor bugfix in
	  boxerbase. Made double-clicking work on class-averages from
	  browser again.

2013-08-05 05:18  jgalaz

	* examples/e2fixheaderparam.py: [no log message]

2013-08-05 03:58  jgalaz

	* programs/e2spt_hac.py: New clusters.json file written, where the
	  indexes of particles are clustered into a user-defined number of
	  groups, simply based on the ranked scores.

2013-08-05 01:27  jgalaz

	* programs/e2spt_hac.py, programs/e2spt_refinemulti.py,
	  examples/e2spt_tomosimjobs.py: --radius option available
	  (functionality described for commit of e2spt_classaverage.py).

2013-08-05 01:24  jgalaz

	* programs/e2spt_classaverage.py: New function to calculat the
	  optimal alignment steps has been implemented, calcAliStep(). The
	  user only needs to provide the hydrodynamic radius of the
	  particles, and make sure that the apix values in the header are
	  correct. This can greatly optimize aligmment time.

2013-08-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-03 22:14  jgalaz

	* programs/e2spt_hac.py: lowpassfine, highpassfine, preprocessfine,
	  etc. options had to be included because they exist in
	  e2spt_classaverage.py and since both programs share the alignmnet
	  functions that uses them, they need to be in e2spt_hac too.

2013-08-03 22:10  jgalaz

	* programs/e2spt_hac.py: [no log message]

2013-08-03 21:59  jgalaz

	* examples/e2fixheaderparam.py: Bug fixed.

2013-08-03 21:58  jgalaz

	* programs/e2spt_refprep.py: Major changes. Entire stacks can now
	  be processed so that stack A matches stack B. Several bugs fixed
	  here and in relate programs.

2013-08-03 21:54  jgalaz

	* programs/e2spt_hac.py: Not sure what changed, but if the program
	  was open in my text editor, and the commit goes through,
	  something must have changed...

2013-08-03 13:14  pawel

	* sparx/bin/sxali3d.py: proposed corrections for shc

2013-08-03 13:13  pawel

	* sparx/libpy/filter.py: [no log message]

2013-08-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-02 19:33  jgalaz

	* programs/e2spt_classaverage.py: Resolved bug	with --shrink and
	  --shrinkrefine options after modifications to the preprocessing()
	  function to accomodate for using the fsc.tomo comparator.

2013-08-02 17:37  pawel

	* sparx/bin/sxali3d.py: [no log message]

2013-08-02 15:16  pawel

	* sparx/libpy/alignment.py: [no log message]

2013-08-02 14:53  pawel

	* sparx/libpy/applications.py: [no log message]

2013-08-02 14:35  fjia

	* sparx/libpy/: alignment.py, applications.py: [no log message]

2013-08-02 14:01  fjia

	* sparx/libpy/applications.py: remove pad from ihrsr

2013-08-02 13:47  pawel

	* sparx/libpy/: alignment.py, applications.py: [no log message]

2013-08-02 12:53  fjia

	* programs/e2helixboxer.py: [no log message]

2013-08-02 12:06  piotr

	* sparx/libpy/utilities.py: add parameter to
	  angles_between_anglesets

2013-08-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-01 21:54  stevel

	* programs/e2refine_easy.py: Trivial

2013-08-01 14:24  pawel

	* doc/build/install.sh: [no log message]

2013-08-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-08-01 11:24  fjia

	* programs/e2helixboxer.py: use distance between particles instead
	  of overlap for extracting particles

2013-08-01 10:35  pawel

	* libEM/sparx/util_sparx.cpp: time stamp

2013-08-01 09:59  piotr

	* libEM/sparx/util_sparx.cpp: hans - add one output parameter
	  (number of checked references) to the routine

2013-08-01 08:41  pawel

	* programs/e2helixboxer.py: type corrected

2013-08-01 00:10  irees

	* libpyEM/qtgui/emimagemx.py: Not quite ready to drop Python 2.6
	  support; the {i:j for i,j in iter} syntax not in 2.6.

2013-07-31 23:32  stevel

	* programs/e2refinemulti.py: multireine work

2013-07-31 14:13  fjia

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-07-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-31 12:00  fjia

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-07-31 10:50  fjia

	* programs/e2helixboxer.py: [no log message]

2013-07-30 23:23  stevel

	* programs/e2ctf.py: trivial

2013-07-30 23:22  stevel

	* programs/e2ctf.py: storeparm limits

2013-07-30 23:10  stevel

	* programs/e2ctf.py: Fix for non-split CTF

2013-07-30 23:07  stevel

	* libpyEM/EMAN2jsondb.py, programs/e2ctf.py: trivial ctf fix

2013-07-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-30 07:48  stevel

	* programs/e2refine_easy.py: trivial

2013-07-29 18:19  fjia

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-07-29 18:13  fjia

	* libEM/sparx/util_sparx.cpp: fix mirror in
	  multiref_polar_ali_helical_local

2013-07-29 16:27  jgalaz

	* programs/e2spt_classaverage.py: The new and correct
	  implementation of the preprocessing() function to accomodate for
	  the fsc.tomo comparator the propper way was broken when --shrink
	  or --shrinkrefine were larger than 1. Fixed now.wq!

2013-07-29 14:22  stevel

	* programs/: e2ctf.py, e2refine_postprocess.py: Fix CTF

2013-07-29 13:56  irees

	* programs/e2pathwalker.py: Fixed problem with subprocess.Popen()
	  with LKH TSP solver

2013-07-29 12:51  fjia

	* sparx/bin/sxhelicon.py: [no log message]

2013-07-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-29 10:37  fjia

	* sparx/libpy/applications.py: back out changes in ehelix_MPI for
	  stopping criterion

2013-07-29 07:51  stevel

	* programs/e2refine2d.py: new acf centering option

2013-07-29 04:31  jgalaz

	* programs/e2spt_classaverage.py: NASTY bug regarding writing
	  alignent parameters for EACH alignment as it happened was fixed.
	  Parameters written after each task is completed, but in
	  get_results() instead of in alignment(), so this presumably is in
	  the "master process" opposed to the "client".

2013-07-29 02:32  jgalaz

	* examples/e2spt_tomosimjobs.py: Changed to be in line with the
	  removal of --fitwedgepost from e2spt_classaverage.py .

2013-07-29 02:31  jgalaz

	* programs/e2spt_classaverage.py: --fidwedgepost has been
	  eliminated (it was only experimental).  In light of how things
	  SHOULD be done, it made no sense to have such option.  When
	  --raligncmp=fsc.tomo or --aligncmp=fsc.tomo, you ALWAYS have to
	  fit the missing wedge parameters AFTER all possible processing
	  steps that don't "put stuff" in the wedge, but BEFORE parameters
	  that can alter the values of the voxels inside the wedge.  The
	  only processor applied which seems to clearly affect the missing
	  wedge is masking.  Therefore, if fsc.tomo is selected, masking is
	  the last step, and the mask-normalize-mask scheme of
	  preprocessing is avoided.

2013-07-28 23:12  jgalaz

	* programs/e2spt_hac.py: [no log message]

2013-07-28 22:15  jgalaz

	* examples/e2figureplot.py, examples/e2spt_ctf.py,
	  examples/e2spt_cudatimetest.py, examples/e2spt_tomosimjobs.py,
	  programs/e2spt_autoboxer.py: [no log message]

2013-07-28 22:13  jgalaz

	* programs/e2spt_hac.py:	matplotlib related imports happen
	  within the plotter function only, to prevent some useless warning
	  messages that occurred when e2spt_classaverage.py was run (and
	  the parallelization tasks were imported)

2013-07-28 22:12  jgalaz

	* programs/e2spt_classaverage.py: Dictionaries for alignment and
	  score results are now opened only ONCE *before* iterating over
	  the particles in a class, and close only ONCE, after the loop.

2013-07-28 21:45  jgalaz

	* libpyEM/EMAN2jsondb.py: Changed an aberrant occurrence of ".js"
	  to ".json".

2013-07-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-28 03:35  jgalaz

	* programs/e2spt_simulation.py: Was broken when ran directly for
	  multiple models simultaneously. Fixed now (presumably).

2013-07-28 02:17  jgalaz

	* programs/e2spt_scramblestack.py: [no log message]

2013-07-28 00:55  jgalaz

	* programs/e2spt_scramblestack.py: This program scrambles the
	  position (n) of particles in a stack.

2013-07-27 23:36  jgalaz

	* programs/: e2spt_hac.py, e2spt_classaverage.py: [no log message]

2013-07-27 17:09  jgalaz

	* programs/e2spt_hac.py: Minor bug tweaks.

2013-07-27 16:49  jgalaz

	* programs/e2spt_hac.py: simmx.hdf files now written for every
	  iteration of all vs all. Plots dsiplaying the decay in
	  correlation written too.

2013-07-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-26 17:26  fjia

	* sparx/bin/sxhelicon.py: [no log message]

2013-07-26 17:20  fjia

	* sparx/libpy/applications.py: :VS:
	  ----------------------------------------------------------------------

2013-07-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-26 10:33  stevel

	* libpyEM/qtgui/embrowser.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emplot2d.py, programs/e2ctf.py,
	  programs/e2evalrefine.py, programs/e2proc2d.py: Fixed plotting
	  problem with same filename in different directories. Working on
	  new e2ctf features. Hopefully not broken.

2013-07-25 15:29  fjia

	* sparx/libpy/applications.py: add stopping criterion (based on
	  pixel errors) to ehelix_MPI

2013-07-25 15:27  fjia

	* sparx/bin/sxhelicon.py: [no log message]

2013-07-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-25 06:17  jgalaz

	* programs/e2spt_subtilt.py: FINALLY working! (It's depressing for
	  how long the SILLIEST bug got in the way...).

2013-07-24 13:23  fjia

	* sparx/libpy/applications.py: [no log message]

2013-07-24 13:21  fjia

	* sparx/libpy/applications.py: comment out printouts

2013-07-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-24 11:36  pawel

	* sparx/bin/sxali3d.py: [no log message]

2013-07-24 01:05  jgalaz

	* programs/e2spt_hac.py: Path where simmx was written was wrong.

2013-07-24 01:02  jgalaz

	* programs/e2spt_hac.py: Plotter buggy.

2013-07-24 00:59  jgalaz

	* programs/e2spt_refinemulti.py: In theory, this program is FINALLY
	  finished, as in there are no crashes. It sucessfully refines a
	  stack of 3D volumes against N-references (in terms of generating
	  the correct files). It still needs to be tested for functionality
	  with data where the answer is known.

2013-07-24 00:58  jgalaz

	* programs/e2spt_classaverage.py: Not sure what changed (can't
	  remember).

2013-07-24 00:57  jgalaz

	* programs/e2spt_hac.py: --minscore implemented to allow/forbid
	  mergers based on a percentage of the maximum score (presumably,
	  when the correlation has fallen enough, the particles are
	  probably no longer in the same "class").

	  Finally, simmx.hdf file written for the first iteration.

	  Scatter plot generated of ranked comparison scores too.

2013-07-23 19:39  stevel

	* libpyEM/EMAN2PAR.py: Fix accidental task directory creation

2013-07-23 17:16  fjia

	* programs/e2helixboxer.py: In cter command line mode, write
	  estimated ctf to micrograph header

2013-07-23 17:16  fjia

	* sparx/libpy/morphology.py: in cter, add option for writing
	  estimated ctf to micrograph header

2013-07-23 16:43  fjia

	* programs/e2boxer.py: [no log message]

2013-07-23 16:30  fjia

	* programs/e2helixboxer.py: [no log message]

2013-07-23 12:23  stevel

	* libpyEM/: EMAN2.py, EMAN2jsondb.py: dir creation

2013-07-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-23 11:57  stevel

	* examples/mpi_test.py: Fixed mpi_test for new mpi system

2013-07-23 11:45  piotr

	* sparx/libpy/alignment.py: prepare_refrings - possibility of set
	  MPI communicator through the parameter named MPI

2013-07-23 11:16  fjia

	* sparx/bin/sxhelicon.py: [no log message]

2013-07-23 11:14  fjia

	* sparx/libpy/applications.py: move ehelix_MPI here

2013-07-23 02:41  jgalaz

	* programs/e2spt_classaverage.py, programs/e2spt_simulation.py,
	  examples/e2spt_tomosimjobs.py: [no log message]

2013-07-22 15:02  pawel

	* sparx/libpy/pixel_error.py: [no log message]

2013-07-22 13:03  pawel

	* sparx/libpy/utilities.py: [no log message]

2013-07-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-22 08:08  stevel

	* programs/e2refinemulti.py: warning message

2013-07-22 00:58  jgalaz

	* programs/e2spt_refinemulti.py: Options not pertaining to this
	  program (copied from e2spt_classaverage) have been commented out.
	  Sensible error message for non existent input file provided to
	  users now.

2013-07-22 00:47  jgalaz

	* programs/e2spt_boxer.py: --path options actually functional now,
	  using sptpathmaker (imported from e2spt_classaverage.py).  All
	  traces of mentioning bdb: format are now commented out.
	  --bruteaverage now saved inside --path (wasn't previously).

2013-07-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-20 23:25  stevel

	* libpyEM/qtgui/emimagemx.py, programs/e2evalparticles.py,
	  programs/e2refine_easy.py, programs/e2refinemulti.py: working on
	  new refinemulti

2013-07-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-20 02:19  jgalaz

	* programs/e2spt_classaverage.py: Preprocessing should never be
	  normalize,mask or normalize,mask,normalize,mask (except perhaps
	  if using normalize.mask? Not sure).  Initial normalization of the
	  entire box can induce artificats if there are strong densities
	  besides protein in your box (which unfortunately has to be twice
	  as large as the particle).  Therefore, you mask first, normalize
	  the density inside the mask only, then mask again to get rid of
	  the aberrant values outside the mask generated from normalizing a
	  masked volume.

2013-07-19 17:20  piotr

	* sparx/libpy/utilities.py: add parameter with mpi communicator

2013-07-19 17:16  piotr

	* sparx/libpy/: reconstruction.py, statistics.py: add parameter
	  with mpi communicator to many functions

2013-07-19 14:35  piotr

	* sparx/libpy/statistics.py: minor bugfix in varf3d_MPI

2013-07-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-19 05:55  jgalaz

	* programs/e2spt_simulation.py: Debugged for circumstances
	  previously described for e2spt_tomosimjobs latest commit.

2013-07-19 05:54  jgalaz

	* programs/e2spt_resolutionplot.py: Can't remember.

2013-07-19 05:54  jgalaz

	* examples/e2spt_rotationalplot.py: Particle symmetrized internally
	  now if --sym is provided, via symmetrize function.

2013-07-19 05:53  jgalaz

	* examples/e2spt_tomosimjobs.py: Debugged for when there is NO
	  --testalignment, and where --saveprjs is on, and when
	  --notrandomize is on

2013-07-18 23:43  jgalaz

	* examples/e2spt_tomosimjobs.py: Hopefully bug free now under every
	  possible circumstance described in last commit. Tested all
	  simultaneously (because it so happens that when you get condition
	  A working, but B is borken, in fixing B you break A, and then in
	  fixing A you break B again...; the point being, the loop of
	  breaking and fixing the script to work under all circumstances
	  previously described has presumably ended).

2013-07-18 23:41  jgalaz

	* programs/e2spt_simulation.py: Who knows. Several small changes
	  while debugging e2spt_tomosimjobs (which calls this program).

2013-07-18 23:40  jgalaz

	* programs/e2spt_classaverage.py: Bugs fixed. Plus more sensible
	  way of writing out class_xxx.hdf files. The number of xxx
	  shouldn't be arbitrary but rather determined by the order of
	  magnitud of the number of classes.

2013-07-18 17:43  jgalaz

	* programs/e2spt_classaverage.py: Compartmentalization of reference
	  generation via the binary tree algorithm into its own function
	  hadn't been fully tested. Thoroughly debugged now.

2013-07-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-18 08:24  jgalaz

	* programs/e2spt_simulation.py: Not sure what changed (can't think
	  at this point :/ ).

2013-07-18 08:23  jgalaz

	* examples/e2spt_tomosimjobs.py: Presumably this works (without
	  breaking) for testing alignment accuracy in ALL of the following
	  cases under different wedge size, noise amount, and/or tilt step
	  size simulated conditions: 1) Test the efficiency of a single
	  comparator, 2) or multiple comparators, 3) the accuracy of the
	  answers after a single fixed value of iterations, 4) after
	  multiple iteration values (for example, if you want to test
	  whether 8 iterations will get you closer to the answer than 4, or
	  than 2, etc...; you can test ALL of those iteration numbers with
	  ONE command).

	  Actual FUNCTIONALITY has to be tested; but for now, there seem to
	  be no bugs that break any of the programs called, and all result
	  files and plots are generated and written as/where they should.

2013-07-18 03:51  jgalaz

	* examples/e2spt_tomosimjobs.py: When --comparators has only ONE
	  comparator, the program should default to the mode where
	  --comparators are NOT provided, but rather ONE comparator is
	  specified through --aligncmp and --raligncmp

2013-07-18 03:34  jgalaz

	* examples/e2spt_tomosimjobs.py: The iteration of adapating/fixing
	  other programs when they depend/work-with others is endless.
	  Testing several comparators at the same time was broken, now
	  fixed.

2013-07-17 21:31  jgalaz

	* examples/e2spt_tomosimjobs.py: Does not crash any more when
	  --iter > 1. Need to perform "real" measurable tests now, more
	  than just debugging.	Verbosity filters improved for this and
	  other programs with changes recently committed (e.g.,
	  e2spt_classaverage and e2spt_simulation).

2013-07-17 21:30  jgalaz

	* examples/e2spt_transformdistance.py: Was buggy when --transform
	  was not a transform but rather a tomo_xforms.json file from
	  e2spt_classaverage.py

2013-07-17 21:29  jgalaz

	* programs/e2spt_simulation.py: Several changes during debugging of
	  e2spt_tomosimjobs to function with --iter > 1

2013-07-17 21:28  jgalaz

	* programs/: e2spt_classaverage.py, e2spt_refinemulti.py: Can't
	  remember what changes (changing so many programs back and
	  forth...). Must have been something trivial related to changes in
	  other programs.

2013-07-17 21:07  pawel

	* sparx/libpy/statistics.py: [no log message]

2013-07-17 18:19  jgalaz

	* programs/e2spt_classaverage.py: IF writing/updating > ONE .json
	  dictionary in the same loop in the same script, it SEEMS like you
	  DO need to close each dictionary, js.close(), to avoid the
	  following error: (e2spt_classaverage changes accordingly)

	  File "/Users/jgalaz/EMAN2/lib/EMAN2jsondb.py", line 773, in
	  setval     if not deferupdate : self.sync()	File
	  "/Users/jgalaz/EMAN2/lib/EMAN2jsondb.py", line 681, in sync
	  raise Exception,"WARNING: file '{}' cannot be created, conflict
	  in writing JSON files. You may consider reporting this if you
	  don't know why this
	  happened.".format(self.normpath[:-3]+"_tmp.js") Exception:
	  WARNING: file
	  '/Volumes/int_3p0/simulations/simulationPaper/ubq/TESTwedge/TR050_NS050_SNR00.00/TR050_NS050_SNR00.00_ali/subtomo_scores.j_tmp.js'
	  cannot be created, conflict in writing JSON files. You may
	  consider reporting this if you don't know why this happened.

2013-07-17 16:35  fjia

	* libEM/sparx/util_sparx.cpp: uncomment old constrained_helix
	  (without SHC) and rename to constrained_helix_exhaustive

2013-07-17 16:34  fjia

	* libEM/sparx/util_sparx.h: add header for
	  constrained_helix_exhaustive (constrained_helix without SHC)

2013-07-17 16:33  fjia

	* libpyEM/libpyUtils2.cpp: add constrained_helix_exhaustive (for
	  ehelix without SHC)

2013-07-17 16:33  fjia

	* sparx/bin/sxhelicon.py: put in --exhaustive option to do ehelix
	  without SHC

2013-07-17 16:03  jgalaz

	* programs/e2spt_refinemulti.py: Radical newbie discovery: Replaced
	  usage of os.system() for subprocess.Popen() [Will have to do this
	  in ALL SPT scripts...].

	  This allows for usage of:

	  p.wait()

	  or even better

	  p.communicate()

	  So that subprocesses can be ran AS COMMANDS ARE BEING GENERATED,
	  AS A SCRIPT PROGRESSES, instead of linking dozens of commands
	  together and executing them till the very end: cmd = cmd1 + '&& '
	  + cmd2 + ' && ' + ... + cmdN os.system( cmd )

2013-07-17 14:22  jgalaz

	* examples/e2spt_tomosimjobs.py: Intermediate (broken after
	  enabling multiple iterations).

2013-07-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-17 11:42  scmurray

	* programs/e2refinetorelion3d.py: Made a change where Relion had
	  renamed files but not mentioned that anywhere.

2013-07-17 03:56  jgalaz

	* programs/e2spt_refinemulti.py: The program now succesfully
	  determines which particles look more like which reference, and
	  extracts the appropriate aignment parameters for that reference.

2013-07-16 23:50  jgalaz

	* examples/e2spt_transformdistance.py: Can now take in a transform
	  via --transform to compensate for the fact that if --iter > 1 the
	  alignment solutions will be respect to the last refined reference
	  and not the original reference from which particles were
	  simulated with e2spt_simulation.  e2spt_tomosimjobs has been
	  modified accordingly to accomodate for this.	One round of
	  alignment CANNOT align all the particles correctly, with varying
	  degrees of challenge (this needs to be accounted for in
	  simulations as well).wq!

2013-07-16 23:47  jgalaz

	* examples/e2spt_tomosimjobs.py: It turns out, for ANY objective
	  test the stack of particles in RANDOM orientations ALWAYS has to
	  be the same as a variable varies.  The SIMULATED stack (which is
	  based on the RANDOME-orientations-stack) will be different at
	  each point in the variable being analized.  Previous commit
	  fixexd this when testing for SNR variations.	This commit fixes
	  the problem for ANY parameter variations. The random stack is
	  computed ONCE, and from that, simulated stacks as needed.

2013-07-16 23:44  jgalaz

	* programs/e2spt_classaverage.py: Trivial

2013-07-16 17:58  fjia

	* sparx/bin/sxlocalhelicon.py: [no log message]

2013-07-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-16 10:30  stevel

	* TODO, libpyEM/EMAN2PAR.py, libpyEM/qtgui/embrowser.py,
	  programs/e2classaverage.py, programs/e2project3d.py,
	  programs/e2projectmanager.py, programs/e2refine_easy.py,
	  programs/e2refine_postprocess.py, programs/e2simmx2stage.py: Fix
	  parallel bug I thought was fixed before...

2013-07-16 04:59  jgalaz

	* programs/e2spt_refinemulti.py: [no log message]

2013-07-16 04:58  jgalaz

	* programs/e2spt_refinemulti.py: UNDER DEVELOPMENT: Public realease
	  version with basic functionality: The program can align a dataset
	  against multiple references and produce an average for each
	  (without classification), and write out tomo_xform.json and
	  subtomo_scores.json files (from the latter, one can know to which
	  reference any given particle in the set is more similar). [I had
	  a VERY old version of this program working, but never translated
	  it into "official" EMAN2 format; doing so was proving too painful
	  and thus I just started again from scratch].

2013-07-16 04:54  jgalaz

	* programs/e2spt_classaverage.py: --makeaverage has been replaced
	  by --donotaverage, and debugged by running e2spt_refinemulti.py

2013-07-16 03:30  jgalaz

	* programs/e2spt_classaverage.py: CCC values for sutomos_score.json
	  file need to be str not int per warnings on the Wiki.

2013-07-16 03:28  jgalaz

	* programs/e2spt_classaverage.py: Modified so that the alignment
	  function does not write tomo_xform.json files when called by
	  e2spt_hac.py.  Also, subtomo_scores.json files are now written,
	  to be used by e2spt_refinemulti.py.  Lastly, preparing a
	  reference using the 'binary tree' approach has been
	  compartmentalized into its own fuction to read the code more
	  easily.

2013-07-16 03:26  jgalaz

	* programs/e2spt_hac.py: e2spt_hac should not write tomo_xform.json
	  files, so this has been disabilitated. Eventually, it needs to
	  write simmx files.

2013-07-15 20:38  jgalaz

	* examples/e2spt_tomosimjobs.py: When exploring alignments under
	  varying levels of noise, you have to use the SAME stack, that is,
	  the same particles with randomized orientation, and only change
	  the noise in their projections before backprojecting them to
	  reconstruct the simulated subtomograms. Previously, a fresh stack
	  of particles was used at each noise point (which wasn't an
	  accurate test).

2013-07-15 20:36  jgalaz

	* programs/e2spt_simulation.py: Adapted to be compatible with
	  e2spt_tomosimjobs.py so that under varying noise conditions ONLY
	  the stack of particles in random orientations (before generating
	  projections and adding noise) doesn't have to be re-computed each
	  time.

2013-07-15 20:34  jgalaz

	* programs/e2spt_classaverage.py: --writewedge now off by default.
	  Other small bug fixed.

2013-07-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-15 10:49  pawel

	* libEM/sparx/util_sparx.cpp: clean constrained SHC

2013-07-15 10:44  scmurray

	* programs/e2refinetorelion3d.py: Fixed an embarassing bug where
	  defocus was in nm, not Angstroms as needed

2013-07-15 01:08  jgalaz

	* programs/e2spt_simulation.py: [no log message]

2013-07-15 01:08  jgalaz

	* programs/e2spt_classaverage.py: Trivial.

2013-07-15 00:41  jgalaz

	* examples/e2spt_tomosimjobs.py: --parallel now passed on to
	  e2spt_simulation.py for significant speedup.

2013-07-15 00:38  jgalaz

	* libpyEM/EMAN2PAR.py: Importing SubtomoSimTask for parallelization
	  in e2spt_simulation.py.

2013-07-15 00:37  jgalaz

	* programs/e2spt_hac.py: Trivial.

2013-07-15 00:29  jgalaz

	* programs/e2spt_classaverage.py: If using the fsc.tomo comparator,
	  the fitted shape of the missing wedge is written out now to
	  wedge.hdf. It can be turned off with --writewedge=False

2013-07-14 23:54  jgalaz

	* programs/e2spt_simulation.py: Function that generates projections
	  of angularly randomized particles and backprojects them to
	  simulate subtomograms is now PARALLELIZED.  [One could still
	  include the randomization of orientations in the parallelization
	  process too... hm]

2013-07-14 22:02  jgalaz

	* programs/e2spt_simulation.py: trivial

2013-07-14 12:59  fjia

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-07-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-13 01:37  stevel

	* programs/: e2proc3d.py, e2refine_postprocess.py: alignment
	  problem in refine_easy

2013-07-13 01:30  stevel

	* programs/: e2proc3d.py, e2refine_easy.py,
	  e2refine_postprocess.py: Fixed bug with Z alignment

2013-07-13 01:16  stevel

	* libpyEM/EMAN2.py: Did someone undo one of my changes ?  I can't
	  check from china...

2013-07-13 00:49  stevel

	* programs/: e2proc3d.py, e2projectmanager.py,
	  e2refine_postprocess.py: oops alignment bug

2013-07-12 22:36  stevel

	* programs/e2rawdata.py: grr

2013-07-12 22:24  stevel

	* libpyEM/EMAN2jsondb.py, libpyEM/qtgui/embrowser.py,
	  programs/e2import.py, programs/e2initialmodel.py,
	  programs/e2proc3d.py, programs/e2rawdata.py,
	  programs/e2refine2d.py, programs/e2refine_postprocess.py: Fix
	  data import issue

2013-07-12 20:14  jgalaz

	* programs/e2spt_hac.py: [no log message]

2013-07-12 20:07  jgalaz

	* programs/e2spt_hac.py: Since the alignment function is now
	  imported from e2spt_classaverage and the writing of
	  tomo_xforms.json happens in there, this had to be enabled and
	  costumized for e2spt_hac. Not sure it's working properly yet, BUT
	  at least it's not broken and tomo_xforms.json files produces by
	  e2spt_hac can be ignored for now.

2013-07-12 20:02  jgalaz

	* programs/e2spt_classaverage.py: Slight changes had to be made
	  after latest changes in tomo_xforms.json files writing to enable
	  funcionality for e2spt_hac

2013-07-12 18:39  jgalaz

	* programs/e2spt_classaverage.py: Changes variables p, ptcl and
	  ptcls to ptclnum, ptclnum and ptclnums, because these were
	  effectively "counters" or indeces of particle numbers, NOT
	  particles themselves. These names make things clearer by being
	  more descriptive.

	  Most significantly, storage of particle orientations in
	  tomo_xforms.json happened AFTER all particles had been aligned
	  (which was absurd).  Now they are stored AS EACH alignment task
	  is completed. This will shortly enable "recovering" completed
	  alignments from crashed jobs. This can potentially be a very
	  significant time-saver for large sets, or for sets involving big
	  particles.

	  Lastly, I changed the labeles for transforms in tomo_xforms.json
	  files so that the label identifying each particle transform
	  doesn't have an arbitrarily large/short numbers of zeros.  For
	  example, in a set of 5 particles, a "tomo_0005" label makes no
	  sense (why the zeros?). On the other hand, the 4 digits in the
	  string would be insufficient for a dataset of 10,000 particles or
	  more.  Thus, the label is NOW determined based on the size of the
	  data set. I.e., particle #5 in a data set of 9 or less, will have
	  a label "tomo_5", whereas particle 5 in a dataset between 1000
	  and 9999 will be labeled "tomo_0005".

2013-07-12 17:45  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-07-12 14:56  fjia

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-07-12 14:42  cailin

	* programs/e2pdb2mrc.py: calculate the box size according to the
	  atom locations.

2013-07-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-12 10:27  piotr

	* libEM/sparx/util_sparx.cpp, sparx/bin/sxali3d.py: change arrays
	  of bool to vector

2013-07-12 02:53  stevel

	* programs/e2spt_hac.py: remove spurious debugging

2013-07-12 02:33  stevel

	* programs/e2boxer.py: e2boxer was broken. Fix to progress

2013-07-12 00:58  jgalaz

	* programs/e2spt_classaverage.py: --inixforms (parameter that takes
	  a .json file where all the alignments of a set are stored) was
	  not working.	Now it is, AND the program can take --inxiforms to
	  align particles even in the ABSENCE of --align and --ralign.

2013-07-11 18:35  jgalaz

	* examples/e2spt_tomosimjobs.py: [no log message]

2013-07-11 13:48  pawel

	* libEM/sparx/util_sparx.cpp: ready for testing

2013-07-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-11 11:36  pawel

	* libEM/sparx/util_sparx.cpp: slow ready?

2013-07-11 10:42  pawel

	* libEM/sparx/: util_sparx.cpp: [no log message]

2013-07-10 19:50  jgalaz

	* examples/e2spt_tomosimjobs.py: There was still a pervading bug
	  concerning usage of bdb files in this script. Fixed now.

2013-07-10 17:08  pawel

	* libEM/sparx/util_sparx.cpp, sparx/libpy/morphology.py: [no log
	  message]

2013-07-10 15:33  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-07-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-10 10:35  fjia

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-07-10 01:39  jgalaz

	* programs/e2spt_classaverage.py: Hadn't tested this for EMAN2.1 in
	  the ABSCENCE of a reference. Was buggy without --ref. Now
	  working.

2013-07-10 01:15  jgalaz

	* programs/e2spt_simulation.py: Default options now produce a
	  sensible outcome to minimize typing for quick testing.

2013-07-10 00:50  jgalaz

	* programs/e2spt_simulation.py: sptmakepath now imported from
	  e2spt_classaverage.py. Plus, --finalboxsize is no longer
	  requiried. If not provided, the boxisze is read from the data
	  provided through --input.

2013-07-10 00:44  jgalaz

	* programs/e2spt_hac.py: [no log message]

2013-07-10 00:41  jgalaz

	* programs/e2spt_hac.py: About 200 lines of code saved from
	  recycling sptmakepath, preprocessing and alignment functions from
	  e2spt_classaverage.py.  Program works with EMAN2.1 now.

2013-07-10 00:40  jgalaz

	* programs/e2spt_classaverage.py: [no log message]

2013-07-09 20:32  jgalaz

	* examples/e2spt_tomosimjobs.py: makepath function was moved to
	  e2spt_classaverage (to recycle across programs) and became
	  sptmakepath.	Other minor changes.

2013-07-09 20:31  jgalaz

	* programs/e2spt_classaverage.py: Fully functional now without BDB
	  stuff.

2013-07-09 18:17  stevel

	* libpyEM/EMAN2jsondb.py: trivial

2013-07-09 17:22  stevel

	* libpyEM/EMAN2jsondb.py: trivial

2013-07-09 16:55  pawel

	* sparx/libpy/statistics.py: randprojdir

2013-07-09 15:21  jgalaz

	* examples/e2spt_tomosimjobs.py: This was broken for running on
	  multiple models after enable simultaneous testing of multiple
	  comparators. It's fixed now. Plus, the code was significantly
	  reduced through elimination of some redundancies/inneficiencies

2013-07-09 14:42  pawel

	* sparx/libpy/: morphology.py, pixel_error.py: additional error
	  info in sxcter

2013-07-09 13:24  pawel

	* libEM/ctf.cpp: blocked annoying printout

2013-07-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-09 11:49  piotr

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: [no log message]

2013-07-09 11:32  cailin

	* libEM/glutil.cpp: l out of boundary(lmax) in pixel averaging.

2013-07-09 11:08  piotr

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: new version of the
	  Util::constrained_helix  function

2013-07-09 09:15  piotr

	* sparx/libpy/global_def.py: bugfix - (print RANDOMSEED)

2013-07-08 14:29  scmurray

	* libEM/pmconfig/spr.json: Removed FreAlign until it is fixed.

2013-07-08 13:47  piotr

	* sparx/libpy/: global_def.py, utilities.py: new routine
	  angles_between_anglesets() calculated minimal angles between
	  projections from two anglesets

2013-07-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-08 11:23  fjia

	* sparx/bin/sxhelicon.py: [no log message]

2013-07-08 11:23  irees

	* libpyEM/qtgui/emimagemx.py: ... accidentally used spaces instead
	  of tabs.

2013-07-08 10:56  pawel

	* sparx/bin/sxcter.py: [no log message]

2013-07-08 09:38  piotr

	* libEM/sparx/util_sparx.cpp: bugifx in hans (ali3d)

2013-07-08 08:51  irees

	* doc/build/: build.py, dep.py, i686-redhat-linux.sh, install.sh,
	  order.txt, x86_64-redhat-linux.sh: Additional updates for pre2-1;
	  merged extlib/python, extlib/qt into extlib; Use $ORIGIN instead
	  of $LD_LIBRARY_PATH on Linux.

2013-07-08 08:45  irees

	* libpyEM/qtgui/emimagemx.py: List comprehensions in {} are a
	  Python 2.7 feature. Switched to dict(...)

2013-07-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-07 01:49  jgalaz

	* programs/e2spt_subtilt.py: Rethought. Needs testing.

2013-07-07 01:33  jgalaz

	* examples/e2fixheaderparam.py: Spurious feedback fixed.

2013-07-07 01:33  jgalaz

	* programs/e2spt_classaverage.py: '>>>' issue resolved. Cleaned
	  minimally in passing.

2013-07-06 23:05  stevel

	* programs/e2projectupdate21.py: Skip bad sets

2013-07-06 17:00  stevel

	* CMakeLists.txt, TODO, examples/mpi_test.py,
	  examples/reconstruct_fill.py, libEM/CMakeLists.txt,
	  libEM/ctf.cpp, libEM/emcache.cpp, libEM/emcache.h,
	  libEM/emdata.cpp, libEM/emdata_io.cpp, libEM/emobject.cpp,
	  libEM/emutil.cpp, libEM/emutil.h, libEM/hdf_filecache.h,
	  libEM/hdfio2.cpp, libEM/lstfastio.cpp, libEM/lstio.cpp,
	  libEM/processor.cpp, libEM/processor.h, libEM/xydata.cpp,
	  libEM/xydata.h, libEM/pmconfig/spr.json, libpyEM/EMAN2.py,
	  libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py, libpyEM/EMAN2fsc.py,
	  libpyEM/EMAN2jsondb.py, libpyEM/emdata_wrapitems.cpp,
	  libpyEM/libpyCmp2.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/typeconverter.h, libpyEM/qtgui/emboxerbase.py,
	  libpyEM/qtgui/embrowser.py, libpyEM/qtgui/emdataitem3d.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emplot2d.py,
	  libpyEM/qtgui/empmtabwidgets.py, libpyEM/qtgui/empmwidgets.py,
	  libpyEM/qtgui/emselector.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2boxer.py, programs/e2buildsets.py,
	  programs/e2buildstacks.py, programs/e2classaverage.py,
	  programs/e2ctf.py, programs/e2eulerxplor.py,
	  programs/e2evalimage.py, programs/e2evalparticles.py,
	  programs/e2import.py, programs/e2initialmodel.py,
	  programs/e2make3d.py, programs/e2montecarlorecon.py,
	  programs/e2proc2d.py, programs/e2proc3d.py,
	  programs/e2project3d.py, programs/e2projectmanager.py,
	  programs/e2projectupdate21.py, programs/e2rct.py,
	  programs/e2refine.py, programs/e2refine2d.py,
	  programs/e2refine_auto.py, programs/e2refine_easy.py,
	  programs/e2refine_evenodd.py, programs/e2refine_postprocess.py,
	  programs/e2refinemulti.py, programs/e2refinetofrealign.py,
	  programs/e2refinetorelion2d.py, programs/e2refinetorelion3d.py,
	  programs/e2simmx.py, programs/e2simmxxplor.py,
	  programs/e2spt_classaverage.py, programs/e2spt_hac.py,
	  programs/e2symsearch3d.py, programs/e2tiltvalidate.py,
	  programs/e2version.py, programs/e2workflow.py: Merge from pre2-1

2013-07-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-05 21:54  scmurray

	* programs/e2refinetofrealign.py: [no log message]

2013-07-05 15:04  fjia

	* sparx/bin/sxhelicon.py: [no log message]

2013-07-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-05 11:59  fjia

	* sparx/bin/sxcter.py: add documentation

2013-07-05 11:37  fjia

	* sparx/libpy/morphology.py: [no log message]

2013-07-05 11:32  fjia

	* sparx/libpy/morphology.py: [no log message]

2013-07-05 08:19  stevel

	* examples/mpi_test.py: Put mpi_test back in distro in examples

2013-07-04 13:11  stevel

	* libpyEM/EMAN2jsondb.py, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/emdataitem3d.py, libpyEM/qtgui/empmwidgets.py,
	  programs/e2ctf.py, programs/e2projectmanager.py: Fixed lockup
	  when looking at read-only directories

2013-07-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-03 17:49  fjia

	* sparx/bin/sxhelicon.py: [no log message]

2013-07-03 16:27  fjia

	* sparx/bin/sxhelicon.py: [no log message]

2013-07-03 14:27  fjia

	* sparx/bin/sxlocalhelicon.py: [no log message]

2013-07-03 13:45  fjia

	* sparx/bin/sxlocalhelicon.py: [no log message]

2013-07-03 12:03  stevel

	* programs/e2ctf.py: Fix problem with CTF refitting failure, and
	  improve autofitting very slightly.

2013-07-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-02 13:41  irees

	* libEM/: emcache.cpp, emcache.h: Fixed macro to turn on/off

2013-07-02 13:40  stevel

	* libpyEM/qtgui/emboxerbase.py, programs/e2import.py: Import tweaks

2013-07-02 12:51  scmurray

	* programs/e2refinetorelion2d.py: Changed to work with Relion 1.2
	  and EMAN2 2.1

2013-07-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-02 11:59  irees

	* CMakeLists.txt, libEM/CMakeLists.txt: Commented out CMake
	  ENABLE_HDFIOCACHE; It's been replaced by ENABLE_IOCACHE

2013-07-02 11:51  irees

	* libEM/emcache.cpp: Cleanup of emcache debugging statements, and
	  some additional safety checks.

2013-07-02 10:54  stevel

	* libpyEM/qtgui/empmwidgets.py, programs/e2projectupdate21.py:
	  Resolution plotting working.

2013-07-02 10:29  pawel

	* sparx/bin/sx3dvariability.py: corrected nomenclature

2013-07-02 10:25  pawel

	* sparx/bin/: sx3Dvariance.py, sx3dvariability.py: [no log message]

2013-07-02 09:37  scmurray

	* programs/e2refinetorelion3d.py: Last Minute changes to 2.1

2013-07-02 09:35  stevel

	* libEM/pmconfig/spr.json, programs/e2projectupdate21.py: disable
	  broken items

2013-07-02 05:49  stevel

	* libpyEM/EMAN2.py, programs/e2projectupdate21.py: work on project
	  update

2013-07-01 17:36  irees

	* libEM/emcache.cpp, libpyEM/qtgui/empmtabwidgets.py: Fix problem
	  with uninitialized quality attr

2013-07-01 17:21  irees

	* libEM/: emcache.cpp, emcache.h, emutil.cpp, hdfio2.cpp:
	  Improvements to global cache: threading, locks, better cache
	  storage, better cache checking, timer to close open files.

2013-07-01 17:20  fjia

	* sparx/libpy/morphology.py: make f_start and f_stop input
	  arguments in cter

2013-07-01 17:12  fjia

	* sparx/bin/sxcter.py: [no log message]

2013-07-01 16:03  scmurray

	* programs/: e2buildstacks.py, e2proc2d.py, e2rct.py,
	  e2refinetorelion2d.py, e2refinetorelion3d.py: MAde 2.1 Related
	  Changes

2013-07-01 15:15  stevel

	* libpyEM/EMAN2db.py, libpyEM/qtgui/embrowser.py,
	  programs/e2projectmanager.py, programs/e2projectupdate21.py:
	  Working on update script.

2013-07-01 14:46  fjia

	* sparx/libpy/morphology.py: put in cross resolution code (from
	  getastcrfNOE.py)

2013-07-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-07-01 11:52  fjia

	* programs/e2boxer.py: [no log message]

2013-07-01 11:08  stevel

	* libEM/hdfio2.cpp, libEM/processor.cpp, libpyEM/EMAN2.py,
	  libpyEM/qtgui/emboxerbase.py, programs/e2boxer.py,
	  programs/e2ctf.py, programs/e2refine_easy.py: ralign bug

2013-07-01 04:38  irees

	* libEM/emcache.cpp: Quick patch to keep things from crashing until
	  I can work on cache again.

2013-07-01 04:27  irees

	* doc/build/install.sh: I noticed eman2-installer was never in
	  source control...

2013-07-01 04:27  irees

	* doc/build/: build.py, build.txt: More 2.1 fixes.

2013-06-30 22:42  stevel

	* libEM/processor.cpp, libpyEM/EMAN2jsondb.py,
	  libpyEM/qtgui/emboxerbase.py, libpyEM/qtgui/empmtabwidgets.py,
	  programs/e2boxer.py, programs/e2evalimage.py: boxing is almost
	  working right

2013-06-30 20:30  irees

	* doc/build/build.py: Build system improvements for 2.1

2013-06-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-28 16:41  fjia

	* programs/e2helixboxer.py: add option --ptcl_dst

2013-06-28 16:19  fjia

	* programs/e2helixboxer.py: for --window option, always window
	  squares

2013-06-28 13:21  fjia

	* programs/e2helixboxer.py: add option for ctf estimation using
	  CTER

2013-06-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-28 01:22  stevel

	* libpyEM/EMAN2.py, libpyEM/qtgui/emplot2d.py,
	  programs/e2eulerxplor.py, programs/e2refine_easy.py: e2eulerxplor
	  fixed

2013-06-27 23:03  stevel

	* TODO, libEM/emdata_io.cpp, libEM/processor.cpp,
	  libEM/processor.h, programs/e2ctf.py, programs/e2evalimage.py,
	  programs/e2refine_easy.py, programs/e2refine_postprocess.py:
	  refine_easy working better. First really good GroEL maps. Using
	  structure factor filter again.

2013-06-27 16:25  fjia

	* programs/e2boxer.py: [no log message]

2013-06-27 13:28  pawel

	* sparx/bin/sxlocal_ali3d.py: [no log message]

2013-06-27 13:17  fjia

	* programs/e2boxer.py: add gui option for CTER in gauss mode

2013-06-27 13:12  fjia

	* sparx/libpy/morphology.py: [no log message]

2013-06-27 12:54  fjia

	* sparx/: bin/sxcter.py, libpy/morphology.py: [no log message]

2013-06-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-26 19:20  stevel

	* libEM/processor.cpp, libEM/processor.h, libpyEM/EMAN2db.py,
	  libpyEM/qtgui/embrowser.py, programs/e2buildsets.py,
	  programs/e2ctf.py, programs/e2evalimage.py,
	  programs/e2refine_easy.py, programs/e2refine_postprocess.py,
	  programs/e2simmx.py, programs/e2simmxxplor.py: Fixed serious
	  problem with misclassification with --twostage.

2013-06-26 17:30  fjia

	* programs/e2boxer.py: add option for ctf estimation using cter

2013-06-26 17:25  fjia

	* programs/e2helixboxer.py: add option to estimate ctf using cter

2013-06-26 16:32  fjia

	* sparx/libpy/morphology.py: [no log message]

2013-06-26 16:20  fjia

	* sparx/bin/sxcter.py: [no log message]

2013-06-26 16:20  fjia

	* sparx/libpy/morphology.py: add cter and related functions

2013-06-26 14:52  fjia

	* sparx/bin/sxcter.py: [no log message]

2013-06-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-26 11:54  fjia

	* sparx/bin/sxcter.py: [no log message]

2013-06-26 11:36  fjia

	* sparx/bin/sxcter.py: [no log message]

2013-06-25 17:07  fjia

	* sparx/bin/sxcter.py: [no log message]

2013-06-25 16:43  piotr

	* sparx/bin/sxali3d.py: saturn2

2013-06-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-25 11:39  irees

	* libEM/: emcache.cpp, emcache.h, emutil.cpp: Cache system can be
	  turned on/off for different file types. In get_imageio(), set
	  persist > 0 to cache a file. Currently just enabled for HDF.

2013-06-25 11:07  irees

	* libEM/: emcache.cpp, emcache.h, emdata_io.cpp, emutil.cpp,
	  emutil.h: Rebuilt GlobalCache system for caching open ImageIOs.
	  It uses a reference counting scheme to know when to open/close a
	  file, and when to switch from read-only to read-write, and has a
	  last-accessed timer to close stale cache items. Note a change:
	  use EMUtil::get_imageio as before to get an ImageIO instance, but
	  close it with EMUtil::close_imageio(filename, imageio) instead of
	  delete imageio. This will keep the reference counts correct. To
	  enable the cache, set ENABLE_IOCACHE in CMake. Currently, only
	  HDF files are kept open longer than needed. Note 2: The timer
	  system is not yet implemented.

2013-06-24 20:48  stevel

	* libEM/processor.cpp, libEM/pmconfig/spr.json,
	  libpyEM/qtgui/emimagemx.py, programs/e2evalparticles.py,
	  programs/e2montecarlorecon.py, programs/e2refine2d.py,
	  programs/e2refine_easy.py, programs/e2refine_postprocess.py:
	  refine_easy working, though still needs tweaks and features.
	  Other related improvements.

2013-06-24 18:36  pawel

	* libEM/sparx/emdata_sparx.cpp, sparx/libpy/alignment.py,
	  sparx/libpy/statistics.py: [no log message]

2013-06-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-21 20:04  stevel

	* libEM/emobject.cpp, libEM/processor.cpp, libEM/pmconfig/spr.json,
	  libpyEM/qtgui/embrowser.py, programs/e2ctf.py,
	  programs/e2make3d.py, programs/e2refine2d.py,
	  programs/e2refine_easy.py, programs/e2refine_postprocess.py:
	  e2refine_easy working, though can use more tweaking and more
	  image analysis. e2ctf problem with bad headers fixed.

2013-06-21 15:49  pawel

	* sparx/libpy/reconstruction.py: [no log message]

2013-06-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-19 19:01  jgalaz

	* programs/e2spt_classaverage.py: Eliminated redundant
	  preprocessing or wedge fitting of particles when there are not
	  preprocessing options on, or when --shrink and --shrinkrefine are
	  identical, or when --ralign is off.

2013-06-19 18:18  jgalaz

	* examples/e2spt_tomosimjobs.py: Modification to make this program
	  compatible with new --fitwedgepost parameter in
	  e2spt_classaverage.py

2013-06-19 18:17  jgalaz

	* programs/e2spt_classaverage.py: Since it is not clear whether the
	  missing wedge should ALWAYS be fit AFTER preprocessing or not
	  when using the FSC.TOMO comparator, the --fitwedgepost parameter
	  now allows the user to decide when fitting the missing wedge will
	  happen.

2013-06-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-18 15:53  fjia

	* sparx/bin/: sxhelicon_utils.py, sxhelicon.py: [no log message]

2013-06-18 15:34  fjia

	* sparx/bin/sxhelicon_utils.py: add symdoc option for entering
	  helical symmetry parameters

2013-06-18 12:55  fjia

	* sparx/libpy/applications.py: fix printout for ihrsr

2013-06-18 12:16  fjia

	* sparx/bin/sxhelicon.py: add --symdoc option

2013-06-18 12:08  pawel

	* sparx/libpy/applications.py: added symmetrization to ihrsr

2013-06-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-18 03:45  jgalaz

	* programs/e2spt_simulation.py: The tilt axis was simulated along x
	  because of the way alt operates by default. Now it is along y, so
	  that the simulated subvolumes are compatible with the conventions
	  of IMOD and e2spt_wedge.py (and the fsc.tomo comparator).

2013-06-17 16:42  pawel

	* sparx/bin/sxhelicon_utils.py: [no log message]

2013-06-17 16:21  fjia

	* sparx/bin/sxhelicon.py: change default padding size from 4 to 2

2013-06-17 16:16  fjia

	* sparx/bin/sxmref_ali3d.py: change default padding size from 4 to
	  2

2013-06-17 16:12  fjia

	* sparx/bin/: sxlocal_ali3dm.py, sxlocalhelicon.py: change default
	  padding size from 4 to 2

2013-06-17 16:07  fjia

	* sparx/bin/sxlocal_ali3d.py: change default npad from 4 to 2

2013-06-17 16:03  fjia

	* sparx/bin/sxhelicon_utils.py: change default npad from 4 to 2

2013-06-17 15:58  fjia

	* sparx/bin/sxrecons3d_f.py: change default npad from 4 to 2

2013-06-17 15:55  fjia

	* sparx/bin/sxihrsr.py: change default npad from 4 to 2

2013-06-17 15:34  fjia

	* sparx/bin/sxhelicon_utils.py: [no log message]

2013-06-17 15:16  fjia

	* sparx/bin/sxhelicon_utils.py: --helicise: symmetrize volume
	  before and after helicising

2013-06-17 14:58  fjia

	* sparx/bin/sxhelicon_utils.py: add option for symmetry search

2013-06-17 13:39  fjia

	* sparx/bin/sxrecons3d_n.py: change npad default to 2

2013-06-17 13:31  fjia

	* sparx/bin/sxali3d.py: default npad to 2

2013-06-17 12:09  fjia

	* programs/e2helixboxer.py: in db_save_particle_coords, do not
	  default  px_overlap=0 to 90% of partcle length so as to match gui
	  mode

2013-06-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-17 10:43  fjia

	* programs/e2helixboxer.py: [no log message]

2013-06-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-15 22:29  stevel

	* libpyEM/EMAN2.py, programs/e2initialmodel.py,
	  programs/e2refine_easy.py: e2refine_easy seems to be working
	  pretty well

2013-06-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-15 02:34  stevel

	* programs/: e2ctf.py, e2refine_easy.py, e2version.py:
	  e2refine_easy should run now, but not tested yet

2013-06-14 14:53  stevel

	* programs/e2refine_easy.py: refine_easy almost ready for testing

2013-06-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-14 11:21  stevel

	* libEM/processor.cpp, libEM/processor.h, programs/e2ctf.py:
	  Trivial

2013-06-14 10:31  stevel

	* libEM/emdata.cpp, libEM/processor.cpp, libEM/processor.h,
	  programs/e2proc3d.py: FSC filter working

2013-06-13 23:53  stevel

	* libEM/: processor.cpp, processor.h: New processor for FSC-based
	  filtration. Not tested yet.

2013-06-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-13 03:46  jgalaz

	* examples/e2spt_tomosimjobs.py: Now you can even supply the same
	  comparator twice, with different parameters, to compare THE same
	  comparator to itself.  For example
	  --comparators=fsc.tomo:sigmas=0.01,fsc.tomo:sigmas=0.05

2013-06-13 02:10  jgalaz

	* examples/e2spt_tomosimjobs.py: When comparing the efficieny of
	  different COMPARATORS, the program can now do it propperly: The
	  SIMULATED SYACK (generated through e2spt_simulation.py) is only
	  generated ONCE, and then tested for different processing
	  parameters through separate runs of e2spt_classaverage.py

2013-06-13 02:08  jgalaz

	* programs/: e2spt_classaverage.py, e2spt_simulation.py: More
	  control of unnecessary printouts under --verbose

2013-06-12 23:40  stevel

	* libEM/processor.cpp, libEM/processor.h,
	  programs/e2refine_easy.py: More work on e2refine_easy

2013-06-12 15:01  pawel

	* sparx/libpy/user_functions.py: [no log message]

2013-06-12 14:44  stevel

	* libEM/processor.cpp, libEM/processor.h, programs/e2ctf.py,
	  programs/e2refine_easy.py: refine_easy work. Almost ready for
	  testing.

2013-06-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-12 11:04  pawel

	* sparx/libpy/user_functions.py: [no log message]

2013-06-12 00:01  stevel

	* libpyEM/qtgui/emimagemx.py, programs/e2ctf.py: Yea ! Set display
	  working !

2013-06-11 21:30  stevel

	* programs/e2ctf.py: another try on the e2ctf.py failure fix

2013-06-11 15:11  stevel

	* libpyEM/qtgui/emimagemx.py: Sets almost working...

2013-06-11 13:39  cailin

	* libEM/amiraio.cpp: remove amira flipping

2013-06-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-11 10:00  stevel

	* libEM/lstfastio.cpp, libpyEM/qtgui/emimagemx.py: Fix problem with
	  LST files not returning data source.

2013-06-10 23:49  stevel

	* libpyEM/qtgui/embrowser.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2ctf.py: sets still broken. Important but minor ctf fix

2013-06-10 19:13  stevel

	* programs/e2ctf.py: Fix for divide by zero crash on autofit.

2013-06-10 18:58  jgalaz

	* programs/e2spt_simulation.py: Bug fix

2013-06-10 15:25  stevel

	* libEM/pmconfig/spr.json, programs/e2refine_auto.py,
	  programs/e2refine_easy.py: First draft of refine_easy.

2013-06-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-10 10:58  pawel

	* sparx/libpy/user_functions.py: user_functions.py

2013-06-10 04:08  jgalaz

	* examples/e2spt_tomogramfiltrator.py: Bugs fixed. Functional
	  (presumably).

2013-06-10 01:56  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2013-06-10 01:41  jgalaz

	* programs/e2spt_simulation.py: [no log message]

2013-06-10 01:34  jgalaz

	* programs/e2spt_simulation.py: Slight inaccuracy corrected for
	  calculation of projection orientation based on --nslices and
	  --tiltrange. Also (unexplicable) bug fixed.

2013-06-10 00:27  jgalaz

	* examples/e2figureplot.py: [no log message]

2013-06-10 00:27  jgalaz

	* examples/e2spt_cudatimetest.py: --boxsizesrange and --boxeslist
	  have been replaced by --boxsizes which now besides taking a comma
	  separated list and a hyphen separated range can also accept a
	  .txt file with a column list of boxsizes to test/plot.

2013-06-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-08 11:24  stevel

	* libEM/lstfastio.cpp, libpyEM/EMAN2.py, libpyEM/EMAN2jsondb.py,
	  libpyEM/qtgui/embrowser.py, libpyEM/qtgui/empmtabwidgets.py,
	  programs/e2projectmanager.py, programs/e2refine.py,
	  programs/e2refinemulti.py: Switch to .json

2013-06-08 01:32  eman

	* doc/build/build.py: One more try...

2013-06-07 17:52  pawel

	* sparx/libpy/utilities.py: [no log message]

2013-06-07 17:00  irees

	* doc/build/: build.py, build.txt: Separated upload command into:
	  install package upload

2013-06-07 16:53  irees

	* doc/build/build.txt: Minor update

2013-06-07 16:50  irees

	* doc/build/build.py: Version information

2013-06-07 16:19  irees

	* programs/e2version.py: Updated version to 2.0.7.

2013-06-07 14:52  stevel

	* programs/e2initialmodel.py: trivial

2013-06-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-07 10:22  stevel

	* libpyEM/EMAN2.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2buildsets.py: Buildset fixed (?)

2013-06-07 00:02  stevel

	* examples/reconstruct_fill.py, programs/e2buildsets.py,
	  programs/e2ctf.py: Fixed a couple of ctf and buildsets bugs.
	  buildsets still fragile as I work out the naming conventions.

2013-06-06 21:52  jgalaz

	* examples/: e2spt_tomosimjobs.py, e2spt_cudatimetest.py: [no log
	  message]

2013-06-06 21:52  jgalaz

	* examples/e2figureplot.py: Most options are functional and
	  debugged now.

2013-06-06 12:51  stevel

	* libEM/processor.h, libpyEM/EMAN2jsondb.py: defocus reading fix

2013-06-06 12:10  stevel

	* examples/reconstruct_fill.py, libEM/hdfio2.cpp, libpyEM/EMAN2.py,
	  programs/e2ctf.py, programs/e2make3d.py,
	  programs/e2refine_evenodd.py: Using __ for modified tag
	  qualifier. Minor make3d fixes

2013-06-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-06 00:29  irees

	* doc/build/: build.py, build.txt, dep.py, i686-apple-darwin10.sh,
	  i686-apple-darwin11.sh, i686-redhat-linux.sh, order.txt,
	  x86_64-pc-mingw.sh, x86_64-redhat-linux.sh: Scripts and
	  documentation for new common build system.

2013-06-05 19:46  jgalaz

	* examples/e2figureplot.py: The purpose of this program (under
	  development) will be to function as a commandline plotter (NO GUI
	  involved) to produce pseudo-publishable figures, where you can
	  fit minima and maxima of curves, do polynonimal fits to the data,
	  smooth raw and fitted curves, plot several curves on the same
	  figure, etc; and have these saved to output as PNG files.  It
	  also automtes the production of plots (that is, you can produce
	  ALL the different kind of plots from a single .txt file with ONE
	  run).  Additionally, this script will host many functions already
	  implemented into SPT programs (e2spt_resolutionplot.py,
	  e2spt_rotationalplot.py, e2spt_cudatimetest.py,
	  e2spt_rotationalplot.py, etc), which are largely redundant.

2013-06-05 13:41  stevel

	* libpyEM/qtgui/empmwidgets.py: fix broken fsc partially

2013-06-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-04 22:52  stevel

	* examples/reconstruct_fill.py: example program for testing number
	  of projections required for a given resolution

2013-06-04 12:47  stevel

	* libpyEM/EMAN2.py, programs/e2refine_evenodd.py: I believe
	  e2refine_evenodd is working now as well !

2013-06-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-04 11:32  stevel

	* libpyEM/EMAN2fsc.py, programs/e2initialmodel.py,
	  programs/e2make3d.py, programs/e2refine.py,
	  programs/e2refine_evenodd.py, programs/e2refinemulti.py: e2refine
	  tested and working with JSON/HDF system

2013-06-03 23:13  stevel

	* programs/e2refine.py: I think e2refine is now working with
	  JSON...

2013-06-03 22:50  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2013-06-03 20:34  jgalaz

	* examples/e2spt_tomosimjobs.py: Now any given number of
	  comparators can be tested simultaneously, that is, in one run,
	  through the --comparators parameter (for now, ccc, ccc.tomo and
	  fsc.tomo are functional).The testing is still NOT completely
	  optimal... because a new simulated stack is generated on each run
	  (yes, with the same parameters... but the orientations of the
	  particles are random...). IDEALLY, to properly and objetively
	  compare different preprocessing and/or alignment parameters, the
	  *SAME* stack would be used as conditions vary. I will turn the
	  program around soon to fix this.  In any case, randomization of
	  conditions on separate runs can still serve a useful purpose: To
	  test for dependence of alignment accuracy on particle
	  orientation. A greater variability in separate runs (using a
	  DIFFERENT randomized stack each time) for a particular specimen
	  indicates the specimen is more susceptible to the orientation of
	  the particles respect to the missing wedge.

2013-06-03 20:21  jgalaz

	* programs/e2spt_classaverage.py: Path numbering should only start
	  if a current subdirectory already exists. For example, if
	  --path=test, and 'test' is already in the directory, 'test_01'
	  should be created, then 'test_02', etc. Otherwise, a non-numbered
	  path should be valid. Previously, 'test_01' was created by
	  default even if 'test' didn't exist yet and the user had
	  specified '--path=test'.

2013-06-03 19:57  jgalaz

	* programs/e2spt_classaverage.py: Since e2spt_classaverage was
	  changed to have an alignment and a preprocessing function, I
	  hadn't tested ALL options. There was a NASTY LITTLE BUG that took
	  almost an entire day to fix... (classoptions are now accessed as
	  classoptions.optionname, instead of classoptions['optionname'];
	  in fact, they shouldn't even be called "classoptions", since the
	  ONLY class in this entire program is now EXCLUSIVELY to set the
	  parallelization tasks -NOT to align; NOT to preprocess. However,
	  clean-up and changes to appropriate nomeclature will have to wait
	  for now....).

2013-06-03 19:14  stevel

	* programs/e2initialmodel.py: Initial models working in parallel.

2013-06-03 16:45  pawel

	* programs/: e2helixboxer.py: cleaning the code

2013-06-03 15:23  stevel

	* libEM/xydata.cpp, libEM/xydata.h, libpyEM/EMAN2.py,
	  libpyEM/EMAN2PAR.py, libpyEM/libpyCmp2.cpp,
	  libpyEM/qtgui/emselector.py, programs/e2initialmodel.py: Parallel
	  e2initialmodel in testing. pickling support for XYData

2013-06-03 15:09  jgalaz

	* examples/e2spt_cudatimetest.py: --logplot implemented.

2013-06-03 13:53  jgalaz

	* examples/e2spt_cudatimetest.py: Conditional statements to prevent
	  specifying redundant invalid options accidentally (such as --test
	  and --extensive at the same time...).

2013-06-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-02 23:06  stevel

	* programs/e2initialmodel.py: Working on e2initialmodel parallelism

2013-06-02 18:09  pawel

	* libEM/symmetry.h: [no log message]

2013-06-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-06-01 11:04  stevel

	* libpyEM/EMAN2PAR.py, libpyEM/EMAN2jsondb.py,
	  libpyEM/qtgui/embrowser.py, programs/e2classaverage.py,
	  programs/e2project3d.py, programs/e2simmx.py,
	  programs/e2spt_classaverage.py, programs/e2spt_hac.py,
	  programs/e2symsearch3d.py, programs/e2tiltvalidate.py:
	  Parallelism seems to be working with JSON now.

2013-05-31 17:00  jgalaz

	* programs/e2spt_resolutionplot.py: [no log message]

2013-05-31 16:52  jgalaz

	* examples/e2fixheaderparam.py: .o

2013-05-31 14:55  jgalaz

	* programs/e2spt_classaverage.py: New major version with
	  proprocessing and alignment functions OUTSIDE of the Task
	  generating alignment class. Non-parallel processing is now
	  possible.  There is no redundancy, so any future changes to
	  preprocessing or alignment schemes would be implemented
	  SIMULTANEOUSLY both for parallel and non-parallel processing.

2013-05-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-31 00:38  jgalaz

	* examples/e2spt_cudatimetest.py: --boxsizerange option implemented
	  to examine the behavior of cuda acceleration of independent
	  ranges of boxsizes without having to write the list explicitely
	  through --boxsizeslist

2013-05-30 14:35  stevel

	* libpyEM/: EMAN2PAR.py, EMAN2jsondb.py, qtgui/embrowser.py:
	  Working on task managing

2013-05-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-30 00:49  jgalaz

	* examples/e2spt_tomogramfiltrator.py: Program to properly filter
	  tomograms avoiding aliasing effects, which e2proc3d.py does NOT
	  do (the propper way is to pad the tomogram, filter, and then crop
	  down the tomogram to the original size).

2013-05-30 00:07  stevel

	* libEM/ctf.cpp, libpyEM/EMAN2jsondb.py,
	  libpyEM/qtgui/embrowser.py: Browsing info in JSON objects.
	  Hierarchical browsing works. Only EMData not fully configured.

2013-05-29 14:23  stevel

	* libpyEM/EMAN2jsondb.py, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/empmtabwidgets.py, programs/e2buildsets.py,
	  programs/e2projectmanager.py, programs/e2refine2d.py: tweaks on
	  set builder. Working on browser additions for JSON files.

2013-05-29 13:17  jgalaz

	* examples/e2spt_cudatimetest.py: Numbered path made more
	  efficiently.

2013-05-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-29 09:51  cailin

	* libEM/dm4io.cpp: gatan dm4io

2013-05-29 09:31  cailin

	* libEM/dm4io.cpp: gatan dm4io, sint, uint, float32, float64

2013-05-29 09:31  cailin

	* libEM/dm4io.h: gatan dm4io

2013-05-28 23:22  stevel

	* libpyEM/emdata_wrapitems.cpp: trivial

2013-05-28 23:20  stevel

	* libEM/: lstfastio.cpp, lstio.cpp: Sets and 2d refinement working

2013-05-28 21:52  stevel

	* libpyEM/EMAN2.py, libpyEM/qtgui/embrowser.py,
	  programs/e2buildsets.py: Set building for JSON working !

2013-05-28 15:08  stevel

	* programs/e2buildsets.py: Starting work on e2buildsets

2013-05-28 13:59  stevel

	* libEM/hdf_filecache.h, libpyEM/EMAN2.py, programs/e2ctf.py,
	  programs/e2projectmanager.py: New Python LSXFile object, to
	  support "fast LST" format files. Specifically this makes it easy
	  to modify the .lst files themselves rather than the images they
	  reference.

2013-05-28 13:50  piotr

	* sparx/libpy/applications.py: patch send by Ambroise Desfosses
	  <ambroisedesfosses@yahoo.fr> (I omitted one of changes, because
	  it was incorrect)

2013-05-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-28 11:13  piotr

	* libEM/sparx/util_sparx.cpp: Critical bugfix in ISAC.

2013-05-27 23:59  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2013-05-27 23:21  stevel

	* libpyEM/EMAN2db.py, libpyEM/EMAN2jsondb.py,
	  libpyEM/qtgui/empmtabwidgets.py, programs/e2ctf.py,
	  programs/e2projectmanager.py: e2ctf now working with JSON. Some
	  fixes for projectmanager too.

2013-05-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-26 02:57  stevel

	* libpyEM/EMAN2jsondb.py, libpyEM/emdata_wrapitems.cpp,
	  libpyEM/typeconverter.h, programs/e2ctf.py: Most EMAN2
	  conversions will now accept unicode arguments as well as strings.
	  Specifically keys and values in EMData attributes, EMObjects and
	  Dict objects can now all accept unicode. However, this assumes
	  that the unicode can be converted to ascii.

2013-05-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-24 21:48  stevel

	* libEM/xydata.cpp, libpyEM/EMAN2.py, libpyEM/EMAN2jsondb.py,
	  programs/e2ctf.py, programs/e2workflow.py: Working on CTF still.
	  Almost done.

2013-05-24 14:14  piotr

	* sparx/libpy/pixel_error.py: correction of the last fix

2013-05-24 14:11  piotr

	* sparx/libpy/pixel_error.py: isac - add checking if pixel_error >0
	  before sqrt

2013-05-24 14:10  piotr

	* sparx/libpy/isac.py: Operation on the filesystem in ISAC code
	  were replaced by os.* functions. Usage of the call routine caused
	  problems with some systems based on OpenMPI (because of fork()).

2013-05-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-23 23:45  stevel

	* programs/e2ctf.py: working on e2ctf with new JSON scheme

2013-05-23 14:35  stevel

	* libpyEM/: EMAN2.py, qtgui/embrowser.py, qtgui/empmtabwidgets.py,
	  qtgui/empmwidgets.py: New browser caching complete, but still
	  testing. Haven't finished related code so it uses JSON.

2013-05-23 14:34  stevel

	* programs/e2projectupdate21.py: Browser caching rewrite complete,
	  but still testing. Beginning of project updating program.

2013-05-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-22 20:28  jgalaz

	* programs/e2spt_resolutionplot.py: [no log message]

2013-05-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-22 11:43  cailin

	* libEM/dm3io.cpp: dm3io float4

2013-05-22 09:01  cailin

	* libEM/glutil.cpp: eliminate mask in histogram distortion.

2013-05-21 23:57  stevel

	* libpyEM/EMAN2db.py, libpyEM/EMAN2jsondb.py,
	  libpyEM/qtgui/embrowser.py, libpyEM/qtgui/empmtabwidgets.py,
	  programs/e2proc2d.py: Working on new jsondb update. New caching
	  mechanism for main browser done. Still retrofitting
	  projectmanager browsers.

2013-05-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-21 00:45  jgalaz

	* programs/e2spt_resolutionplot.py: --fit option now fits a
	  polynomial given a user defined number of expansion terms.

2013-05-20 14:57  piotr

	* libEM/: symmetry.cpp, symmetry.h, sparx/util_sparx.cpp: Add
	  Icosahedron2Sym to symmetry

2013-05-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-20 09:42  pawel

	* libEM/sparx/emdata_sparx.cpp: [no log message]

2013-05-19 21:35  jgalaz

	* programs/e2spt_resolutionplot.py: Curves can	now be "smoothed"
	  through --smooth, and different threshold (horizontal, dashed)
	  lines can be optionally plotted through --threshold

2013-05-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-17 20:04  stevel

	* programs/e2refine2d.py: convert from bdb to js

2013-05-17 15:21  fjia

	* programs/e2helixboxer.py: handle dm3 files for --window option

2013-05-17 14:55  scmurray

	* programs/e2RCTboxer.py: Fixed an issue where the tiltangle,
	  tiltaxis, and tiltgamma were not being saved to the particles.

2013-05-17 13:29  fjia

	* programs/e2helixboxer.py: [no log message]

2013-05-17 13:18  fjia

	* programs/e2helixboxer.py: add option to specify directory where
	  box coordinates are

2013-05-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-16 15:16  cailin

	* libEM/dm3io.cpp: read dm3

2013-05-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-15 14:58  pawel

	* programs/e2bdb.py: [no log message]

2013-05-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-14 15:33  piotr

	* sparx/libpy/applications.py: bugfix in project3d

2013-05-14 12:23  fjia

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-05-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-14 11:13  fjia

	* sparx/libpy/pixel_error.py: uncomment getnewhelixcoords

2013-05-14 10:58  fjia

	* sparx/bin/sxave_ali.py: add option --filament for calculating
	  averages by filament membership

2013-05-13 12:54  fjia

	* libEM/sparx/util_sparx.cpp: fix how mirror is handled in
	  helical_local

2013-05-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-13 10:29  scmurray

	* programs/e2refinetorelion3d.py: Fixed a bug

2013-05-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-10 17:41  pawel

	* sparx/libpy/pixel_error.py: [no log message]

2013-05-10 14:23  stevel

	* libpyEM/: EMAN2.py, EMAN2jsondb.py, libpyEMData2.cpp: Big
	  improvements in jsondb library

2013-05-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-09 16:33  stevel

	* libpyEM/EMAN2jsondb.py: Some changes to new JSDB system.
	  Branching now, because incompatible changes starting.

2013-05-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-08 12:51  piotr

	* sparx/libpy/applications.py: sxheader - no shifts in text file
	  means shifts = 0

2013-05-08 12:38  piotr

	* sparx/libpy/utilities.py: minor change

2013-05-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-08 11:03  cailin

	* libpyEM/qtgui/emimagemx.py: removed the refresh in the particle
	  window

2013-05-07 23:32  stevel

	* libpyEM/qtgui/embrowser.py: Minor bugfix

2013-05-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-06 17:40  fjia

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-05-06 13:25  stevel

	* libpyEM/EMAN2.py, libpyEM/EMAN2db.py, libpyEM/EMAN2jsondb.py,
	  programs/e2ddd_movie.py, programs/e2evalimage.py: Some ddd_movie
	  work.  New EMAN2jsondb module complete and partially tested. This
	  will be a replacement for BDB !

2013-05-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-06 11:33  fjia

	* programs/e2helixboxer.py: sort file list to be processed by
	  windowing option

2013-05-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-03 20:31  jgalaz

	* programs/e2spt_classaverage.py: bugs bugs bugs...

2013-05-03 17:04  pawel

	* sparx/libpy/filter.py: [no log message]

2013-05-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-03 10:41  fjia

	* sparx/bin/sxshiftali.py: [no log message]

2013-05-02 16:08  fjia

	* sparx/bin/sxshiftali.py: check if ctf_applied is 1 or 0 before
	  multiplying segments by ctf

2013-05-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-05-01 17:20  fjia

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-05-01 15:27  fjia

	* libEM/sparx/util_sparx.cpp: add constrained_helix_test function
	  for dealing with general case where inter-segment distances are
	  not assumed to be multiples of rise

2013-05-01 15:26  fjia

	* libpyEM/libpyUtils2.cpp, sparx/bin/sxhelicon.py,
	  libEM/sparx/util_sparx.h: [no log message]

2013-05-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-30 13:43  cailin

	* libpyEM/qtgui/emimageutil.py: 2d histo bug fixed

2013-04-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-30 07:47  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2013-04-30 02:13  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2013-04-29 14:33  jgalaz

	* examples/e2spt_cudatimetest.py: So many files are saved... there
	  were bugs concerning the different endings that differentiate one
	  type of file from another (full plots, plot of subsets, and plots
	  of the minima for both)

2013-04-29 13:43  jgalaz

	* programs/e2spt_classaverage.py, examples/e2spt_tomosimjobs.py:
	  [no log message]

2013-04-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-29 10:00  cailin

	* libpyEM/qtgui/emimageutil.py: volume rendering with color and
	  coordinate.

2013-04-29 04:06  jgalaz

	* examples/e2spt_cudatimetest.py: Util.nonconvex(data,0) now used
	  ADDITIONALLY to create a smoother, non-convex curve for plots
	  that go along the minima of cuda-time-test plots, either for CPU
	  or GPU.

2013-04-28 23:10  jgalaz

	* examples/e2spt_cudatimetest.py: --rotonlyoff flag to control
	  whether you get plots for rotations only (no preprocessing, no
	  calls to e2spt_classaverage.py), or not.

2013-04-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-28 01:42  jgalaz

	* examples/: e2spt_tomosimjobs.py: [no log message]

2013-04-28 01:32  jgalaz

	* programs/e2spt_simulation.py: [no log message]

2013-04-28 01:08  jgalaz

	* programs/e2spt_simulation.py: Persistent, irrational bug :@ .
	  Taken care of.

2013-04-28 00:40  jgalaz

	* programs/e2spt_classaverage.py: Program now has a preprocessing
	  function outside of the alignment class to minimize code and
	  avoid redundancies.  It is also capable of taking filtration
	  parameters for the "fine alignment" round that might be different
	  from those in the "coarse alginment" round.

2013-04-28 00:15  jgalaz

	* programs/e2spt_simulation.py: [no log message]

2013-04-28 00:09  jgalaz

	* examples/e2spt_tomosimjobs.py: [no log message]

2013-04-27 23:41  jgalaz

	* programs/e2spt_simulation.py: [no log message]

2013-04-27 12:11  pawel

	* libEM/sparx/util_sparx.cpp: version updated

2013-04-27 12:05  pawel

	* libEM/: reconstructor.cpp, sparx/emdata_sparx.cpp: corrected
	  astigmatism in reconstructor

2013-04-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-27 11:33  pawel

	* sparx/libpy/applications.py: corrected ctf in project

2013-04-26 17:36  fjia

	* sparx/bin/sxlocalhelicon.py: [no log message]

2013-04-26 12:54  cailin

	* libpyEM/qtgui/: emdataitem3d.py, emimageutil.py: histogram for
	  volume rendering

2013-04-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-25 13:52  piotr

	* libEM/sparx/util_sparx.cpp: removing NULL from parameters of
	  vector's constructor (it didn't compile on some compilers)

2013-04-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-24 17:57  piotr

	* libEM/sparx/util_sparx.cpp: hans - problem with shifts solved

2013-04-24 15:42  fjia

	* sparx/bin/sxlocalhelicon.py: [no log message]

2013-04-24 15:29  fjia

	* sparx/libpy/applications.py: handle rectangular segments and CTF
	  in gendisk

2013-04-24 12:29  fjia

	* sparx/libpy/applications.py: [no log message]

2013-04-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-24 11:32  fjia

	* sparx/libpy/applications.py: modify ihrsr_MPI to handle
	  rectangular segments

2013-04-23 15:32  cailin

	* libpyEM/qtgui/emdataitem3d.py: volume histogram

2013-04-23 14:47  cailin

	* libpyEM/qtgui/emdataitem3d.py: add volume histogram

2013-04-23 14:46  cailin

	* libpyEM/qtgui/emdataitem3d.py: add histogram to volume.

2013-04-22 18:58  fjia

	* sparx/bin/sxhelical_demo.py: [no log message]

2013-04-22 18:54  fjia

	* sparx/bin/sxhelical_demo.py: [no log message]

2013-04-22 17:42  piotr

	* sparx/libpy/isac.py: correction for the last commit

2013-04-22 16:45  piotr

	* sparx/libpy/isac.py: Improvement of memory management in ISAC (2)
	  -> peak_list in isac_MPI

2013-04-22 16:37  irees

	* rt/pyem/rt.py: Changed rt.py to use sys.executable (current
	  interpreter) for test scripts.

2013-04-22 15:59  fjia

	* sparx/bin/sxhelical_demo.py: [no log message]

2013-04-22 15:32  fjia

	* sparx/bin/sxhelical_demo.py: [no log message]

2013-04-22 15:14  pawel

	* sparx/bin/sxshiftali.py: corrected inclined in sxshiftali

2013-04-22 15:01  fjia

	* sparx/bin/: sxhelical_demo.py: [no log message]

2013-04-22 14:39  pawel

	* sparx/bin/sxshiftali.py: corrected inclined in sxshiftali

2013-04-22 14:35  fjia

	* sparx/bin/sxhelical_demo.py: [no log message]

2013-04-22 14:28  pawel

	* sparx/bin/sxshiftali.py: corrected inclined in sxshiftali

2013-04-22 13:58  fjia

	* sparx/bin/sxhelical_demo.py: [no log message]

2013-04-22 13:40  fjia

	* sparx/bin/sxhelical_demo.py: [no log message]

2013-04-22 13:23  fjia

	* sparx/bin/sxhelical_demo.py: file containing utilities for
	  helical demo

2013-04-22 11:23  pawel

	* sparx/bin/: sxhelicon_utils.py, sxshiftali.py: [no log message]

2013-04-22 11:17  fjia

	* sparx/libpy/applications.py: update import statement for
	  chunks_distribution

2013-04-22 11:15  fjia

	* sparx/bin/sxshiftali.py: import chunks_distribution from
	  utilities instead of pixel_error

2013-04-22 11:12  fjia

	* sparx/libpy/pixel_error.py: move chunks_distribution to utilities

2013-04-22 11:11  fjia

	* sparx/libpy/utilities.py: move chunks_distribution here from
	  pixel_error

2013-04-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-21 11:13  fjia

	* sparx/bin/sxshiftali.py: fix import

2013-04-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-19 17:54  piotr

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  sparx/libpy/isac.py: Improvement of memory management in ISAC

2013-04-19 14:56  fjia

	* sparx/bin/sxlocalhelicon.py: [no log message]

2013-04-19 14:33  fjia

	* sparx/bin/sxlocalhelicon.py: [no log message]

2013-04-19 13:04  piotr

	* sparx/libpy/isac.py: change method of reading data

2013-04-19 12:26  pawel

	* sparx/libpy/isac.py: suggestions

2013-04-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-19 11:20  pawel

	* sparx/libpy/applications.py: [no log message]

2013-04-19 10:19  pawel

	* sparx/libpy/isac.py: [no log message]

2013-04-19 04:58  jgalaz

	* examples/e2spt_tomosimjobs.py: [no log message]

2013-04-19 04:51  jgalaz

	* examples/: e2spt_tomosimjobs.py: [no log message]

2013-04-19 04:48  jgalaz

	* examples/e2spt_tomosimjobs.py: [no log message]

2013-04-19 04:46  jgalaz

	* examples/e2spt_tomosimjobs.py: When etomo0 was upgraded to have
	  more space (which apparently hasn't worked yet), and cuda was
	  re-installed (which works fine), my EMAN2 build broke. Unaware
	  that there were chagnes to this program that I had not commited
	  (and that were developed on etomo0), I deleted my EMAN2 build to
	  recompile freshly.  Anyway, I've reinstated the changes:
	  --lowpass, --highpass, and --iter options.  *Sigh*.

2013-04-19 03:35  jgalaz

	* programs/e2spt_boxer.py: Not sure if I've submitted this before,
	  but normalize.edgemean should  NOT be the default choice. It
	  messes up virus particles with high-density DNA (the densities
	  corresponding to the molecule end up being negative, even after
	  contrast inversion). --normproc is in place now. Plus, no
	  normalization should occur if mean density and sigma of the
	  particles are to be used for analyses.

2013-04-18 13:55  piotr

	* CMakeLists.txt, libpyEM/EMAN2PAR.py, libpyEM/mpi_eman.py,
	  mpi_eman/0README, mpi_eman/CMakeLists.txt,
	  mpi_eman/Makefile.linux, mpi_eman/Makefile.linux2,
	  mpi_eman/Makefile.osx, mpi_eman/mpi_eman.c, mpi_eman/mpi_eman.py,
	  mpi_eman/mpi_test.py, mpi_eman/mpi_test_basic.py,
	  mpi_eman/pbs.example, mpi_eman/test.sge: Merge with branch
	  EMAN2_Before_changes_in_MPI_branch.  Now MPI calls are handled by
	  pydusa wrapper.

2013-04-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-17 16:31  fjia

	* sparx/libpy/applications.py: [no log message]

2013-04-17 16:12  fjia

	* sparx/: libpy/applications.py, bin/sxhelicon_utils.py: [no log
	  message]

2013-04-17 15:02  fjia

	* sparx/: bin/sxhelicon_utils.py, libpy/applications.py: [no log
	  message]

2013-04-17 14:43  fjia

	* sparx/: libpy/applications.py, bin/sxhelicon_utils.py: [no log
	  message]

2013-04-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-16 15:39  scmurray

	* libpyEM/qtgui/emplot2d.py, programs/e2tiltvalidate.py: Changing
	  the Right Click functionality in e2tiltvalidate when it plots

2013-04-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-16 08:10  stevel

	* programs/: e2ddd_movie.py, e2iminfo.py: bugfix in iminfo

2013-04-15 17:13  fjia

	* sparx/bin/sxlocalhelicon.py: [no log message]

2013-04-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-13 14:33  pawel

	* libEM/sparx/util_sparx.cpp: OK?

2013-04-13 14:25  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-04-13 12:58  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-04-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-13 07:55  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-04-12 18:03  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-04-12 17:59  fjia

	* sparx/libpy/utilities.py: add type checking to write_text_row

2013-04-12 17:56  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-04-12 17:21  fjia

	* sparx/bin/sxhelicon_utils.py: [no log message]

2013-04-12 17:15  fjia

	* sparx/libpy/applications.py: modify imgstat_hfsc and gendisks_MPI

2013-04-12 16:43  fjia

	* sparx/libpy/applications.py: [no log message]

2013-04-12 16:37  fjia

	* sparx/libpy/applications.py: put gendisks_MPI back

2013-04-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-12 11:05  fjia

	* sparx/libpy/applications.py: [no log message]

2013-04-11 17:42  fjia

	* sparx/bin/sxhelicon_utils.py: [no log message]

2013-04-11 17:38  fjia

	* sparx/bin/sxhelicon_utils.py: add new options for gendisks_MPI

2013-04-11 17:37  fjia

	* sparx/libpy/applications.py: fixed up match_pixel_rise (and move
	  gendisks_MPI to development for modifications...will move it
	  back)

2013-04-11 16:39  fjia

	* sparx/libpy/pixel_error.py: move chunks_distribution here from
	  development.py

2013-04-11 13:29  fjia

	* sparx/bin/: sxhelicon_utils.py, sxhelicon.py: [no log message]

2013-04-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-11 04:27  jgalaz

	* examples/e2spt_cudatimetest.py: New --setcudadevice option.

2013-04-10 22:56  jgalaz

	* programs/e2spt_classaverage.py: --inixforms was not working. Now
	  it seems to be.

2013-04-10 16:57  fjia

	* sparx/bin/sxlocalhelicon.py: [no log message]

2013-04-10 16:36  fjia

	* sparx/bin/sxihrsr.py: remove helical consistency related options

2013-04-10 16:17  fjia

	* sparx/bin/sxhelicon_utils.py: sx file for various helical
	  consistency related utilities

2013-04-10 16:09  fjia

	* sparx/bin/sxihrsr.py: remove --ehelix option

2013-04-10 16:01  fjia

	* sparx/bin/sxihrsr.py: remove --localcons option for calling
	  ihrsrlocalcons

2013-04-10 15:54  fjia

	* sparx/bin/sxhelicon.py: change --nearby option to --xwobble

2013-04-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-10 09:28  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-04-10 01:03  jgalaz

	* examples/e2spt_cudatimetest.py: Minor bugs fixed.

2013-04-09 21:33  pawel

	* libEM/sparx/util_sparx.cpp: removed printout from hans

2013-04-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-09 11:10  piotr

	* libEM/sparx/util_sparx.cpp: comment out the boost/format header

2013-04-08 15:30  piotr

	* sparx/bin/sxali3d.py: sxali3d - hans and saturn versions

2013-04-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-08 10:45  fjia

	* sparx/bin/sxlocalhelicons.py: remove sxlocalhelicons.py from
	  system

2013-04-08 10:44  fjia

	* sparx/bin/sxhelicons.py: removing sxhelicons.py from system

2013-04-08 10:43  fjia

	* sparx/bin/sxhelicon.py: add sx file for ehelix

2013-04-08 10:42  fjia

	* sparx/bin/sxlocalhelicon.py: put local helical refinement with
	  consistency into its own sx file

2013-04-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-06 11:21  pawel

	* sparx/bin/sxisc.py: [no log message]

2013-04-05 18:55  jgalaz

	* examples/e2spt_cudatimetest.py: More efficient organization of
	  code through elimination of redundancies.  Plus, text files are
	  now created for ALL cases (they were written for --oneicos only
	  before).

2013-04-05 18:31  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2013-04-05 17:24  fjia

	* sparx/bin/sxhelicons.py: add sx file for ehelix

2013-04-05 17:23  fjia

	* sparx/bin/sxlocalhelicons.py: [no log message]

2013-04-05 16:54  fjia

	* sparx/bin/sxlocalhelicons.py: add sx file for local refinement
	  with helical consistency

2013-04-05 14:25  jgalaz

	* examples/e2spt_cudatimetest.py: All new modalities ('onefull' and
	  'oneccf') fully tested and presumably bug free.

2013-04-05 12:04  pawel

	* sparx/: bin/sxali3d.py, libpy/alignment.py: [no log message]

2013-04-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-04 18:12  pawel

	* libEM/sparx/util_sparx.cpp: constrained fixed

2013-04-04 17:19  fjia

	* sparx/libpy/applications.py: remove logging from ssnr3d

2013-04-04 16:57  fjia

	* sparx/libpy/applications.py: remove logging from transform2d

2013-04-04 16:47  fjia

	* sparx/libpy/applications.py: move ali3d_a to development.py (and
	  comment it out there)

2013-04-04 16:20  fjia

	* sparx/libpy/applications.py: remove logging from
	  ali2d_rotationaltop and fix error with nx

2013-04-04 15:42  pawel

	* sparx/libpy/pixel_error.py: corrected 2D pixel error name

2013-04-04 15:39  fjia

	* sparx/bin/sxproj_stability.py: remove logging

2013-04-04 14:44  fjia

	* sparx/libpy/applications.py: remove logging from recons3d_n and
	  recons3d_n_MPI

2013-04-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-04 11:54  cailin

	* libpyEM/qtgui/embrowser.py: windows title update

2013-04-04 11:52  cailin

	* libpyEM/qtgui/embrowser.py: window title updates

2013-04-04 10:39  cailin

	* programs/: e2ctf.py, e2evalimage.py: update window title

2013-04-03 21:32  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2013-04-03 16:50  pawel

	* sparx/libpy/applications.py, libEM/sparx/util_sparx.cpp,
	  sparx/bin/sxali3d.py: [no log message]

2013-04-03 15:50  cailin

	* programs/e2filtertool.py: location restore

2013-04-03 15:40  pawel

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, sparx/bin/sxshiftali.py: [no log
	  message]

2013-04-03 14:41  cailin

	* programs/e2projectmanager.py: location and size restore

2013-04-03 14:39  cailin

	* libpyEM/qtgui/embrowser.py: e2display location size restore

2013-04-03 14:28  cailin

	* programs/e2ctf.py: e2ctf window location and size restore

2013-04-03 14:14  cailin

	* libpyEM/qtgui/emrctboxergui.py, programs/e2RCTboxer.py:
	  e2rctboxer location and size restore

2013-04-03 14:06  pawel

	* sparx/bin/sxshiftali.py: [no log message]

2013-04-03 13:02  cailin

	* libpyEM/EMAN2.py, programs/e2evalimage.py: windows location
	  restore

2013-04-03 13:01  cailin

	* libpyEM/qtgui/emboxerbase.py: window location restore

2013-04-03 12:15  cailin

	* libpyEM/qtgui/emboxerbase.py: e2boxer locations restore

2013-04-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-03 11:40  fjia

	* sparx/bin/sxshiftali.py: [no log message]

2013-04-03 11:15  piotr

	* libpyEM/mpi_eman.py: bugfix in serialization

2013-04-02 18:14  fjia

	* sparx/bin/sxshiftali.py: add helishiftali_MPI for one dimensional
	  x-shift search over filaments

2013-04-02 16:47  fjia

	* sparx/bin/sxshiftali.py: handle rectangular input data for 2D
	  search

2013-04-02 15:20  scmurray

	* libpyEM/qtgui/emplot2d.py, programs/e2tiltvalidate.py: Working on
	  fixing a right clicking issue in the polar plot

2013-04-02 15:19  fjia

	* sparx/bin/sxshiftali.py: consider rectangular images where nx !=
	  ny

2013-04-02 15:02  cailin

	* libpyEM/EMAN2.py: location restoration

2013-04-02 14:11  fjia

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-04-02 12:05  pawel

	* sparx/bin/sxihrsr.py: [no log message]

2013-04-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-01 18:07  fjia

	* sparx/libpy/applications.py: [no log message]

2013-04-01 18:03  fjia

	* sparx/libpy/alignment.py: add y restriction argument to function
	  call Util.multiref_polar_ali_helical_90_local

2013-04-01 18:01  fjia

	* libEM/sparx/util_sparx.cpp: add y search restriction to
	  multiref_polar_ali_helical_90_local

2013-04-01 17:59  fjia

	* libEM/sparx/util_sparx.h: add input argument to
	  multiref_polar_ali_helical_90_local

2013-04-01 17:58  fjia

	* libpyEM/libpyUtils2.cpp: add one more input argument to
	  multiref_polar_ali_helical_90_local

2013-04-01 16:40  fjia

	* libEM/sparx/: util_sparx.cpp: [no log message]

2013-04-01 14:31  fjia

	* sparx/libpy/alignment.py: remove mirror_only flag from
	  proj_ali_helical_local

2013-04-01 14:29  fjia

	* libEM/sparx/util_sparx.cpp: clean up code in
	  multiref_polar_ali_helical_local

2013-04-01 14:26  fjia

	* libpyEM/libpyUtils2.cpp, libEM/sparx/util_sparx.h: remove
	  mirror_only argument from multiref_polar_ali_helical_local

2013-04-01 13:25  fjia

	* sparx/libpy/applications.py: remove print statement

2013-04-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-04-01 11:40  pawel

	* libEM/sparx/emdata_sparx.cpp: helicise - error when the section
	  size it too small

2013-03-31 23:18  stevel

	* libEM/processor.cpp: Added error checking in center of mass

2013-03-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-29 16:42  fjia

	* programs/e2helixboxer.py: [no log message]

2013-03-29 15:24  fjia

	* sparx/bin/sxihrsr.py: move option --window for windowing segments
	  out of sxihrsr and into e2helixboxer

2013-03-29 15:19  fjia

	* programs/e2helixboxer.py: [no log message]

2013-03-29 15:16  fjia

	* programs/e2helixboxer.py: add option --window for windowing
	  segments from multiple micrographs located in different
	  directories

2013-03-29 15:04  fjia

	* sparx/libpy/applications.py: moving window segment code out of
	  applications and into e2helixboxer

2013-03-29 14:49  pawel

	* sparx/libpy/: applications.py, global_def.py, utilities.py:
	  modified code so logfile goes to the output directory

2013-03-29 13:35  pawel

	* sparx/bin/sxproj_stability.py: [no log message]

2013-03-29 13:31  fjia

	* sparx/libpy/pixel_error.py: [no log message]

2013-03-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-29 08:06  stevel

	* libEM/averager.cpp, libEM/averager.h, libEM/util.h,
	  libpyEM/EMAN2.py, programs/e2ddd_movie.py: Improvements to
	  e2ddd_movie

2013-03-29 04:51  jgalaz

	* examples/e2spt_cudatimetest.py: --plotonly fully functional now
	  with different linestyles and markers for differnet curves on the
	  same plot.  Added --subset option, to see ripples or variations
	  at the lower end of the curves (opposed to calculating log plots
	  which are less straight-forward or intuitive to interpret).

2013-03-29 01:59  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2013-03-29 01:56  jgalaz

	* examples/e2spt_cudatimetest.py: Committing as I change things to
	  prevent losses...

2013-03-29 01:17  jgalaz

	* examples/e2spt_cudatimetest.py: Different markers for each curve
	  automatically picked when plotting multiple curves on the same
	  figure in grey scale.

2013-03-28 23:37  jgalaz

	* programs/e2spt_boxer.py: The boxer used to be able to take
	  "normalize" as the only --normproc. Now it can take ANY
	  normalizing processor.  Also, --thresh option added. It is
	  somtimes useful to "clamp" the min and max values to get rid of
	  possibly surving xrays, and to minimize the influence of gold on
	  alignments (some golds are very close to the particles, or lie
	  within the normalization volume or mask).

2013-03-28 22:01  jgalaz

	* examples/e2fixheaderparam.py: Program to add and/or change
	  parameters on the header of EM files.  hdf, mrc, bdb, st, ali and
	  rec formatts are supported.

2013-03-28 16:22  pawel

	* sparx/libpy/reconstruction.py: [no log message]

2013-03-28 15:28  scmurray

	* programs/e2tiltvalidate.py: Changed it to always generate new
	  projections from the given model. It used to only make them the
	  first time but now, with the need to try different models, it
	  needs to regenerate each time.

2013-03-28 15:19  pawel

	* sparx/libpy/pixel_error.py: modified ordersegm

2013-03-28 14:38  piotr

	* libpyEM/mpi_eman.py: bugfixes

2013-03-28 13:48  fjia

	* libEM/sparx/util_sparx.cpp: changed the way mirroring is handled
	  in multiref_polar_ali_helical_local

2013-03-28 13:30  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2013-03-28 13:13  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2013-03-28 13:03  piotr

	* libpyEM/mpi_eman.py:
	  Bugfix

2013-03-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-27 16:04  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2013-03-27 15:53  pawel

	* libEM/sparx/fourierfilter.cpp: [no log message]

2013-03-27 12:19  pawel

	* sparx/libpy/filter.py: cleaning

2013-03-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-27 11:57  pawel

	* sparx/libpy/morphology.py: in rotavg_ctf Cs should appear as the
	  third argument)

2013-03-27 11:40  cailin

	* libEM/glutil.cpp: histo gauss/equal/normal

2013-03-27 11:39  cailin

	* libpyEM/qtgui/emimage2d.py: button for histogram
	  gauss/equal/normal

2013-03-26 15:55  cailin

	* libEM/glutil.cpp: update historgram range

2013-03-26 13:56  cailin

	* libEM/glutil.cpp: histogram matching gaussian

2013-03-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-26 05:40  jgalaz

	* examples/e2spt_cudatimetest.py: Included --onefft and --onefull
	  options to test alignment time against boxsize for a single
	  orientation (one fft, not rotations) through
	  e2spt_classaverage.py without any preprocessing done (--onefft),
	  and with preprocessing done (--onefull). Previously, alignments
	  defaulted to scanning the icosahedral asymmetric unit (which can
	  now be selected through --icosali). All three tests can be run in
	  parallel. The first two are meant to indirectly meassure
	  preprocessing time. (Option to test for overhead soon to
	  come...).

2013-03-26 05:32  jgalaz

	* programs/e2spt_boxer.py: Fixed --normalize bug that came up when
	  boxing particles with the GUI and selecting to save the boxed
	  data (instead of just the coordinates).

2013-03-26 05:32  jgalaz

	* programs/e2spt_autoboxer.py: --Llowpass and --highpass of
	  tomograms were not working when the tomogram wasn't in the local
	  directory where the autoboxer was run (fixed now).  Also added
	  --invert (so that you don't have to pre-invert the contrast),
	  --threshold (so that you can take benefit of knowing that given
	  the proper contrast, protein should be positive or "white"), and
	  --normalize options (some of these were listed among the options
	  already but had NOT been implemented). Thresholding negative
	  densities DRAMMATICALLY facilitates visualization of particles
	  (at least for e15).

2013-03-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-25 11:11  piotr

	* sparx/libpy/: applications.py, pixel_error.py: change the name of
	  max_2D_pixel_error to pixel_error_2D

2013-03-25 10:45  pawel

	* sparx/libpy/applications.py: applications.py

2013-03-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-23 15:31  fjia

	* sparx/: bin/sxihrsr.py, libpy/applications.py: [no log message]

2013-03-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-22 15:39  fjia

	* programs/e2helixboxer.py: add option --invert_contrast to invert
	  contast of loaded micrograph so contrast of boxed helices and
	  windowed particles are inverted

2013-03-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-22 11:51  pawel

	* libEM/sparx/util_sparx.cpp: removed printout from ehelix

2013-03-22 11:46  pawel

	* sparx/libpy/pixel_error.py: [no log message]

2013-03-22 10:52  pawel

	* libEM/sparx/util_sparx.cpp: added directional search

2013-03-22 10:51  pawel

	* sparx/libpy/pixel_error.py: moved helical code around to logical
	  places, more corrections

2013-03-22 06:48  jgalaz

	* programs/e2spt_autoboxer.py: [no log message]

2013-03-22 06:41  jgalaz

	* programs/e2spt_autoboxer.py: [no log message]

2013-03-22 06:40  jgalaz

	* programs/e2spt_autoboxer.py: Can't get ALL good partilces to be
	  picked :/ ; only ~80% ... (at least, no golds or carbon edges are
	  picked, and only > 10% false positive "empty" boxes).

2013-03-21 19:08  jgalaz

	* examples/e2spt_cudatimetest.py: Troubleshooting the addition of
	  options like --onefft (to test the alignment time of ONE
	  orientation only, with NO preprocessing) and --onefull (to test
	  the alignment of one orientation, including all possible
	  preprocessing options).  Also cleaned up code a bit.	Also fixed
	  bug where "fine alignments" were scanning too many positions (the
	  range for fine alignments does NOT  need to be equal to delta
	  coarse; rather, 1/2 of delta coarse).

2013-03-21 19:06  jgalaz

	* programs/e2spt_autoboxer.py: No repeated elementes anymore.

2013-03-21 15:33  pawel

	* sparx/libpy/fundamentals.py: [no log message]

2013-03-21 14:22  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-03-21 12:47  fjia

	* sparx/: libpy/applications.py, bin/sxihrsr.py: [no log message]

2013-03-21 12:27  fjia

	* sparx/: libpy/applications.py, bin/sxihrsr.py: [no log message]

2013-03-21 12:20  piotr

	* libEM/sparx/util_sparx.cpp: bugfix

2013-03-21 12:12  piotr

	* libEM/sparx/util_sparx.cpp: constrained_helix - last bugfix

2013-03-21 12:03  piotr

	* libEM/sparx/util_sparx.cpp: constrained_helix - add last changes

2013-03-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-21 11:52  piotr

	* libEM/sparx/util_sparx.cpp: constrained_helix - some bugs removed

2013-03-21 11:40  fjia

	* sparx/libpy/applications.py: [no log message]

2013-03-21 06:00  jgalaz

	* programs/e2spt_autoboxer.py: [no log message]

2013-03-21 05:41  jgalaz

	* programs/e2spt_autoboxer.py: [no log message]

2013-03-21 05:38  jgalaz

	* programs/e2spt_autoboxer.py: Improvements by using alignment of
	  projections to better center the particles and detect false
	  positives, in particular, using autocorrelation to prune out
	  carbon edges, and mean/sigma/max/min stats of particles (or their
	  projections) to prune out golds and empty boxes (ice).

2013-03-20 14:55  piotr

	* sparx/libpy/: applications.py, reconstruction.py, utilities.py:
	  recons3d_4nn_mpi - reading images from stack one by one
	  (implementing 2 iterators)

2013-03-20 14:40  fjia

	* sparx/libpy/applications.py: add windowing program

2013-03-20 14:25  piotr

	* libpyEM/: EMAN2PAR.py, mpi_eman.py: Removing bugs (type of int
	  variables, string deserialization)

2013-03-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-20 11:24  piotr

	* CMakeLists.txt: Removing directory mpi_eman - update
	  CMakeList.txt

2013-03-20 11:16  piotr

	* mpi_eman/: 0README, CMakeLists.txt, Makefile.linux,
	  Makefile.linux2, Makefile.osx, mpi_eman.c, mpi_eman.py,
	  mpi_test.py, mpi_test_basic.py, pbs.example, test.sge: Removing
	  directory mpi_eman

2013-03-20 11:01  piotr

	* libpyEM/mpi_eman.py: Moving the file mpi_eman.py from mpi_eman to
	  libpyEM

2013-03-20 10:40  piotr

	* libpyEM/EMAN2PAR.py: Remove dependency from mpi_eman.c wrapper.
	  Now MPI based on mpi library (wrapper from sparx).

2013-03-20 10:36  piotr

	* mpi_eman/mpi_eman.py:
	  Remove dependency from mpi_eman.c wrapper. Now MPI based on mpi
	  library (wrapper from sparx).

2013-03-20 01:15  jgalaz

	* programs/e2spt_autoboxer.py: [no log message]

2013-03-19 23:44  stevel

	* libpyEM/qtgui/emimage2d.py: Further improved "Probe"

2013-03-19 23:20  stevel

	* libpyEM/qtgui/emimage2d.py: Fixed probing. Still incomplete.

2013-03-19 22:48  stevel

	* libpyEM/qtgui/emimage2d.py: Working on new probe tab for 2D
	  widget

2013-03-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-19 11:49  pawel

	* sparx/bin/sxihrsr.py: ywobble

2013-03-18 16:22  pawel

	* sparx/libpy/applications.py: applications.py

2013-03-18 13:13  piotr

	* libEM/sparx/util_sparx.cpp: constrained_helix - I have removed
	  memory leaks

2013-03-18 12:06  piotr

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: constrained_helix - first version

2013-03-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-16 20:27  stevel

	* programs/: e2align3d.py, e2ddd_movie.py: Working on movie
	  processing

2013-03-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-16 02:59  jgalaz

	* programs/e2spt_autoboxer.py: meancalc function decoupled into two
	  functions: meancalc and pruner.  (Also, experimenting with
	  thresholding the tomogram before particle search...).

2013-03-16 02:57  jgalaz

	* examples/e2spt_cudatimetest.py: ...

2013-03-15 19:33  jgalaz

	* examples/e2spt_cudatimetest.py: Debugging latest introduced
	  options (--plotonly and --plotminima).

2013-03-15 16:31  pawel

	* sparx/: bin/sxali2d.py, libpy/alignment.py,
	  libpy/applications.py: added rotational 2D alignment with limited
	  angle

2013-03-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-15 10:46  cailin

	* libpyEM/qtgui/emboxerbase.py: window location restore

2013-03-14 17:16  pawel

	* sparx/libpy/applications.py: corrected nonsensical transform2d

2013-03-14 15:24  fjia

	* sparx/libpy/applications.py: [no log message]

2013-03-14 13:55  piotr

	* sparx/libpy/reconstruction.py: remove some spaces

2013-03-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-14 10:37  pawel

	* sparx/libpy/applications.py: corrected (again!) ordersegments

2013-03-14 10:33  pawel

	* sparx/libpy/applications.py: corrected ordersegments

2013-03-13 15:47  pawel

	* sparx/libpy/applications.py: corrected ordersegments

2013-03-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-12 21:14  jgalaz

	* examples/e2spt_cudatimetest.py: Implementation of --plotonly if
	  .txt files with data are provided, and of --plotminima, if
	  extensive tests are performed but one wants to plot only the data
	  corresponding to the "good box sizes"

2013-03-12 21:13  jgalaz

	* examples/e2spt_rotationalplot.py: [no log message]

2013-03-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-11 14:03  cailin

	* libpyEM/EMAN2.py: restore window location

2013-03-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-10 11:20  pawel

	* sparx/: bin/sxali2d.py, libpy/applications.py: added option
	  friedel to 2D alignment

2013-03-09 13:08  pawel

	* sparx/libpy/applications.py: align2d_friedel

2013-03-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-08 17:47  fjia

	* sparx/libpy/applications.py: [no log message]

2013-03-08 16:46  fjia

	* sparx/libpy/fundamentals.py: [no log message]

2013-03-08 13:42  fjia

	* sparx/libpy/applications.py: add code for windowing segments from
	  boxed helices

2013-03-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-08 10:14  cailin

	* programs/e2evalimage.py: remove a lowerbar typo.

2013-03-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-06 13:59  pawel

	* sparx/libpy/morphology.py: rotavg_ctf

2013-03-06 13:16  pawel

	* sparx/libpy/morphology.py: rotavg_ctf

2013-03-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-06 09:21  pawel

	* libEM/sparx/util_sparx.cpp: change the direction of astigmatism
	  rotation to correspond to standard in sparx

2013-03-06 08:22  pawel

	* sparx/libpy/fundamentals.py: commented out original golden search

2013-03-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-05 08:06  stevel

	* programs/e2ctf.py: oops. typo in e2ctf

2013-03-04 17:02  jgalaz

	* examples/e2spt_coordsrefactor.py: Same thing: Can't remember what
	  changed, but my file is different from the CVS version...
	  (otherwise you're not asked  for a log file).

2013-03-04 17:00  jgalaz

	* programs/e2spt_simulation.py: Can't remember what I changed
	  during the weekend but the file is different from the one in CVS.

2013-03-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-04 10:15  stevel

	* libEM/util.cpp, libEM/util.h, libpyEM/libpyUtils2.cpp,
	  programs/e2ctf.py, programs/e2ddd_movie.py: Finally made the
	  iterative non-convex function a C++ function for speed.

2013-03-04 05:13  jgalaz

	* programs/e2spt_resolutionplot.py: --mask and --lowpass shouldn't
	  be parsed. They actually NEED to remain strings.

2013-03-04 03:36  jgalaz

	* examples/e2slicer.py: Bugs fixed. Presumably fully functional
	  now.

2013-03-04 01:03  jgalaz

	* examples/e2slicer.py: Program to extract orthogonal slices
	  through the mid sections of subvolumes.  It can also extract all
	  consecutive slices along each of the carthesian axes (it executes
	  e2proc2d.py at the command line for this, using the --threed2twod
	  option).

2013-03-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-02 16:54  jgalaz

	* examples/e2orthoproject.py: --mask default should be None.

2013-03-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-01 22:45  jgalaz

	* programs/e2spt_hac.py: --autocenter was broken and messing up
	  alignments when on...

2013-03-01 16:51  fjia

	* sparx/libpy/statistics.py: modify ave_var to take listID as one
	  of the argments

2013-03-01 16:50  fjia

	* sparx/libpy/applications.py: in ave_ali, pass name of stack to
	  ave_var instead of reading stack into memory

2013-03-01 13:32  stevel

	* TODO, libEM/processor.cpp, libEM/processor.h, programs/e2ctf.py,
	  programs/e2ddd_movie.py: New horizontal/vertical stripe removal.
	  Improvements to e2ddd_movie, but still incomplete

2013-03-01 13:29  scmurray

	* libpyEM/qtgui/embrowser.py, programs/e2refinetorelion3d.py: Small
	  changes. e2refinetorelion.py now pulls the amplitude contrast
	  from the ctf parameters and embrowser.py recieved a small change
	  where it will no longer spit out a warning when the '...'
	  particle number is selected.

2013-03-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-03-01 11:01  pawel

	* sparx/: bin/sxihrsr.py, libpy/applications.py: [no log message]

2013-03-01 04:29  jgalaz

	* examples/e2orthoproject.py: [no log message]

2013-03-01 04:25  jgalaz

	* examples/: e2orthoproject.py: [no log message]

2013-03-01 04:20  jgalaz

	* examples/e2orthoproject.py: --normproc implemented.

2013-03-01 04:12  jgalaz

	* programs/e2spt_resolutionplot.py: [no log message]

2013-02-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-28 10:55  scmurray

	* programs/: e2proc2d.py, e2refinetorelion3d.py: Fixed an extra
	  debugging line in e2proc2d.py and am integrating new features
	  into e2refinetorelion3d.py

2013-02-28 08:19  stevel

	* libEM/processor.cpp, libEM/processor.h, programs/e2ddd_movie.py:
	  updates to ddd processor, but still not done

2013-02-27 15:02  pawel

	* sparx/libpy/: alignment.py, applications.py, isac.py,
	  projection.py, statistics.py, utilities.py: some cleaning in util
	  in alignment.py

2013-02-27 14:53  pawel

	* libEM/sparx/util_sparx.cpp, sparx/libpy/alignment.py: some
	  cleaning in util in alignment.py

2013-02-27 14:46  pawel

	* sparx/libpy/alignment.py: some cleaning in util in alignment.py

2013-02-27 14:45  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-02-27 13:38  fjia

	* libEM/sparx/util_sparx.cpp: change the way psi_pos is calculated
	  in Crosrng_sm_psi and Crosrng_psi so psi_pos = 1 when psi=0
	  (indicating no change in in-plane rotation)

2013-02-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-27 11:13  fjia

	* libEM/sparx/util_sparx.cpp: remove function
	  Crosrng_psi_0_180_no_mirror (not used, replaced by
	  Crosrng_sm_psi)

2013-02-27 11:12  fjia

	* libEM/sparx/util_sparx.h: remove declaration for
	  Crosrng_psi_0_180_no_mirror

2013-02-27 11:08  fjia

	* sparx/libpy/applications.py: [no log message]

2013-02-27 10:57  fjia

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-02-27 10:50  fjia

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-02-27 04:58  jgalaz

	* examples/e2orthoproject.py: Bug fixes for latest implemented
	  parameters.

2013-02-27 03:57  jgalaz

	* examples/e2orthoproject.py: [no log message]

2013-02-27 03:38  jgalaz

	* examples/e2orthoproject.py: Program can now save the volume
	  rotated in the directions use to project it by turning on
	  --saverotvol Also, the program now accepts a rotation to apply
	  (--angles=az,alt,phi) before projecting the volume (and
	  optionally a --tag, to easily label output projections either as
	  "top", "side" or whatever one might want), or a list of
	  projection orientations by supplying a text file through
	  --transformsfile=

2013-02-26 17:14  fjia

	* libEM/sparx/util_sparx.cpp: remove old comments

2013-02-26 15:33  pawel

	* sparx/libpy/applications.py: modified transform2d

2013-02-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-25 14:53  cailin

	* libEM/marchingcubes.cpp, libpyEM/qtgui/emdataitem3d.py: update
	  opengl version control

2013-02-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-24 23:17  jgalaz

	* programs/e2spt_resolutionplot.py: [no log message]

2013-02-24 23:17  jgalaz

	* examples/e2orthoproject.py: --lowpass option implemented.

2013-02-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-23 17:51  jgalaz

	* examples/e2orthoproject.py: New --mask param that tajes mask
	  processor. Improves quality of projections by removing noise in
	  the 3D box, that doesn't need to be projected with the actual
	  molecule.

2013-02-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-22 09:54  pawel

	* sparx/libpy/morphology.py: [no log message]

2013-02-22 02:48  jgalaz

	* examples/e2spt_tomosimjobs.py: The --plotonly option had never
	  been checked for functionality. It was broken. I now fixed it,
	  and made a function that analyses the error files, instead of
	  having redundant code.  The allowed to analyse/plot many files
	  from previous runs where the analysis of the results (the plots)
	  were buggy, and needed to be re-done, but the simulation did not
	  need to be redone itself.

2013-02-22 01:13  jgalaz

	* programs/e2spt_boxer.py: --normproc was implemented for
	  --helixboxer, but not for the normal tomo boxer. Normalization
	  was on by default; then I turned it off; now I added it back,
	  optionally, through --normproc.

	  Also, new --bruteaverage computes the average of picked particles
	  (what the "average" window was supposed to have done for the GUI,
	  but it was never implemented), which is useful in determining
	  whether on average you have picked the correct specimen and
	  whether the particles are reasonably centered.

2013-02-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-21 04:57  jgalaz

	* programs/e2spt_refprep.py: Output edited reference has now origin
	  parameters equal to zero for ease of visualization with chimera.

2013-02-21 04:10  jgalaz

	* programs/e2spt_tiltstacker.py:
	  New program so that one won't have to manually convert dm3 or
	  tiff images to mrc, and then stack them with IMOD using
	  "newstack".  A .rawtlt file is also generatd if the theoretical
	  tilt range limits and tiltstep are provided.

	  It all works perfect, EXCEPT that EMAN2's images of data type
	  "EMUtil.EMDataType.EM_FLOAT" have messed-up contrast in IMOD's
	  programs.  IMOD requires EMUtil.EMDataType.EM_SHORT; but, for
	  some reason, when --mrc16bit or --mrc8bit are on, e2proc2d.py
	  fails with a segmentation fault and thus the output of the type
	  desired by IMOD is never written... :/

2013-02-21 04:04  jgalaz

	* programs/e2proc2d.py: --twod2threed was not working EITHER. Now
	  it is (it puts all images in an HDF stack into a pseudo-3D MRC
	  volume).

2013-02-20 22:40  jgalaz

	* examples/e2orthoproject.py: Fixed program description.

2013-02-20 19:05  jgalaz

	* programs/e2proc2d.py: --exclude and --list are fixed now for
	  --threed2threed (they were COMPLETELY non-functional).

2013-02-20 17:29  pawel

	* sparx/libpy/morphology.py: correct limitctf

2013-02-20 16:57  jgalaz

	* examples/e2orthoproject.py: Cleaned code a bit. Also, program now
	  allows to generate ONE projection, selected from the three
	  orthogonal options.

2013-02-20 16:36  pawel

	* sparx/libpy/fundamentals.py: normalize tilemic

2013-02-20 15:15  cailin

	* libEM/pointarray.cpp: windows compile error fixed(sqrt)

2013-02-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-20 10:26  pawel

	* sparx/demo/demo_user_funcs.py: [no log message]

2013-02-20 09:22  piotr

	* libEM/sparx/fundamentals.cpp: cleanings

2013-02-20 05:52  jgalaz

	* examples/e2spt_rotationalplot.py: Just in case I didn't commit
	  latest changes... (can't remember/think).

2013-02-20 03:45  jgalaz

	* examples/e2spt_tomosimjobs.py: Fixed 'nslicestag'

2013-02-20 03:38  jgalaz

	* programs/e2spt_classaverage.py: --savedpreprocessed rendered
	  unusable because "preprocessing" functionis buggy and therefore
	  commented out for now.

2013-02-19 17:37  jgalaz

	* examples/e2spt_tomosimjobs.py:

	  When using fsc.tomo, the wedge size was not being properly passed
	  on to e2spt_classaverage and defaulted to +-60 (this might
	  partially explain the negative results in the extensive
	  simulations of TRiC testing fsc.tomo to characterize its "sigmas"
	  parameter...).

2013-02-19 17:09  piotr

	* sparx/tests/test_fundamentals.py: unit test for all acf* and ccf*
	  routines

2013-02-19 17:08  piotr

	* libEM/sparx/fundamentals.cpp: corrections of normalization in
	  fourierproduct (it has impact on the ccf*, acf* and cnv*
	  routines)

2013-02-19 15:38  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2013-02-19 14:47  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2013-02-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-19 06:14  jgalaz

	* programs/e2spt_autoboxer.py:
	  CVS
	  ----------------------------------------------------------------------
	  Improvements, and EXTENSIVE attempts to get --mask to function
	  (not working fully yet though...).

2013-02-19 04:31  jgalaz

	* programs/e2spt_resolutionplot.py:
	  ...

2013-02-19 00:47  jgalaz

	* examples/e2spt_rotationalplot.py: Bug fixes when --plotonly on
	  and no titles on plot now.

2013-02-19 00:26  jgalaz

	* examples/e2spt_coeffplot.py: --normalizeplot now available. Also
	  ticks and labels are larger and bolder, and x axis limit extends
	  a bit beyond last value for better visualization.

2013-02-18 20:50  jgalaz

	* examples/e2spt_transformdistance.py: Got rid of spt_ali_param,
	  now properly stored in xform.align3d.

2013-02-18 20:45  jgalaz

	* programs/e2spt_classaverage.py:
	  Got rid of spt_ali_param, now properly stored in xform.align3d.

2013-02-18 19:30  jgalaz

	* programs/e2spt_resolutionplot.py: Program can now limit the
	  extent of resolution shown on the X-axis (which makes low
	  resolution plots look better).  Also, bug displaying the first
	  tick is fixed (it is now always "0"); also, a variable number of
	  ticks are shown depending on the number of Fourier pixels
	  plotted, to avoid overcrowding.  Furthermore, colors are
	  generated automatically and are now virtually litmitless
	  (previously, an error would come up if plotting to many FSC on
	  the same plot).

2013-02-18 18:29  stevel

	* examples/e2spt_extract_align.py: Simple example script for
	  extracting alignments

2013-02-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-18 11:12  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2013-02-18 05:36  jgalaz

	* examples/e2spt_rotationalplot.py: Although --plotonly was on the
	  list of parameters, its functionality was NOT implemented. Now it
	  IS.

2013-02-18 03:51  jgalaz

	* examples/e2spt_rotationalplot.py: Removed labels (they aren't
	  very useful).  Plotting range on axis is back to min and max
	  values of data (no padding).	Fixed bug that was producing 2d
	  plots even when not requested.

2013-02-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-15 17:31  pawel

	* sparx/libpy/: morphology.py, user_functions.py: [no log message]

2013-02-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-13 14:34  stevel

	* examples/e2ptclzvssim.py, programs/e2ddd_movie.py: work on ddd
	  processing

2013-02-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-13 00:19  jgalaz

	* programs/e2spt_autoboxer.py: Picking particles that are gold
	  fiducials is now effectively avoided (still picking empty boxes
	  and carbon though, and neglecting some good particles...; all
	  based on translational alignment of a sphere the size the radius
	  of gyration of the partilce)

2013-02-12 16:11  jgalaz

	* programs/e2spt_boxer.py: Implemented --normproc because particles
	  should NOT be normalized by default. e2spt_classaverage and
	  e2spt_hac already take care of normalization internally. The
	  non-normalized mean and sigma information for boxed out particles
	  can be used for other purposes and thus should not be made 0 and
	  1 by default.

2013-02-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-12 10:27  stevel

	* programs/e2ddd_movie.py: Adding first version of e2ddd_movie.py

2013-02-11 20:43  irees

	* programs/e2proc2dmulti.py: Fixed typo when using "--postfix"
	  option.

2013-02-11 16:50  jgalaz

	* examples/e2spt_tomosimjobs.py: mpi parallelization doesn't seem
	  to be working for this program.  Fix attempt.

2013-02-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-10 23:12  jgalaz

	* programs/e2spt_classaverage.py: Functionality of --cmp=fsc.tomo
	  fully implemented now (presumably in the proper way now, AFTER
	  subtomogram processing, and WITHOUT having to run your particles
	  through e2spt_wedge.py. [Since the comparator depends on
	  arbitrary parameters, it needs more/extensive testing]).

2013-02-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-08 14:06  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2013-02-08 13:56  pawel

	* sparx/libpy/utilities.py: [no log message]

2013-02-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-08 07:18  stevel

	* libEM/cmp.cpp: Maxres default was claimed to be 10 but was
	  actually 2 in phase and fsc comparators !

2013-02-07 22:48  jgalaz

	* programs/e2proc2d.py:
	  Changed line 587, to write out files properly when --unstacking
	  is on and --mrc8bit and --mrc16bit are off:

	  #d.write_image(outfile.split('.')[0]+'-'+str(i+1).zfill(len(str(nimg)))+'.'+outfile.split('.')[-1])
	  d.write_image(outfile.split('.')[0]+'-'+str(i+1).zfill(len(str(nimg)))+'.'+outfile.split('.')[-1],
	  0, EMUtil.get_image_ext_type(options.outtype), False, None,
	  EMUtil.EMDataType.EM_FLOAT, not(options.swap))

2013-02-07 13:24  stevel

	* libEM/: averager.cpp, averager.h: added normimage option to mean
	  averager

2013-02-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-06 15:02  stevel

	* libEM/aligner.cpp, libEM/aligner.h, libEM/emdata.cpp,
	  libEM/emdata.h, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emplot2d.py, programs/e2ptcltrace.py: Several
	  significant changes to the coarse "rotate_translate_flip" aligner
	  series. This includes adding a new "zscore" option, and also
	  reverting a change from last fall where the rotational precision
	  was marginally reduced. There are some indications that this
	  caused a subtle worsening of map quality, even when the 'refine'
	  aligners were used. The "zscore" option is experimental.

2013-02-06 14:22  cailin

	* programs/e2evalimage.py: add a lock to redisplay.

2013-02-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-04 17:26  jgalaz

	* programs/e2spt_resolutionplot.py: Bug fix

2013-02-04 15:31  scmurray

	* libpyEM/qtgui/embrowser.py, programs/e2refinetorelion3d.py:
	  Changed some options in e2refinetorelion3d and removed a
	  debugging statement in embrowser.py where it would print "isc" to
	  the terminal whenever you looked at a new image in the browser.

2013-02-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-02 22:21  jgalaz

	* programs/e2spt_subtilt.py: [no log message]

2013-02-02 22:20  jgalaz

	* programs/e2spt_subtilt.py: Ugh. I had advanced on this program
	  quite a bit, long ago, but I never submitted it. Now, apparently,
	  I deleted my old /src/ directory and lost it. Submitting this as
	  it is being developed to prevent losses. UNDER DEVELOPMENT.

2013-02-02 21:07  jgalaz

	* programs/e2spt_resolutionplot.py: [no log message]

2013-02-02 18:57  jgalaz

	* examples/e2spt_coeffplot.py: Things where broken when --cutoff
	  option was on. Fixed them.  Also fixed annoying bug that brought
	  up an error when "-h" was specified (to see the options). It
	  turns out, you cannot have the percent symbol (%) inside the
	  string that describes each options, otherwise arparse.py crashes.
	  Furthermore, added --path and --verbose options, as well as
	  --ppid and logger capability.

2013-02-02 17:43  jgalaz

	* examples/e2spt_coeffplot.py: Txt file with indx numbers of
	  selected "good particles" is now written out.  Txt file with
	  coordinates from original tomogram of selected "good particles"
	  is also now written out.  Additional option to select kept
	  particles, now based on --topn, that is, the top N particles you
	  want to keep (ranked by ccc) and make into a new, clean substack.
	  Fixed old way of prunning bad particles out (used to throw out
	  those with half the score of the particle in the middle of the
	  rank data set; now you can select a number of standard deviations
	  below the mean through --sigmaprune to throw particles out).

2013-02-02 17:23  jgalaz

	* programs/e2spt_resolutionplot.py: A bit more script cleaning.

2013-02-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-01 20:28  jgalaz

	* programs/e2spt_resolutionplot.py: Fixed trivial bugs when --sym
	  option is on.  [Some output path bugs endure, but the new version
	  of the program seems to be fully functional now...] [Some output
	  path bugs endure, but the new version of the program seems to be
	  fully functional now...]..

2013-02-01 18:51  jgalaz

	* programs/e2spt_resolutionplot.py: Trivial bugs fixed when
	  --mirror on, and cleaned script a bit.

2013-02-01 18:04  jgalaz

	* programs/e2spt_resolutionplot.py: Logic and efficieny of program
	  much improved (in many ways); e.g., --sym and --mirror are now
	  applied internally, same as --fsc, instead of calling/running
	  e2proc3d.py.	Most significantly, the program can now plot fscs
	  for entire stacks against a reference, either as individual
	  figures, or with all plots in a single figure.

2013-02-01 14:43  cailin

	* libEM/glutil.cpp: add delete to grayhe

2013-02-01 13:48  cailin

	* libEM/glutil.cpp: fixed broken histoequal problem. removal an
	  intermedium matrix which can lead to segmentation fault with
	  eevalimage.py

2013-02-01 13:20  scmurray

	* programs/e2refinetorelion3d.py: Option Changes

2013-02-01 13:04  stevel

	* libEM/ctf.cpp, programs/CMakeLists.txt, programs/e2help.py,
	  programs/e2ptcltrace.py, pyemtbx/boxertools.py: Minor bugfix.

2013-02-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-02-01 11:41  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2013-01-31 19:03  jgalaz

	* programs/e2spt_resolutionplot.py: [no log message]

2013-01-31 17:40  jgalaz

	* programs/e2spt_resolutionplot.py: [no log message]

2013-01-31 16:51  scmurray

	* programs/e2refinetorelion3d.py: More Small Changes

2013-01-31 16:33  scmurray

	* programs/e2refinetorelion3d.py: logic error

2013-01-31 16:21  scmurray

	* programs/e2refinetorelion3d.py: More changes

2013-01-31 16:05  scmurray

	* programs/e2refinetorelion3d.py: fixed a silly logic error I made

2013-01-31 15:44  scmurray

	* programs/e2refinetorelion3d.py: Changes

2013-01-31 15:39  scmurray

	* programs/e2refinetorelion2d.py: Fixed some bugs

2013-01-31 15:07  pawel

	* libEM/sparx/util_sparx.cpp, sparx/libpy/morphology.py: [no log
	  message]

2013-01-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-30 18:31  jgalaz

	* examples/e2spt_tomosimjobs.py: --tiltstep was added back, becase
	  for varying missing wedge sizes, a constant --nslices parameter
	  would cram the same number of tilts in narrower tilt ranges.
	  Also, naming tangs for --nslices was fixed.

2013-01-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-30 09:17  pawel

	* sparx/libpy/morphology.py: [no log message]

2013-01-29 19:21  jgalaz

	* programs/e2spt_classaverage.py: bug fix writing preprocessed
	  stack.

2013-01-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-29 11:54  pawel

	* libEM/sparx/util_sparx.cpp, sparx/libpy/morphology.py: more ctfs

2013-01-29 08:48  pawel

	* libpyEM/libpyUtils2.cpp, sparx/libpy/morphology.py: [no log
	  message]

2013-01-29 08:31  pawel

	* libEM/sparx/: fundamentals.cpp, util_sparx.cpp, util_sparx.h:
	  corrections of real ctfs

2013-01-28 17:56  jgalaz

	* programs/e2spt_classaverage.py: Testing --randomizewedge and
	  building towards a preprocessing function (subtomogram
	  preprocessing should be independent from the alignment class).

2013-01-28 14:19  pawel

	* sparx/libpy/fundamentals.py: [no log message]

2013-01-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-24 14:43  jgalaz

	* examples/e2spt_rotationalplot.py: Bug fix

2013-01-24 14:38  fjia

	* sparx/libpy/applications.py: [no log message]

2013-01-24 13:58  fjia

	* libEM/sparx/util_sparx.cpp: in
	  multiref_polar_ali_helical_90_local: replace
	  Crosrng_psi_0_180_no_mirror with Crosrng_sm_psi (no checking for
	  mirror, and searches only around current psi of input data)

2013-01-24 13:01  jgalaz

	* programs/e2proc3d.py: Fixed output writing to the outputfile
	  format when using --unstacking option.

2013-01-24 12:27  pawel

	* sparx/libpy/pixel_error.py: cleaned code for pixel_error, added
	  angle_ave

2013-01-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-24 10:31  pawel

	* sparx/libpy/applications.py: [no log message]

2013-01-23 17:48  fjia

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-01-23 17:12  fjia

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-01-23 15:29  irees

	* programs/e2simmx.py: Fixed typo in error message in e2simmx.py;
	  if given a bad data file, gave error message for bad reference
	  file. Reported by Jason.

2013-01-23 15:27  jgalaz

	* examples/e2spt_rotationalplot.py: Capacities largely extenxed to
	  deal with particle stacks, and to plot rotational correlation
	  agreement in pseudo-3D if both alt and az are varied continously,
	  and to produce plots of rotational agreement of one particle
	  against another (except of only producing plots to see the
	  agreement of one particle with itself).

2013-01-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-23 11:57  stevel

	* programs/e2proc3d.py: oops

2013-01-23 11:55  stevel

	* libpyEM/EMAN2.py, programs/e2proc3d.py: Shrink big maps

2013-01-23 09:22  stevel

	* CMakeLists.txt: trivial

2013-01-23 09:17  stevel

	* CMakeLists.txt, programs/e2initialmodel.py: Improvements to
	  CMakeLists, mostly for Mac

2013-01-22 16:15  stevel

	* libpyEM/EMAN2.py: oops

2013-01-22 16:00  scmurray

	* programs/: e2refinetorelion2d.py, e2refinetorelion3d.py: Changed
	  to add better error handling and changed some options

2013-01-22 14:55  stevel

	* libpyEM/EMAN2.py, programs/e2proc3d.py: Improvements to
	  e2proc3d.py. incomplete

2013-01-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-18 12:59  pawel

	* sparx/libpy/: applications.py, morphology.py: corrected rintout
	  of ctf in sxheader

2013-01-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-17 16:21  jgalaz

	* programs/e2spt_boxer.py: Bug fix. Commandline boxer was
	  apparently not being able to write out particles to the correct
	  directory when a path wasn't provided.

2013-01-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-16 17:20  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2013-01-16 15:09  jgalaz

	* programs/e2spt_autoboxer.py: [no log message]

2013-01-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-15 15:19  cailin

	* libEM/pointarray.cpp: update gauss width

2013-01-15 15:15  cailin

	* libEM/pointarray.cpp: test

2013-01-15 14:35  scmurray

	* libEM/pmconfig/spr.json, programs/e2refinetofrealign.py,
	  programs/e2refinetorelion2d.py, programs/e2refinetorelion3d.py:
	  Changed GUI parameters and made small changes to 2D to work with
	  relion 1.1 better

2013-01-15 14:18  cailin

	* libpyEM/qtgui/emimage2d.py: add histo equalizaiton button

2013-01-15 14:18  cailin

	* libEM/glutil.cpp: add histo equlization

2013-01-15 13:58  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-01-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-14 16:11  irees

	* programs/e2iminfo.py: If a header or informational option is
	  specified (--header, --stat, --euler) is specified, assume the
	  first image (-N 0) if none is given.

2013-01-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-14 11:15  pawel

	* sparx/bin/sxihrsr.py: [no log message]

2013-01-14 11:11  pawel

	* sparx/bin/sxihrsr.py: [no log message]

2013-01-14 11:07  pawel

	* sparx/bin/: sxihrsr.py: [no log message]

2013-01-14 10:10  pawel

	* sparx/: bin/sxihrsr.py, libpy/morphology.py: [no log message]

2013-01-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-11 17:46  jgalaz

	* examples/e2spt_radialdensityplot.py: Previously, multiple plots
	  could be on one png file if each stack contained an individual
	  image, or if only one stack was provided. Now, you can plot all
	  curves in one plot regardless of how many stacks you provide and
	  how many images each stack has. This is done through
	  --singleplotperfile and --singlefinalplot. If none of these is
	  specified, you get one plot for each each image in each stack,
	  for each desired plotting "mode" (density along a certain axis,
	  or radial density, or cilyndrical, etc.). Redundancies were
	  eliminated as well, so the code is shorter.

2013-01-11 14:25  pawel

	* sparx/libpy/: morphology.py, statistics.py: corrected
	  defocus_guess

2013-01-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-11 11:14  pawel

	* sparx/libpy/alignment.py: [no log message]

2013-01-10 19:05  fjia

	* sparx/libpy/applications.py: [no log message]

2013-01-10 14:00  fjia

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-01-10 13:25  fjia

	* sparx/bin/sxshiftali.py: [no log message]

2013-01-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-10 11:44  stevel

	* examples/mergeproject2.py: Trivial

2013-01-10 11:31  fjia

	* sparx/bin/sxshiftali.py: [no log message]

2013-01-10 10:49  stevel

	* examples/mergeproject2.py: New version of mergeproject should
	  work with e2projectmanager

2013-01-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-09 11:15  fjia

	* sparx/libpy/applications.py: [no log message]

2013-01-09 09:49  stevel

	* programs/e2eotest.py: Fix for new option

2013-01-08 15:40  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2013-01-08 14:24  stevel

	* programs/e2import.py: trivial

2013-01-08 13:47  stevel

	* programs/e2helixboxer.py: whitespace fix

2013-01-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-08 02:24  irees

	* libEM/: hdfio2.cpp, hdfio2.h: Patch for HDF5 to respect
	  render_min & render_max attributes when writing integer output
	  format. Implemented in the same was as for PNG.

2013-01-07 14:16  stevel

	* programs/e2refinevariance.py: Fix for renamed processor

2013-01-07 13:54  fjia

	* libpyEM/libpyUtils2.cpp: [no log message]

2013-01-07 13:18  fjia

	* sparx/libpy/alignment.py: [no log message]

2013-01-07 13:14  fjia

	* libpyEM/libpyUtils2.cpp, libEM/sparx/util_sparx.h,
	  libEM/sparx/util_sparx.cpp: [no log message]

2013-01-07 12:33  stevel

	* TODO, libEM/emutil.cpp, programs/e2evalimage.py,
	  programs/e2evalparticles.py, programs/e2helixboxer.py: Tweaks to
	  e2helixboxer to improve workflow for Ed

2013-01-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-04 16:22  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2013-01-04 16:03  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2013-01-04 15:58  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2013-01-04 15:16  fjia

	* sparx/libpy/applications.py: [no log message]

2013-01-04 14:43  fjia

	* sparx/libpy/applications.py: [no log message]

2013-01-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-04 11:14  pawel

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, sparx/libpy/fundamentals.py,
	  sparx/libpy/morphology.py: added ctf2_img

2013-01-03 14:41  fjia

	* sparx/libpy/applications.py: [no log message]

2013-01-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-02 15:30  scmurray

	* libEM/pmconfig/relion3d.json, programs/e2align3d.py,
	  programs/e2refinefromfrealign.py, programs/e2refinetorelion3d.py:
	  Changed e2refinetorelion3d.py to be more user-friendly by
	  removing certain options from the GUI but leaving them
	  command-line accessible. I also changed the wizard for
	  e2refinetorelion3d accordingly. I changed the parser that
	  e2refinefromfrealign.py was using to the newer one and fixed an
	  error that the old style was causing.

2013-01-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2013-01-02 11:58  fjia

	* sparx/libpy/applications.py: [no log message]

2013-01-02 11:50  fjia

	* sparx/libpy/applications.py: [no log message]

2013-01-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-30 23:38  stevel

	* libEM/ctf.cpp: Quick fix for EMAN1 CTF reading

2012-12-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-22 08:50  pawel

	* sparx/: bin/sxihrsr.py, libpy/applications.py: [no log message]

2012-12-21 19:00  pawel

	* sparx/bin/sxihrsr.py: [no log message]

2012-12-21 13:42  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2012-12-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-21 11:34  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2012-12-20 14:15  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2012-12-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-20 11:42  pawel

	* sparx/libpy/applications.py: [no log message]

2012-12-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-18 15:28  pawel

	* libEM/sparx/emdata_sparx.cpp: [no log message]

2012-12-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-17 15:56  cailin

	* programs/e2pdb2mrc.py: [no log message]

2012-12-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-17 11:55  fjia

	* sparx/bin/sxihrsr.py: import gendisks_MPI from applications
	  instead of development

2012-12-17 11:53  fjia

	* sparx/libpy/applications.py: move gendisks_MPI from development
	  to applications

2012-12-17 10:46  fjia

	* sparx/: bin/sxihrsr.py, libpy/applications.py: moving
	  imgstat_hfsc from development to applications

2012-12-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-14 20:17  jgalaz

	* examples/e2spt_tomosimjobs.py:
	  --tiltstep and associated parameters deprecated and fully
	  replaced by --nslices and associated parameters. A major bug
	  resulting from this redundancy was fixed (need to redo ALL in
	  silico tests)

2012-12-14 20:15  jgalaz

	* programs/e2spt_simulation.py:
	  --tiltstep parameter deprecated and fully replaced by --nslices
	  (so that the --tiltrange is always evenly covered).

2012-12-14 18:23  jgalaz

	* examples/e2spt_radialdensityplot.py: --normalizeplot used to
	  scale the values so that the maximum value in the plot would be
	  equal to 1. Now, it also scales them so that the minimum value is
	  equal to 0.

2012-12-14 18:15  jgalaz

	* examples/e2spt_radialdensityplot.py: Masking and normalization
	  defaults are now "None".

2012-12-14 18:06  jgalaz

	* examples/e2spt_radialdensityplot.py: This program could not
	  handle 2D images. Now it can.  Crashed when shrinking factor was
	  larger than at least one of the image dimensiones. The crash is
	  now avoided.	When shrinking, the x-axis of the plots was
	  inaccurate (it is in angstroms; therefore, x needed to be
	  multiplied by the shrinking factor).

2012-12-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-13 19:27  jgalaz

	* examples/e2spt_tomosimjobs.py:
	  assdfg

2012-12-13 19:22  jgalaz

	* examples/e2spt_radialdensityplot.py:
	  Error message when supplying repeated files.

2012-12-13 19:03  jgalaz

	* examples/e2spt_tomosimjobs.py:
	  Outfile naming improved. Bugs that resulted as a consequence
	  fixed. Split --shrinking into two options, --shrinksim and
	  --shrinkalign.

2012-12-13 19:02  jgalaz

	* programs/e2spt_simulation.py:
	  Shrinking issue on this program too...

2012-12-13 19:01  jgalaz

	* programs/e2spt_classaverage.py:
	  Fixed small issue with shrinking.

2012-12-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-13 11:02  fjia

	* sparx/libpy/applications.py: remove unnecesary import statement
	  from diskali

2012-12-13 01:03  jgalaz

	* programs/e2spt_autoboxer.py: FINALLY, this works!! To some
	  reasonable extent...	:) Sure, it picks up some garbage (golds
	  and carbon edges mostly), BUT those should be relatively easy to
	  get rid of.  The important point is, it finds tons of real
	  partilces too (and I have many several prunning ideas yet to
	  implement and test).

	  Plus, I tested the e2spt_autoboxer on a not-particularly good
	  ZSHORT, REAL tomogram of apo-TRiC.

	  Eager to test on esier cases (better quality tomograms), with
	  much easier particles (large viruses).  [Very optimistic].

2012-12-12 16:11  cailin

	* libpyEM/qtgui/em3Dhelloworld.py, sparx/bin/sxfit_error.py: [no
	  log message]

2012-12-12 16:05  cailin

	* libpyEM/qtgui/: emfoldhunterstat.py, emlights.py, emglobjects.py:
	  [no log message]

2012-12-12 16:02  cailin

	* libpyEM/qtgui/emscene3d.py, libEM/marchingcubes.cpp: [no log
	  message]

2012-12-12 15:57  cailin

	* libpyEM/qtgui/: emimage3dmorph.py, emanimationutil.py: [no log
	  message]

2012-12-12 15:53  cailin

	* libpyEM/qtgui/: emitem3d.py, emimageutil.py: [no log message]

2012-12-12 15:46  cailin

	* libEM/aligner.cpp: [no log message]

2012-12-12 15:40  cailin

	* examples/: e2simmxptclqual.py, e2spt_transformdistance.py: [no
	  log message]

2012-12-12 15:36  cailin

	* programs/e2procpdb.py, rt/pyem/test_transform.py: update
	  spin-omega

2012-12-12 15:33  cailin

	* libEM/transform.h, libEM/transform.cpp,
	  programs/e2tiltvalidate.py: update spin-omega

2012-12-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-12 10:48  fjia

	* sparx/libpy/applications.py: move get_dist from development to
	  applicatiosn

2012-12-12 08:20  stevel

	* programs/e2refine_evenodd.py: Added new sffile option to
	  refine_evenodd

2012-12-11 16:58  jgalaz

	* programs/e2spt_resolutionplot.py: The name of output files was
	  messed up if one of the volumes supplied was not in the current
	  directory, but rather within a subdirectory, or elsewhere
	  (../../wherever.hdf, e.g.).  Now the output files are propperly
	  named.

2012-12-11 15:54  fjia

	* programs/e2bdb.py: remove list printout from --exlist option

2012-12-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-11 02:15  jgalaz

	* programs/e2spt_autoboxer.py: Getting this to work has been a
	  NIGHTMARE. But I'm masochistic :) Previous tests on simulated
	  tomograms were superficial, and did not cover all possibilities.
	  Re-did lots of this program from scratch, and added several
	  options.  NOW *exhaustive* testing in-silico yields promising
	  results for autoboxing ZSHORT tomograms.  (I'll soon test with
	  real data, and I'll enable autoboxing of YSHORT tomograms).

2012-12-10 15:42  cailin

	* programs/e2procpdb.py: update program with eman2 and eman
	  conventions

2012-12-10 13:26  fjia

	* programs/e2bdb.py: add option --exlist for specifying name of
	  file with a list of images to exclude in creation of virtual
	  stack using makevstack

2012-12-10 12:17  stevel

	* programs/e2evalimage.py: Fixed defaults, I think...

2012-12-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-10 09:09  stevel

	* programs/e2helixboxer.py: Fixed box size default in GUI issue

2012-12-09 22:04  jgalaz

	* examples/e2spt_radialdensityplot.py: The program was working
	  without bugs only when you supplied more than one volume (to
	  compare density plots of, for example, a complex with vs without
	  substrate).  I fixed the section of the code for when only one
	  volume is supplied.

2012-12-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-07 18:17  pawel

	* sparx/libpy/morphology.py: [no log message]

2012-12-07 16:04  jgalaz

	* examples/e2spt_radialdensityplot.py: The output text file now
	  contains two columns: position, density.  The position is in
	  pixels, and must be interpreted depending on the --mode selected
	  for the program to operate (depending on whether you are plotting
	  density along consecutive spherical or cylindrical shells, or
	  along consecutive planes across the volume in a particular
	  direction).

2012-12-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-07 09:26  cailin

	* libEM/emfft.cpp: update mutex wrapper

2012-12-07 08:48  stevel

	* libpyEM/qtgui/emplot2d.py: Trivial

2012-12-06 15:51  cailin

	* libEM/emfft.cpp: [no log message]

2012-12-06 15:48  cailin

	* libEM/sparx/emdata_sparx.cpp: [no log message]

2012-12-06 14:52  cailin

	* libEM/: util.h, util.cpp, emfft.cpp: mutex wrapper

2012-12-06 13:32  stevel

	* programs/e2ctf.py: Massively important patch. CTF parameters were
	  incorrectly being read from the raw particle header rather than
	  the better values determined by e2ctf.py, unless the --store_parm
	  option was set, which is was NOT.

2012-12-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-05 16:48  jgalaz

	* programs/e2spt_simulation.py: Of course, whenever you program
	  something without testing it, bugs ensue.  I have NOW tested the
	  newly implemented functionality of simulating entire tomograms
	  (opposed to only sub-tomogram stacks).  NOW this new
	  functionality works -only for small tomgorams (on most computers)
	  though due to the high memory requirements.

2012-12-05 14:56  pawel

	* sparx/libpy/applications.py: [no log message]

2012-12-05 12:15  pawel

	* sparx/libpy/applications.py: findall fixed in mref

2012-12-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-05 07:29  stevel

	* programs/e2refine.py: Added file-based setsf option to refine

2012-12-05 07:19  stevel

	* TODO, libpyEM/EMAN2.py, programs/e2eulerxplor.py,
	  programs/e2proc2d.py: Deal with list files better in e2proc2d.py

2012-12-05 07:18  stevel

	* libEM/: averager.cpp, cmp.cpp: Tweak to prevent negative SNR
	  impacts

2012-12-04 16:29  jgalaz

	* examples/e2spt_radialdensityplot.py: The --help section has been
	  updated.  Also, this program can now: 1) Normalize the density in
	  each curve/plot so that the maximum value is equal to 1 2)
	  Produce plots in different modes with ONE command,
	  --mode=x,y,z,cylinder,sphere, instead of having to run the
	  program multiple times.

2012-12-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-04 09:03  stevel

	* programs/e2ctf.py: Fitting improvement for some virues and dense
	  particles.

2012-12-04 06:44  pawel

	* sparx/: bin/sxihrsr.py, libpy/alignment.py,
	  libpy/applications.py, libpy/morphology.py, libpy/utilities.py:
	  [no log message]

2012-12-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-12-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-30 18:13  jgalaz

	* programs/e2spt_simulation.py: This program already generated
	  simulated subtomograms and their corresponding subtiltseries
	  (from more than one model at a time).  NOW, it can (presumably)
	  ALSO randomly distribute all the subtomograms in a larger volume,
	  effectively simulating a TOMOGRAM (need to test for bugs, but am
	  committing it now just to 'save' the code; I've lost changes to
	  programs before for waiting till they're polished to commit
	  them...).

2012-11-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-29 14:40  fjia

	* sparx/libpy/applications.py: stop program and return error if
	  number of filaments is less than number of CPUs

2012-11-29 14:20  fjia

	* sparx/libpy/applications.py: stop program and return error if
	  number of filaments is less than number of CPUs in diskali_MPI

2012-11-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-29 10:14  stevel

	* libEM/pmconfig/spr.json: Re-enable box import. Works on singapore
	  data anyway...

2012-11-28 17:32  jgalaz

	* examples/e2spt_rotationalplot.py: plot scaling/normalization to
	  make max value = 1 should only be on if explicitly solicited by
	  the user. Implemented the --normalizeplot flag for such purpose.

2012-11-28 17:16  jgalaz

	* examples/e2spt_rotationalplot.py: The program now 1) takes .mrc
	  files for input.  2) checks whether the input is .hdf or .mrc,
	  shuts off otherwise (instead of crashing) 3) can plot the
	  rotational correlation at either altitude separately (0 vs 180),
	  or, actually, starting at any given altitude --alti, ending in
	  180, varying in --dalt steps.  4) The correlations are
	  normalized, such that the maximum value in the plot is 1.

2012-11-28 15:35  fjia

	* sparx/libpy/applications.py: moved from development to
	  applications: predict_helical_params, volalixshift_MPI,
	  diskali_MPI, stack_disks, iang, alihelical3, alihelical4,
	  cylindrical_trans

2012-11-28 15:32  fjia

	* sparx/bin/sxihrsr.py: moving predict_helical_params,
	  volalixshift_MPI, diskali_MPI, stack_disks from development to
	  applications

2012-11-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-27 23:21  jgalaz

	* programs/e2spt_classaverage.py:
	  Fixing minor break after last edits.

2012-11-27 20:34  jgalaz

	* programs/e2spt_classaverage.py: There were too many things being
	  printed out that were NOT under the control of the "verbose"
	  option.  Deleted a bunch of prints that were there from testing
	  phases of the program, and added many if options.verbose filters
	  to ensure printing happenes only if the user wants to see it,
	  since it is now to slow things down significantly.

2012-11-27 19:50  jgalaz

	* programs/e2iminfo.py: [no log message]

2012-11-27 19:49  jgalaz

	* programs/e2iminfo.py: My computer crashed when running
	  "e2iminfo.py tomogram.rec -H -N0". I had noticed previously that
	  reading the header info for tomograms took unreasonably long. It
	  turned out, the entire tomogram was being loaded, opposed to just
	  the header. I added "True" in 3 different places (labeld with a
	  side comment, "#Jesus"), and now e2iminfo.py doesn't crash and
	  prints out the header info on the screen much faster.

2012-11-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-26 12:00  fjia

	* programs/e2helixboxer.py: add attribute for filament membership
	  in saved particles

2012-11-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-25 06:11  jgalaz

	* programs/e2spt_autoboxer.py: This is not only functional now (as
	  in it doesn't crash), but it also seems to find (and rank
	  correctly) the correct coordinates for simulated tomograms.

2012-11-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-23 18:33  jgalaz

	* programs/e2spt_autoboxer.py: [no log message]

2012-11-23 18:30  jgalaz

	* examples/e2spt_tomosimjobs.py:
	  bugs bugs bugs...

2012-11-23 17:43  jgalaz

	* programs/e2spt_autoboxer.py: [no log message]

2012-11-23 17:11  jgalaz

	* examples/e2spt_tomosimjobs.py: [no log message]

2012-11-23 16:46  jgalaz

	* examples/e2orthoproject.py: Cleaned up the code a bit.  Fixed the
	  name of default path.  The program used to generate 5 projections
	  (two were redundant); now it correctly generates 3 orthogonal
	  projections only.

2012-11-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-21 19:31  jgalaz

	* programs/e2spt_resolutionplot.py: Multiple plots can now be
	  plotted and their color will be different automatically.  If the
	  script runs out of colors, it will change the marker, and make
	  all combinations of markers and colors.  Axes and labels are
	  bigger and bolder too.

2012-11-21 17:46  jgalaz

	* programs/e2spt_refprep.py: Mirroring the prepared reference
	  wasn't working, now it is.  Also, more efficient code for both
	  mirroring and applying symmetry.

2012-11-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-21 11:15  jgalaz

	* programs/e2spt_autoboxer.py: [no log message]

2012-11-21 09:58  cailin

	* programs/e2pdb2mrc.py, libEM/pointarray.cpp: [no log message]

2012-11-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-20 11:30  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2012-11-20 11:09  fjia

	* sparx/bin/sxihrsr.py: :VS:
	  ----------------------------------------------------------------------

2012-11-20 11:06  pawel

	* sparx/bin/sxihrsr.py: [no log message]

2012-11-20 10:39  pawel

	* sparx/bin/sxihrsr.py: [no log message]

2012-11-20 04:31  jgalaz

	* examples/e2spt_coordsrefactor.py: This program was in a
	  non-functional state. Not sure if I never finished/test it... or
	  just somehow lost it and never commited a functional update.
	  Anyway, basic functionally is now available.

2012-11-20 04:12  jgalaz

	* examples/e2spt_coordsrefactor.py: [no log message]

2012-11-20 03:30  jgalaz

	* programs/e2spt_autoboxer.py: Perhaps functional now.

2012-11-19 14:36  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2012-11-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-19 07:17  stevel

	* libpyEM/EMAN2PAR.py: Adjust DC parallelism timing

2012-11-18 21:25  stevel

	* libpyEM/qtgui/valslider.py, programs/e2eotest.py,
	  programs/e2proc2d.py, programs/e2refine2d.py,
	  programs/e2stacksort.py: Improvements to e2refine2d by selecting
	  better alignment references

2012-11-18 13:05  pawel

	* sparx/libpy/isac.py: [no log message]

2012-11-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-17 18:40  jgalaz

	* programs/e2spt_autoboxer.py: Changes in plans after talking to
	  Mike about this.

2012-11-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-16 17:05  jgalaz

	* examples/e2spt_autocenter.py: Past log for e2spt_autoboxer.py was
	  intended for THIS program: Improvements by applying preprocessing
	  options and centeroffmass.  [Improvements to e2spt_autoboxer.py
	  not logged; heavily under development].

2012-11-16 17:03  jgalaz

	* programs/e2spt_autoboxer.py: Attempt to improve by applyin
	  preprocessing options and centeroffmass.

2012-11-16 14:43  cailin

	* programs/e2pdb2mrc.py: add pdb2mrc_summation option, --usenufft
	  --addpdbbfactor --boxsize.

2012-11-16 14:39  cailin

	* libEM/pointarray.cpp: update pdb2mrc_summation. use different
	  bfactor to filer each atom.

2012-11-16 14:37  cailin

	* libEM/pointarray.h: add a bfactor pointer.

2012-11-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-16 03:35  jgalaz

	* programs/e2spt_autoboxer.py: In development.

2012-11-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-15 07:57  pawel

	* libEM/emdata.cpp, sparx/bin/sxstability.py,
	  sparx/libpy/pixel_error.py: [no log message]

2012-11-15 04:16  jgalaz

	* programs/e2spt_autoboxer.py: [no log message]

2012-11-15 04:03  jgalaz

	* programs/e2spt_autoboxer.py: Program to autobox subvolumes from
	  tomograms.

2012-11-15 04:01  jgalaz

	* examples/e2spt_ctf.py: [no log message]

2012-11-15 04:01  jgalaz

	* programs/e2spt_refprep.py: Slight reorganization of script.

2012-11-14 21:16  jgalaz

	* libpyEM/qtgui/embrowser.py: Fixed a small detail I broke with
	  previous changes.

2012-11-14 15:37  jgalaz

	* programs/e2spt_refprep.py: Bug fixes.

2012-11-14 12:25  piotr

	* sparx/bin/sxisac.py: add support for parameter indep_run equals 2
	  or 3

2012-11-14 12:21  piotr

	* sparx/libpy/alignment.py: new function align2d_no_mirror

2012-11-14 12:20  piotr

	* sparx/libpy/isac.py: add support for parameter indep_run equals 2
	  or 3

2012-11-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-14 09:46  stevel

	* libpyEM/libpyEMData2.cpp: Fix for segfaults due to threadsafety.
	  Exceptions returned are still a bit funny though.

2012-11-13 23:49  jgalaz

	* programs/e2spt_refprep.py: [no log message]

2012-11-13 18:46  jgalaz

	* programs/e2spt_refprep.py: Program to make a reference file (in
	  various formats) match a certain data image. The refernece can
	  also be edited independently.

2012-11-13 14:21  piotr

	* sparx/libpy/applications.py: cleanings

2012-11-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-11 19:32  jgalaz

	* libpyEM/qtgui/embrowser.py: Info Pane window for stacks now has
	  column labels ("Images" and "Header Information").  The browser
	  window for e2display is also labeled (titled) now.

2012-11-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-09 15:37  pawel

	* sparx/libpy/statistics.py: [no log message]

2012-11-09 12:57  jgalaz

	* examples/e2spt_tomosimjobs.py:
	  Default for raligncmp and aligncmp is now ccc.tomo instead of
	  ccc.

2012-11-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-08 19:50  jgalaz

	* examples/e2spt_tomosimjobs.py:
	  Fixed bug regarding fine step angular search.  Results for final
	  plot (a list of the angular errors and translational errors with
	  the average results from each run) is now written (before, you
	  would only get a plot, but not a text file; you only got text
	  files for the per-particle error for each run).  Plot linewidth
	  is thicker.

2012-11-08 14:57  stevel

	* programs/e2boxer.py: remove spurious prints

2012-11-08 14:56  stevel

	* TODO, libEM/ctf.cpp, libEM/emutil.cpp, libEM/hdfio2.cpp,
	  libpyEM/EMAN2.py, libpyEM/qtgui/empmtabwidgets.py,
	  programs/e2boxer.py, programs/e2ctf.py, programs/e2evalimage.py,
	  programs/e2initialmodel.py, programs/e2projectmanager.py,
	  pyemtbx/boxertools.py: Fixed e2boxer

2012-11-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-07 22:52  stevel

	* programs/: e2msa.py, e2refine_auto.py: Added first draft of
	  e2refine_auto

2012-11-07 21:57  jgalaz

	* programs/e2spt_boxer.py: [no log message]

2012-11-07 21:55  jgalaz

	* programs/e2spt_boxer.py: Resuls now logged when using the
	  e2spt_boxer in commandline mode.

	  Also, for commandline mode, saving to bdb: format was not
	  working. It's working now (I haven't tested it from the GUI
	  though...).

2012-11-07 21:17  jgalaz

	* programs/e2spt_boxer.py:
	  Path option wasn't working (it is now).

2012-11-07 15:13  jgalaz

	* programs/e2spt_boxer.py: Fixed bug reported by user regarding
	  boxing out subtomograms as individual .mrc files

2012-11-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-07 10:14  piotr

	* sparx/libpy/isac.py: fix in commented code

2012-11-06 22:12  jgalaz

	* programs/e2spt_boxer.py: [no log message]

2012-11-06 22:08  jgalaz

	* programs/e2spt_boxer.py:
	  More efficient way of passing options to commadline_tomoboxer
	  function.  Plus, this function now accurately overwrites the apix
	  if the user specifies a new apix, and resets the origin to 0
	  (which it wasn't doing, and should, because Chimera messes up
	  displaying paricles if the origin is some other aberrant number).

2012-11-06 16:29  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2012-11-06 15:32  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2012-11-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-06 09:43  pawel

	* sparx/bin/sxihrsr.py: [no log message]

2012-11-05 21:21  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2012-11-05 19:19  fjia

	* sparx/bin/: sxihrsr.py: [no log message]

2012-11-05 17:01  fjia

	* sparx/bin/sxihrsr.py: add option for testing consistency

2012-11-05 16:49  pawel

	* sparx/libpy/: user_functions.py: [no log message]

2012-11-05 16:41  pawel

	* sparx/bin/: sxihrsr.py: [no log message]

2012-11-05 16:38  pawel

	* sparx/libpy/user_functions.py: [no log message]

2012-11-05 15:18  pawel

	* sparx/bin/sxihrsr.py: [no log message]

2012-11-05 14:48  pawel

	* sparx/libpy/utilities.py: [no log message]

2012-11-05 14:43  pawel

	* sparx/libpy/: utilities.py: [no log message]

2012-11-05 14:35  pawel

	* sparx/libpy/utilities.py: [no log message]

2012-11-05 12:56  pawel

	* sparx/bin/sxihrsr.py: [no log message]

2012-11-05 12:44  fjia

	* sparx/bin/sxihrsr.py: line up columns

2012-11-05 12:36  pawel

	* sparx/bin/sxihrsr.py: [no log message]

2012-11-05 12:28  pawel

	* sparx/bin/sxihrsr.py: [no log message]

2012-11-05 12:23  pawel

	* sparx/bin/sxihrsr.py: [no log message]

2012-11-05 12:19  pawel

	* sparx/: bin/sxihrsr.py, libpy/utilities.py: [no log message]

2012-11-05 12:05  pawel

	* sparx/bin/sxihrsr.py: [no log message]

2012-11-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-05 11:58  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2012-11-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-02 17:50  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2012-11-02 17:18  fjia

	* sparx/bin/: sxihrsr.py: [no log message]

2012-11-02 17:07  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2012-11-02 16:03  fjia

	* sparx/libpy/applications.py: pass mask in to user function in
	  ihrsr_MPI

2012-11-02 13:27  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2012-11-02 13:03  pawel

	* sparx/libpy/utilities.py: [no log message]

2012-11-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-01 13:14  piotr

	* libEM/sparx/util_sparx.cpp: correction in BPCQ - now works for
	  cases when nz < n[xy]

2012-11-01 13:03  piotr

	* sparx/libpy/applications.py: correct obvious error in project3d

2012-11-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-11-01 10:35  stevel

	* examples/feiraw2hdf.py: New program to read 'raw' files from
	  Falcon cameras

2012-11-01 07:53  stevel

	* TODO, libEM/emutil.cpp: Recognize .st as mrc files

2012-10-31 15:06  fjia

	* sparx/bin/sxihrsr.py: restrict inner iteration (--maxit) of disk
	  alignment (option --vol_ali) and x-shift determination
	  (--searchxshisft) to 1

2012-10-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-30 16:36  fjia

	* sparx/libpy/applications.py: change the way y search range is
	  handled for local refinement in ihrsr_MPI

2012-10-30 16:36  fjia

	* sparx/bin/sxihrsr.py: change format of input arguments from
	  pixels to Angstroms

2012-10-30 12:58  pawel

	* sparx/libpy/filter.py: [no log message]

2012-10-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-30 09:58  stevel

	* libpyEM/EMAN2.py, programs/e2proc3d.py: eman-style --rot fix CVS
	  ----------------------------------------------------------------------

2012-10-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-27 14:51  pawel

	* sparx/libpy/applications.py: [no log message]

2012-10-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-26 17:52  jgalaz

	* examples/e2spt_ctf.py: [no log message]

2012-10-26 15:56  jgalaz

	* examples/: e2spt_tomosimjobs.py, e2spt_cudatimetest.py: [no log
	  message]

2012-10-26 14:20  fjia

	* sparx/bin/sxshiftali.py: fix indentation

2012-10-26 13:34  jgalaz

	* examples/e2spt_tomosimjobs.py: [no log message]

2012-10-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-26 09:45  scmurray

	* programs/: e2refinetorelion2d.py, e2refinetorelion3d.py: Added
	  and removed comments

2012-10-26 09:40  scmurray

	* programs/e2refinetorelion3d.py: Added Comment

2012-10-26 07:29  stevel

	* TODO, libpyEM/EMAN2.py, programs/e2proc3d.py,
	  programs/e2rawdata.py, programs/e2refine_evenodd.py: Fixed broken
	  e2proc3d.py

2012-10-26 01:37  jgalaz

	* examples/e2spt_tomosimjobs.py: [no log message]

2012-10-26 01:25  jgalaz

	* programs/e2spt_classaverage.py: [no log message]

2012-10-25 15:56  jgalaz

	* examples/e2spt_cudatimetest.py:
	  Text file with cpu/gpu ratio written now. Plot lines thicker (3
	  vs 1 linewidth).

2012-10-25 15:05  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2012-10-25 13:40  piotr

	* sparx/tests/test_fundamentals.py: some cleanings

2012-10-25 13:39  piotr

	* sparx/tests/test_fundamentals.py: unit test for ccf* acf* and
	  cnv* routines from fundamentals.py For now, 5 last tests for cnv*
	  functions fail

2012-10-25 13:38  piotr

	* libEM/sparx/fundamentals.cpp: solve problem with acfp and ccfp
	  functions

2012-10-25 13:17  pawel

	* sparx/libpy/: alignment.py, applications.py, fundamentals.py: [no
	  log message]

2012-10-25 12:29  pawel

	* libEM/sparx/util_sparx.cpp: ::

2012-10-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-24 16:00  fjia

	* sparx/bin/sxihrsr.py: add option for disk alignment
	  (filrecons3d_MPI)

2012-10-24 15:27  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2012-10-24 14:45  fjia

	* sparx/bin/sximgstat.py: [no log message]

2012-10-24 14:40  fjia

	* sparx/bin/sxihrsr.py: add option for generating two lists of
	  image indices used to split image stack for calculating helical
	  fsc

2012-10-24 14:28  fjia

	* sparx/bin/sxihrsr.py: add option for helicising volume

2012-10-24 13:45  stevel

	* libEM/emutil.cpp, libpyEM/libpyUtils2.cpp: New routine for
	  reading raw data from python, and FEI raw image input

2012-10-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-24 11:59  piotr

	* sparx/tests/test_pixel_error.py: minor changes

2012-10-24 11:38  pawel

	* libEM/sparx/fundamentals.cpp: [no log message]

2012-10-23 22:33  jgalaz

	* programs/: e2spt_simulation.py: [no log message]

2012-10-23 22:28  jgalaz

	* examples/e2spt_tomosimjobs.py: [no log message]

2012-10-23 18:08  fjia

	* sparx/bin/sximgstat.py: add option for calculationg helical fsc

2012-10-23 17:46  jgalaz

	* examples/e2spt_tomosimjobs.py: [no log message]

2012-10-23 17:34  jgalaz

	* examples/e2spt_tomosimjobs.py: SNR increasable by non-integer
	  amounts now.

2012-10-23 14:31  pawel

	* libEM/sparx/fundamentals.cpp: [no log message]

2012-10-23 13:57  pawel

	* libEM/sparx/fundamentals.cpp: [no log message]

2012-10-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-22 15:41  pawel

	* libEM/sparx/util_sparx.cpp, sparx/libpy/alignment.py,
	  sparx/libpy/applications.py: more cleaning of helical code

2012-10-22 13:06  cailin

	* programs/e2proc3d.py, libpyEM/EMAN2.py: [no log message]

2012-10-22 12:56  jgalaz

	* programs/e2spt_simulation.py: [no log message]

2012-10-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-21 22:55  jgalaz

	* examples/e2orthoproject.py: Program to generate orthogonal
	  projections from multiple models (separated by commas), or
	  multiple stacks of models (.hdf files separated by commas).

2012-10-21 22:13  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2012-10-21 22:09  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2012-10-21 21:37  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2012-10-21 21:31  jgalaz

	* examples/e2spt_cudatimetest.py:
	  Coarse amd fine steps are user defined now.

2012-10-21 15:00  pawel

	* sparx/libpy/alignment.py: various clarifications of helical code

2012-10-21 14:32  pawel

	* libEM/sparx/util_sparx.cpp, sparx/bin/sxihrsr.py,
	  sparx/libpy/alignment.py, sparx/libpy/applications.py: various
	  clarifications of helical code

2012-10-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-19 17:42  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2012-10-19 15:24  cailin

	* libpyEM/EMAN2.py: [no log message]

2012-10-19 14:05  stevel

	* programs/e2refine_evenodd.py: ugg

2012-10-19 14:02  stevel

	* programs/e2refine_evenodd.py: oops

2012-10-19 14:01  stevel

	* examples/local_correlation.py, libEM/processor.cpp,
	  libEM/processor.h, programs/e2refine.py,
	  programs/e2refine_evenodd.py: Usefilt fix

2012-10-19 13:11  piotr

	* sparx/libpy/fundamentals.py: bugfix

2012-10-19 13:09  piotr

	* sparx/libpy/fundamentals.py: bugfix - broken import

2012-10-19 12:21  scmurray

	* libEM/emfft.cpp: Fixed a warning where someone had used a
	  python-style comment in a c++ file.

2012-10-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-18 14:15  stevel

	* libpyEM/libpyUtils2.cpp: oops

2012-10-18 14:13  stevel

	* examples/boxscale.py, libpyEM/EMAN2.py, libpyEM/libpyUtils2.cpp,
	  libpyEM/qtgui/emapplication.py, programs/e22.py: Fix for binary
	  file i/o, few other minor fixes.

2012-10-18 14:04  stevel

	* libpyEM/libpyUtils2.cpp: New function in EMUtil for reading raw
	  data from binary files

2012-10-18 12:34  scmurray

	* libEM/pmconfig/relion3d.json, programs/e2refinetorelion3d.py:
	  Changed the GUI as it would appear in the project manager and
	  changed the wizard for e2refinetorelion3d as well.

2012-10-18 12:32  pawel

	* sparx/bin/sxihrsr.py: [no log message]

2012-10-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-18 11:02  piotr

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, sparx/libpy/utilities.py: omit memory
	  leak in get_params2D, get_params3D and get_params_proj by using
	  get_transform_params from util_sparx.cpp

2012-10-18 10:43  pawel

	* sparx/libpy/morphology.py: [no log message]

2012-10-18 03:26  jgalaz

	* examples/e2spt_tomosimjobs.py: [no log message]

2012-10-18 03:18  jgalaz

	* examples/e2spt_tomosimjobs.py: [no log message]

2012-10-18 03:14  jgalaz

	* examples/e2spt_tomosimjobs.py: [no log message]

2012-10-18 03:09  jgalaz

	* examples/e2spt_tomosimjobs.py: [no log message]

2012-10-18 03:05  jgalaz

	* examples/e2spt_tomosimjobs.py: [no log message]

2012-10-18 02:48  jgalaz

	* examples/e2spt_tomosimjobs.py: Controlling the missing wedge
	  compensation method (ccc, ccc.tomo, fsc.tomo) is now possible for
	  simulations.

2012-10-17 22:31  stevel

	* programs/e2refine.py: minor fix

2012-10-17 15:17  scmurray

	* programs/e2refinetorelion3d.py: More changes to update to RELION
	  1.1

2012-10-17 15:13  fjia

	* sparx/libpy/applications.py: remove ihrsr_MPI_no_wrap

2012-10-17 14:50  fjia

	* sparx/libpy/applications.py: make wrapping optional in ihrsr_MPI

2012-10-17 13:52  fjia

	* sparx/libpy/applications.py: pixel_size is no longer read from
	  ctf or image header but part of input argument list in ihrsr and
	  ihrsr_MPI

2012-10-17 13:47  fjia

	* sparx/bin/sxihrsr.py: add pixel size as input argument to ihrsr

2012-10-17 13:34  fjia

	* sparx/bin/sximgstat.py: add option for calculating fsc of helical
	  structures

2012-10-17 13:20  cailin

	* programs/e2procpdb.py: [no log message]

2012-10-17 13:15  fjia

	* sparx/bin/sxihrsr.py: remove chunk and consnbr options

2012-10-17 13:14  fjia

	* sparx/libpy/applications.py: remove ihrsr_chunk_MPI code

2012-10-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-17 11:49  scmurray

	* programs/e2refinetorelion3d.py: [no log message]

2012-10-17 11:22  scmurray

	* programs/e2refinetorelion3d.py: Removed some debugging.

2012-10-17 11:16  fjia

	* sparx/libpy/applications.py: remove MPI and chunk from control
	  flow of ihrsr

2012-10-17 11:08  fjia

	* sparx/libpy/applications.py: remove ihrsr_MPI_cons

2012-10-17 11:02  fjia

	* sparx/libpy/applications.py: removed old commented out code in
	  ihrsr

2012-10-17 11:01  scmurray

	* programs/e2refinetorelion3d.py: Changes were made to adjust the
	  program to RELION v1.1 from v1.0

2012-10-17 10:27  pawel

	* sparx/bin/sxihrsr.py: [no log message]

2012-10-17 10:18  pawel

	* sparx/bin/: sxihrsr.py: [no log message]

2012-10-17 09:54  pawel

	* sparx/bin/sxihrsr.py: [no log message]

2012-10-17 09:50  pawel

	* sparx/libpy/applications.py: [no log message]

2012-10-16 18:09  pawel

	* sparx/bin/sxihrsr.py: [no log message]

2012-10-16 17:48  pawel

	* sparx/bin/sxfilrecons3d.py: [no log message]

2012-10-16 17:40  piotr

	* sparx/libpy/utilities.py: cleanings

2012-10-16 17:32  piotr

	* libEM/sparx/util_sparx.h, sparx/libpy/isac.py: ISAC - cleanings

2012-10-16 17:23  pawel

	* sparx/: bin/sxfilrecons3d.py, libpy/applications.py: [no log
	  message]

2012-10-16 17:09  piotr

	* libEM/sparx/util_sparx.cpp: bugfix

2012-10-16 16:58  piotr

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, sparx/bin/sxisac.py,
	  sparx/libpy/utilities.py: ISAC: - omit memory leak in
	  get_params2D - new parameter set from command line - rand_seed

2012-10-16 16:25  cailin

	* programs/e2procpdb.py: [no log message]

2012-10-16 14:16  pawel

	* sparx/bin/sx3Dvariance.py: [no log message]

2012-10-16 14:13  fjia

	* sparx/bin/sxfilrecons3d.py: [no log message]

2012-10-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-15 14:41  stevel

	* libpyEM/EMAN2db.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2buildsets.py: Fixed problem with iterator in
	  emimagemx. Added 'i' option for inverting displayed stacks on
	  disk.

2012-10-15 14:41  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2012-10-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-15 09:57  pawel

	* sparx/libpy/utilities.py: added finding all positions on a list

2012-10-14 21:05  pawel

	* sparx/: bin/sxali3d.py, libpy/applications.py: [no log message]

2012-10-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-12 15:15  cailin

	* programs/e2procpdb.py:

	  procpdb is used for process pdb coordinate, such as transform
	  rotation posttransform, ect.

2012-10-12 14:30  fjia

	* sparx/bin/sxihrsr.py: [no log message]

2012-10-12 12:07  fjia

	* sparx/bin/sxihrsr.py: add option for searching x-shift

2012-10-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-11 09:46  pawel

	* libEM/emdata_core.h: spelling corrected

2012-10-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-10 00:48  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2012-10-09 18:45  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2012-10-09 18:04  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2012-10-09 17:18  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2012-10-09 17:12  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2012-10-09 17:05  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2012-10-09 16:50  jgalaz

	* examples/e2spt_cudatimetest.py: Bug fix.

2012-10-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-09 08:11  pawel

	* libEM/sparx/emdata_sparx.cpp: rewritten helicise, the previous
	  code was atrocious

2012-10-08 20:09  stevel

	* TODO, libEM/pifio.cpp, libEM/pifio.h, libpyEM/qtgui/embrowser.py,
	  programs/e2motion.py: PIF improvements. Support mode 46

2012-10-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-07 16:19  pawel

	* sparx/bin/sx3Dvariance.py: [no log message]

2012-10-07 14:18  pawel

	* sparx/bin/sx3Dvariance.py: [no log message]

2012-10-07 12:33  pawel

	* sparx/bin/sx3Dvariance.py: [no log message]

2012-10-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-05 15:59  pawel

	* libEM/sparx/util_sparx.cpp: [no log message]

2012-10-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-04 10:48  piotr

	* sparx/libpy/alignment.py: correct whitespaces

2012-10-03 16:42  pawel

	* sparx/: bin/sxheader.py, libpy/applications.py: added set to
	  sxheader

2012-10-03 14:31  jgalaz

	* programs/e2spt_simulation.py: [no log message]

2012-10-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-01 17:01  irees

	* libpyEM/EMAN2db.py: Better error message in the event bsddb3 does
	  not import.

2012-10-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-10-01 01:20  jgalaz

	* examples/e2spt_tomosimjobs.py:
	  bla bla

2012-10-01 01:20  jgalaz

	* programs/e2spt_simulation.py: [no log message]

2012-09-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-29 23:32  jgalaz

	* examples/e2spt_tomosimjobs.py:
	  Now you can plot results from results files directly and skip the
	  rest of the process if necessary (for exaple, if you want to
	  merge results from separate runs).

2012-09-29 19:09  pawel

	* sparx/: bin/sxproj_stability.py, libpy/pixel_error.py: [no log
	  message]

2012-09-29 18:57  pawel

	* sparx/: bin/sxproj_stability.py, libpy/pixel_error.py: [no log
	  message]

2012-09-29 18:18  pawel

	* sparx/: bin/sxproj_stability.py, libpy/pixel_error.py: [no log
	  message]

2012-09-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-28 17:33  piotr

	* sparx/bin/sxave_ali.py: add parameters to sxave_ali (setting
	  header parameters in output image)

2012-09-28 17:27  piotr

	* sparx/libpy/applications.py: add parameters to ave_ali (setting
	  header parameters in output image)

2012-09-28 16:28  pawel

	* sparx/libpy/pixel_error.py: [no log message]

2012-09-28 16:18  pawel

	* sparx/: libpy/pixel_error.py, bin/sxproj_stability.py: [no log
	  message]

2012-09-28 16:04  pawel

	* sparx/bin/sxproj_stability.py: [no log message]

2012-09-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-27 17:08  jgalaz

	* examples/: e2spt_cudatimetest.py: [no log message]

2012-09-27 17:07  jgalaz

	* examples/e2spt_cudatimetest.py:
	  "extensive" option added, to test gain in GPU vs CPU speed
	  continuously for boxsizes from 12 to 256

2012-09-27 16:44  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2012-09-27 15:20  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2012-09-27 15:13  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2012-09-27 15:10  jgalaz

	* programs/e2spt_hac.py:
	  Fixed path writing.

2012-09-27 14:48  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2012-09-27 14:33  fjia

	* libEM/sparx/emdata_sparx.cpp: change sign in helicise

2012-09-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-25 11:16  piotr

	* libEM/emdata_metadata.cpp: undo the last change (EMAN2 stopped
	  working properly after that)

2012-09-24 18:05  piotr

	* libEM/emdata_metadata.cpp: change realloc() to malloc() in EMData

2012-09-24 18:01  pawel

	* sparx/bin/sxproj_stability.py: [no log message]

2012-09-24 17:25  pawel

	* sparx/bin/sxproj_stability.py: block empty classes

2012-09-24 15:41  pawel

	* sparx/: bin/sxproj_stability.py, bin/sxstability.py,
	  libpy/pixel_error.py: more or less fine

2012-09-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-24 11:52  pawel

	* sparx/bin/sxstability.py: [no log message]

2012-09-24 01:23  stevel

	* libEM/emfft.h, libpyEM/libpyEMData2.cpp, programs/e2motion.py: A
	  lot of work on e2motion, but still a work in progress

2012-09-23 20:09  pawel

	* sparx/: bin/sxstability.py, libpy/pixel_error.py: still trying

2012-09-23 16:36  pawel

	* sparx/bin/sxstability.py: [no log message]

2012-09-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-23 11:20  pawel

	* sparx/libpy/pixel_error.py: corrected

2012-09-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-22 00:19  stevel

	* libEM/emfft.cpp, libEM/emfft.h, programs/e2motion.py: Threadsafe
	  FFTs (I think)...

2012-09-21 16:48  pawel

	* programs/e2ctf.py, sparx/libpy/pixel_error.py: [no log message]

2012-09-21 15:01  stevel

	* libpyEM/EMAN2.py, libpyEM/libpyEMData2.cpp, programs/e2motion.py,
	  programs/e2proc3d.py, programs/e2refine.py: Beginning of Python
	  threadsafety for EMData. still broken in some ways due to FFTW
	  non-threadsafety.

2012-09-21 13:16  jgalaz

	* programs/e2symsearch3d.py: [no log message]

2012-09-21 13:10  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2012-09-21 12:04  pawel

	* sparx/bin/sxproj_stability.py: memleak, replaced stability

2012-09-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-20 14:23  pawel

	* libEM/: emdata_transform.cpp, emfft.cpp: formatting

2012-09-20 13:14  pawel

	* libEM/emdata_transform.cpp: fixing native fft

2012-09-20 13:05  pawel

	* libEM/: emdata_transform.cpp, sparx/native_fft.cpp: [no log
	  message]

2012-09-20 12:57  pawel

	* libEM/: emdata_transform.cpp: corrected ifdef in emdata_transform

2012-09-20 12:48  pawel

	* libEM/emfft.cpp, sparx/libpy/applications.py: [no log message]

2012-09-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-20 10:08  pawel

	* sparx/libpy/applications.py: [no log message]

2012-09-19 15:56  jgalaz

	* programs/e2symsearch3d.py: I can finally commit this successfuly.
	  Path bug fixed. Screens for adequate output format, otherwise
	  program terminates instead of crashing.

2012-09-19 15:34  pawel

	* sparx/: libpy/applications.py, bin/sxali_vol.py: [no log message]

2012-09-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-19 11:51  fjia

	* libEM/sparx/util_sparx.cpp: [no log message]

2012-09-18 19:04  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2012-09-18 18:48  jgalaz

	* examples/e2spt_cudatimetest.py: [no log message]

2012-09-18 18:20  jgalaz

	* examples/e2spt_cudatimetest.py:
	  Test GPU vs CPU performace for SPT alignment ona computer that
	  has an EMAN2 cuda build.

2012-09-18 17:06  piotr

	* sparx/libpy/isac.py: correction of fatal bug in ISAC - at the end
	  of second round output of SAC was copied erroneously to output of
	  2-way matching (in the last 3 SAC)

2012-09-18 16:09  jgalaz

	* programs/e2spt_boxer.py: [no log message]

2012-09-18 14:33  stevel

	* programs/e2motion.py: trivial

2012-09-18 14:19  jgalaz

	* programs/e2spt_classaverage.py: --bin has been changes to
	  --shrink. --cbin to --cshrink. --reverse_contrast to --invert.

2012-09-18 13:18  stevel

	* programs/e2motion.py: e2motion beginning to do something

2012-09-18 12:34  pawel

	* sparx/: libpy/utilities.py, templates/import_SPIDER_refi.py: [no
	  log message]

2012-09-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-17 22:42  stevel

	* programs/e2motion.py: more work

2012-09-17 15:34  stevel

	* programs/: e2bdb.py, e2motion.py, e2refinemulti.py: Working on
	  e2motion logic. Tweaks for e2bdb.py

2012-09-17 14:13  scmurray

	* programs/e2proc2d.py: Change a small logic issue.

2012-09-17 14:09  stevel

	* programs/e2motion.py: GUI complete. Logic not.

2012-09-17 12:42  scmurray

	* programs/: e2proc2d.py, e2proc3d.py: Changed a couple of places
	  where help info was spelled incorrectly

2012-09-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-17 11:11  scmurray

	* programs/e2proc3d.py: Added support for a --step option. This
	  option will let a user step through a stack when doing stack
	  related things similar to the option in e2bdb.py. The --step
	  option can work in conjunction with the --last option but not
	  with the --first option as the --step option contains that
	  information already. Use of --step and --frst together raises an
	  error now.

2012-09-17 09:36  stevel

	* programs/: e2ctf.py, e2motion.py: New keyboard shortcuts for
	  e2ctf.py

2012-09-16 23:34  stevel

	* programs/e2motion.py: GUI Layout work

2012-09-16 16:37  pawel

	* sparx/libpy/applications.py: [no log message]

2012-09-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-14 15:55  stevel

	* programs/: e2evalimage.py, e2motion.py: Evalimage z stack support

2012-09-14 14:48  stevel

	* programs/: e2motion.py, e2spt_boxer.py: sptboxer fix. e2motion
	  incomplete

2012-09-14 13:40  stevel

	* examples/average.py: New program

2012-09-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-12 13:45  stevel

	* libpyEM/EMAN2.py: trivial

2012-09-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-11 10:08  piotr

	* sparx/libpy/applications.py: sxali2d - add checking if whole
	  particle lie inside image (radius & shifts)

2012-09-10 17:23  piotr

	* sparx/libpy/isac.py: switch off logging

2012-09-10 16:33  pawel

	* sparx/libpy/statistics.py: [no log message]

2012-09-10 15:25  stevel

	* TODO, libpyEM/EMAN2PAR.py, libpyEM/qtgui/emboxerbase.py,
	  libpyEM/qtgui/emplot2d.py, programs/e2eotest.py,
	  programs/e2refine_evenodd.py: Fix refine_evenodd to work with
	  usefilt. Other minor bugfixes

2012-09-10 13:59  piotr

	* sparx/bin/sxisac.py: set threshold for pixel error back to 0.7

2012-09-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-10 10:42  piotr

	* sparx/: bin/sxisac.py, libpy/applications.py, libpy/isac.py:
	  Corrected ISAC version.  For now I set the default threshold of
	  pixel error to 1.0.

2012-09-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-07 17:30  piotr

	* sparx/libpy/pixel_error.py: bugfix in multi_align_stability
	  (divide H elements by sqrtP)

2012-09-07 17:28  piotr

	* sparx/tests/test_pixel_error.py: unit tests for
	  multi_align_stability

2012-09-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-05 21:39  jgalaz

	* examples/e2spt_tomosimjobs.py: 1D, 2D and 3D plotting enabled,
	  depending on whether what parameters you vary simulatneously
	  (noise level, tilt step, tilt range).

2012-09-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-04 10:29  piotr

	* sparx/libpy/applications.py: Return to version of ISAC from EMAN
	  2_05 (May 2012)

2012-09-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-09-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-31 16:14  jgalaz

	* examples/e2spt_tomosimjobs.py: [no log message]

2012-08-30 21:22  jgalaz

	* examples/e2spt_tomosimjobs.py: Fully functional for single and
	  multiple references.

2012-08-30 13:44  pawel

	* sparx/libpy/applications.py: grammar corrections in ISAC

2012-08-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-30 02:41  jgalaz

	* examples/e2spt_transformdistance.py: .-

2012-08-30 02:40  jgalaz

	* examples/e2spt_tomosimjobs.py: [no log message]

2012-08-30 01:57  jgalaz

	* programs/e2spt_simulation.py: Further development...

2012-08-30 01:57  jgalaz

	* programs/e2symsearch3d.py: Bug with options.path. Not sure if
	  fixed (haven't tested, but code was definitely wrong).

2012-08-29 12:41  fjia

	* programs/e2boxer.py: Modified clear_all so that user set
	  parameters are NOT cleared when 'Clear Boxes' is clicked.

	  Also, if gauss width slider is adjusted because the float value
	  in the gauss width box is adjusted by user, then the approximate
	  value the slider is adjusted to is not propagated back to the
	  gauss width box.

2012-08-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-29 11:06  fjia

	* programs/e2boxer.py: comment out part in set_data that changes
	  Threshold Low and Threshold High after particles are picked

2012-08-28 12:54  pawel

	* sparx/libpy/applications.py: [no log message]

2012-08-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-28 09:25  stevel

	* CMakeLists.txt: Mountain lion cmake fixes

2012-08-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-26 08:32  pawel

	* sparx/libpy/: statistics.py, utilities.py: [no log message]

2012-08-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-24 00:31  jgalaz

	* programs/e2spt_classaverage.py: It is now possible to randomize
	  the position of the particles from the start (which minimizes
	  missing wedge bias under certain conditions), avoiding multiple
	  interpolations. Also, if a transform is provided to "prealign"
	  the particles, coarse alignment SHOULD NOT be skipped by default.
	  Coarse alignment should ONLY be skipped IF --align=None.

2012-08-24 00:29  jgalaz

	* programs/e2spt_simulation.py: A simulated reference is now
	  generated if requested by the user. Also, it is now possible to
	  simulate particles without randomizing there orientation and
	  translation by default. Lastly, runs of this programs are now
	  logged.

2012-08-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-20 02:26  jgalaz

	* programs/e2spt_simulation.py: Tweaks.

2012-08-19 23:59  jgalaz

	* programs/e2spt_simulation.py: Multiple models can be suplied now
	  and a separate simulation will be run/generated for each.  Also,
	  the path where to save results for a run can now be defined by
	  the user.

2012-08-19 13:13  gtang

	* libEM/CMakeLists.txt, libEM/all_imageio.h, libEM/dm4io.cpp,
	  libEM/dm4io.h, libEM/emutil.cpp, libEM/emutil.h,
	  libpyEM/libpyUtils2.cpp, pyemtbx/imagetypes.py,
	  rt/pyem/test_utils.py: Gatan DM4 reading support. Not tested yet.

2012-08-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-17 18:55  jgalaz

	* programs/e2spt_simulation.py: Numbered path working correctly
	  now. Apix propperly written to projections and simulated
	  subtomograms now. Padding used to be fixed, user defined now,
	  same thing for final size of simulated subtomograms.

2012-08-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-16 22:30  stevel

	* libpyEM/EMAN2.py, libpyEM/qtgui/valslider.py,
	  programs/e2eulerxplor.py: Fix problem with Euler explorer display

2012-08-16 18:27  jgalaz

	* programs/e2spt_resolutionplot.py: Wrong python called on first
	  line. Fixed.

2012-08-16 17:21  piotr

	* sparx/bin/sxstability.py: switch to proper multi_align_stability
	  function

2012-08-16 14:30  piotr

	* sparx/bin/sxgui.py: change default value for isac parameter:
	  thld_err

2012-08-16 14:29  pawel

	* sparx/libpy/applications.py: [no log message]

2012-08-16 13:46  stevel

	* TODO, programs/e2classaverage.py, programs/e2filtertool.py,
	  programs/e2refine2d.py, programs/e2stacksort.py: Changes to
	  alignment reference selection for e2refine2d.py. Testing to see
	  if it improves averages of IP3R.

2012-08-16 13:27  pawel

	* sparx/demo/mpi_bdb_ctf/run_through_example: [no log message]

2012-08-16 13:01  piotr

	* sparx/demo/mpi_bdb/run_through_example: ISAC description -
	  corrections

2012-08-16 12:40  pawel

	* sparx/demo/mpi_bdb/run_through_example: [no log message]

2012-08-16 12:34  piotr

	* sparx/demo/: mpi_bdb/run_through_example,
	  mpi_bdb_ctf/run_through_example: ISAC description

2012-08-16 12:29  piotr

	* sparx/demo/mpi_bdb_ctf/run_through_example: ISAC description

2012-08-16 12:25  piotr

	* sparx/libpy/: applications.py, statistics.py: pcanalyzer -
	  problem with missing parameter (outdir)

2012-08-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-16 11:35  pawel

	* sparx/: libpy/applications.py, demo/mpi_bdb/run_through_example:
	  [no log message]

2012-08-16 10:41  piotr

	* sparx/demo/: mpi_bdb/run_through_example,
	  mpi_bdb_ctf/run_through_example: ISAC parameters - set threshold
	  for pixel error to 0.75

2012-08-16 10:13  piotr

	* sparx/: demo/mpi_bdb/run_through_example,
	  demo/mpi_bdb_ctf/run_through_example, libpy/applications.py,
	  libpy/pixel_error.py: corrected ISAC version - alignment
	  parameters of stable images are set to H matrix (average
	  transformation) value of threshold_error in demo was set to 1.0
	  (instead of 5.1)

2012-08-16 09:06  gtang

	* programs/: e2spt_wedge.py, e2wedge.py: change file name
	  e2wedge.py to e2spt_wedge.py

2012-08-16 02:08  jgalaz

	* programs/e2spt_hac.py: Bug fix

2012-08-16 01:52  jgalaz

	* examples/e2spt_rotationalplot.py:
	  Grid lines turned off.

2012-08-16 01:51  jgalaz

	* programs/e2spt_resolutionplot.py:
	  Horizontal lines now plotted at FSC cuttof values of 0.5 and
	  0.143

2012-08-15 17:06  fjia

	* sparx/demo/mpi_bdb/run_through_example: add directions for using
	  e2boxer interactively and deleting individual particle files

2012-08-15 17:00  pawel

	* sparx/demo/SPARX_intro.pdf: [no log message]

2012-08-15 16:33  fjia

	* sparx/demo/mpi_bdb_ctf/run_through_example: [no log message]

2012-08-15 15:46  fjia

	* sparx/demo/mpi_bdb_ctf/run_through_example: add directions for
	  using e2boxer in interactive mode for parameter adjustment and
	  also delete specific particle files using e2bdb

2012-08-15 15:06  piotr

	* sparx/libpy/pp.py: file added by accident

2012-08-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-15 11:41  gtang

	* CMakeLists.txt: windows GUI file e2projectmanager.pyw

2012-08-14 17:06  piotr

	* sparx/libpy/pixel_error.py: multi_align_stability - correction of
	  error caused by different types of transformation matrices used
	  in paper about ISAC and EMAN2

2012-08-14 17:01  piotr

	* sparx/libpy/pp.py: multi_align_stability - correction of error
	  caused by different types of transformation matrices used in
	  paper about ISAC and EMAN2

2012-08-14 16:37  piotr

	* libEM/sparx/util_sparx.cpp: multi_align_error - correction of
	  error caused by different types of transformation matrices used
	  in ISAC article and EMAN2

2012-08-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-13 13:29  pawel

	* sparx/bin/sxproj_stability.py: done??

2012-08-13 12:32  pawel

	* sparx/bin/sxproj_stability.py: done?

2012-08-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-13 11:39  pawel

	* sparx/bin/sxproj_stability.py: [no log message]

2012-08-13 10:17  gtang

	* programs/e2version.py: minor fix

2012-08-13 10:13  gtang

	* programs/: e2version.py: minor fix

2012-08-12 17:03  pawel

	* sparx/bin/sxproj_stability.py: [no log message]

2012-08-12 16:07  pawel

	* sparx/bin/sxproj_stability.py: [no log message]

2012-08-12 15:15  pawel

	* sparx/bin/sxproj_stability.py: [no log message]

2012-08-12 13:16  pawel

	* sparx/bin/sxproj_stability.py: [no log message]

2012-08-12 13:15  eman-vm

	* programs/e2version.py: new date stamp

2012-08-12 13:12  pawel

	* sparx/bin/sxproj_stability.py: [no log message]

2012-08-12 13:02  pawel

	* sparx/bin/sxproj_stability.py: [no log message]

2012-08-12 11:57  pawel

	* sparx/bin/sxproj_stability.py: [no log message]

2012-08-12 11:49  pawel

	* sparx/bin/sxproj_stability.py: [no log message]

2012-08-12 11:01  pawel

	* sparx/bin/sxproj_stability.py: [no log message]

2012-08-12 10:57  pawel

	* sparx/bin/sxproj_stability.py: [no log message]

2012-08-11 12:26  pawel

	* sparx/: bin/sxproj_stability.py, libpy/utilities.py: [no log
	  message]

2012-08-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-11 11:08  pawel

	* sparx/bin/sxproj_stability.py: [no log message]

2012-08-10 15:00  scmurray

	* programs/e2refinetorelion3d.py: Made several changes. Refined the
	  program to work only with EMAN2 reconstructions and added some
	  functionality of per-micrograph defocus values

2012-08-10 13:58  pawel

	* sparx/libpy/applications.py: [no log message]

2012-08-10 13:42  pawel

	* sparx/libpy/applications.py: [no log message]

2012-08-10 12:57  eman-vm

	* programs/e2version.py: new date stamp

2012-08-10 12:56  gtang

	* programs/e2version.py: 2.0.6

2012-08-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-10 11:42  pawel

	* sparx/libpy/applications.py: [no log message]

2012-08-10 11:39  pawel

	* sparx/libpy/applications.py: [no log message]

2012-08-10 10:59  stevel

	* TODO, libEM/pmconfig/spr.json, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/empmwidgets.py: disable  . broken import

2012-08-09 13:49  pawel

	* sparx/libpy/applications.py: [no log message]

2012-08-09 12:54  pawel

	* sparx/libpy/applications.py: [no log message]

2012-08-09 12:30  pawel

	* sparx/: bin/sxali3d.py, libpy/applications.py: [no log message]

2012-08-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-09 11:49  pawel

	* sparx/: bin/sxali3d.py, bin/sxproj_stability.py,
	  libpy/applications.py: [no log message]

2012-08-08 22:11  pawel

	* sparx/bin/sxproj_stability.py: [no log message]

2012-08-08 19:30  pawel

	* sparx/bin/sxproj_stability.py: sxstability.py

2012-08-08 17:24  pawel

	* sparx/libpy/applications.py: [no log message]

2012-08-08 14:40  pawel

	* sparx/: bin/sxproj_stability.py, libpy/applications.py,
	  libpy/pixel_error.py: [no log message]

2012-08-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-07 16:10  pawel

	* sparx/libpy/pixel_error.py: variance corrected

2012-08-07 15:51  piotr

	* sparx/libpy/pixel_error.py: subrotine func working properly

2012-08-07 15:42  pawel

	* sparx/: bin/sxproj_stability.py, libpy/pixel_error.py: [no log
	  message]

2012-08-07 15:31  pawel

	* sparx/libpy/pixel_error.py: [no log message]

2012-08-07 15:14  pawel

	* sparx/: bin/sxproj_stability.py, bin/sxstability.py,
	  libpy/applications.py: [no log message]

2012-08-07 14:42  stevel

	* TODO, libpyEM/qtgui/valslider.py, programs/e2cmpxplor.py,
	  programs/e2eotest.py, programs/e2filtertool.py,
	  programs/e2proc2d.py, programs/e2refine2d.py: Progress dialog in
	  filtertool. updates for mask alignment

2012-08-07 13:45  pawel

	* sparx/libpy/: applications.py, pixel_error.py: pixer

2012-08-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-07 11:16  gtang

	* programs/e2version.py: Now we can display Ubuntu version properly

2012-08-07 11:14  pawel

	* sparx/libpy/pixel_error.py: [no log message]

2012-08-07 08:08  stevel

	* programs/e2refine_evenodd.py: Automaskalign in refine_evenodd

2012-08-06 17:37  pawel

	* sparx/bin/sxproj_stability.py: work on proj_stab

2012-08-06 17:33  pawel

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, sparx/bin/sxproj_stability.py,
	  sparx/libpy/pixel_error.py, sparx/libpy/utilities.py: work on
	  proj_stab

2012-08-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-05 19:45  stevel

	* TODO, examples/alignnrg.py, libEM/aligner.cpp, libEM/aligner.h,
	  libEM/projector.cpp, libEM/projector.h,
	  programs/e2initialmodel.py, programs/e2proc2d.py,
	  programs/e2refine.py, programs/e2simmx.py,
	  programs/e2simmx2stage.py: New masking option seems to be working
	  properly for classification. Haven't incorporated into
	  class-averaging yet.

2012-08-05 17:31  pawel

	* sparx/bin/sxstability.py: sxstab OK

2012-08-05 14:42  pawel

	* sparx/bin/sxstability.py: sxstab removed mpi

2012-08-05 14:38  pawel

	* sparx/bin/sxstability.py: [no log message]

2012-08-05 14:11  pawel

	* sparx/: bin/sxstability.py, libpy/alignment.py,
	  libpy/applications.py: sxstab ok

2012-08-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-03 17:18  piotr

	* sparx/libpy/applications.py: New method of scattering stability
	  checking among MPI processes

2012-08-03 16:07  pawel

	* sparx/bin/sxstability.py: ::

2012-08-03 15:51  pawel

	* sparx/libpy/pixel_error.py: I think I am done with pixer

2012-08-03 12:37  pawel

	* sparx/libpy/pixel_error.py: more new functions

2012-08-03 12:17  pawel

	* sparx/: bin/sxstability.py, libpy/applications.py: [no log
	  message]

2012-08-03 12:17  pawel

	* sparx/libpy/pixel_error.py: new version inserted

2012-08-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-08-02 09:41  gtang

	* libEM/emutil.cpp: check BOOST_VERSION make conditional
	  compilation for boost::filesystem::absolute and
	  boost::filesystem::complete

2012-08-01 20:01  gtang

	* libEM/: emdata_io.cpp, emutil.cpp: fix the bug when HDFIO_CACHE
	  is defined, imageio object will not get deleted. Check the
	  runtime type of imageio, if not HdfIO or HdfIO2, then delete it.

2012-08-01 15:48  gtang

	* libEM/emobject.cpp: miss return for short

2012-08-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-31 16:03  pawel

	* sparx/bin/: sx3Dvariance.py, sxstability.py: minor corrections,
	  not done yet

2012-07-31 14:37  stevel

	* libEM/: processor.cpp, processor.h: New version of mask.auto3d
	  processor. Parameters unchanged, but Gaussian decay now generated
	  much more smoothly. Nonzero mask size may be slightly increased.

2012-07-31 12:24  stevel

	* TODO, examples/alignnrg.py, libEM/aligner.cpp, libEM/aligner.h,
	  libEM/processor.h, libpyEM/qtgui/empmwidgets.py,
	  programs/e2bdb.py, programs/e2speedtest.py: New RegineCG aligner.
	  Same purpose as normal refine aligner, but uses conjugate
	  gradient rather than simplex. Generally sufficiently accurate,
	  and significantly faster, particularly when used with expensive
	  comparators like FRC.

2012-07-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-28 16:10  pawel

	* sparx/: bin/sx3Dvariance.py, bin/sxproj_stability.py,
	  libpy/applications.py, libpy/utilities.py: [no log message]

2012-07-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-28 04:38  pawel

	* sparx/bin/sxproj_stability.py: [no log message]

2012-07-27 17:14  gtang

	* libEM/serio.cpp: fix for Windows visual c++ compilation.

2012-07-27 16:41  piotr

	* sparx/bin/sxstability.py: make second parameter (file with
	  averages) optional

2012-07-27 15:24  gtang

	* libEM/: serio.cpp, serio.h: finish up the SER I/O routine. clean
	  up the prints.

2012-07-27 15:23  gtang

	* libpyEM/typeconverter.cpp: support short in EMObject

2012-07-27 14:15  piotr

	* sparx/bin/sxstability.py: New  command line parameters

2012-07-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-26 17:36  gtang

	* libEM/: CMakeLists.txt, all_imageio.h, emobject.cpp, emobject.h,
	  emutil.cpp, emutil.h, hdfio2.cpp, serio.cpp, serio.h: Implement
	  the I/O for TIA (Emispec) file format (.ser). Initial version,
	  need remove those print out.

2012-07-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-26 08:33  pawel

	* sparx/bin/sx3Dvariance.py: [no log message]

2012-07-26 07:45  stevel

	* TODO, examples/alignnrg.py, libEM/aligner.cpp, libEM/aligner.h,
	  libpyEM/qtgui/emimagemx.py: Working on alignnrg. Fixed some
	  debugging issues.

2012-07-25 16:19  pawel

	* sparx/bin/sxstability.py: [no log message]

2012-07-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-24 12:55  gtang

	* utils/CMakeLists.txt: stop compile e2speedtest executable file

2012-07-24 12:55  stevel

	* examples/alignnrg.py, libEM/aligner.cpp: Fixed problem with
	  infinities not being handled properly in inequalities.

2012-07-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-23 13:25  fjia

	* sparx/bin/sxshiftali.py: add mask option

2012-07-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-23 08:03  stevel

	* programs/e2speedtest.py: Update speedtest

2012-07-23 06:58  stevel

	* TODO, programs/e2speedtest.py: e2speedtest now uses refine
	  aligner as well. Adjusted so numbers same on reference machine,
	  but processing is different.

2012-07-22 23:09  stevel

	* TODO, libEM/aligner.cpp, libEM/aligner.h, libEM/emdata.cpp: Ok,
	  the previous fix for the segfault with certain sizes actually
	  messed up the alignments somewhat. Still testing this patch, but
	  initial indications are that it fixes the problem.

2012-07-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-20 15:22  stevel

	* programs/e2speedtest.py: Speedtest updates

2012-07-20 14:46  stevel

	* libEM/: emdata.cpp, emdata.h: Tweak to the unwrap algorithm to
	  give it better performance on certain box sizes. May have a minor
	  impact on rotate_translate_flip alignments. Not to say they will
	  be worse, just not identical to previous results. Need to do some
	  testing to confirm ok.

2012-07-20 13:35  stevel

	* libEM/emdata.cpp: patch to prevent SSE crashes in calc_ccfx.
	  Insures 128 bit alignment of rows

2012-07-20 12:08  stevel

	* libpyEM/qtgui/emboxerbase.py, programs/e2speedtest.py: Speedtest
	  update

2012-07-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-20 03:05  jgalaz

	* programs/e2spt_hac.py: "normalize.mask" is now supported.

2012-07-20 01:59  jgalaz

	* programs/e2spt_hac.py: Bug fixes regarding NOT overwriting a
	  directory if the specified PATH already exists.

2012-07-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-18 12:13  gtang

	* CMakeLists.txt: compilation optimization flag for visual c++ on
	  Windows

2012-07-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-18 03:07  jgalaz

	* programs/e2spt_simulation.py: This program was still using
	  OptParser; changed to EMparser. Also using Better noise
	  simulation now (supposedly).

2012-07-18 03:06  jgalaz

	* programs/e2spt_hac.py: Reordered some lines.

2012-07-17 12:22  gtang

	* programs/: e2ctf.py, e2evalimage.py: Fix the angstrom sign
	  display in x axis label. Use matplotlib's mathtext rendering.

2012-07-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-17 10:58  pawel

	* sparx/bin/sxali3d.py: [no log message]

2012-07-17 07:31  stevel

	* libpyEM/: EMAN2jsondb.py, qtgui/empmwidgets.py: New JSON module.
	  Just starting, not ready for use

2012-07-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-14 11:11  pawel

	* programs/e2bdb.py: deleted line 225

2012-07-13 12:48  fjia

	* sparx/libpy/morphology.py: remove helical consistency code

2012-07-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-12 23:37  stevel

	* programs/e2speedtest.py: trivial

2012-07-12 23:35  stevel

	* programs/e2speedtest.py: indent oops

2012-07-12 23:31  stevel

	* programs/e2speedtest.py: oops

2012-07-12 23:30  stevel

	* libpyEM/qtgui/empmwidgets.py, programs/e2simmxxplor.py,
	  programs/e2speedtest.py: Fix bug in gui generator.

2012-07-12 16:11  fjia

	* sparx/libpy/morphology.py: [no log message]

2012-07-12 15:55  fjia

	* sparx/libpy/morphology.py: [no log message]

2012-07-12 14:30  fjia

	* sparx/libpy/morphology.py: [no log message]

2012-07-12 13:39  fjia

	* sparx/libpy/morphology.py: [no log message]

2012-07-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-12 09:44  piotr

	* sparx/libpy/applications.py: add efficiency warning to ISAC

2012-07-12 02:02  stevel

	* programs/e2speedtest.py: Update speedtest stats.

2012-07-11 18:39  fjia

	* sparx/libpy/morphology.py: [no log message]

2012-07-11 18:13  fjia

	* sparx/libpy/morphology.py: [no log message]

2012-07-11 15:58  pawel

	* libEM/sparx/util_sparx.cpp, sparx/bin/sxali3d.py,
	  sparx/libpy/applications.py: restriction of psi in ali3d

2012-07-11 14:52  fjia

	* sparx/libpy/morphology.py: [no log message]

2012-07-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-11 10:37  fjia

	* libEM/sparx/util_sparx.cpp: formatting

2012-07-11 09:19  stevel

	* programs/e2helixboxer.py: Fix max size issue

2012-07-11 09:13  stevel

	* libpyEM/qtgui/empmwidgets.py, programs/e2refinetofrealign.py: Fix
	  refinetofrealign conventions

2012-07-10 19:14  pawel

	* libEM/sparx/util_sparx.cpp: formatting

2012-07-10 18:32  fjia

	* sparx/libpy/morphology.py: [no log message]

2012-07-10 16:02  fjia

	* sparx/: bin/sxihrsr.py, libpy/applications.py: [no log message]

2012-07-10 14:24  fjia

	* sparx/libpy/morphology.py: [no log message]

2012-07-10 14:00  stevel

	* libpyEM/qtgui/emboxerbase.py, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2import.py,
	  programs/e2proc3d.py, programs/e2rawdata.py: Major improvements
	  for box db import naming issues

2012-07-10 13:25  fjia

	* sparx/libpy/morphology.py: [no log message]

2012-07-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-10 11:52  fjia

	* libEM/sparx/util_sparx.cpp: fix bug with phi angle restriction in
	  multiref_polar_ali_helical_local

2012-07-09 18:28  fjia

	* sparx/libpy/morphology.py: [no log message]

2012-07-09 17:46  fjia

	* libEM/sparx/util_sparx.cpp: add restricted search based on
	  helical consistency constraints in
	  multiref_polar_ali_helical_local

2012-07-09 17:46  gtang

	* programs/e2projectmanager.py: fix the Windows "Task manager"
	  display issue

2012-07-09 17:43  fjia

	* libpyEM/libpyUtils2.cpp, libEM/sparx/util_sparx.h: modify
	  argument list for multiref_polar_ali_helical_local

2012-07-09 17:41  fjia

	* sparx/libpy/alignment.py: add flag for checking helical
	  consistency constraints in call to
	  multiref_polar_ali_helical_local

2012-07-09 17:38  fjia

	* sparx/libpy/applications.py: add ihrsr_MPI_cons for refinement
	  whiel maintaining helical consistency

2012-07-09 17:35  fjia

	* sparx/bin/sxihrsr.py: add --CONS option for restricting angular
	  search to maintain helical consistency

2012-07-09 17:12  fjia

	* sparx/libpy/morphology.py: [no log message]

2012-07-09 16:44  fjia

	* sparx/libpy/morphology.py: added helical consistency code

2012-07-09 14:04  pawel

	* sparx/libpy/utilities.py: reshape_1d

2012-07-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-08 01:53  stevel

	* programs/e2import.py: Unfixing a fix that was fixed elsewhere

2012-07-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-06 11:40  pawel

	* sparx/libpy/applications.py: [no log message]

2012-07-06 08:10  stevel

	* libpyEM/qtgui/emscene3d.py: Oops

2012-07-06 08:08  stevel

	* libpyEM/qtgui/emscene3d.py: trivial divide by zero fix

2012-07-05 13:14  stevel

	* libpyEM/EMAN2db.py: Fixed problem with creating new databases in
	  non-existent directories.

2012-07-05 12:45  stevel

	* programs/e2evalimage.py: trivial

2012-07-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-05 11:41  stevel

	* examples/redo_convergence.py, libpyEM/qtgui/embrowser.py: Windows
	  fixes

2012-07-04 20:48  jgalaz

	* programs/e2spt_simulation.py: Better noise simulation. Changed
	  some parameter names.

2012-07-04 20:47  jgalaz

	* programs/e2spt_classaverage.py: [no log message]

2012-07-04 18:03  pawel

	* sparx/bin/sxali3d.py: [no log message]

2012-07-04 12:34  stevel

	* libEM/processor.cpp: Fix ringmean processor

2012-07-04 12:30  stevel

	* programs/e2refine_evenodd.py: Options checking

2012-07-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-04 11:24  stevel

	* programs/e2refine.py: trivial

2012-07-04 11:23  stevel

	* programs/e2classaverage.py: Trivial

2012-07-04 11:01  stevel

	* libpyEM/EMAN2fsc.py: oops, missed one

2012-07-04 11:00  stevel

	* examples/redo_convergence.py, libpyEM/qtgui/emplot2d.py,
	  programs/e2proc3d.py, programs/e2refine.py: Convergence plot fix

2012-07-04 09:19  stevel

	* libpyEM/EMAN2db.py: Fix error reporting bug

2012-07-03 20:43  jgalaz

	* programs/e2import.py: [no log message]

2012-07-03 20:38  jgalaz

	* programs/e2projectmanager.py: Bla.

2012-07-03 17:17  gtang

	* libpyEM/qtgui/emboxerbase.py, programs/e2import.py: bug fix for
	  windows. It's an issue with '/' and '\' in path name, especially
	  as db key.

2012-07-03 17:08  jgalaz

	* programs/e2spt_classaverage.py: Bug fix.

2012-07-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-02 22:57  stevel

	* libEM/processor.cpp: Undo a change Stephen made to radial fourier
	  processors

2012-07-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-01 21:22  stevel

	* libpyEM/qtgui/: empmtabwidgets.py, empmwidgets.py: Trivial

2012-07-01 18:51  stevel

	* libpyEM/qtgui/: empmtabwidgets.py, emsprworkflow.py: Fixes for
	  filter in browser in CTF

2012-07-01 13:52  stevel

	* libpyEM/qtgui/emboxerbase.py, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2evalimage.py: Fixes
	  for ./

2012-07-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-07-01 11:10  gtang

	* libpyEM/EMAN2PAR.py: fix the threading launching for Windows

2012-06-30 23:22  stevel

	* programs/e2evalimage.py: Fix processing

2012-06-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-29 12:57  gtang

	* libEM/emobject.cpp: support string to float conversion in meta
	  data

2012-06-29 12:55  gtang

	* libEM/emobject.cpp: support string to

2012-06-29 12:31  pawel

	* sparx/bin/sx3Dvariance.py: [no log message]

2012-06-29 12:12  pawel

	* sparx/bin/sx3Dvariance.py: [no log message]

2012-06-29 12:04  stevel

	* libpyEM/qtgui/emboxerbase.py, programs/e2ctf.py: Fix apix problem

2012-06-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-29 11:22  pawel

	* sparx/libpy/applications.py: [no log message]

2012-06-29 10:53  pawel

	* sparx/: bin/sx3Dvariance.py, bin/sxmref_ali3d.py,
	  libpy/applications.py: [no log message]

2012-06-29 09:55  stevel

	* libpyEM/qtgui/embrowser.py, libpyEM/qtgui/empmwidgets.py,
	  programs/e2import.py: Box DB import fixes

2012-06-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-27 11:50  pawel

	* sparx/bin/sx3Dvariance.py: [no log message]

2012-06-27 00:41  jgalaz

	* programs/e2spt_resolutionplot.py: Modified program to enable
	  plotting multiple resolution curves in one plot.

2012-06-26 16:52  zyang

	* sparx/bin/sx3Dvariance.py: [no log message]

2012-06-26 15:24  zyang

	* sparx/libpy/utilities.py: Trivial change.

2012-06-26 12:43  pawel

	* sparx/libpy/applications.py: [no log message]

2012-06-26 12:31  pawel

	* sparx/bin/: sx3Dvariance.py: [no log message]

2012-06-26 12:13  zyang

	* sparx/bin/sx3Dvariance.py: Change to eigenvolume program

2012-06-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-26 11:59  pawel

	* sparx/: bin/sx3Dvariance.py, libpy/applications.py: [no log
	  message]

2012-06-26 09:21  gtang

	* libpyEM/EMAN2PAR.py: import the name get_platform

2012-06-25 20:03  zyang

	* sparx/bin/sx3Dvariance.py: Fix a minor bug.

2012-06-25 17:53  zyang

	* sparx/: bin/sx3Dvariance.py, libpy/reconstruction.py: Add the
	  eigenvolumes part of the 3D variance.

2012-06-25 15:04  pawel

	* sparx/libpy/applications.py: [no log message]

2012-06-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-25 11:59  gtang

	* libpyEM/EMAN2.py: enable both bdb: and BDB: in option string
	  parse

2012-06-25 11:32  gtang

	* libpyEM/EMAN2PAR.py: fix the threading launch for windows

2012-06-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-23 11:38  stevel

	* libpyEM/qtgui/empmwidgets.py: Fixed issue with automask
	  parameters in projectmanager not going through properly.

2012-06-23 10:01  stevel

	* libpyEM/qtgui/empmwidgets.py, programs/e2refine.py: Automask
	  improperly configured in GUI

2012-06-23 02:19  stevel

	* libpyEM/EMAN2PAR.py, programs/e2refine.py: Fix accidental
	  parallelism problem

2012-06-23 02:00  stevel

	* libEM/pmconfig/spr.json, libpyEM/EMAN2db.py,
	  libpyEM/qtgui/embrowser.py, programs/e2ctf.py,
	  programs/e2filtertool.py, programs/e2proc2d.py: A bunch of fixes
	  for e2projectmanager workflow.

2012-06-22 20:45  stevel

	* libpyEM/qtgui/emboxerbase.py, programs/e2buildsets.py: New
	  program

2012-06-22 16:33  astrocytus

	* sparx/bin/sxpca.py: parameters

2012-06-22 16:33  astrocytus

	* sparx/libpy/applications.py: pca

2012-06-22 16:25  astrocytus

	* sparx/libpy/statistics.py: pcanalizer

2012-06-22 14:03  pawel

	* sparx/libpy/applications.py: [no log message]

2012-06-22 12:41  pawel

	* sparx/libpy/applications.py: [no log message]

2012-06-22 12:38  stevel

	* programs/e2evalimage.py: Few more GUI niceities

2012-06-22 12:34  pawel

	* sparx/libpy/morphology.py: [no log message]

2012-06-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-22 11:59  pawel

	* sparx/libpy/applications.py: chunk corrected

2012-06-22 10:43  stevel

	* programs/e2evalimage.py: another tweak to gui

2012-06-22 10:40  stevel

	* programs/e2evalimage.py: Trivial fix

2012-06-22 10:40  gtang

	* programs/e2pathwalker.py: set shell=True, otherwise winodws
	  doesnot recognize the first string as a command

2012-06-22 10:39  gtang

	* libpyEM/EMAN2PAR.py: set shell=True, otherwise winodws doesnot
	  recognize the e2*.py as a command

2012-06-22 10:29  stevel

	* programs/e2refine.py: oops, scaling wrong

2012-06-22 10:10  stevel

	* libpyEM/qtgui/empmwidgets.py, programs/e2initialmodel.py,
	  programs/e2refine.py: Improvements to initial model generation,
	  automatic input model scaling in e2refine.py

2012-06-22 10:06  gtang

	* libpyEM/EMAN2.py: os.waitpid() dows not work on windows, replace
	  with Popen.wait()

2012-06-21 22:40  stevel

	* libEM/pmconfig/spr.json, libpyEM/EMAN2.py,
	  libpyEM/qtgui/emapplication.py, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/emplot2d.py, libpyEM/qtgui/empmtabwidgets.py,
	  libpyEM/qtgui/valslider.py, programs/e2eotest.py,
	  programs/e2evalimage.py, programs/e2refine.py: Fixes to
	  e2projectmanager set building.

2012-06-21 15:37  zyang

	* sparx/bin/sx3Dvariance.py: A brand new version, did a complete
	  makeover

2012-06-21 15:36  gtang

	* programs/: e2proc3d.py, e2proc2d.py: fix the --process option.
	  try to convert non-digit parameter followed by filter name to
	  EMData object. If not a valid image file name, just ignore.

2012-06-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-20 16:57  gtang

	* programs/e2boxer.py: fix the bug when the '--gui' option is
	  specified, the following image file name is hidden by this
	  option.

2012-06-20 16:45  gtang

	* libpyEM/EMAN2.py, programs/e2proc2d.py, programs/e2proc3d.py:
	  move the "bdb:" parsing code to parsemodopt in EMAN2.py

2012-06-20 13:33  fjia

	* sparx/demo/mpi_bdb/run_through_example: change sxali3d and
	  sxlocal_ali3d commands to use external user function

2012-06-20 13:30  fjia

	* sparx/demo/mpi_bdb_ctf/run_through_example: use external user
	  function for sxali3d and sxlocal_ali3d commands

2012-06-20 13:28  fjia

	* sparx/demo/demo_user_funcs.py: contains external user functions
	  used by sxali3d and sxlocal_ali3d in run_through_example

2012-06-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-20 11:36  gtang

	* programs/: e2proc2d.py, e2proc3d.py: bug fix. The paramenter for
	  --process option could be float number.

2012-06-19 21:37  jgalaz

	* examples/e2spt_radialdensityplot.py: Update.

2012-06-19 14:59  gtang

	* programs/e2proc2d.py: parse the --process option to convert the
	  image file to EMData object

2012-06-19 14:51  gtang

	* programs/e2proc3d.py: parse the --process option to convert the
	  image file to EMData object

2012-06-19 14:05  scmurray

	* programs/e2refinetorelion3d.py: Fixed a small issue

2012-06-19 13:42  scmurray

	* programs/e2refinetorelion3d.py: Removed debugging statements

2012-06-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-19 10:58  zyang

	* sparx/libpy/statistics.py: Switch snr default back to 1.e23 per
	  Pawel's request

2012-06-19 09:49  scmurray

	* libEM/processor.cpp, programs/e2proc3d.py: Fixed an issue with
	  setSF

2012-06-18 16:18  jgalaz

	* examples/e2spt_radialdensityplot.py: Updated to allow to plot
	  radial density plots that are non-spherical, but rather
	  cylindrical, keeping the height constant, or varying it
	  continuously. It is now also possible to make plots of density
	  along any give axis (x, y or z).

2012-06-18 15:51  jgalaz

	* programs/e2spt_classaverage.py: Masking/normalizing
	  modified/fixed.

2012-06-18 15:06  zyang

	* sparx/libpy/reconstruction.py: Set the default value of snr to
	  1.0

2012-06-18 14:59  zyang

	* sparx/libpy/statistics.py: Change default snr to 1.0

2012-06-18 13:49  zyang

	* sparx/bin/sxisac.py: Add mpi_finalize()

2012-06-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-18 11:26  fjia

	* programs/e2boxer.py: correct spelling

2012-06-17 20:08  jgalaz

	* programs/e2spt_boxer.py: [no log message]

2012-06-17 20:01  jgalaz

	* programs/e2spt_boxer.py: Fixed bugs concerning saving
	  subtomograms and reading coordinates from binned/expanded coords
	  files.

2012-06-17 08:09  pawel

	* sparx/bin/sxlocal_ali3d.py: [no log message]

2012-06-17 04:16  pawel

	* sparx/libpy/applications.py: [no log message]

2012-06-16 12:55  pawel

	* sparx/: bin/sxlocal_ali3d.py, libpy/applications.py: minor
	  corrections

2012-06-15 17:14  pawel

	* sparx/libpy/applications.py, sparx/libpy/reconstruction.py,
	  libEM/reconstructor.cpp: [no log message]

2012-06-15 15:50  zyang

	* sparx/libpy/reconstruction.py: Add radius as a parameter of
	  recons3d_em (and _MPI)

2012-06-15 12:20  gtang

	* programs/e2speedtest.py: add test score for new cpu type

2012-06-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-15 10:45  gtang

	* programs/e2proc2d.py: let --list option work with
	  --twod2threed/--threed2threed

2012-06-14 17:10  jgalaz

	* examples/e2spt_coordsrefactor.py: Program to refactor coordinate
	  files for SPT in multiple flexible ways. Some people have
	  aberrant files, with extra characters, in various formats, or
	  binned, or with z or y flipped respect to the tomogram, etc. This
	  program cleans empty lines, deletes garbage characters, allows to
	  scale coordinate values (up and down), and writes the coordinates
	  in the format "X Y Z"; for example, "10 32 23", with no comas, no
	  "x=" or "y=" or "z=" characters, no tabs, no dots, etc.  It also
	  allows to produce a subcoordinates file with a subset of the
	  coordinates, to sort them by any scheme selected (xyz, y, zy, zx,
	  etc...), or to randomize the coordinates.

2012-06-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-14 09:44  zyang

	* sparx/libpy/utilities.py: Fix a small bug in nearest_ang

2012-06-13 15:14  gtang

	* libpyEM/qtgui/: embrowser.py, emdataitem3d.py: fix the 3D stack
	  image display problem

2012-06-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-12 15:49  pawel

	* sparx/libpy/reconstruction.py: [no log message]

2012-06-12 15:29  piotr

	* sparx/: bin/sx3Dvariance.py, libpy/reconstruction.py: New stop
	  criterions in recons3d_em_MPI

2012-06-12 14:51  jgalaz

	* examples/e2spt_rotationalplot.py: Major changes.

2012-06-12 14:50  jgalaz

	* examples/e2spt_radialdensityplot.py: Major redesign and expanded
	  capabilities.

2012-06-12 14:50  gtang

	* programs/: e2proc2d.py, e2proc3d.py: for unstacking option, fill
	  the output name with 0.

2012-06-12 14:49  jgalaz

	* programs/e2spt_resolutionplot.py: Modifications...

2012-06-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-12 11:23  piotr

	* sparx/libpy/reconstruction.py: recons3d_em_MPI - now it reads
	  only part of projections instead of whole stack

2012-06-12 10:46  gtang

	* libEM/: emdata_io.cpp, lstio.cpp: set "source_path" to reference
	  image full path for LstIO

2012-06-11 15:46  gtang

	* programs/e2proc3d.py: fix the bug when the --first is not equal
	  to zero

2012-06-11 14:11  gtang

	* CMakeLists.txt, libEM/CMakeLists.txt: make hdfcache work with
	  MacOS

2012-06-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-11 10:40  gtang

	* libEM/: hdf_filecache.cpp, hdf_filecache.h: set cache size limit
	  to 1/2 of the system's per process file descriptor size limit

2012-06-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-08 17:06  astrocytus

	* sparx/bin/sx3Dvariance.py: not woring version

2012-06-08 15:47  pawel

	* sparx/libpy/statistics.py: keep working

2012-06-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-08 09:36  pawel

	* libEM/sparx/util_sparx.cpp, sparx/libpy/statistics.py: keep
	  trying

2012-06-07 14:51  astrocytus

	* sparx/bin/sx3Dvariance.py: new approach - moving averages - not
	  ready for testing yet

2012-06-07 14:41  gtang

	* examples/e2tomosim.py, programs/e2tomohunter.py: remove redundant
	  file for Jesus

2012-06-07 14:35  gtang

	* libEM/emutil.cpp: boost::filesystem::complete is deprecated, now
	  replaced by boost::filesystem::absolute

2012-06-07 14:01  pawel

	* sparx/libpy/statistics.py: avgvarctf

2012-06-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-07 11:51  astrocytus

	* sparx/bin/sxpca.py: [no log message]

2012-06-07 11:50  astrocytus

	* sparx/libpy/applications.py: pca

2012-06-07 09:55  gtang

	* examples/e2spt_simulation.py, examples/e2sptsimulation.py,
	  programs/e2spt_simulation.py: massive rename and move files for
	  Jesus

2012-06-07 09:53  gtang

	* examples/: e2spt_fftamp.py, e2spt_resolutionplot.py,
	  e2sptcoeffplot.py: [no log message]

2012-06-07 09:51  gtang

	* examples/e2spt_simulation.py, libEM/pmconfig/breaksym.json,
	  libEM/pmconfig/classaverage3d.json, libEM/pmconfig/spr.json,
	  libEM/pmconfig/symaligner.json, libEM/pmconfig/symsearch.json,
	  libEM/pmconfig/tomo.json, libEM/pmconfig/tomoboxer.json,
	  libEM/pmconfig/tomores.json, libpyEM/EMAN2PAR.py,
	  libpyEM/qtgui/emtprworkflow.py, programs/CMakeLists.txt,
	  programs/e2classaverage3d.py, programs/e2classaveragebysym.py,
	  programs/e2montecarlorecon.py, programs/e2preferences.py,
	  programs/e2proc3d.py, programs/e2spt_boxer.py,
	  programs/e2spt_classaverage.py, programs/e2spt_fftamp.py,
	  programs/e2spt_hac.py, programs/e2spt_refinemulti.py,
	  programs/e2spt_resolutionplot.py, programs/e2symsearch.py,
	  programs/e2symsearch3d.py, programs/e2tomoallvsall.py,
	  programs/e2tomoboxer.py, examples/e2spt_autocenter.py,
	  examples/e2spt_coeffplot.py: massive rename and move files for
	  Jesus

2012-06-07 01:26  jgalaz

	* examples/e2sptsimulation.py: [no log message]

2012-06-06 22:31  stevel

	* examples/e2extractctf.py: New simple example program to extract
	  ctf parms

2012-06-06 17:39  jgalaz

	* examples/e2spt_radialdensityplot.py: Program to automatically
	  compute radial density plots on a single volume or stack of
	  subtomograms.

2012-06-06 17:24  zyang

	* sparx/libpy/utilities.py: Add function nearest_proj(), the code
	  to determine the k nearest projections

2012-06-06 16:43  astrocytus

	* sparx/: libpy/applications.py, bin/sx3Dvariance.py: pca

2012-06-06 16:42  astrocytus

	* sparx/bin/sxpca.py: [no log message]

2012-06-06 14:35  gtang

	* libEM/emobject.h: fix the printf compilation error on gcc 4.7

2012-06-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-06 09:54  zyang

	* libEM/sparx/util_sparx.cpp: Fix all the warnings.

2012-06-06 08:49  stevel

	* programs/e2evalimage.py: Minor tweak to prevent occasional crash

2012-06-05 15:45  gtang

	* libEM/averager.cpp, libEM/averager.h, rt/pyem/test_averager.py:
	  Add a new averager class AbsMaxMinAverager

2012-06-05 15:02  astrocytus

	* sparx/libpy/statistics.py: class pcanalyzer

2012-06-05 12:57  piotr

	* sparx/libpy/alignment.py: prepare_refrings - use Applyws routine
	  from util_sparx.cpp instead of version implemented in Python

2012-06-05 12:21  piotr

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Move Applyws routine from alignment.py
	  to util_sparx.cpp (speedup > 100x)

2012-06-05 12:14  piotr

	* sparx/libpy/alignment.py: correct type of indices

2012-06-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-05 11:05  scmurray

	* programs/e2refinetorelion3d.py: Small changes. Removed some
	  debugging.

2012-06-05 08:02  piotr

	* libEM/sparx/util_sparx.cpp: bugfix - add conversion in
	  group_by_phi_theta()

2012-06-05 07:27  stevel

	* examples/e2ptclzvssim.py, libpyEM/EMAN2PAR.py,
	  libpyEM/qtgui/emimage2d.py, programs/e2evalimage.py: Fix for 2d
	  stack saving. Tweaks to parallelism to reduce timeouts.

2012-06-05 03:21  jgalaz

	* examples/e2spt_rotationalplot.py: Program to calculate the
	  rotational correlation plot (.txt and .png files are generated)
	  of a volume with itself, or another volume, with an angular
	  variation refined by the user. The volumes can be pre-processed
	  in multiple ways.

2012-06-05 03:07  jgalaz

	* programs/e2classaverage3d.py: Fixed conceptual bug regarding
	  normalization (normalize-mask-normalize-mask should be applied on
	  BOTH subvolumes)

2012-06-05 02:31  jgalaz

	* examples/e2spt_resolutionplot.py: Multiple changes. Now you can
	  calculate the FSC only, for particles assumed to be aligned
	  already, through --fsconly. You can also generate only the plots,
	  without alignment or FSC computation, through --curves. Multiple
	  FSC curves can be plotted at the same time (in separate plots),
	  if you already have the files generated. Also, the program aligns
	  mirrored and symmetrized versions of the structures and generates
	  FSC files and PLOTS automatically through simple --sym and
	  --mirror flags. Furthermore, the program generates a .txt file
	  with automatic resolution calculations (two different methods,
	  and the average of the two, all printed on the screen as well).

2012-06-04 17:10  gtang

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: fix for windows
	  compilation

2012-06-04 17:00  astrocytus

	* sparx/libpy/statistics.py: pcanalyzer - not ready yet

2012-06-04 16:59  astrocytus

	* sparx/libpy/applications.py: pca

2012-06-04 16:58  astrocytus

	* sparx/bin/sxpca.py: --incore

2012-06-04 12:14  astrocytus

	* sparx/bin/sx3Dvariance.py: [no log message]

2012-06-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-04 11:59  astrocytus

	* sparx/bin/sx3Dvariance.py: [no log message]

2012-06-03 18:33  piotr

	* sparx/bin/sx3Dvariance.py: Bugfix

2012-06-03 15:48  astrocytus

	* sparx/bin/sx3Dvariance.py: SND in progress

2012-06-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-06-01 07:15  jgalaz

	* examples/e2spt_resolutionplot.py: Expanded capabilities. Symmetry
	  can be accounted for automatically now (bot during alignment and
	  fsc calculation). X axis plotted as frequency = 1/resolution. Got
	  rid of labels.

2012-05-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-05-31 09:40  piotr

	* libEM/sparx/util_sparx.cpp: Util::WTF(...) - optimization +
	  remove bug (condition in if statement)

2012-05-31 07:26  piotr

	* sparx/libpy/reconstruction.py: recons3d_wbp - remove old comments

2012-05-30 16:55  gtang

	* programs/e2evalparticles.py: fix the bdb name issue caused by hdf

2012-05-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-05-29 17:48  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, sparx/libpy/utilities.py: Add the
	  program group_proj_by_phitheta()

2012-05-29 14:47  piotr

	* libEM/sparx/util_sparx.cpp: Util::WTF -  optimizing (details)

2012-05-29 14:19  piotr

	* libEM/sparx/util_sparx.cpp: Util::WTF - cleaning and optimizing

2012-05-29 12:46  piotr

	* sparx/libpy/reconstruction.py: recons3d_wbp - new parameter
	  "radius"

2012-05-29 12:40  piotr

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  sparx/libpy/reconstruction.py: Util::BPCQ - now volume is updated
	  within sphere only (radius is given as parameter)

2012-05-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-05-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-05-27 13:33  piotr

	* libEM/sparx/util_sparx.cpp: Util::BPCQ - refactoring

2012-05-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-05-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-05-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-05-24 17:39  jgalaz

	* programs/e2classaverage3d.py: Bug fix.

2012-05-24 17:13  gtang

	* libEM/util.h: change 'long int' to 'long long', because 'long
	  int' is 32 bit on windows.

2012-05-24 17:12  jgalaz

	* programs/e2classaverage3d.py: Fixed error/deficiency in the
	  normalization/masking strategy.

2012-05-24 16:51  gtang

	* libEM/: randnum.cpp, randnum.h, util.cpp, util.h: make 'long int'
	  to 'long long' to make it 64 bit integer on windows.

2012-05-24 14:52  gtang

	* libEM/util.h: long int is 32bit on windows, use long long for 64
	  bit integer is cross-platform safe.

2012-05-24 14:15  jgalaz

	* examples/e2spt_resolutionplot.py: Modification to how accurately
	  the polynomial fit is calculated.

2012-05-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-05-23 19:31  jgalaz

	* programs/e2tomoallvsall.py: Bug fix

2012-05-23 14:44  stevel

	* examples/redo_convergence.py, libEM/processor.cpp,
	  libpyEM/qtgui/valslider.py, programs/e2classify.py: Playing with
	  simvec option

2012-05-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-05-22 16:58  fjia

	* sparx/libpy/applications.py: back out yesterday's changes for
	  ihrsr_mpi...don't set xform.projection attribute internally if
	  the user didn't set it in image headers

2012-05-22 13:19  stevel

	* libpyEM/qtgui/embrowser.py, programs/e2make3d.py,
	  programs/e2refine.py, programs/e2refinevariance.py: keepabs added
	  to make3d

2012-05-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-05-21 18:41  stevel

	* libpyEM/EMAN2PAR.py, mpi_eman/pbs.example,
	  programs/e2parallel.py: Patch to specify path for dcclient for
	  mpirun use

2012-05-21 17:27  fjia

	* sparx/libpy/applications.py: in ihrsr_MPI: if xform.projection
	  attribute is not in the headers of the input stack, and the
	  angular neighbor specified for the first iteration is -1
	  (exhaustive), then set xform.projection parameters of the input
	  stack to zero.

2012-05-21 14:13  zyang

	* sparx/libpy/applications.py: Fix a small bug in mref_ali3d_MPI()

2012-05-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-05-21 08:19  stevel

	* examples/redo_convergence.py, libpyEM/EMAN2.py,
	  programs/e2classify.py, programs/e2eotest.py,
	  programs/e2evalrefine.py, programs/e2refine.py,
	  programs/e2refine_evenodd.py: New classification option in
	  e2refine and e2classify (untested, but doesn't crash). New time
	  diagnostic in e2evalrefine.

2012-05-21 07:17  pawel

	* sparx/libpy/reconstruction.py: added a test wbp function

2012-05-20 23:38  stevel

	* programs/e2classify.py: New option in e2classify to permit
	  pattern-based classification rather than peak-pased
	  classification

2012-05-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-05-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-05-18 18:30  jgalaz

	* examples/e2spt_resolutionplot.py: Bugfixes

2012-05-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-05-17 13:42  jgalaz

	* examples/e2spt_meanintensityplot.py:
	  Multiple improvements.

2012-05-17 13:42  jgalaz

	* examples/e2tomosim.py:
	  Noise issues fixed

2012-05-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-05-17 10:40  stevel

	* libpyEM/qtgui/: emapplication.py, emscene3d.py: Fixed window
	  closing problem with new browser.

2012-05-16 17:13  gtang

	* programs/e2proc3d.py: support multiple '--trans' and '--rot'
	  options.

2012-05-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-05-15 19:49  jgalaz

	* examples/e2sptcoeffplot.py:
	  Many modifications to divide the data into any arbitrary number
	  of groups.

2012-05-15 13:32  stevel

	* libpyEM/qtgui/emapplication.py: Minor tweak to new patch

2012-05-15 13:30  stevel

	* examples/filespeedtest.py, libpyEM/EMAN2.py,
	  libpyEM/qtgui/emapplication.py: Patch so opened images are the
	  right size on the Mac

2012-05-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-05-15 10:25  stevel

	* libpyEM/qtgui/emplot2d.py: Fix name conflict

2012-05-15 09:57  scmurray

	* libEM/pmconfig/spr.json, programs/e2eulerxplor.py: Added
	  e2eulerxplor.py to the Project Manager and added a
	  header/description for it to the Project Manager

2012-05-14 17:16  jgalaz

	* examples/e2spt_meanintensityplot.py: [no log message]

2012-05-14 17:14  jgalaz

	* examples/e2spt_meanintensityplot.py:
	  Bug fix

2012-05-14 17:07  jgalaz

	* examples/e2spt_meanintensityplot.py: Program to plot the mean
	  intensity distribution of a subvolume stack, or specific masked
	  out/in parts of the volumes in the stack

2012-05-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-05-13 16:39  jgalaz

	* examples/e2sptcoeffplot.py: Bug fix

2012-05-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-05-13 01:53  stevel

	* libpyEM/EMAN2PAR.py: New method using UNIX domain socket seems to
	  work now, though it hasn't solved the underlying torus problem.

2012-05-13 01:10  stevel

	* libpyEM/EMAN2PAR.py: Still fine-tuning MPI parallelism change

2012-05-13 00:22  stevel

	* libpyEM/EMAN2PAR.py: Experimental new mpi code using unix domain
	  socket rather than a named FIFO

2012-05-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-05-12 00:04  stevel

	* programs/e2refine_evenodd.py: refine_evenodd was messed up. Was
	  using all of the data for each of the 2 refinements. ie - was
	  doing self-consistency test, not resolution test !

2012-05-11 16:27  gtang

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/emutil.cpp,
	  libEM/emdata_io.cpp, libEM/hdf_filecache.cpp,
	  libEM/hdf_filecache.h, libEM/hdfio2.cpp: Implement HDFCache for
	  caching the HDF5 I/O object.

2012-05-11 15:49  eman-vm

	* programs/e2version.py: new date stamp

2012-05-11 15:48  zyang

	* sparx/libpy/utilities.py: Fix a bug in group_proj_by_phitheta()
	  and make some changes to make it more robust.

2012-05-11 14:35  pawel

	* sparx/libpy/: fundamentals.py, statistics.py: I think I got CTF
	  variance

2012-05-11 13:58  jgalaz

	* examples/e2sptcoeffplot.py: Update.

2012-05-11 12:22  stevel

	* libpyEM/EMAN2.py, libpyEM/qtgui/emplot2d.py, programs/e2ctf.py,
	  programs/e2evalimage.py: Fix for defocus autofitting. Bug.

2012-05-10 17:42  pawel

	* sparx/libpy/statistics.py: some more work on 2D CTF variance

2012-05-10 13:59  pawel

	* sparx/libpy/statistics.py: corrected 2D variance with CTF

2012-05-10 11:35  john

	* libpyEM/qtgui/emrctstrategy.py: #^#^$ ANother CVS screw up!!!!

2012-05-10 11:33  john

	* programs/e2tiltvalidate.py: reverted what CVS screwed up

2012-05-10 11:28  john

	* libEM/pmconfig/spr.json, libpyEM/qtgui/emplot2d.py,
	  libpyEM/qtgui/emrctstrategy.py, programs/e2tiltvalidate.py:
	  reverted somebody breaking my ploarplot widget

2012-05-10 11:16  stevel

	* libpyEM/qtgui/embrowser.py, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emplot2d.py, libpyEM/qtgui/emplot3d.py,
	  programs/e2evalimage.py: Updates

2012-05-10 10:32  john

	* libpyEM/qtgui/embrowser.py: bugfixs for the browser

2012-05-10 09:39  piotr

	* libEM/sparx/util_sparx.cpp: Util::BPCQ - cleaning and optimizing

2012-05-09 16:03  astrocytus

	* sparx/bin/sx3Dvariance.py: [no log message]

2012-05-09 15:39  astrocytus

	* sparx/bin/sx3Dvariance.py: logfile

2012-05-09 15:36  piotr

	* libEM/sparx/util_sparx.cpp, sparx/libpy/reconstruction.py: repair
	  compilation error in EMAN::Util::BPCQ recons3d_wbp - new version
	  (now it works for symmetry != c1)

2012-05-09 15:17  scmurray

	* libEM/pmconfig/relion2d.json, libEM/pmconfig/relion3d.json,
	  libEM/pmconfig/spr.json, programs/e2refinetorelion2d.py,
	  programs/e2refinetorelion3d.py: Adding e2refinetorelion2d.py,
	  e2refinetorelion3d.py and the associated json files for wizards.

2012-05-09 14:41  astrocytus

	* sparx/libpy/reconstruction.py: removing printouts

2012-05-09 13:51  piotr

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  sparx/libpy/reconstruction.py, sparx/libpy/statistics.py: remove
	  DM parameter from Util::BPCQ routines Util::BPCQ, Util::WTF and
	  Util::WTM can accept fft images on input from now

2012-05-09 11:43  astrocytus

	* sparx/libpy/reconstruction.py: printouts removed form
	  recons3d_em()

2012-05-08 16:23  john

	* libpyEM/qtgui/: emimage.py, emplot3d.py, emshapeitem3d.py: Added
	  new 3D plotting widget

2012-05-08 14:21  zyang

	* sparx/libpy/utilities.py: Fix a small bug
	  group_proj_by_phitheta()

2012-05-08 13:33  fjia

	* sparx/demo/generate_projections.py: Deleting
	  generate_projections.py from cvs; it has been replaced by
	  sxprocess using generate_projections option.

2012-05-08 13:29  fjia

	* sparx/demo/: filldb_demo.py, filldb_mpibdb.py: [no log message]

2012-05-08 13:04  john

	* libpyEM/qtgui/emplot3d.py, programs/e2import.py: bugfix for
	  e2import.pyO

2012-05-08 12:13  john

	* examples/redo_convergence.py, programs/e2refine_evenodd.py:
	  updated redo_convergence.py

2012-05-08 11:09  john

	* libpyEM/qtgui/empmwidgets.py: fscplot

2012-05-08 10:52  john

	* libpyEM/qtgui/empmwidgets.py: fsc table fixes

2012-05-08 10:46  astrocytus

	* sparx/bin/sx3Dvariance.py: averages do not have CTF

2012-05-08 10:21  john

	* libEM/aligner.h, libpyEM/EMAN2fsc.py,
	  libpyEM/qtgui/empmwidgets.py: FSC table fix

2012-05-08 08:51  stevel

	* libpyEM/qtgui/emimage.py: Fix 1-D plotting.

2012-05-07 22:36  stevel

	* programs/e2classify.py: Working on new classification option for
	  refinement.

2012-05-07 14:49  zyang

	* sparx/libpy/user_functions.py: Trivial change

2012-05-06 15:29  piotr

	* sparx/libpy/user_functions.py: revert to revision 1.75 (removes
	  ref_empty function)

2012-05-06 15:11  pawel

	* sparx/libpy/statistics.py: [no log message]

2012-05-06 12:29  stevel

	* examples/ctf_first_zero.py, programs/e2refine.py: fix
	  continuation option so it uses the right starting file

2012-05-06 11:05  pawel

	* sparx/libpy/statistics.py: comments in reconstruction

2012-05-06 10:13  pawel

	* sparx/libpy/reconstruction.py: comments in reconstruction

2012-05-05 18:44  piotr

	* sparx/libpy/user_functions.py:
	  ref_empty - removes bug

2012-05-05 18:40  piotr

	* sparx/libpy/user_functions.py:
	  ref_empty - remove bug

2012-05-05 18:32  piotr

	* sparx/libpy/user_functions.py:
	  ref_empty - return parameters

2012-05-05 17:42  piotr

	* sparx/libpy/user_functions.py:
	  add empty function

2012-05-05 12:15  stevel

	* examples/e2simmxptclqual.py: Improved thresholds

2012-05-05 11:47  stevel

	* libpyEM/EMAN2fsc.py: Fix missing import

2012-05-04 16:20  john

	* libpyEM/qtgui/empmwidgets.py, programs/e2plotFSC.py: fsc
	  enhancements and bug fixes

2012-05-04 15:02  john

	* libpyEM/qtgui/emplot2d.py, programs/e2plotEulers.py: decoupled
	  polar and 2D plotting widgets. Previously polar inherited from 2D
	  cartesian, but this caused coupling issues. When 2D cartesian
	  plot was modified it broke the 2D ploar plot. This casues a bit
	  of code duplication, but it is worth it. Avoi heche....

2012-05-04 14:13  stevel

	* libpyEM/qtgui/emplot2d.py: unreverting 2d plot

2012-05-04 14:07  john

	* libpyEM/qtgui/emplot2d.py, programs/e2projectmanager.py: Reverted
	  to an stable version of emplot2d.py (last weeks). The new version
	  broke the polar plot opengL, and I couldn't track down the
	  reason.

2012-05-04 11:38  astrocytus

	* sparx/bin/sx3Dvariance.py: writing files to the disk

2012-05-03 16:44  astrocytus

	* sparx/libpy/applications.py: project3d() --CTF now works - it had
	  used the old format for ctf

2012-05-03 16:18  john

	* libpyEM/qtgui/empmwidgets.py, programs/e2projectmanager.py:
	  bugfix for PM

2012-05-03 14:47  pawel

	* sparx/bin/sx3Dvariance.py: [no log message]

2012-05-03 13:53  john

	* libpyEM/qtgui/empmtabwidgets.py: two bugs for the price of one,

2012-05-03 13:48  john

	* libpyEM/qtgui/empmtabwidgets.py: bugfix

2012-05-03 13:35  john

	* libEM/pmconfig/spr.json, libEM/pmconfig/tomo.json,
	  libpyEM/EMAN2fsc.py, programs/e2symsearch.py: changed default
	  output dir for e2symsearch

2012-05-03 11:20  john

	* libpyEM/EMAN2.py, libpyEM/EMAN2fsc.py,
	  libpyEM/qtgui/empmwidgets.py, programs/e2plotFSC.py,
	  programs/e2refine.py, programs/e2refine_evenodd.py: refactored
	  code to remove function duplication

2012-05-03 10:42  john

	* libpyEM/EMAN2.py, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/emimage.py, libpyEM/qtgui/empmwidgets.py,
	  libpyEM/qtgui/emselector.py, programs/e2display.py,
	  programs/e2plotFSC.py, programs/e2refine.py,
	  programs/e2refine_evenodd.py: Added e2refine_even_odd to FSC
	  scheme

2012-05-03 10:31  astrocytus

	* sparx/bin/sx3Dvariance.py: reconstruction from averages based on
	  recons3d_4nn()

2012-05-03 08:10  stevel

	* examples/e2simmxptclqual.py, programs/e2display.py,
	  programs/e2fsc.py: Browser fixes

2012-05-02 17:25  pawel

	* sparx/bin/sx3Dvariance.py: added indeces to output 2D

2012-05-02 17:17  john

	* libpyEM/qtgui/: embrowser.py, emdataitem3d.py, emimage.py,
	  emscene3d.py, emselector.py: Added isosurface display upon
	  e2display and browser 3D widget loading

2012-05-02 17:11  pawel

	* sparx/bin/sx3Dvariance.py: [no log message]

2012-05-02 16:45  piotr

	* sparx/libpy/reconstruction.py: removing bug from recons3d_em

2012-05-02 14:51  astrocytus

	* sparx/bin/sx3Dvariance.py: [no log message]

2012-05-02 11:29  astrocytus

	* sparx/bin/sx3Dvariance.py: calculation of volumes from averages

2012-05-02 11:20  gtang

	* rt/pyem/test_processor.py: unit test update

2012-05-02 11:19  gtang

	* rt/pyem/test_processor.py: small fix

2012-05-02 11:01  gtang

	* programs/e2version.py: change popen4 to subprocess call

2012-05-02 10:57  gtang

	* programs/: e2version.py: small fix

2012-05-02 10:46  gtang

	* programs/e2version.py: change popen4 to subprocess call

2012-05-01 17:15  john

	* libEM/emdata_cuda.cpp: Documentation

2012-05-01 15:25  stevel

	* libpyEM/qtgui/emplot2d.py: Autoscaling fixes

2012-05-01 15:24  stevel

	* examples/e2simmxptclqual.py, libpyEM/qtgui/emplot2d.py,
	  programs/e2display.py: 2d plotting autoscaling massively improved

2012-05-01 14:13  john

	* libEM/aligner.cpp, libEM/aligner.h, libpyEM/qtgui/emscene3d.py,
	  libpyEM/qtgui/emselector.py: Added Jesus's suggestions for 3D
	  aligner and enhanced 3D widget map swcaling

2012-05-01 11:19  john

	* libpyEM/qtgui/: embrowser.py, emdataitem3d.py, emimage.py,
	  emscene3d.py: Implmented widget filling of the viewport upon SG
	  showEvent

2012-05-01 07:37  stevel

	* libEM/transform.cpp: Transform angle fix

2012-04-30 22:46  stevel

	* examples/e2simmxptclqual.py, libEM/transform.cpp: Some trivial
	  fixes to transform. May not really have fixed anything.

2012-04-30 15:23  pbaldwin

	* libEM/transform.cpp:
	  modified get_rotation calls for quaternionic types,	 PRB

2012-04-30 15:17  john

	* libpyEM/qtgui/emdataitem3d.py: fix for 3D tecture slices as well

2012-04-30 15:17  john

	* libpyEM/qtgui/emdataitem3d.py: opps I forgot to fix the 3D
	  textures as well for slices

2012-04-30 15:06  john

	* libpyEM/qtgui/empmwidgets.py: Added multi to FSC dirs

2012-04-30 15:05  john

	* libpyEM/qtgui/emdataitem3d.py: bug fix for slices

2012-04-30 14:19  john

	* libpyEM/qtgui/: embrowser.py, emdataitem3d.py, empmtabwidgets.py,
	  empmwidgets.py: bugfix for browser and slice viewer

2012-04-30 02:53  jgalaz

	* examples/e2spt_resolutionplot.py: Should be functional now.

2012-04-30 00:06  jgalaz

	* examples/e2spt_resolutionplot.py: Debugging.

2012-04-30 00:05  jgalaz

	* programs/e2classaverage3d.py: Bug fix regarding supplied
	  symmetry. If statement filter "if X AND Y not Z" does not work
	  the same as "If X not X AND Y not Z".

2012-04-29 23:31  jgalaz

	* examples/e2spt_resolutionplot.py: Program to align two 3D volumes
	  and obtain a resolution plot automatically.

2012-04-27 17:34  john

	* programs/e2filtertool.py: new 3d widget tweaks

2012-04-27 17:31  john

	* programs/e2filtertool.py: Replaced old 3d widget with new 3d
	  widget

2012-04-27 17:10  john

	* libpyEM/qtgui/embrowser.py: bugfix for 3d viewing in info pain

2012-04-27 14:30  stevel

	* libpyEM/qtgui/embrowser.py, programs/e2refinemulti.py: Minor
	  patches for release 2.05

2012-04-27 14:26  stevel

	* libpyEM/qtgui/embrowser.py: Minor tweak on timing.

2012-04-27 14:21  stevel

	* libpyEM/qtgui/embrowser.py: Individual image buttons in Info
	  panes.

2012-04-27 13:48  stevel

	* libpyEM/qtgui/embrowser.py, libpyEM/qtgui/emdataitem3d.py,
	  programs/e2filtertool.py, programs/e2refinemulti.py: More browser
	  improvements.

2012-04-27 11:49  piotr

	* sparx/: bin/sx3Dvariance.py, libpy/reconstruction.py: [no log
	  message]

2012-04-27 11:36  astrocytus

	* sparx/bin/sx3Dvariance.py: testing

2012-04-26 17:13  zyang

	* sparx/libpy/utilities.py: Trivial change to some formatting.

2012-04-26 14:08  john

	* libpyEM/qtgui/empmwidgets.py, programs/e2projectmanager.py: PM
	  documentation

2012-04-26 12:30  stevel

	* libpyEM/qtgui/embrowser.py: Double-click triggers default action

2012-04-26 11:11  stevel

	* libpyEM/qtgui/embrowser.py: Added refresh button. Improved arrows

2012-04-26 11:09  eman-vm

	* programs/e2version.py: new date stamp

2012-04-26 11:08  gtang

	* libEM/: aligner.cpp, emdata.cpp, processor.cpp,
	  sparx/util_sparx.cpp: fix warning message

2012-04-26 10:55  stevel

	* libpyEM/EMAN2.py, libpyEM/qtgui/embrowser.py, programs/e2fsc.py:
	  Browser improvements

2012-04-26 08:44  pawel

	* sparx/libpy/projection.py: [no log message]

2012-04-25 18:53  jgalaz

	* examples/e2sptsimulation.py: Program to correctly simulate
	  subtomograms (adding CTF does not seem to be working though).

2012-04-25 17:15  john

	* libpyEM/qtgui/empmwidgets.py, programs/e2projectmanager.py,
	  programs/e2refinemulti.py: Fixed multirefine PM

2012-04-25 12:50  astrocytus

	* sparx/bin/sx3Dvariance.py: testing

2012-04-25 12:50  astrocytus

	* sparx/libpy/utilities.py: group_proj_by_phitheta

2012-04-25 11:38  john

	* libEM/pmconfig/spr.json, libpyEM/qtgui/empmwidgets.py,
	  programs/e2projectmanager.py: Finshed fsc table

2012-04-24 19:41  jgalaz

	* programs/: e2wedge.py: [no log message]

2012-04-24 17:34  john

	* libEM/cmp.cpp, libEM/emdata.cpp, libEM/emdata.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/qtgui/emplot2d.py,
	  libpyEM/qtgui/empmwidgets.py, programs/e2RCTboxer.py,
	  programs/e2plotEulers.py, programs/e2plotFSC.py,
	  programs/e2projectmanager.py, programs/e2wedge.py: Bugfixes and
	  added a table for FSC info. Also added table base class for the
	  PM

2012-04-24 16:13  jgalaz

	* libEM/emdata.cpp: Change in parameter names mean_wedge_amp and
	  sigma_wedge_amp to spt_wedge_mean and spt_wedge_sigma

2012-04-24 16:11  jgalaz

	* libEM/cmp.cpp: Change in name of header parameters mean_wedge_amp
	  and sigma_wedge_amp to spt_wedge_mean and spt_wedge_sigma.

2012-04-24 16:04  astrocytus

	* sparx/bin/sx3Dvariance.py: testing

2012-04-24 14:30  astrocytus

	* sparx/: bin/sx3Dvariance.py, libpy/utilities.py: [no log message]

2012-04-24 12:10  astrocytus

	* sparx/bin/: sx3Dvariance.py: [no log message]

2012-04-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-24 12:01  astrocytus

	* sparx/bin/sx3Dvariance.py: [no log message]

2012-04-24 11:42  astrocytus

	* sparx/bin/sx3Dvariance.py: working version

2012-04-24 11:38  astrocytus

	* sparx/bin/sx3Dvariance.py: working version

2012-04-24 11:15  pawel

	* sparx/libpy/statistics.py: [no log message]

2012-04-24 07:15  stevel

	* programs/e2fsc.py: Warning messages so people don't misinterpret
	  the intent.

2012-04-23 18:31  astrocytus

	* sparx/bin/sx3Dvariance.py: [no log message]

2012-04-23 18:15  astrocytus

	* sparx/bin/sx3Dvariance.py: [no log message]

2012-04-23 16:06  astrocytus

	* sparx/libpy/utilities.py: group_proj_by_phitheta() returns a list
	  of lists of projections indexes and Eulerian angles assigned to
	  these groups

2012-04-23 14:58  astrocytus

	* sparx/libpy/utilities.py: adding a function
	  group_proj_by_phitheta

2012-04-23 14:25  astrocytus

	* sparx/bin/sx3Dvariance.py: 04/23/12 embedding Yangs program

2012-04-23 14:12  stevel

	* programs/e2fsc.py: e2fsc seems to be working pretty well. No idea
	  yet if the results are meaningful though

2012-04-23 13:39  piotr

	* sparx/bin/sx3Dvariance.py: sx3Dvariance - temp version

2012-04-23 12:59  stevel

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/processor.cpp,
	  programs/e2fsc.py: e2fsc.py now working. Renamed translation
	  processor from math to xform

2012-04-23 12:46  gtang

	* libEM/cmp.cpp: Fix for Visual C++ 2010 compilation. The max is
	  defined as macro in windows.h.

2012-04-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-21 14:17  stevel

	* programs/: e2fsc.py, e2refinemulti.py: trivial

2012-04-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-20 14:42  eman-vm

	* programs/e2version.py: new date stamp

2012-04-20 14:22  john

	* libpyEM/qtgui/empmtabwidgets.py, programs/e2RCTboxer.py: Bugfixes

2012-04-20 13:04  stevel

	* programs/e2refinemulti.py: more sym fixes

2012-04-20 12:45  john

	* libEM/sparx/processor_sparx.h, libpyEM/qtgui/emsprworkflow.py:
	  Bugfixes for workflow and documentation fix for resolv

2012-04-20 12:27  stevel

	* libpyEM/qtgui/embrowser.py, programs/e2refinemulti.py:
	  multirefine multi-sym fix. embrowser sorting selection fix

2012-04-20 10:30  piotr

	* sparx/: bin/sx3Dvariance.py, libpy/reconstruction.py: recons3d_em
	  and recons3d_em_MPI - remove projections_indexes parameter

2012-04-20 10:16  piotr

	* sparx/bin/sx3Dvariance.py: sx3Dvariance - remove [begin end step]
	  parameters

2012-04-20 08:18  piotr

	* sparx/: bin/sx3Dvariance.py, libpy/reconstruction.py:
	  sx3Dvariance - beta - works only with --var parameter

2012-04-19 19:02  fjia

	* libEM/sparx/util_sparx.cpp: clean up code for
	  multiref_polar_ali_helical_90

2012-04-19 16:08  john

	* programs/e2import.py: bugfixO

2012-04-19 15:00  fjia

	* libEM/sparx/util_sparx.cpp: replace Crosrng_psi_0_180 with
	  Crosrng_psi, clean up multiref_polar_ali_helical

2012-04-19 14:58  fjia

	* libEM/sparx/util_sparx.h: remove Crosrng_psi_0_180, add
	  Crosrng_psi

2012-04-19 14:28  piotr

	* sparx/: bin/sx3Dvariance.py, libpy/reconstruction.py: Program for
	  3D variance reconstruction (version alpha)

2012-04-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-19 11:58  john

	* programs/: e2buildstacks.py, e2import.py: CHuan's bugfixes. Added
	  more support for IMAGE style files

2012-04-19 10:32  john

	* libpyEM/qtgui/embrowser.py, libpyEM/qtgui/emplot2d.py,
	  libpyEM/qtgui/empmwidgets.py, programs/e2plotEulers.py,
	  programs/e2refine.py: Bugfixes for steve

2012-04-19 08:18  piotr

	* sparx/libpy/reconstruction.py: reconstruction algorithm based on
	  EM - MPI version

2012-04-19 07:29  piotr

	* sparx/libpy/reconstruction.py: recons_em_MPI

2012-04-18 17:06  gtang

	* programs/e2proc2d.py: for --average option in e2proc2d.py, write
	  only the average to output file, i.e., skip writing the input
	  into output stack

2012-04-18 14:09  piotr

	* sparx/libpy/reconstruction.py: New version of recons3d_em_MPI
	  (MPI version of EM reconstruction)

2012-04-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-18 11:56  john

	* libpyEM/qtgui/empmtabwidgets.py, programs/e2RCTboxer.py: bugfixes
	  for derived browsers

2012-04-18 09:20  stevel

	* libpyEM/qtgui/emplot2d.py, programs/e2ctf.py,
	  programs/e2refine.py: glut, more work on 2-d plot capabilites

2012-04-17 18:19  fjia

	* programs/e2boxer.py: add micrograph name to screen print out of
	  estimated defocus (gauss mode)

2012-04-17 14:45  pawel

	* sparx/libpy/reconstruction.py: [no log message]

2012-04-17 14:27  piotr

	* .pydevproject, sparx/libpy/reconstruction.py: recons3d_em -
	  second version

2012-04-17 14:02  pawel

	* sparx/: bin/sxproject3d.py, libpy/applications.py: added real
	  space projector option to sxproject3d

2012-04-17 13:03  john

	* libpyEM/EMAN2.py, libpyEM/qtgui/emboxerbase.py,
	  libpyEM/qtgui/empmtabwidgets.py, libpyEM/qtgui/emrctboxergui.py,
	  programs/e2RCTboxer.py, programs/e2boxer.py,
	  programs/e2buildstacks.py, programs/e2ctf.py,
	  programs/e2eotest.py, programs/e2evalimage.py,
	  programs/e2import.py, programs/e2plotEulers.py,
	  programs/e2plotFSC.py, programs/e2rawdata.py,
	  programs/e2refinefromfrealign.py, programs/e2refinetofrealign.py,
	  programs/e2resolution.py, programs/e2tomoboxer.py,
	  programs/e2tomoresolution.py, programs/e2wedge.py: Reverted back
	  to using fullpaths for micreographs in the database

2012-04-17 12:48  pawel

	* sparx/libpy/reconstruction.py: [no log message]

2012-04-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-17 11:53  pawel

	* sparx/libpy/statistics.py: [no log message]

2012-04-17 11:45  piotr

	* sparx/libpy/reconstruction.py: Reconstruction algorithm basing on
	  the Expectation Maximization method

2012-04-16 19:08  fjia

	* programs/e2boxer.py: fix pixel related bug for batch ctf
	  estimation in Gauss mode

2012-04-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-13 14:40  stevel

	* libpyEM/qtgui/emplot2d.py: Drag and drop working between plots
	  now.

2012-04-13 13:49  john

	* programs/e2tomoboxer.py: Bugfixs for helixboxing using yshort

2012-04-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-13 10:09  john

	* libEM/aligner.cpp, libpyEM/qtgui/emboxerbase.py,
	  programs/e2boxer.py, programs/e2rawdata.py, programs/e2rct.py,
	  programs/e2tomoboxer.py: bugfixes for e2boxer

2012-04-13 03:47  jgalaz

	* examples/e2sptcoeffplot.py: Modifications

2012-04-12 18:30  john

	* libEM/cuda/cuda_util.cu, programs/e2tomoboxer.py: bugfix for
	  binning while helixboxing

2012-04-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-12 10:56  gtang

	* programs/e2proc3d.py: add --unstacking option to convert a stack
	  of 3D image to a series of single 3D images.

2012-04-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-11 08:15  pawel

	* libEM/projector.cpp: minor inconsequential mistake fixed

2012-04-09 17:47  john

	* programs/e2resolution.py: GUI fix for e2resolution.py

2012-04-09 17:04  john

	* libEM/: cmp.cpp, cmp.h: updates

2012-04-09 17:00  john

	* libEM/cmp.cpp, libEM/pmconfig/RCTboxer.json,
	  libEM/pmconfig/RCTboxergo.json, libEM/pmconfig/boxer.json,
	  libEM/pmconfig/boxergo.json, libEM/pmconfig/breaksym.json,
	  libEM/pmconfig/buildstacks.json, libEM/pmconfig/coordimport.json,
	  libEM/pmconfig/ctftuning.json, libEM/pmconfig/evalrawdata.json,
	  libEM/pmconfig/particleimport.json, libEM/pmconfig/raw,
	  libEM/pmconfig/rawdata.json, libEM/pmconfig/rawdataimport.json,
	  libEM/pmconfig/symaligner.json, libEM/pmconfig/tomo.json,
	  libEM/pmconfig/tomores.json, programs/e2eotest.py,
	  programs/e2tiltvalidate.py, programs/e2wedge.py: Added wizards,
	  and enhanced fsc.tomo to allow resolution domains

2012-04-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-06 16:33  jgalaz

	* examples/e2sptcoeffplot.py: Program to plot the cross correlation
	  scores of sub-volumes that have been aligned with
	  e2classaverage3d and contain the "spt_score" or "spt_coefficient"
	  parameters on the header.  The script can also divide the data
	  into two sets based on a correlation value used as the threshold.

2012-04-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-06 11:26  stevel

	* libpyEM/qtgui/emplot2d.py, programs/e2evalimage.py: Working on
	  drag/drop in plot. Not done, but shouldn't break anything.

2012-04-05 17:30  zyang

	* sparx/: bin/sxstability.py, libpy/applications.py: Two trivial
	  changes.

2012-04-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-04 12:04  john

	* libpyEM/qtgui/embrowser.py: cleanup

2012-04-04 12:01  john

	* libEM/pmconfig/tomo.json, libpyEM/qtgui/embrowser.py,
	  programs/e2classaverage3d.py, programs/e2montecarlorecon.py,
	  programs/e2rct.py, programs/e2symsearch.py,
	  programs/e2tiltvalidate.py: Fixed browser circular array

2012-04-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-04 08:36  stevel

	* libpyEM/qtgui/empmtabwidgets.py: trivial

2012-04-03 17:43  zyang

	* sparx/bin/sxstability.py: Fix some bugs

2012-04-03 17:03  john

	* libEM/pmconfig/classaverage3d.json, libEM/pmconfig/spr.json,
	  libEM/pmconfig/tomo.json, libEM/pmconfig/tomoboxer.json,
	  libEM/pmconfig/tomoimport.json, libEM/pmconfig/wedge.json,
	  libpyEM/qtgui/embrowser.py, libpyEM/qtgui/empmtabwidgets.py,
	  programs/e2rawdata.py, programs/e2tiltvalidate.py,
	  programs/e2wedge.py: Added some wizards, fixed the browser, and
	  updated micrograph import as per Steve's suggestions

2012-04-03 17:02  zyang

	* sparx/bin/sxstability.py: Add an option for sxstability.py

2012-04-03 14:05  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, sparx/libpy/utilities.py: Change
	  assign_projangles() into C++ code. Speedup > 100 times!

2012-04-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-04-02 09:47  zyang

	* sparx/libpy/filter.py: Trivial change.

2012-04-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-30 17:01  john

	* libEM/pmconfig/: ctfautofit.json, ctfgo.json, ctfsf.json,
	  spr.json: added CTF wizards

2012-03-30 15:47  john

	* libEM/pmconfig/ctfautofit.json, libEM/pmconfig/spr.json,
	  libpyEM/qtgui/embrowser.py: enhaced the bowser and added wizard
	  info

2012-03-30 13:14  fjia

	* sparx/libpy/alignment.py: small change in proj_ali_helical_local

2012-03-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-29 16:56  john

	* libEM/pmconfig/montecarlo.json, libEM/pmconfig/ploteulers.json,
	  libEM/pmconfig/plotfsc.json,
	  libEM/pmconfig/plottiltvalidation.json, libEM/pmconfig/rct.json,
	  libEM/pmconfig/runtiltvalidation.json, libEM/pmconfig/spr.json,
	  libEM/pmconfig/symsearch.json, libpyEM/qtgui/empmtabwidgets.py,
	  libpyEM/qtgui/empmwidgets.py, programs/e2ctf.py,
	  programs/e2projectmanager.py, programs/e2refine.py,
	  programs/e2tiltvalidate.py: added wizard info

2012-03-29 16:30  fjia

	* sparx/libpy/applications.py: [no log message]

2012-03-29 16:21  fjia

	* sparx/libpy/alignment.py: [no log message]

2012-03-29 16:15  fjia

	* sparx/libpy/applications.py: change comparison order in ihrsr_mpi

2012-03-29 16:04  pawel

	* sparx/libpy/applications.py: [no log message]

2012-03-29 15:48  fjia

	* sparx/libpy/utilities.py: changes to even_angles for helical
	  symmetry case

2012-03-29 15:46  fjia

	* sparx/libpy/applications.py: changes to unique range code in
	  ihrsr_MPI

2012-03-29 15:20  fjia

	* sparx/libpy/applications.py: changes to unique range code in
	  ihrsr_MPI

2012-03-29 14:33  fjia

	* sparx/libpy/applications.py: change call to
	  proj_ali_helical_local, add changes for y search range
	  restriction

2012-03-29 14:32  fjia

	* sparx/libpy/alignment.py: add changes to proj_ali_helical_local

2012-03-29 14:28  fjia

	* sparx/bin/sxihrsr.py: add y search range restriction

2012-03-29 14:27  fjia

	* libpyEM/libpyUtils2.cpp: change number of arguments for
	  multiref_polar_ali_helical_local

2012-03-29 14:26  fjia

	* libEM/sparx/util_sparx.cpp: add changes for
	  multiref_polar_ali_helical_local

2012-03-29 14:26  fjia

	* libEM/sparx/util_sparx.h: change multiref_polar_ali_helical_local

2012-03-29 13:47  pawel

	* sparx/libpy/: reconstruction.py, utilities.py: [no log message]

2012-03-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-27 11:04  gtang

	* programs/e2proc2d.py: fix the broken --interlv option for
	  e2proc2d.py

2012-03-27 10:24  john

	* programs/: e2RCTboxer.py, e2ctf.py, e2projectmanager.py: bugfixes
	  to stop manditory computesf in e2ctf

2012-03-27 00:54  irees

	* programs/e2pathwalker.py: TODO: Update all EMAN2 programs using
	  argparse to have the correct %prog formatting.

2012-03-27 00:46  irees

	* programs/e2seq2pdb.py: Added e2seq2pdb.py.

2012-03-27 00:43  irees

	* programs/e2pathwalker.py: Minor fixes to e2pathwalker.py Added
	  better error messages if Concorde/LKH are not installed.  Added
	  links to wiki pages.	Manuscript text had older "--fixed" option
	  instead of "--edgefile." Added an alias for --fixed to
	  --edgefile.  Added warning that "iterations" isn't working at the
	  moment.

2012-03-26 16:50  zyang

	* sparx/libpy/: applications.py, alignment.py: Trivial change.

2012-03-26 14:17  gtang

	* libEM/mrcio.cpp: Do not write CTF information into mrc.

2012-03-26 13:50  zyang

	* sparx/libpy/applications.py: Many trivial changes. (I cannot help
	  it.)

2012-03-26 13:24  pawel

	* sparx/bin/sxresample.py: import corrected

2012-03-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-26 09:37  john

	* libEM/aligner.cpp, programs/e2classaverage.py: Bugfix for
	  alingers, previouslyt caused segfault

2012-03-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-24 14:44  fjia

	* libpyEM/libpyUtils2.cpp: update argument list for Crosrng_sm_psi

2012-03-24 14:07  fjia

	* libEM/sparx/util_sparx.cpp: modify crosrng_sm_psi

2012-03-24 14:06  fjia

	* libEM/sparx/util_sparx.h: update signature for modified
	  crosrng_sm_psi

2012-03-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-23 14:17  zyang

	* sparx/libpy/applications.py: Change the way how centering of the
	  volume is conducted in ali3d (ali3d_MPI) such that: (1) For c_n
	  (n>1) symmetry, only perform centering in z-axis (2) For d_n
	  symmetry, no centering is performed.

2012-03-23 14:14  zyang

	* sparx/libpy/fundamentals.py: Trivial change.

2012-03-23 13:58  stevel

	* examples/: e2ptclzvssim.py, e2simmxptclqual.py, e2simmxsort.py:
	  More work on bad particle identification

2012-03-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-23 12:00  astrocytus

	* sparx/libpy/projection.py: there was a small bug

2012-03-23 10:29  gtang

	* libEM/glutil.cpp: fix for windows compilation

2012-03-22 18:09  astrocytus

	* sparx/libpy/applications.py: in function project3d() as a default
	  for stack I set None

2012-03-22 17:05  astrocytus

	* sparx/libpy/projection.py: I modified the prg() so it works with
	  cubic and rectangular volumes

2012-03-22 13:01  pawel

	* sparx/bin/sxresample.py: rationalized resampling code

2012-03-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-22 11:45  john

	* libEM/: aligner.cpp, aligner.h: mem leak bugfixes

2012-03-21 18:57  stevel

	* libpyEM/: EMAN2_cppwrap.py, qtgui/emimagemx.py,
	  qtgui/emplot2d.py: Minor fix to cppwrap

2012-03-21 14:35  astrocytus

	* sparx/libpy/utilities.py: new version of read_spider_doc

2012-03-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-20 16:49  john

	* examples/mergeproject.py, libEM/aligner.cpp, libEM/aligner.h,
	  programs/e2buildstacks.py: Added scaling aligners

2012-03-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-20 00:31  jgalaz

	* examples/e2spt_stackrandomize.hdf: Takes an .hdf stack and
	  scrambles de images in it into random positions.

2012-03-19 16:31  gtang

	* libpyEM/: libpyTypeConverter2.cpp, libpyUtils2.cpp,
	  typeconverter.cpp, typeconverter.h: for Python3K compilation

2012-03-19 15:06  john

	* libpyEM/qtgui/emscene3d.py, programs/e2classaverage3d.py,
	  programs/e2classaveragebysym.py: Bugfix for sym breaking and
	  update to 3D widget

2012-03-19 14:57  john

	* libEM/aligner.cpp, libEM/aligner.h, libEM/emdata_metadata.h,
	  libEM/processor.h, libpyEM/qtgui/emdataitem3d.py,
	  libpyEM/qtgui/emitem3d.py, libpyEM/qtgui/emrctstrategy.py,
	  libpyEM/qtgui/emshapeitem3d.py, programs/e2RCTboxer.py: Added
	  scale aligner and adjusted 3D widget geometry

2012-03-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-15 18:04  john

	* libEM/pmconfig/montecarlo.json, libEM/pmconfig/ploteulers.json,
	  libEM/pmconfig/plotfsc.json, libEM/pmconfig/rct.json,
	  libEM/pmconfig/runtiltvalidation.json, libEM/pmconfig/spr.json,
	  libEM/pmconfig/symsearch.json, libEM/pmconfig/tomo.json,
	  programs/e2montecarlorecon.py: Added wizard files

2012-03-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-14 17:21  john

	* libEM/pmconfig/icons.json, libEM/pmconfig/spr.json,
	  libpyEM/qtgui/empmtabwidgets.py, programs/e2classaveragebysym.py,
	  programs/e2ctf.py, programs/e2plotEulers.py,
	  programs/e2projectmanager.py, programs/e2tiltvalidate.py: PM
	  updates, added plot Eulers

2012-03-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-13 14:18  jgalaz

	* programs/e2tomoallvsall.py: [no log message]

2012-03-13 13:38  fjia

	* sparx/libpy/applications.py: comment out body of ihrsr after mpi
	  version(s) of ihrsr is called

2012-03-13 13:26  fjia

	* sparx/bin/sxihrsr.py: block non-mpi call to IHRSR

2012-03-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-13 09:59  jgalaz

	* programs/e2tomoallvsall.py: Bug fix concerning naming of new
	  averages.

2012-03-13 04:35  jgalaz

	* examples/e2tomosim.py: [no log message]

2012-03-13 04:17  jgalaz

	* examples/e2tomosim.py: Continued development. Added --orthogonal
	  option.

2012-03-13 02:25  jgalaz

	* programs/e2classaverage3d.py: [no log message]

2012-03-13 01:50  jgalaz

	* programs/e2classaverage3d.py: Bug fixed concerning output writing
	  when --groups is urned on

2012-03-13 01:49  jgalaz

	* programs/e2tomoboxer.py: Bug fixed concerning boxsize for command
	  line boxing.

2012-03-12 18:02  jgalaz

	* programs/e2classaverage3d.py: Bug fix. It doesn't make sense to
	  define groups > 1 if there's only one particle in the input
	  stack.  Implemented a conditional statement that checks for this
	  to prevent crashes.

2012-03-12 15:46  john

	* libpyEM/qtgui/emplot2d.py, programs/e2plotEulers.py,
	  programs/e2tiltvalidate.py: Added Euler plotting

2012-03-12 15:16  john

	* programs/e2classaverage3d.py: Bugfixes. More bugs than my apt....

2012-03-12 14:12  john

	* programs/e2classaverage3d.py: bugfixes

2012-03-12 12:16  gtang

	* libpyEM/libpyTransform2.cpp: pass equality operator to c++

2012-03-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-12 09:50  john

	* libEM/glutil.cpp, libEM/glutil.h,
	  libEM/pmconfig/plottiltvalidation.json,
	  libpyEM/libpyGLUtils2.cpp, libpyEM/qtgui/valslider.py: Bugfix for
	  3D widget

2012-03-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-10 16:42  jgalaz

	* examples/e2spt_variance.py: Compute variance for stack of SPT
	  particles.

2012-03-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-09 23:42  jgalaz

	* programs/e2tomoallvsall.py:
	  UGH. Bug fixes.

2012-03-09 22:49  jgalaz

	* programs/e2tomoallvsall.py: [no log message]

2012-03-09 21:42  jgalaz

	* programs/e2tomoallvsall.py: [no log message]

2012-03-09 20:22  jgalaz

	* programs/e2tomoallvsall.py:
	  The header parameter 'spt_ptcl_indxs' which stores the indxs for
	  ptcls that went into an average in each iteration is now sorted.
	  Cleared some redundancies or commented out text.  Included a
	  function that puts mutually exclusive classes with a minimum
	  number of particles in it into a new subdirectory. Users define
	  this minimum number through --exclusive_class_min

2012-03-09 15:53  john

	* libEM/pmconfig/plottiltvalidation.json, libEM/pmconfig/spr.json,
	  programs/e2tiltvalidate.py: Added wizard for tiltvalidation
	  plotting

2012-03-09 15:18  gtang

	* programs/e2proc2d.py: [no log message]

2012-03-09 15:04  john

	* libEM/pmconfig/spr.json, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/emplot2d.py, libpyEM/qtgui/empmtabwidgets.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2buildstacks.py,
	  programs/e2tiltvalidate.py: bugfix for buildstacks and added
	  color by Z for tilt validation

2012-03-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-08 16:35  john

	* programs/e2classaverage3d.py: Jesus's bugfix

2012-03-08 16:07  john

	* libEM/pmconfig/spr.json, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/empmtabwidgets.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2projectmanager.py: Bugfixes for PM and added tables

2012-03-08 16:01  zyang

	* libEM/cmp.cpp: Remove the unnecessary comments.

2012-03-08 15:29  zyang

	* libEM/cmp.cpp: Fix the way of calculating the dot product of two
	  3-D complex images

2012-03-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-08 09:45  john

	* libpyEM/qtgui/empmtabwidgets.py, programs/e2tiltvalidate.py:
	  Reversed somebody breaking tiltvalidate

2012-03-08 08:41  stevel

	* examples/e2ptclzvssim.py, programs/e2bdb.py,
	  programs/e2refine_evenodd.py: e2refine_evenodd technically done.
	  Needs testing

2012-03-07 15:25  stevel

	* examples/e2ptclzvssim.py, libEM/processor.cpp,
	  libEM/sparx/processor_sparx.h, programs/e2bdb.py,
	  programs/e2refine_evenodd.py, programs/e2resolution.py: More
	  e2ptclzvssim improvements. incomplete e2refine_evenodd.
	  filter.lowpass.randomphase works in 3-D now.

2012-03-07 12:22  john

	* programs/e2tomoboxer.py: enabled reverse contrast GUI

2012-03-07 12:15  gtang

	* libEM/emdata_io.cpp: fix for visual c++ compilation

2012-03-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-07 11:19  gtang

	* libEM/emdata_transform.cpp: fix for big size image

2012-03-07 10:32  gtang

	* libEM/mrcio.cpp: fix for big size image reading

2012-03-07 09:35  john

	* libEM/: emdata_io.cpp, emdata_io.h: added steve's comments

2012-03-07 09:09  john

	* programs/e2projectmanager.py: Bugfixes for the wizard

2012-03-06 16:56  john

	* libEM/emdata_io.cpp, libEM/emdata_io.h, libpyEM/libpyEMData2.cpp,
	  programs/e2tomoboxer.py: bining enhancments

2012-03-06 16:37  john

	* libEM/emdata_io.cpp, libEM/emdata_io.h, libpyEM/libpyEMData2.cpp,
	  programs/e2tomoboxer.py: added a C side binning command and
	  intergrated it into e2tomoboxer.py

2012-03-06 12:39  john

	* libpyEM/qtgui/emrctstrategy.py, programs/e2RCTboxer.py,
	  programs/e2classaveragebysym.py: added writing of tiltangle/axis
	  to e2boxercache. Also enabled metadata writing when using
	  generate output

2012-03-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-06 09:47  gtang

	* libEM/: omapio.cpp, omapio.h: fix the Omap reading routine

2012-03-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-03 00:28  jgalaz

	* programs/e2classaverage3d.py:
	  Several bugs came up under different running conditions because
	  of --nocenterofmass relocation to the correct place. Presumably
	  fixed all now.

2012-03-02 17:49  jgalaz

	* programs/e2tomoallvsall.py:
	  Added --lowpass and --highpass options so that e2tomoallvsall can
	  be done propperly on phaseplate data.  Also fixed a bug regarding
	  output files when --path is not defined but defaulted.

2012-03-02 16:10  jgalaz

	* programs/e2classaverage3d.py:
	  --nocenterofmass was misplaced to be in the postprocess function.
	  Applying centerofmass should NOT be dependent on postprocessing.
	  Bug fixed.

2012-03-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-03-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-29 17:01  stevel

	* programs/e2classaverage.py: Accidentally committed a bug to
	  classaverage yesterday

2012-02-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-28 09:51  stevel

	* programs/: e2classaverage.py, e2make3d.py: Fixes for apix issue

2012-02-27 13:43  stevel

	* examples/e2ptclzvssim.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2tiltvalidate.py: Improvements to ptclzvssim.py & fixes
	  for tiltvalidate parallelism

2012-02-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-25 22:57  stevel

	* examples/e2ptclzvssim.py, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/emplot2d.py, libpyEM/qtgui/valslider.py: New
	  capabilities for 2D plotting.

2012-02-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-24 10:31  zyang

	* sparx/libpy/applications.py: Trivial change.

2012-02-24 10:29  zyang

	* sparx/libpy/applications.py: Slightly change the way of how ISAC
	  program keep tab of the index to make it more robust, also add an
	  error handling.

2012-02-24 10:27  zyang

	* sparx/libpy/pixel_error.py: Just clean up some printouts.

2012-02-23 15:52  fjia

	* sparx/bin/sxprocess.py: put in option for --order

2012-02-23 14:00  scmurray

	* programs/e2refine.py: Fixed some spelling errors with the help
	  text and updated some of the help text to be more user friendly

2012-02-23 13:39  jgalaz

	* programs/e2classaverage3d.py: Fixed output writting bug.  Added
	  lowpass and highpass options/parameters since you need BOTH for
	  phaseplate data and PREPROCESS does not suffice (plus
	  "preprocess" is a vague name; users are better off with parameter
	  names that evoque a specific process).

2012-02-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-22 14:39  gtang

	* programs/e2proc3d.py: suppress print info when verbose=0

2012-02-22 12:34  scmurray

	* programs/: e2refinefromfrealign.py, e2refinetofrealign.py: Adding
	  icosahedral symmetry support.

2012-02-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-22 11:49  scmurray

	* programs/: e2refinefromfrealign.py, e2refinetofrealign.py: Fixed
	  an issue where e2proc2d was being used instead of e2proc3d

2012-02-21 12:49  scmurray

	* programs/: e2refinefromfrealign.py, e2refinetofrealign.py: Both
	  files were changed to fix an issue where the icosahedral symmetry
	  was different between EMAN2 and MRC formats. Now the symmetry is
	  changed to MRC format going into FreAlign and changed back to
	  EMAN2 coming out.

2012-02-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-21 06:26  jgalaz

	* examples/e2tomosim.py: [no log message]

2012-02-21 06:06  jgalaz

	* examples/e2tomosim.py: Program pretty much finished (re-written).
	  Minor issues/options to add.

2012-02-21 03:08  jgalaz

	* programs/e2classaverage3d.py: [no log message]

2012-02-21 01:29  jgalaz

	* programs/e2classaverage3d.py: [no log message]

2012-02-21 01:27  jgalaz

	* programs/e2classaverage3d.py: Fixed "randomizedwedge" typo
	  reported by Rossi.

2012-02-20 13:40  john

	* programs/e2classaveragebysym.py: bugfix

2012-02-20 13:13  john

	* programs/e2classaveragebysym.py: bugfix

2012-02-20 13:02  john

	* programs/e2classaveragebysym.py: Added Wei's ideas

2012-02-20 12:25  john

	* programs/: e2classaveragebysym.py, e2symsearch.py: Bug fixes for
	  sym align by xform

2012-02-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-19 11:43  stevel

	* libpyEM/qtgui/emplot2d.py, libpyEM/qtgui/valslider.py,
	  programs/e2evalimage.py: Improvements to evalimage 45 mode and
	  other general 2d plot improvements

2012-02-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-17 16:42  john

	* programs/e2classaveragebysym.py: Bug fixes

2012-02-17 16:30  john

	* libEM/pmconfig/tomo.json, programs/e2classaveragebysym.py: Added
	  classaver3d using symmetry

2012-02-17 15:51  john

	* libpyEM/qtgui/emplot2d.py, libpyEM/qtgui/empmwidgets.py,
	  programs/e2projectmanager.py: PM bug fixes

2012-02-17 13:53  stevel

	* programs/e2evalimage.py: Directional evalimage

2012-02-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-17 10:39  john

	* libEM/pmconfig/runtiltvalidation.json,
	  libpyEM/qtgui/empmwidgets.py, programs/e2projectmanager.py: Added
	  Wizard

2012-02-17 10:28  stevel

	* examples/e2ptclzvssim.py, libEM/emdata.cpp, libEM/emdata.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/qtgui/emplot2d.py,
	  programs/e2evalimage.py: Fixed calc_radial_dist with rotational
	  divisions. Working on new capabilities for e2evalimage and
	  e2ptclzvssim

2012-02-16 17:28  john

	* libEM/glutil.cpp, libEM/pmconfig/runtiltvalidation.json,
	  libEM/pmconfig/spr.json, libpyEM/qtgui/empmwidgets.py,
	  programs/e2projectmanager.py: Added Some Wizard structure

2012-02-16 14:40  john

	* libEM/pmconfig/tomo.json, programs/e2tomoboxer.py: Autoset apix

2012-02-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-16 10:48  gtang

	* libEM/glutil.cpp: John's fix for glIsBuffer failure on Ubuntu 11
	  and MacOS Lion.

2012-02-15 17:29  john

	* libEM/cmp.cpp, libpyEM/qtgui/emscene3d.py,
	  programs/e2symsearch.py: Fixed axis bug in SG, and added
	  documentation

2012-02-15 12:50  scmurray

	* libpyEM/qtgui/: empmwidgets.py, pmwidgets.py: We (John and Steve
	  M) fixed automasked widget, previous was JUNK!

2012-02-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-14 16:41  gtang

	* libEM/: glutil.cpp, marchingcubes.cpp, marchingcubes.h: fix the
	  opengl linking error on visual c++.

2012-02-14 13:47  stevel

	* libEM/processor.cpp: More tweaking to phase randomizer

2012-02-14 13:06  stevel

	* libEM/processor.cpp, mpi_eman/pbs.example: Fix phase randomizer
	  parameters

2012-02-14 12:56  stevel

	* libEM/processor.cpp: Fix for randomphase processor

2012-02-14 12:08  stevel

	* programs/e2classaverage.py: Fix an accidental debugging change.

2012-02-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-14 10:09  john

	* programs/e2projectmanager.py: Added SL suggestions

2012-02-13 15:37  pawel

	* sparx/libpy/statistics.py: mpi stuff corrected in kmenas_groups

2012-02-13 13:51  john

	* programs/e2classaverage3d.py: CVS conflict fix

2012-02-13 13:01  gtang

	* libEM/marchingcubes.cpp: fix for Visual C++ compilation

2012-02-13 12:35  gtang

	* libEM/hdfio2.cpp: fix for Visual C++ compilation

2012-02-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-13 10:26  zyang

	* sparx/libpy/applications.py: Trivial change.

2012-02-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-10 23:21  stevel

	* examples/filespeedtest.py, programs/e2classaverage.py: New test
	  program

2012-02-10 17:48  john

	* libpyEM/qtgui/embrowser.py, libpyEM/qtgui/emplot2d.py,
	  libpyEM/qtgui/empmtabwidgets.py, programs/e2RCTboxer.py,
	  programs/e2boxer.py: Added Steve GUI suggestion #2

2012-02-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-10 10:28  john

	* libpyEM/qtgui/embrowser.py: Row numbering bug fix

2012-02-10 09:23  zyang

	* sparx/libpy/applications.py: Fix a strange ASCII-coding issue.

2012-02-09 18:13  jgalaz

	* examples/e2tomosim.py: Continued development/testing (committing
	  just to "backup" changes).

2012-02-09 17:29  john

	* libEM/cmp.cpp, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/empmtabwidgets.py: Bugfix for rows in browser

2012-02-09 15:08  jgalaz

	* programs/e2classaverage3d.py: Bug fixed, concerning missing wedge
	  randomization.

2012-02-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-09 11:02  zyang

	* sparx/libpy/applications.py: Just add a simple note.

2012-02-08 19:59  stevel

	* libEM/processor.cpp, libpyEM/qtgui/emplot2d.py: Fix breakage
	  without annoying syntax. 2-D plotting should be working
	  more-or-less properly with new capabilities now.

2012-02-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-08 10:34  zyang

	* libEM/processor.cpp: Fix a small bug.

2012-02-08 10:04  john

	* programs/e2projectmanager.py: Added dump terminal option in menu

2012-02-07 20:45  stevel

	* libEM/: processor.cpp, processor.h: other part of changes just
	  checked in. Still not complete, but hopefully not broken.

2012-02-07 20:44  stevel

	* examples/e2ptclzvssim.py, examples/transalignavg2.py,
	  libEM/averager.cpp, libpyEM/qtgui/emplot2d.py,
	  programs/e2filtertool.py: Incomplete update for 2-D plotting.
	  Will complete soon. New filter.

2012-02-07 13:22  john

	* libEM/cmp.cpp: Reomve debugging code

2012-02-07 13:20  john

	* libEM/: cmp.cpp, cuda/cuda_cmp.cu: CUDA bugfix

2012-02-07 12:59  john

	* libEM/: cmp.cpp, emdata.cpp, cuda/cuda_cmp.cu: CUDA bugfix

2012-02-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-07 09:18  john

	* libEM/cmp.cpp, libpyEM/qtgui/emimageutil.py,
	  libpyEM/qtgui/empmwidgets.py: Bug fixes for Jesus

2012-02-06 21:35  jgalaz

	* examples/e2tomosim.py: Extremely outdated. Under extensive
	  re-writting.

2012-02-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-03 13:33  john

	* libEM/cuda/cuda_cmp.cu, programs/e2classaverage3d.py: fsc.tomo
	  stuff

2012-02-03 13:20  john

	* libEM/cmp.cpp, libEM/cuda/cuda_cmp.cu, libEM/cuda/cuda_cmp.h,
	  libpyEM/qtgui/empmwidgets.py, programs/e2classaverage3d.py: CUDA
	  enabled fsc_tomo aligner

2012-02-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-02 15:21  john

	* libEM/: cmp.cpp, cmp.h: Finished adding 'NEW' way of accounting
	  for the missing wedge

2012-02-02 13:31  john

	* libEM/cmp.cpp: Added fsc.tomo cmp

2012-02-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-02 11:04  john

	* libEM/cmp.cpp: bugfixes

2012-02-02 10:50  john

	* libEM/cmp.cpp, libEM/cmp.h, libEM/emdata.cpp,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2wedge.py,
	  programs/e2workflow.py: Cleaned up comments

2012-02-01 15:17  john

	* libEM/emdata.cpp, programs/e2wedge.py: bugfix for e2wedge.py

2012-02-01 15:00  john

	* libEM/pmconfig/tomo.json, libpyEM/qtgui/emform.py,
	  programs/e2wedge.py: Added e2wedge.pg, a program for wedge
	  visuablization and wedge stats computation

2012-02-01 12:43  john

	* libEM/emdata.cpp, libEM/emdata.h, libEM/glutil.cpp,
	  libpyEM/libpyEMData2.cpp, libpyEM/qtgui/emform.py: Bugfix for
	  workflow

2012-02-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-02-01 10:17  zyang

	* sparx/libpy/applications.py: Add date to the ISAC program.

2012-02-01 06:53  stevel

	* libpyEM/EMAN2PAR.py: Undo previous change.

2012-02-01 06:48  stevel

	* libpyEM/EMAN2PAR.py, programs/e2speedtest.py: Fix FIFO opening
	  order for MPI. I hope...

2012-01-31 17:22  jgalaz

	* programs/e2tomoallvsall.py: [no log message]

2012-01-31 15:47  jgalaz

	* programs/e2tomoallvsall.py: [no log message]

2012-01-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-30 12:29  gtang

	* libEM/mrcio.cpp: fix mrc region writing

2012-01-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-28 00:46  stevel

	* programs/e2proc3d.py: Undo is_new_file change until it can be
	  fixed

2012-01-27 14:28  john

	* libpyEM/qtgui/: emdataitem3d.py, emimageutil.py: 3D widget bugfix

2012-01-27 13:36  john

	* programs/e2evalimage.py: Bug fix for evalimage

2012-01-27 12:50  john

	* programs/e2evalimage.py: Bugzilla, EMAN2CTf usage in eval image

2012-01-27 12:27  john

	* programs/e2evalimage.py: Bugzilla, fixed e2evalimage bug

2012-01-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-27 11:58  john

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/libpyEMData2.cpp,
	  programs/e2projectmanager.py: PM bugfixes

2012-01-27 10:11  john

	* programs/e2projectmanager.py: PM bugfix

2012-01-27 09:32  john

	* programs/e2tiltvalidate.py: Pawel bugfix

2012-01-26 16:34  john

	* libEM/pmconfig/spr.json, libpyEM/EMAN2.py,
	  libpyEM/qtgui/empmwidgets.py, programs/e2RCTboxer.py,
	  programs/e2classaverage3d.py, programs/e2eotest.py,
	  programs/e2montecarlorecon.py, programs/e2plotFSC.py,
	  programs/e2projectmanager.py, programs/e2refine.py,
	  programs/e2refine2d.py, programs/e2refinemulti.py,
	  programs/e2symsearch.py, programs/e2tiltvalidate.py,
	  programs/e2workflow.py: Fixed PM bugs foudn by Alexy

2012-01-26 14:21  pawel

	* libpyEM/EMAN2db.py: blocked John's parallel_process_exit which
	  crashes the system

2012-01-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-26 10:54  pawel

	* programs/e2bdb.py: [no log message]

2012-01-25 19:25  jgalaz

	* programs/e2spt_refinemulti.py: Program (scraps) to do
	  multiple-model refinement of SPT data with a fixed or growing
	  number of references/models, and with supplied references or
	  self-generated from the data.

2012-01-25 19:07  jgalaz

	* programs/e2spt_refinemsa.py: Cleanup

2012-01-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-24 16:07  gtang

	* programs/e2proc3d.py: bug fix for subsetting a stack.

2012-01-24 13:34  stevel

	* libEM/cmp.cpp: Fixed CCC to not return NanZ

2012-01-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-24 01:06  jgalaz

	* programs/e2tomoallvsall.py:
	  Bug fix concerning write-out directory and subdirectories.

2012-01-24 00:21  jgalaz

	* programs/e2tomoallvsall.py: The all vs all program can now break
	  down a huge stack into substacks through the --groups parameter,
	  and will do all vs all for each substack independently.

2012-01-23 13:16  john

	* libEM/pmconfig/spr.json, libpyEM/qtgui/empmwidgets.py,
	  programs/e2refine.py, programs/e2refinemulti.py: Bug fixes

2012-01-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-23 11:51  john

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/qtgui/pmicons.py: bug fixes for Madriva builds

2012-01-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-22 11:45  gtang

	* libEM/hdfio2.cpp: fix the HDF5 regional writing routine

2012-01-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-20 15:34  gtang

	* examples/e2spt_fft.py, examples/e2spt_fftamp.py,
	  examples/e2spt_msa.py, programs/e2spt_refinemsa.py,
	  programs/e2tomoallvall.py: file change for Jesus

2012-01-20 12:33  john

	* libpyEM/EMAN2.py, libpyEM/qtgui/emdataitem3d.py,
	  libpyEM/qtgui/emimage.py, programs/e2display.py: Added new widget
	  to python prompt

2012-01-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-20 09:45  john

	* programs/e2simmx.py: Fixed version conflict

2012-01-20 09:40  john

	* programs/: e2projectmanager.py, e2simmx.py: e2simmx flushing
	  revert

2012-01-19 19:43  stevel

	* libEM/cmp.cpp, libEM/util.h, libEM/xydata.cpp,
	  programs/e2classifykmeans.py, programs/e2simmx.py: Apparently the
	  'fpclassify' functions in the standard library on linux are
	  completely broken (possibly other platforms as well). So, all of
	  that careful goodf() checking to avoid sporadic crashes was
	  accomplishing exactly nothing. !@#!@ std library. It is now using
	  direct interrogation of bit patterns, and seems to be working
	  well.

2012-01-19 18:44  jgalaz

	* examples/e2spt_fft.py: Program to write out the fft (amplitudes)
	  in 3D for a subvolume or a stack of subvolumes.

2012-01-19 17:08  john

	* libpyEM/EMAN2.py, programs/e2projectmanager.py: PM bugfix

2012-01-19 16:30  john

	* libpyEM/EMAN2.py, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/emplot2d.py, libpyEM/qtgui/empmtabwidgets.py,
	  programs/e2project3d.py, programs/e2projectmanager.py,
	  programs/e2simmx.py, programs/e2tiltvalidate.py: PM updates

2012-01-19 14:14  jgalaz

	* programs/e2tomoboxer.py: --Coordinats for each subvolume were
	  stored in the header only when boxing from the command line.
	  Fixed this so that they're ALWAYS stored (boxing from the GUI
	  too).  --If using binned coordinates, they were stored binned in
	  the header. Changed this to write to the header the coordinates
	  of the particle in the ACTUAL tomogram (not the binned one).
	  --Reduced redundancies concerning normalization, setting the
	  origin to zero and contrast reversal (there were three separate
	  portions of code for this, depending on which boxing mode you
	  chose; now this things are done idependently from the mode
	  chosen).  --Cleaned the code extensively.

2012-01-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-18 17:15  astrocytus

	* libEM/sparx/util_sparx.cpp: corrected bug reports in window

2012-01-18 17:11  astrocytus

	* sparx/libpy/global_def.py: correcting wrong setting of cash

2012-01-18 17:10  astrocytus

	* sparx/libpy/global_def.py: corrected bug reports in window

2012-01-18 13:31  jgalaz

	* programs/e2proc3d.py: Option --average added to generate the
	  normalized average of a given 3D stack.

2012-01-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-17 23:10  jgalaz

	* programs/e2tomoboxer.py: autocentering (doesn't seem very
	  useful...).

2012-01-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-17 10:56  john

	* libpyEM/qtgui/empmwidgets.py: bugfix

2012-01-17 10:54  stevel

	* libpyEM/: EMAN2db.py, qtgui/embrowser.py: Fix some image display
	  dimensions issues in the browser.

2012-01-17 10:02  john

	* libEM/pmconfig/spr.json, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emplot2d.py, programs/e2projectmanager.py,
	  programs/e2tiltvalidate.py: PM bugfix

2012-01-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-13 14:36  stevel

	* libpyEM/EMAN2db.py, programs/e2classaverage.py: Fix problem with
	  final alignment in class-averaging with some comparators.

2012-01-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-12 18:50  jgalaz

	* examples/e2spt_msa.py: update

2012-01-12 15:58  fjia

	* programs/e2helixboxer.py: add micrograph of origin to the header
	  when writing helix segments to file

2012-01-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-12 09:20  john

	* libEM/averager.cpp, programs/e2classaverage3d.py: Fixed avg
	  header info bug

2012-01-11 18:41  jgalaz

	* examples/e2spt_msa.py: Automated MSA based K-means classification
	  for subtomograms.

2012-01-11 16:46  john

	* programs/: e2projectmanager.py, e2tomoboxer.py: bugfix for
	  tomoboxer

2012-01-11 15:57  john

	* libpyEM/qtgui/empmwidgets.py: update

2012-01-11 15:49  john

	* libpyEM/qtgui/empmwidgets.py, programs/e2classaverage3d.py:
	  bugfix

2012-01-11 15:04  john

	* programs/e2classaverage3d.py: bugfix

2012-01-11 15:03  john

	* libpyEM/qtgui/empmwidgets.py, programs/e2projectmanager.py:
	  updates

2012-01-11 13:47  john

	* libpyEM/qtgui/embrowser.py, libpyEM/qtgui/emplot2d.py,
	  libpyEM/qtgui/empmwidgets.py, libpyEM/qtgui/pmicons.py,
	  programs/e2projectmanager.py, programs/e2tiltvalidate.py: bug
	  fixes

2012-01-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-11 09:40  zyang

	* sparx/libpy/reconstruction.py: Fix a minor bug.

2012-01-10 18:05  fjia

	* sparx/bin/sxprocess.py: add more noise paramters as user input
	  options for generate_projections option

2012-01-10 17:52  fjia

	* sparx/bin/sxprocess.py: let parameters determining amount of
	  noise added to micrograph and projections (for
	  --generate_projections option) be optional user input

2012-01-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-09 17:42  fjia

	* sparx/bin/sxprocess.py: [no log message]

2012-01-09 17:27  fjia

	* sparx/bin/sxprocess.py: [no log message]

2012-01-09 17:16  fjia

	* sparx/bin/sxprocess.py: add box size as user input option

2012-01-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-09 10:29  zyang

	* sparx/libpy/: applications.py, reconstruction.py: Trivial change.

2012-01-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-06 16:56  john

	* libpyEM/qtgui/: emdataitem3d.py, emshapeitem3d.py: More bug fixes

2012-01-06 15:42  john

	* libpyEM/qtgui/: emdataitem3d.py, emscene3d.py, emshapeitem3d.py:
	  simplification of EMRuler

2012-01-06 15:05  john

	* libpyEM/qtgui/: emitem3d.py, emscene3d.py, emshapeitem3d.py:
	  Ruler saving bug fix

2012-01-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-06 11:16  fjia

	* sparx/libpy/statistics.py: [no log message]

2012-01-06 10:17  john

	* libpyEM/qtgui/emshapeitem3d.py: bugfix for ruler

2012-01-06 10:03  john

	* libpyEM/qtgui/: emscene3d.py, emshapeitem3d.py: Added Ruler, no
	  scale adjustment yet

2012-01-05 16:48  john

	* libpyEM/qtgui/: emdataitem3d.py, emitem3d.py, emscene3d.py,
	  emshapeitem3d.py: Added measuring stick to the 3D widget

2012-01-05 16:47  john

	* programs/e2classaverage3d.py: com disbaled flag added

2012-01-05 13:45  fjia

	* sparx/libpy/statistics.py: [no log message]

2012-01-05 13:39  fjia

	* sparx/libpy/statistics.py: added avgvar_CTF for calculating avg
	  and variance with ctf correction

2012-01-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-05 10:23  fjia

	* sparx/libpy/statistics.py: added avgvar function for calculating
	  avg and variance without ctf correction

2012-01-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-04 11:31  john

	* programs/: e2help.py, e2projectmanager.py: Added GUI to HELP

2012-01-04 10:43  john

	* libEM/CMakeLists.txt, libEM/glutil.cpp, libEM/marchingcubes.cpp,
	  libpyEM/CMakeLists.txt: Added glDelete buffers to MC destructor

2012-01-03 19:34  stevel

	* programs/: e2ctf.py, e2evalparticles.py: Mark good option. Fix
	  writing parameters to image headers.

2012-01-03 15:51  john

	* libpyEM/qtgui/emdataitem3d.py: bugfix

2012-01-03 15:48  gtao

	* sparx/libpy/fundamentals.py: [no log message]

2012-01-03 15:16  john

	* libpyEM/qtgui/emscene3d.py, programs/e2projectmanager.py:
	  bugfixes

2012-01-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-03 10:57  john

	* images/SirEMAN2.png, libpyEM/qtgui/embrowser.py,
	  programs/e2projectmanager.py: PM updates

2012-01-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2012-01-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-29 17:49  astrocytus

	* sparx/libpy/applications.py: astigmatism added to sxheader.py

2011-12-29 16:53  astrocytus

	* sparx/libpy/user_functions.py: set aa = 0.2 in reference3

2011-12-29 16:34  john

	* programs/e2projectmanager.py: help updates to PM

2011-12-29 12:51  john

	* libpyEM/qtgui/: embrowser.py, emdataitem3d.py, emscene3d.py:
	  Capping updates

2011-12-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-29 09:47  pawel

	* libEM/: cmp.cpp, cmp.h, processor.cpp: [no log message]

2011-12-29 09:34  pawel

	* programs/e2help.py: [no log message]

2011-12-28 16:50  john

	* libEM/marchingcubes.cpp, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/emdataitem3d.py, libpyEM/qtgui/empmtabwidgets.py:
	  Bug fix for color by radius

2011-12-28 15:09  john

	* libEM/glutil.cpp, libEM/glutil.h, libEM/marchingcubes.cpp,
	  libEM/marchingcubes.h, libpyEM/qtgui/emdataitem3d.py,
	  programs/e2classaverage3d.py: Reverted what CVS screwed
	  up(yesterdays changes)

2011-12-28 14:31  john

	* libpyEM/qtgui/: emdataitem3d.py, emscene3d.py: capping clipping
	  planes

2011-12-28 13:40  john

	* libpyEM/qtgui/: emdataitem3d.py, emitem3d.py, emscene3d.py: iso
	  capping

2011-12-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-27 16:05  john

	* libEM/: glutil.cpp, glutil.h, marchingcubes.cpp, marchingcubes.h:
	  openGL criticasl bug fix

2011-12-27 15:43  john

	* libpyEM/qtgui/emdataitem3d.py, programs/e2projectmanager.py:
	  color by map updates

2011-12-27 13:29  john

	* programs/e2classaverage3d.py: var bugfix

2011-12-27 13:27  john

	* libEM/isosurface.h, libEM/marchingcubes.cpp,
	  libEM/marchingcubes.h, libpyEM/libpyMarchingCubes2.cpp,
	  libpyEM/qtgui/emdataitem3d.py, libpyEM/qtgui/empmtabwidgets.py,
	  libpyEM/qtgui/valslider.py: ColorbyMap updates

2011-12-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-23 17:30  fjia

	* sparx/bin/sxprocess.py: change help message

2011-12-23 17:20  fjia

	* sparx/demo/mpi_bdb_ctf/run_through_example: change the way
	  database is initialized using sxprocess's makedb option

2011-12-23 17:20  fjia

	* sparx/demo/mpi_bdb/run_through_example: change the way database
	  is initialized by sxprocess's --makedb option

2011-12-23 17:19  fjia

	* sparx/bin/sxprocess.py: change the way parameters are set by
	  makedb option

2011-12-23 14:02  astrocytus

	* sparx/demo/mpi_bdb_ctf/run_through_example: comment

2011-12-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-23 11:15  astrocytus

	* sparx/demo/mpi_bdb_ctf/run_through_example: comment

2011-12-23 10:54  astrocytus

	* sparx/demo/mpi_bdb/run_through_example: comment

2011-12-22 16:46  john

	* libEM/pmconfig/spr.json, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/empmtabwidgets.py, libpyEM/qtgui/pmicons.py,
	  programs/e2RCTboxer.py, programs/e2projectmanager.py: PM updates

2011-12-22 13:01  john

	* libEM/aligner.cpp: Removed debugging statement

2011-12-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-22 10:55  john

	* libEM/pmconfig/tomo.json, programs/e2tomoboxer.py: bugfixes

2011-12-21 17:42  fjia

	* sparx/demo/mpi_bdb_ctf/run_through_example: phase flip data set

2011-12-21 15:59  fjia

	* sparx/bin/sxprocess.py: [no log message]

2011-12-21 15:48  fjia

	* sparx/demo/mpi_bdb_ctf/run_through_example: update the way
	  sxprocess is used to generate projections

2011-12-21 15:41  fjia

	* sparx/demo/mpi_bdb/run_through_example: update line using
	  sxprocess to generate projections

2011-12-21 15:38  fjia

	* sparx/bin/sxprocess.py: add input/output for generate_projections
	  option

2011-12-21 14:07  fjia

	* sparx/bin/sxprocess.py: [no log message]

2011-12-21 13:44  john

	* libEM/glutil.h, libpyEM/qtgui/emshapeitem3d.py: Bugfix for
	  lighting

2011-12-21 13:31  john

	* libEM/glutil.cpp, libEM/glutil.h, libpyEM/libpyGLUtils2.cpp,
	  libpyEM/qtgui/emdataitem3d.py, libpyEM/qtgui/emitem3d.py,
	  libpyEM/qtgui/emshapeitem3d.py: Bugfix for 3D widget

2011-12-21 12:59  pawel

	* libEM/sparx/emdata_sparx.cpp: [no log message]

2011-12-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-21 11:35  john

	* libpyEM/qtgui/emdataitem3d.py, programs/e2classaverage3d.py:
	  Added variance map to 3dCA

2011-12-21 10:50  john

	* libpyEM/qtgui/: empmtabwidgets.py, emshapeitem3d.py: PM updates

2011-12-21 10:44  astrocytus

	* libEM/sparx/util_sparx.cpp: fix a miner bug in verifying whether
	  the input image exists

2011-12-21 09:58  john

	* libpyEM/qtgui/empmtabwidgets.py: [no log message]

2011-12-20 17:50  john

	* libEM/aligner.cpp: [no log message]

2011-12-20 17:48  john

	* libEM/aligner.cpp, libEM/aligner.h, libEM/processor.cpp,
	  libpyEM/qtgui/emdataitem3d.py: Addedrotateinfs to aligners

2011-12-20 13:44  john

	* libEM/glutil.cpp, libEM/glutil.h, libEM/marchingcubes.cpp,
	  libEM/marchingcubes.h, libpyEM/libpyGLUtils2.cpp,
	  libpyEM/qtgui/emdataitem3d.py: Deprecated 3D display lists and
	  replaced with buffer objects

2011-12-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-20 10:51  john

	* libEM/aligner.cpp, libEM/glutil.cpp, libEM/glutil.h,
	  libEM/marchingcubes.cpp, libEM/marchingcubes.h,
	  libEM/pmconfig/spr.json, libEM/pmconfig/tomo.json,
	  libpyEM/libpyGLUtils2.cpp, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/emdataitem3d.py, libpyEM/qtgui/emitem3d.py,
	  libpyEM/qtgui/empmwidgets.py, libpyEM/qtgui/emscene3d.py,
	  programs/e2projectmanager.py: PM updates, openGL updates, and
	  Phils aligners

2011-12-19 15:39  fjia

	* sparx/demo/: mpi_bdb/run_through_example,
	  mpi_bdb_ctf/run_through_example: update the way sxprocess is used
	  to generate projections

2011-12-19 15:39  fjia

	* sparx/bin/sxprocess.py: change the way arguments for
	  --generate_projections options is input

2011-12-19 14:59  pbaldwin

	* libEM/: processor.cpp, processor.h:
	       Changed RotateinFS to accept default values for
	  interpolation distance,
		and have it so that the function doesn't need to be carried
	  out in place.
	       Done with JFlanagan.

2011-12-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-19 10:52  fjia

	* sparx/demo/: mpi_bdb/run_through_example,
	  mpi_bdb_ctf/run_through_example: [no log message]

2011-12-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-18 10:22  pawel

	* libEM/aligner.cpp: [no log message]

2011-12-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-16 12:59  fjia

	* sparx/demo/mpi_bdb_ctf/run_through_example: [no log message]

2011-12-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-16 11:54  fjia

	* sparx/demo/mpi_bdb/run_through_example: [no log message]

2011-12-16 11:47  fjia

	* sparx/bin/sxboxer.py: removing sxboxer from distribution

2011-12-16 10:42  gtang

	* libEM/marchingcubes.cpp: fix compilation error for Windows

2011-12-15 15:59  pawel

	* sparx/bin/: sxresample.py, sxvar.py: [no log message]

2011-12-15 15:39  pawel

	* sparx/bin/sxbmask.py: [no log message]

2011-12-15 15:34  fjia

	* sparx/bin/sxgui.py: removed Applyparams option from pre-centering
	  (sxshiftali) gui

2011-12-15 15:06  pbaldwin

	* libEM/: processor.cpp, processor.h:
	  Added  the RotateInFS    processor. Is working for even and odd
	  images, 2d and 3d.

2011-12-15 14:56  fjia

	* sparx/demo/mpi_bdb/run_through_example: modified to use sxprocess

2011-12-15 14:49  john

	* libEM/aligner.cpp, libEM/aligner.h, libEM/glutil.cpp,
	  libEM/isosurface.h, libEM/marchingcubes.cpp,
	  libEM/marchingcubes.h, libpyEM/libpyMarchingCubes2.cpp,
	  libpyEM/qtgui/embrowser.py, libpyEM/qtgui/emdataitem3d.py,
	  libpyEM/qtgui/empmtabwidgets.py, libpyEM/qtgui/empmwidgets.py,
	  libpyEM/qtgui/valslider.py, programs/e2RCTboxer.py,
	  programs/e2evalimage.py, programs/e2projectmanager.py,
	  programs/e2symsearch.py: Added color by radius, and worked on PM

2011-12-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-15 11:08  fjia

	* sparx/bin/sxprocess.py: [no log message]

2011-12-14 16:59  fjia

	* sparx/bin/sxprocess.py: carry out various sparx img processing
	  commands on 2-D images

2011-12-14 13:33  fjia

	* sparx/demo/: 5_mpi_bdb/run_through_example,
	  7_mpi_bdb_ctf/run_through_example: removing old demos

2011-12-14 13:17  fjia

	* sparx/demo/3_bdb_ctf/run_through_example: removing old demo files

2011-12-14 13:15  fjia

	* sparx/demo/1_bdb/run_through_example: deleting old demo

2011-12-14 13:03  gtang

	* programs/e2proc2d.py: fix the file name issue when output slice
	  of a 3D image to a bunch of 2D images.

2011-12-14 12:11  fjia

	* sparx/demo/: mpi_bdb/run_through_example,
	  mpi_bdb_ctf/run_through_example: new demo file

2011-12-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-14 11:29  fjia

	* sparx/demo/mpi_bdb_ctf2/: run_through_example, dummy.txt: [no log
	  message]

2011-12-14 11:22  fjia

	* sparx/demo/mpi_bdb/: run_through_example, dummy.txt: [no log
	  message]

2011-12-14 10:55  scmurray

	* programs/e2refinetorelion2d.py: This program will run the 2D
	  relion module on particles that have been previously boxed out
	  and made into a "set" in EMAN2.

2011-12-14 10:54  gtang

	* libEM/imagicio2.cpp, libpyEM/qtgui/emboxerbase.py: fixt the bug
	  when writing boxed particles to image files, the A/pix numbers
	  were not written to header.

2011-12-14 09:58  fjia

	* sparx/demo/: mpi_bdb/run_through_example,
	  mpi_bdb_ctf2/run_through_example: updated demo file

2011-12-14 07:50  stevel

	* libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libpyEM/EMAN2db.py, libpyEM/libpyEMData2.cpp,
	  libpyEM/qtgui/embrowser.py, libpyEM/qtgui/emimage2d.py,
	  programs/CMakeLists.txt, programs/e2bdb.py,
	  programs/e2classaverage.py, programs/e2remoted.py: Fixed problem
	  with nx/ny/nz setting in EMAN2db

2011-12-14 03:44  jgalaz

	* examples/e2spt_autocenter.py: Bug fixes.

2011-12-13 18:10  jgalaz

	* examples/e2spt_autocenter.py: 95% finalized and tested.

2011-12-13 16:43  jgalaz

	* examples/e2spt_autocenter.py: Iterative auto-centering of a data
	  set based on the spherical average of the average blob.

2011-12-13 16:05  gtang

	* libpyEM/EMAN2db.py: do not set attribute for nx,ny,nz

2011-12-13 15:40  gtang

	* sparx/demo/mpi_bdb_ctf2/dummy.txt: add for Jia

2011-12-13 15:24  gtang

	* sparx/demo/mpi_bdb/dummy.txt: add for Jia

2011-12-13 14:44  fjia

	* sparx/demo/: 7_mpi_bdb_ctf/run_through_example,
	  5_mpi_bdb/run_through_example: [no log message]

2011-12-13 14:39  fjia

	* sparx/demo/7_mpi_bdb_ctf/run_through_example: [no log message]

2011-12-13 14:23  jgalaz

	* programs/e2tomoallvsall.py: [no log message]

2011-12-13 14:17  jgalaz

	* programs/e2tomoallvsall.py: blah

2011-12-13 14:02  scmurray

	* programs/e2evalparticles.py: Added support to e2evalparticles.py
	  for reading classes that are generated in the 2D relion module in
	  EMAN2

2011-12-13 13:23  gtang

	* programs/e2version.py: for Mac OS X

2011-12-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-13 11:41  fjia

	* sparx/demo/filldb_mpibdb.py: create and fill in db for autoboxing

2011-12-13 11:35  fjia

	* sparx/bin/sxgui.py: add option to switch between different demo
	  input parameters

2011-12-13 10:20  fjia

	* sparx/demo/filldb_demo.py: create and fill database for e2boxer
	  line in run through example

2011-12-12 17:31  gtang

	* programs/e2version.py: print user system information

2011-12-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-09 15:30  gtang

	* libEM/: emdata_io.cpp, emdata_metadata.cpp, emdata_metadata.h:
	  remove 'nx','ny','nz' from EMData's attribute dictionary. The
	  image dimension is stored in member variables.

2011-12-09 15:27  gtang

	* rt/pyem/test_aligner.py: unit test update

2011-12-09 15:24  gtang

	* rt/pyem/test_emdata.py: unit test update

2011-12-09 12:25  fjia

	* programs/e2boxer.py: added command line mode for Gauss autoboxer
	  plus some other Gauss autoboxer related changes

2011-12-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-08 11:56  gtang

	* libEM/mrcio.cpp: cell angles not correctly set when reading mrc
	  image

2011-12-07 21:52  jgalaz

	* programs/e2tomoboxer.py: [no log message]

2011-12-07 21:49  jgalaz

	* programs/e2tomoboxer.py: Fixed command line lowpass filtering
	  bug.

2011-12-07 20:38  stevel

	* libpyEM/qtgui/: embrowser.py, emplot2d.py: plot improvements

2011-12-07 20:36  jgalaz

	* programs/e2tomoboxer.py: Command line boxer was broken. Fixed
	  typos too.

2011-12-07 17:03  john

	* libEM/pmconfig/spr.json, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/empmtabwidgets.py, libpyEM/qtgui/empmwidgets.py,
	  programs/e2classaverage3d.py, programs/e2evalimage.py,
	  programs/e2import.py, programs/e2initialmodel.py,
	  programs/e2montecarlorecon.py, programs/e2projectmanager.py,
	  programs/e2symsearch.py: PM browser caching updates

2011-12-07 15:08  fjia

	* sparx/bin/: sxgui.py: [no log message]

2011-12-07 14:19  fjia

	* sparx/bin/sxgui.py: add --demo option to initialize input fields
	  with demo specific values

2011-12-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-06 16:18  john

	* libpyEM/qtgui/: embrowser.py, empmtabwidgets.py: PM bug fixes

2011-12-06 16:09  john

	* libpyEM/qtgui/empmtabwidgets.py, programs/e2montecarlorecon.py,
	  programs/e2tomoboxer.py: tomoboxer updates

2011-12-06 15:56  john

	* libEM/emdata_cuda.cpp, libpyEM/qtgui/empmtabwidgets.py,
	  programs/e2classaverage3d.py, programs/e2import.py,
	  programs/e2tomoboxer.py: bugfixes for tomo mode

2011-12-06 14:34  john

	* programs/e2buildstacks.py: PM program

2011-12-06 14:05  fjia

	* sparx/libpy/applications.py: [no log message]

2011-12-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-06 11:58  john

	* libEM/pmconfig/tomo.json, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/empmtabwidgets.py, libpyEM/qtgui/empmwidgets.py,
	  programs/e2classaverage3d.py, programs/e2import.py,
	  programs/e2initialmodel.py, programs/e2montecarlorecon.py,
	  programs/e2projectmanager.py, programs/e2rct.py,
	  programs/e2refine.py, programs/e2refine2d.py,
	  programs/e2refinefromfrealign.py, programs/e2refinemulti.py,
	  programs/e2symsearch.py, programs/e2tiltvalidate.py,
	  programs/e2tomoboxer.py: PM updates

2011-12-06 11:14  zyang

	* sparx/libpy/applications.py: Just fix some wordings of the error
	  message in the ISAC program

2011-12-06 10:51  zyang

	* sparx/libpy/applications.py: A trivial bug.

2011-12-06 10:50  zyang

	* sparx/libpy/applications.py: Add some error messages for the ISAC
	  program

2011-12-06 10:46  gtao

	* sparx/libpy/applications.py: add code to check whether the out
	  radius is reasonable.

2011-12-06 10:29  gtang

	* libEM/emdata_metadata.cpp: update the attribute nx,ny,nz at
	  set_size(). They were updated too late.

2011-12-05 16:31  gtang

	* programs/e2proc2d.py: [no log message]

2011-12-05 16:27  john

	* libEM/pmconfig/spr.json, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/emform.py, libpyEM/qtgui/empmtabwidgets.py,
	  libpyEM/qtgui/emrctboxergui.py, programs/e2RCTboxer.py,
	  programs/e2ctf.py, programs/e2import.py: pmtables addition plus
	  embrowser enhyancements and bugvfixes

2011-12-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-05 09:27  john

	* libpyEM/qtgui/embrowser.py: [no log message]

2011-12-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-03 01:11  stevel

	* libpyEM/EMAN2PAR.py, mpi_eman/pbs.example: Fix for caching 3D
	  stacks

2011-12-02 16:41  john

	* libpyEM/qtgui/empmtabwidgets.py, programs/e2import.py: GUI
	  updates

2011-12-02 16:37  john

	* libEM/pmconfig/spr.json, libpyEM/EMAN2.py,
	  libpyEM/qtgui/emboxerbase.py, libpyEM/qtgui/embrowser.py,
	  libpyEM/qtgui/empmtabwidgets.py, libpyEM/qtgui/empmwidgets.py,
	  libpyEM/qtgui/emrctboxergui.py, programs/e2RCTboxer.py,
	  programs/e2boxer.py, programs/e2projectmanager.py,
	  programs/e2rawdata.py: GUI updates

2011-12-02 12:20  gtang

	* libEM/xplorio.cpp: fix the wrong cell size for writing xplor
	  image.

2011-12-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-12-02 11:38  gtang

	* libEM/emdata_core.cpp: fix for >8GB image

2011-12-01 12:34  gtang

	* libEM/glutil.cpp: fix for compilation failure on Fedora 12

2011-12-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-30 14:33  john

	* images/EMAN2Icon.png, libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libpyEM/qtgui/embrowser.py, programs/e2projectmanager.py: PM
	  updates

2011-11-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-30 02:04  jgalaz

	* programs/e2tomoallvsall.py: Fixed averaging bug.

2011-11-30 00:02  jgalaz

	* programs/e2tomoallvsall.py: Normalization bug fixed.

2011-11-29 22:11  jgalaz

	* programs/e2tomoallvsall.py: Fixed hard-drive consumption issue.
	  Particles are now read from files directly, for all rounds. This
	  is NOT parallelizable on a cluster, but works well for an
	  individual workstation.

2011-11-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-29 11:22  zyang

	* sparx/libpy/: applications.py, user_functions.py: Fix two small
	  bugs

2011-11-29 10:17  john

	* libEM/aligner.cpp, libEM/aligner.h, libEM/pmconfig/tomo.json,
	  libpyEM/qtgui/empmwidgets.py, programs/e2classaverage3d.py,
	  programs/e2projectmanager.py: PM updates

2011-11-29 09:26  john

	* libpyEM/EMAN2.py, programs/e2RCTboxer.py, programs/e2boxer.py,
	  programs/e2ctf.py, programs/e2projectmanager.py,
	  programs/e2tiltvalidate.py: guidefault removed from PM

2011-11-28 17:48  john

	* programs/e2projectmanager.py: bugfix

2011-11-28 17:47  john

	* libpyEM/EMAN2.py, libpyEM/qtgui/empmwidgets.py,
	  programs/e2RCTboxer.py, programs/e2projectmanager.py,
	  programs/e2tiltvalidate.py: pm mode upgrade

2011-11-28 16:39  gtang

	* libEM/emdata_metadata.h: get_xsize return zero when do the header
	  only	reading from database.

2011-11-28 16:29  gtang

	* libEM/emdata.cpp: small fix for "warning: extra tokens at end of
	  #endif directive"

2011-11-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-27 23:20  stevel

	* programs/: e2remoted.py, e2scp.py: Remote communication daemon.
	  Not done yet

2011-11-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-23 10:58  stevel

	* libpyEM/qtgui/embrowser.py: Can use embrowser in modal mode.

2011-11-22 14:52  john

	* libEM/pmconfig/spr.json, libEM/pmconfig/tomo.json,
	  programs/e2RCTboxer.py, programs/e2projectmanager.py,
	  programs/e2tiltvalidate.py: BUgfixes

2011-11-22 14:19  john

	* libEM/emdata_metadata.h, programs/e2classaverage3d.py: CA updates

2011-11-22 14:01  stevel

	* libpyEM/qtgui/embrowser.py: new embrowser inspector working now
	  for all (?) data types !

2011-11-22 12:52  gtang

	* libEM/emdata.cpp: fix for windows compilation

2011-11-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-22 11:25  gtao

	* sparx/libpy/applications.py: fix the bug for helical wrapping in
	  the ihrsr_MPI.

2011-11-22 10:00  fjia

	* sparx/bin/sxgui.py: resized main window

2011-11-21 17:05  john

	* libEM/: aligner.cpp, emdata.cpp, emdata_cuda.cpp, emdata_cuda.h,
	  emdata_metadata.h, reconstructor.cpp: Enhancement of CUDA emem
	  managment based on commentys from Steven Murray

2011-11-21 15:20  jgalaz

	* programs/e2tomoallvsall.py: Individual particle writing out
	  capabilities (through --saveali) per average per round, and
	  further code cleanup.

2011-11-21 14:51  scmurray

	* libpyEM/qtgui/emimagemx.py: Changed a line where if you tried to
	  save a snapshot, it called itself recursively to infinity and
	  crashed. Fixed now.

2011-11-21 14:31  fjia

	* programs/e2boxer.py: [no log message]

2011-11-21 13:38  jgalaz

	* programs/e2tomoallvsall.py: Bug fix.

2011-11-21 13:02  gtang

	* libEM/emdata.cpp, libEM/emdata_core.h, libpyEM/libpyEMData2.cpp,
	  rt/pyem/test_emdata.py, rt/pyem/test_imageio.py,
	  rt/pyem/test_processor.py: add funciton equal() for testing
	  equality of two EMData object by their pixel values.

2011-11-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-21 10:03  john

	* libEM/: emdata.cpp, emdata_core.cpp, emdata_transform.cpp,
	  projector.cpp, reconstructor.cpp, cuda/cuda_processor.cu,
	  cuda/cuda_projector.cu, cuda/cuda_reconstructor.cu,
	  cuda/cuda_util.cu: CUDA updates

2011-11-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-18 15:44  gtang

	* libEM/emdata_metadata.cpp, libpyEM/EMAN2db.py: fix the header
	  only reading from database. Previously a set of attributes like
	  "sigma" etc. were read out as 0.

2011-11-18 15:44  john

	* libEM/reconstructor.cpp: CUDA updates

2011-11-18 15:42  john

	* libEM/: projector.cpp, reconstructor.cpp: LRU CUDA updates

2011-11-18 15:23  john

	* libEM/emdata_cuda.cpp: Documentation

2011-11-18 14:23  john

	* libEM/aligner.cpp: tweked code to remove posssible mem leak

2011-11-18 13:16  john

	* libEM/: emdata_cuda.cpp, cuda/cuda_cmp.cu,
	  cuda/cuda_processor.cu: CDUA bug fix for large volumes

2011-11-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-17 16:33  gtang

	* libEM/emdata.cpp, libEM/glutil.cpp, libEM/processor.cpp,
	  libpyEM/libpyGLUtils2.cpp: Fix for Windows compilation.

2011-11-17 15:56  jgalaz

	* programs/e2tomoallvsall.py: Cleaning up code

2011-11-17 12:59  zyang

	* sparx/libpy/applications.py: Fix a bug in the ISAC program

2011-11-17 12:29  gtao

	* sparx/: bin/sxihrsr.py, libpy/applications.py: for helical
	  refiment, add option to avoid helical wrapping.

2011-11-17 12:07  gtang

	* programs/e2version.py: version 2.0.4

2011-11-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-17 11:45  john

	* libpyEM/EMAN2db.py, libpyEM/qtgui/emplot2d.py,
	  programs/e2tiltvalidate.py: Empty directory bugfix

2011-11-17 11:19  stevel

	* examples/e2ptclzvssim.py, libpyEM/qtgui/embrowser.py: browser
	  work

2011-11-17 09:26  zyang

	* sparx/libpy/applications.py: Fix a bug in header() function.

2011-11-17 00:51  jgalaz

	* programs/e2tomoallvsall.py: Supposedly now avoids multiple
	  interpolations!

2011-11-16 17:09  pawel

	* libEM/reconstructor.cpp: added clarifying comments

2011-11-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-16 07:08  stevel

	* libpyEM/qtgui/embrowser.py: Work on browser. May be broken.

2011-11-15 20:43  jgalaz

	* programs/e2tomoallvsall.py: Finished! I still need to prevent
	  multiple interpolations (complicated for all vs all)

2011-11-15 17:01  john

	* programs/e2tiltvalidate.py: Tiltvalidate non quaterion calcuation

2011-11-15 15:25  fjia

	* sparx/bin/sxshiftali.py: [no log message]

2011-11-15 14:49  pawel

	* sparx/bin/sxshiftali.py: still needs corrections

2011-11-15 14:14  john

	* libEM/cuda/cuda_emfft.cu, programs/e2projectmanager.py: PM bugfix

2011-11-15 13:52  fjia

	* sparx/bin/sxshiftali.py: [no log message]

2011-11-15 12:15  fjia

	* sparx/bin/sxshiftali.py: [no log message]

2011-11-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-15 11:10  pawel

	* sparx/: bin/sxshiftali.py, libpy/applications.py: [no log
	  message]

2011-11-15 10:53  fjia

	* sparx/bin/sxshiftali.py: take into account initial align2d params
	  in header

2011-11-14 13:36  john

	* libEM/aligner.cpp, libEM/aligner.h, libEM/cmp.cpp,
	  libEM/processor.cpp, libpyEM/qtgui/emscene3d.py,
	  programs/e2tiltvalidate.py: Symmetry aligner updates

2011-11-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-14 11:40  fjia

	* sparx/bin/sxshiftali.py: transform images from fourier back to
	  real space when writing xform.align2d parameterss to header

2011-11-14 10:40  john

	* libpyEM/qtgui/empmwidgets.py, programs/e2classaverage3d.py:
	  DFixed PM boolbox bug

2011-11-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-11 17:48  gtang

	* libEM/hdfio2.cpp: fix the HDF5 region writing bug, the header
	  should not be changed by region writing

2011-11-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-11 10:40  john

	* libpyEM/qtgui/: emimage2d.py, emplot2d.py, emscene3d.py: Added
	  additional image saving formats

2011-11-10 13:02  john

	* libpyEM/qtgui/: emdataitem3d.py, emitem3d.py, emscene3d.py,
	  emshapeitem3d.py: Added Steve's 4 buttons to the root node

2011-11-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-10 01:51  jgalaz

	* programs/e2tomoallvsall.py: troubleshooting...

2011-11-09 16:36  john

	* libpyEM/EMAN2PAR.py, libpyEM/qtgui/emshapeitem3d.py,
	  programs/e2basis.py, programs/e2tiltvalidate.py: Changed cude
	  highlights

2011-11-09 15:54  eman-vm

	* programs/e2version.py: new date stamp

2011-11-09 15:00  fjia

	* sparx/bin/sxgui.py: add gui for sxfind_struct.py

2011-11-09 14:18  jgalaz

	* libpyEM/: EMAN2PAR.py: [no log message]

2011-11-09 14:07  jgalaz

	* programs/e2tomoallvsall.py: [no log message]

2011-11-09 12:26  stevel

	* libpyEM/EMAN2PAR.py: Mpi fixed (broken by earlier changes)

2011-11-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-09 10:59  stevel

	* libpyEM/EMAN2PAR.py: Jesus broke something

2011-11-09 10:56  stevel

	* libpyEM/EMAN2PAR.py: oops

2011-11-09 10:53  stevel

	* libpyEM/EMAN2PAR.py, programs/e2parallel.py: Added nocache, fixed
	  caching problem in mpi

2011-11-09 10:46  gtang

	* libEM/emdata.cpp: change the operator== to check memory address.

2011-11-09 10:46  john

	* libEM/processor.cpp, libpyEM/qtgui/emdataitem3d.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emitem3d.py,
	  libpyEM/qtgui/emscene3d.py, libpyEM/qtgui/emshapeitem3d.py,
	  programs/e2projectmanager.py, programs/e2tiltvalidate.py:
	  Decoupling of the SG, and I have enabled saving 2D 'snapshots' as
	  tiff as well as pgm and ppm Also fixes to PM and tiltvalidate

2011-11-08 17:38  jgalaz

	* libpyEM/EMAN2PAR.py: Needed to import a new alignment class for
	  e2tomoallvsall so that parallelization works.

2011-11-08 17:25  jgalaz

	* programs/e2tomoallvsall.py: All vs all script under
	  development/testing.

2011-11-08 17:25  jgalaz

	* programs/e2classaverage3d.py: Symmetry was being enforced even if
	  not specified and gave an error when "emtpy". Fixed.

2011-11-08 15:39  gtao

	* sparx/libpy/applications.py: fix a bug for helical wrapping.

2011-11-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-07 14:58  john

	* libpyEM/: EMAN2PAR.py, EMAN2db.py: Cods

2011-11-07 14:53  john

	* libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py, programs/e2parallel.py,
	  programs/e2projectmanager.py: Fixed killing of e2parallel
	  processes

2011-11-07 12:02  pawel

	* sparx/libpy/applications.py: [no log message]

2011-11-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-04 12:59  stevel

	* programs/e2filtertool.py: trivial

2011-11-04 12:57  stevel

	* libEM/processor.cpp: CTF simulating filter working now.

2011-11-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-04 09:36  stevel

	* libEM/processor.cpp: A little messed up in scaling still...

2011-11-04 09:14  stevel

	* libEM/processor.cpp, libpyEM/qtgui/emimagemx.py,
	  programs/e2filtertool.py: Fixed filtertool. CTF working I
	  think...

2011-11-04 08:33  stevel

	* libEM/: processor.cpp, processor.h: Compiles again...

2011-11-03 17:54  john

	* libEM/processor.cpp, libpyEM/qtgui/emdataitem3d.py,
	  libpyEM/qtgui/emitem3d.py, libpyEM/qtgui/emscene3d.py,
	  libpyEM/qtgui/emshapeitem3d.py, programs/e2rct.py,
	  programs/e2tiltvalidate.py: cleanedup SG and improved
	  tiltvalidate

2011-11-03 15:58  stevel

	* libEM/processor.h: oops

2011-11-03 15:56  stevel

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/embrowser.py: Browser work

2011-11-03 13:12  pawel

	* sparx/libpy/fundamentals.py: [no log message]

2011-11-03 12:51  eman-vm

	* programs/e2version.py: new date stamp

2011-11-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-03 11:48  zyang

	* sparx/bin/sxstability.py: Fix help message.

2011-11-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-02 11:05  gtang

	* libEM/mrcio.cpp: Treat FEI MRC image as a single image format,
	  not a stack of tilt series

2011-11-02 10:19  zyang

	* sparx/libpy/morphology.py: Add adaptive mask 2D

2011-11-02 10:19  zyang

	* libEM/sparx/util_sparx.cpp: Fix typoes.

2011-11-02 09:04  stevel

	* libpyEM/qtgui/: embrowser.py, emimagemx.py: Imagemx fix for
	  classes with no excluded particles

2011-11-01 16:38  gtao

	* libEM/sparx/emdata_sparx.cpp, sparx/libpy/fundamentals.py,
	  sparx/libpy/utilities.py: recover the resample code for 3D.

2011-11-01 12:59  stevel

	* libpyEM/EMAN2db.py, libpyEM/qtgui/embrowser.py,
	  programs/e2filtertool.py, programs/e2iminfo.py: Fixed e2iminfo
	  and filtertool broken recently. embrowser improvements

2011-11-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-11-01 11:12  john

	* programs/e2classaverage3d.py: Make sym fixes to
	  e2classaverage3d.py

2011-10-31 18:58  pawel

	* sparx/libpy/statistics.py: corrected criteria

2011-10-31 16:11  john

	* programs/e2tomoresolution.py: Tomores update and Hack

2011-10-31 15:58  john

	* libEM/pmconfig/spr.json, libpyEM/qtgui/emdataitem3d.py,
	  libpyEM/qtgui/emrctboxergui.py, programs/e2RCTboxer.py,
	  programs/e2tiltvalidate.py: updates

2011-10-31 15:38  pawel

	* sparx/libpy/statistics.py: [no log message]

2011-10-31 14:39  eman-vm

	* programs/e2version.py: new date stamp

2011-10-31 14:04  fjia

	* sparx/bin/sxgui.py: add gui for sxlocal_ali3d

2011-10-31 11:42  fjia

	* programs/e2boxer.py: Added sxboxer's gauss convolution option for
	  autoboxing, and sxboxer's ctf estimation tool (accessed under the
	  gauss convolution option).

2011-10-28 22:31  stevel

	* libEM/sparx/util_sparx.cpp, libpyEM/qtgui/embrowser.py,
	  programs/e2evalimage.py: Fix for some new compiler issues.

2011-10-28 17:17  gtang

	* libEM/jpegio.cpp: change the way to flip image when write to PNG
	  format. Do not flip the image in the memory.

2011-10-28 17:11  gtang

	* libEM/pngio.cpp: change the way to flip image when write to PNG
	  format. Do not flip the image in the memory.

2011-10-28 16:11  zyang

	* libEM/sparx/util_sparx.cpp: Delete all unnecessary 'extern'

2011-10-28 14:16  stevel

	* libEM/marchingcubes.cpp: Fix extern issue

2011-10-28 14:06  pawel

	* sparx/libpy/statistics.py: [no log message]

2011-10-28 12:12  gtang

	* libEM/imagicio2.cpp: c_str() appends a terminating null
	  character, which cause overflow on Ubuntu 10.04.

2011-10-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-27 11:37  gtang

	* libpyEM/libpyEMData2.cpp: comment out unnecessary methods
	  wrapping. It cause "import libpyEMData2" segfault on CentOS 4.8
	  with gcc 3.4.6.

2011-10-26 18:52  jgalaz

	* programs/e2classaverage3d.py: Alignment paraments and cc
	  coefficient properly stored now in particle headers for SPT.

2011-10-26 17:16  jgalaz

	* programs/e2classaverage3d.py: Changed the name of directories
	  generated by e2classaverage3d to "spt" instead of "job" as
	  suggested by Steve.

2011-10-26 17:09  john

	* libpyEM/qtgui/valslider.py: More docs

2011-10-26 17:06  john

	* libEM/sparx/processor_sparx.h, libpyEM/qtgui/valslider.py: Added
	  code documentation

2011-10-26 16:38  john

	* libpyEM/qtgui/: emitem3d.py, emscene3d.py: Implemented 'don't
	  call us we'll call you' for the inspector. As Steven L suggested

2011-10-26 12:23  john

	* libpyEM/qtgui/emitem3d.py: Found another bug

2011-10-26 12:20  john

	* libpyEM/qtgui/emdataitem3d.py: BUGfix for 3d widget

2011-10-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-26 11:51  john

	* libEM/pmconfig/tomo.json, programs/e2tomoresolution.py: Added
	  tomores to workflow

2011-10-26 11:13  john

	* libpyEM/qtgui/emimage.py, libpyEM/qtgui/emscene3d.py,
	  libpyEM/qtgui/emselector.py, programs/e2symsearch.py,
	  programs/e2tomoresolution.py: New tomoreso routin and implmented
	  Steve's 3D widget default state

2011-10-25 17:05  john

	* libpyEM/EMAN2db.py, libpyEM/qtgui/emscene3d.py,
	  programs/e2project3d.py, programs/e2tiltvalidate.py: PPID bugfix

2011-10-25 17:04  john

	* programs/: e2classaverage.py, e2classaverage3d.py,
	  e2project3d.py, e2simmx.py, e2symsearch.py, e2tiltvalidate.py:
	  Fixed PPID

2011-10-25 16:17  john

	* libpyEM/EMAN2.py, libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py,
	  programs/e2align3d.py, programs/e2classaverage.py,
	  programs/e2classaverage3d.py, programs/e2montecarlorecon.py,
	  programs/e2parallel.py, programs/e2project3d.py,
	  programs/e2projectmanager.py, programs/e2rct.py,
	  programs/e2simmx.py, programs/e2symsearch.py,
	  programs/e2tiltvalidate.py: Fixed a CUDA lock bug and enabled the
	  EMLocalTaskHandler to pass the PID to e2parallel.py so that it
	  can be registered as a child of whatever program ran it.  This
	  required that each TASK set ppid

2011-10-25 12:54  gtang

	* libEM/emdata_transform.cpp: fix bug for >8GB image do_ift

2011-10-25 12:27  john

	* libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/cuda/cuda_util.cu, libEM/cuda/cuda_util.h,
	  libpyEM/EMAN2.py, libpyEM/libpyEMData2.cpp: Enabled the system to
	  reome dead cuda lock files. Uses PID

2011-10-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-25 09:59  john

	* programs/e2tomoboxer.py: Bugfix, when I change boxisze and there
	  is no boxes then upon picking the next box, a IndexError was
	  raised in UpdateBoxes (Program was tring to get a box that
	  doesn't exists. I put a try except to cath any valueerror and
	  then return

2011-10-25 07:06  stevel

	* libpyEM/qtgui/: embrowser.py, emimage2d.py, emplot2d.py: More
	  browser work

2011-10-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-22 15:55  stevel

	* examples/e2ptclzvssim.py, programs/e2bdb.py: New program to
	  compare particle sim metrics and Z scores. Experimental.

2011-10-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-21 17:41  john

	* libpyEM/qtgui/emitem3d.py, programs/e2tiltvalidate.py: Updated 3D
	  widget to remove lighting from bounding boxes... looked stupid

2011-10-21 16:33  ross

	* libpyEM/qtgui/emdataitem3d.py: documenting code

2011-10-21 15:12  john

	* libEM/aligner.cpp, libEM/aligner.h, libEM/processor.cpp,
	  libEM/processor.h, libEM/pmconfig/spr.json,
	  libEM/pmconfig/tomo.json, libpyEM/EMAN2PAR.py,
	  programs/e2symsearch.py, programs/e2tiltvalidate.py: Added
	  mechanism to efficiently align to sym axis

2011-10-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-21 10:45  ross

	* libEM/glutil.h: documented a change I made a while back

2011-10-20 14:46  stevel

	* libpyEM/: EMAN2db.py, qtgui/embrowser.py, qtgui/emimage2d.py,
	  qtgui/emimagemx.py: Browser starting to actually let you view
	  images !

2011-10-20 13:20  john

	* programs/e2tiltvalidate.py: Improved img alignment

2011-10-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-19 15:21  ross

	* programs/e2helixboxer.py: added license message to top of file

2011-10-19 15:19  ross

	* libpyEM/qtgui/emitem3d.py: added license message at top of file

2011-10-19 15:06  stevel

	* libEM/emdata.cpp: No update without data

2011-10-19 15:02  stevel

	* libEM/emdata_io.cpp, libpyEM/qtgui/embrowser.py: Fix for
	  allocation on header-only

2011-10-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-19 10:59  john

	* libEM/transform.cpp, libpyEM/qtgui/emitem3d.py,
	  libpyEM/qtgui/emscene3d.py, programs/e2tiltvalidate.py: SG
	  update, based on SteveL comments

2011-10-18 13:04  john

	* libEM/: emdata_cuda.cpp, emdata_cuda.h: CUDA cleanup

2011-10-18 12:44  john

	* libEM/cuda/cuda_util.cu: Docs

2011-10-18 12:42  john

	* libEM/cuda/cuda_util.cu: Bugfix

2011-10-18 12:40  john

	* libEM/emdata_cuda.cpp, libEM/cuda/cuda_util.cu,
	  libEM/cuda/cuda_util.h, libpyEM/qtgui/empmwidgets.py: CUDA fixes

2011-10-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-18 09:08  stevel

	* examples/e2fftsynth.py: Additions to fourier synthesis program

2011-10-17 16:57  john

	* libpyEM/EMAN2PAR.py, libpyEM/qtgui/empmwidgets.py,
	  programs/e2tiltvalidate.py: Bugfixes for the GUI

2011-10-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-17 11:06  zyang

	* libEM/sparx/util_sparx.cpp: Trivial change.

2011-10-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-14 14:42  john

	* libpyEM/EMAN2.py, libpyEM/qtgui/emplot2d.py,
	  libpyEM/qtgui/empmwidgets.py, programs/e2display.py,
	  programs/e2eotest.py, programs/e2help.py, programs/e2iminfo.py,
	  programs/e2proc2d.py, programs/e2proc3d.py,
	  programs/e2projectmanager.py, programs/e2refinetofrealign.py,
	  programs/e2resolution.py, programs/e2tiltvalidate.py,
	  programs/e2workflow.py: PM updates

2011-10-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-14 10:03  fjia

	* libEM/sparx/util_sparx.cpp: add in branch_factor_0 option in
	  matching code

2011-10-14 10:03  fjia

	* libEM/sparx/util_sparx.h: add declaration for branch_factor_0

2011-10-13 12:24  john

	* libEM/: emdata_cuda.cpp, cuda/cuda_util.cu, cuda/cuda_util.h:
	  CUDA bugfix

2011-10-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-12 21:36  jgalaz

	* programs/e2classaverage3d.py: [no log message]

2011-10-12 15:48  john

	* libEM/pmconfig/spr.json, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emplot2d.py, libpyEM/qtgui/empmwidgets.py,
	  libpyEM/qtgui/emscene3d.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/valslider.py, programs/e2projectmanager.py,
	  programs/e2tiltvalidate.py: Polar ploting new validation stuff,
	  improvement to 3D widget

2011-10-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-12 08:01  jgalaz

	* programs/e2classaverage3d.py: fixes

2011-10-12 06:25  jgalaz

	* programs/e2classaverage3d.py: .  -

2011-10-12 04:00  jgalaz

	* programs/e2classaverage3d.py: [no log message]

2011-10-11 17:43  fjia

	* sparx/libpy/statistics.py: updated documentation for
	  k_means_stab_bbenum

2011-10-11 17:23  zyang

	* sparx/libpy/applications.py: Fix a small bug in the ISAC
	  algorithm

2011-10-11 17:01  john

	* libpyEM/qtgui/empmwidgets.py, programs/e2tiltvalidate.py:
	  Tiltvalidate improvements

2011-10-11 13:29  fjia

	* sparx/libpy/statistics.py: For case of two partitions in the
	  matching algorithm, I modified the input to the Hungarian
	  algorithm so only matchings with weight greater than threshold T
	  are considered. Previously, the Hungarian algorithm considered
	  all matchings, and only matches with weight greater than T was
	  returned.

2011-10-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-11 07:23  stevel

	* libpyEM/EMAN2PAR.py, programs/e2bdb.py: New option in e2bdb.py.
	  Patch for EMAN2PAR for JF

2011-10-10 12:43  stevel

	* programs/e2filtertool.py: Better platform dependent fix for
	  filtertool

2011-10-10 12:24  stevel

	* libpyEM/EMAN2PAR.py, programs/e2filtertool.py: Filtertool gui
	  tweak

2011-10-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-10 11:53  scmurray

	* programs/e2refinetofrealign.py: Changed the Euler Angles as per
	  discussion with Phil. This line "unflips" the flipped particles.

2011-10-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-08 21:56  ross

	* programs/e2helixboxer.py: improved save dialog layout

2011-10-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-07 19:02  ross

	* libpyEM/qtgui/emimage3d.py: EMImage3DWidget.set_data() now has
	  replace parameter default to false. When it is false, it reuses
	  viewables (slices, volumes, isosurfaces, and euler viewers). If
	  there are no viewables, an isosurface is added regardless of the
	  "replace" parameter.

2011-10-07 17:19  john

	* libpyEM/qtgui/empmwidgets.py, programs/e2classaverage3d.py:
	  Updates Jesus suggested

2011-10-07 16:21  john

	* programs/e2projectmanager.py: bugfix

2011-10-07 16:08  john

	* programs/: e2projectmanager.py, e2tiltvalidate.py: Docs and
	  updates

2011-10-07 16:05  john

	* libpyEM/qtgui/emselector.py, programs/e2classaverage3d.py: Fixed
	  Steves bugs

2011-10-07 15:30  stevel

	* libpyEM/qtgui/embrowser.py, programs/e2classaverage3d.py: New
	  option in classaverage3d

2011-10-07 13:04  stevel

	* libEM/emutil.cpp, libpyEM/EMAN2db.py, libpyEM/qtgui/embrowser.py,
	  programs/e2iminfo.py: write_image("bdb:...") works

2011-10-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-07 10:14  john

	* libEM/emdata.cpp, libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/cuda/cuda_util.cu, programs/e2classaverage3d.py: CUDA
	  bugfixes

2011-10-07 10:07  john

	* programs/e2classaverage3d.py: Added path option to
	  classaverage3d.py

2011-10-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-06 11:44  john

	* programs/e2unwrap3d.py: Bug Fix

2011-10-06 09:53  john

	* programs/: e2basis.py, e2classptcl.py, e2cmpxplor.py,
	  e2modeleval.py, e2pathwalker.py: Bugfixes

2011-10-05 17:00  john

	* programs/: e2align2d.py, e2align3d.py, e2basis.py, e2bdb.py,
	  e2classaverage.py, e2classify.py, e2classifykmeans.py,
	  e2classifyligand.py, e2classptcl.py, e2cmmtomrc.py,
	  e2cmpxplor.py, e2ctf2eman1.py, e2display.py, e2eulerxplor.py,
	  e2evalimage.py, e2evalrefine.py, e2fileinfo.py, e2filtertool.py,
	  e2findsubunit.py, e2flick.py, e2foldfitter.py,
	  e2helical_recons.py, e2helixboxer.py, e2help.py, e2history.py,
	  e2iminfo.py, e2make3d.py, e2modeleval.py, e2msa.py,
	  e2parallel.py, e2pathwalker.py, e2pdb2em.py, e2pdb2mrc.py,
	  e2proc2d.py, e2proc2dmulti.py, e2project3d.py, e2ptcltrace.py,
	  e2refinemultinoali.py, e2refinevariance.py, e2refmerge.py,
	  e2scannereval.py, e2scp.py, e2segment3d.py, e2simmx.py,
	  e2simmx2stage.py, e2simmxxplor.py, e2skelpath.py, e2speedtest.py,
	  e2ssehunter.py, e2ssematch.py, e2stackanim.py, e2stacksort.py,
	  e2symbest.py, e2tilefile.py, e2tomoallvall.py, e2tomoallvsall.py,
	  e2tomoaverage.py, e2tomogram.py, e2tomohunter.py: argparser
	  update

2011-10-05 14:37  john

	* programs/: e2ctf.py, e2eotest.py, e2projectmanager.py,
	  e2refinemulti.py, e2resolution.py, e2runfrealign.py: Removed %
	  symbols from these programs so that argpraser doesn't have any
	  pbs

2011-10-05 14:23  john

	* programs/: e2ctf.py, e2projectmanager.py: Fixed bloody percent in
	  e2ctf.py

2011-10-05 14:10  john

	* programs/: e2ctf.py, e2projectmanager.py: CTF bugfix

2011-10-05 13:52  john

	* libEM/pmconfig/icons.json: icons file

2011-10-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-05 11:53  john

	* programs/e2projectmanager.py: Updates

2011-10-05 11:17  john

	* programs/e2projectmanager.py: BugFix

2011-10-05 10:28  john

	* programs/e2projectmanager.py: BugFixO

2011-10-05 09:58  john

	* programs/e2refinetofrealign.py: BugFix

2011-10-04 19:09  stevel

	* libpyEM/qtgui/embrowser.py: Browser work

2011-10-04 17:31  john

	* programs/e2projectmanager.py: NoteBook Updates

2011-10-04 14:27  john

	* libEM/cuda/cuda_util.cu: up

2011-10-04 14:21  john

	* libEM/: emdata.cpp, emdata_cuda.cpp, emdata_cuda.h,
	  cuda/cuda_util.cu: CUDA device lock

2011-10-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-03 17:25  john

	* programs/e2projectmanager.py: update

2011-10-03 16:00  john

	* libpyEM/qtgui/valslider.py, programs/e2projectmanager.py: PM
	  updates

2011-10-03 15:56  john

	* libpyEM/qtgui/empmwidgets.py: Renamed to fix cvs bug

2011-10-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-10-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-30 22:42  stevel

	* libpyEM/: EMAN2.py, EMAN2db.py, qtgui/embrowser.py: browser work

2011-09-30 17:08  zyang

	* libEM/: amiraio.cpp, imagicio.cpp, imagicio2.cpp, pdbreader.cpp,
	  processor.cpp, symmetry.cpp: Fix a bunch of warnings.

2011-09-30 16:24  gtao

	* sparx/libpy/applications.py: [no log message]

2011-09-30 15:53  john

	* programs/e2basis.py: Added basis list for tomography

2011-09-30 12:09  john

	* libpyEM/EMAN2.py, libpyEM/qtgui/emapplication.py,
	  programs/e2RCTboxer.py, programs/e2align2d.py,
	  programs/e2align3d.py, programs/e2basis.py, programs/e2bdb.py,
	  programs/e2boxer.py, programs/e2classaverage.py,
	  programs/e2classaverage3d.py, programs/e2classify.py,
	  programs/e2classifykmeans.py, programs/e2classifyligand.py,
	  programs/e2cmmtomrc.py, programs/e2ctf.py,
	  programs/e2ctf2eman1.py, programs/e2display.py,
	  programs/e2eotest.py, programs/e2eulerxplor.py,
	  programs/e2evalimage.py, programs/e2evalparticles.py,
	  programs/e2evalrefine.py, programs/e2fileinfo.py,
	  programs/e2filtertool.py, programs/e2findsubunit.py,
	  programs/e2flick.py, programs/e2foldfitter.py,
	  programs/e2helical_recons.py, programs/e2helixboxer.py,
	  programs/e2help.py, programs/e2history.py, programs/e2iminfo.py,
	  programs/e2initialmodel.py, programs/e2make3d.py,
	  programs/e2montecarlorecon.py, programs/e2msa.py,
	  programs/e2parallel.py, programs/e2pdb2em.py,
	  programs/e2pdb2mrc.py, programs/e2proc2d.py,
	  programs/e2proc2dmulti.py, programs/e2proc3d.py,
	  programs/e2proc3d_huge.py, programs/e2project3d.py,
	  programs/e2projectmanager.py, programs/e2ptcltrace.py,
	  programs/e2rct.py, programs/e2refine.py, programs/e2refine2d.py,
	  programs/e2refinefromfrealign.py, programs/e2refinemulti.py,
	  programs/e2refinemultinoali.py, programs/e2refinetofrealign.py,
	  programs/e2refinevariance.py, programs/e2refmerge.py,
	  programs/e2resolution.py, programs/e2runfrealign.py,
	  programs/e2scannereval.py, programs/e2scp.py,
	  programs/e2segment3d.py, programs/e2simmx.py,
	  programs/e2simmx2stage.py, programs/e2simmxxplor.py,
	  programs/e2skelpath.py, programs/e2speedtest.py,
	  programs/e2ssehunter.py, programs/e2ssematch.py,
	  programs/e2stackanim.py, programs/e2stacksort.py,
	  programs/e2symbest.py, programs/e2tilefile.py,
	  programs/e2tiltvalidate.py, programs/e2tomoallvall.py,
	  programs/e2tomoallvsall.py, programs/e2tomoaverage.py,
	  programs/e2tomoboxer.py, programs/e2tomogram.py,
	  programs/e2tomohunter.py: Changed os.system to
	  launch_childprocess, a conv function in EMAN2.py

2011-09-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-30 11:42  gtao

	* sparx/libpy/applications.py: [no log message]

2011-09-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-28 15:06  john

	* programs/e2projectmanager.py: PM updates

2011-09-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-27 14:49  john

	* programs/e2projectmanager.py: pm updates

2011-09-27 14:41  john

	* programs/e2projectmanager.py: z

2011-09-27 14:32  stevel

	* libpyEM/qtgui/embrowser.py, programs/e2evalimage.py: Major
	  progress on the, still incomplete, browser

2011-09-27 14:27  john

	* programs/: e2ctf.py, e2projectmanager.py: projectmanager updates

2011-09-27 13:22  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-09-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-27 11:39  john

	* libEM/pmconfig/spr.json, libpyEM/qtgui/pmwidgets.py,
	  programs/e2boxer.py, programs/e2ctf.py,
	  programs/e2projectmanager.py: PM bugfixes and updates

2011-09-27 09:57  john

	* libpyEM/qtgui/pmwidgets.py: Widget for the project manager

2011-09-26 16:48  john

	* libEM/pmconfig/spr.json, libpyEM/EMAN2.py,
	  programs/e2classaverage3d.py, programs/e2ctf.py,
	  programs/e2projectmanager.py: GUI updates

2011-09-26 15:26  gtang

	* libEM/emdata_transform.cpp: fix the 8GB inverse FFT limit.

2011-09-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-26 10:59  gtang

	* CMakeLists.txt: ftgl library is mandatory

2011-09-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-24 22:56  ross

	* programs/e2helixboxer.py: Adding gui and command line options to
	  save all particles to a single stack file. Adding this safely
	  required changing save_particles() to accept a list of lists of
	  particles for all the helices at once rather than one at a time.

2011-09-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-23 17:09  john

	* libEM/pmconfig/spr.json, libEM/pmconfig/tomo.json,
	  libpyEM/EMAN2.py, programs/e2RCTboxer.py, programs/e2boxer.py,
	  programs/e2classaverage3d.py, programs/e2eotest.py,
	  programs/e2evalparticles.py, programs/e2montecarlorecon.py,
	  programs/e2projectmanager.py, programs/e2rct.py,
	  programs/e2refine.py, programs/e2refine2d.py,
	  programs/e2refinefromfrealign.py, programs/e2refinemulti.py,
	  programs/e2refinetofrealign.py, programs/e2resolution.py,
	  programs/e2runfrealign.py, programs/e2tiltvalidate.py,
	  programs/e2tomoboxer.py: GUI update and e2program to argparser

2011-09-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-23 10:06  john

	* libEM/pmconfig/spr.json, libpyEM/EMAN2.py,
	  programs/e2initialmodel.py, programs/e2montecarlorecon.py,
	  programs/e2projectmanager.py, programs/e2refine.py,
	  programs/e2refine2d.py, programs/e2refinemulti.py: argparser
	  updates and projectmanager updates

2011-09-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-22 08:17  stevel

	* libpyEM/qtgui/emsprworkflow.py: someone left debugging prints in

2011-09-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-20 18:05  john

	* libEM/pmconfig/spr.json, libpyEM/EMAN2.py,
	  libpyEM/qtgui/emdataitem3d.py, libpyEM/qtgui/emitem3d.py,
	  libpyEM/qtgui/emrctstrategy.py, libpyEM/qtgui/emscene3d.py,
	  libpyEM/qtgui/emshapeitem3d.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2RCTboxer.py, programs/e2boxer.py,
	  programs/e2projectmanager.py, programs/e2rct.py,
	  programs/e2refine2d.py: SG documentation, PM updates, and
	  argparser for e2boxer and e2refine2d

2011-09-20 12:10  stevel

	* programs/e2refine.py: oops

2011-09-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-20 09:14  stevel

	* programs/e2refine.py: New second postprocessor in refinement.
	  Changed how post-processing was handled.

2011-09-20 07:02  stevel

	* programs/: e2refine.py, e2speedtest.py: Minor bugfix

2011-09-19 15:29  ppenczek

	* sparx/libpy/: projection.py, reconstruction.py: [no log message]

2011-09-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-16 16:05  ross

	* libpyEM/qtgui/emdataitem3d.py: Added brightness and contrast
	  controls for Volume node. Made slice node textures use GL_ALPHA
	  channel for 2D textures (already true for 3D textures).

2011-09-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-16 08:03  stevel

	* examples/recoverctf.py: New script to help recovering lost CTF
	  parameters

2011-09-16 07:32  stevel

	* programs/: e2eotest.py, e2make3d.py: Fix a couple of minor bugs

2011-09-15 22:42  ross

	* libpyEM/qtgui/emdataitem3d.py: added brightness and contrast
	  controls to slice node. Moved 3D texture generation back to C++
	  (after adding format parameter to GLUtils::gen_gl_texture() that
	  lets us specify GL_ALPHA), which resulted in a huge performance
	  improvement.

2011-09-15 22:22  ross

	* libEM/glutil.cpp, libEM/glutil.h, libpyEM/libpyGLUtils2.cpp:
	  const EMData* const emdata, GLenum format = GL_LUMINANCE)...
	  added format parameter to allow for things other than
	  GL_LUMINANCE in this function

2011-09-15 14:20  stevel

	* programs/e2ctf.py: Really fixed now

2011-09-15 14:18  stevel

	* programs/e2ctf.py: oops

2011-09-15 14:17  stevel

	* libpyEM/qtgui/embrowser.py, libpyEM/qtgui/emimage2d.py,
	  programs/e2ctf.py: Display images and invert capability in ctfit

2011-09-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-14 23:03  ross

	* libpyEM/qtgui/emdataitem3d.py: Moving 3D texture generation from
	  data node to volume node and slice node (3d texture optional).
	  Setting brightness and contrast for them, though brightness and
	  contrast controls are still needed in the inspector.

2011-09-14 17:10  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Add a function cml_spin_psi_now()

2011-09-14 15:50  ppenczek

	* sparx/libpy/: projection.py, reconstruction.py: [no log message]

2011-09-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-14 09:30  stevel

	* libpyEM/qtgui/embrowser.py, programs/e2evalparticles.py: Minor
	  fix to evalparticles

2011-09-13 17:17  john

	* libpyEM/qtgui/emscene3d.py, libpyEM/qtgui/emshapeitem3d.py,
	  programs/e2align3d.py, programs/e2projectmanager.py: Text3D
	  wigdte update

2011-09-13 14:46  ppenczek

	* sparx/libpy/projection.py: [no log message]

2011-09-13 14:45  ppenczek

	* libEM/: emdata.cpp, sparx/util_sparx.cpp: cosmetics on max_3D

2011-09-13 12:57  fjia

	* sparx/bin/: sxshftali.py, sxshiftali.py: [no log message]

2011-09-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-13 10:23  john

	* libEM/pmconfig/CMakeLists.txt: One more pm file

2011-09-13 10:21  john

	* images/EMAN2Icon.png, libEM/CMakeLists.txt,
	  libEM/pmconfig/spr.json, libEM/pmconfig/tomo.json,
	  libpyEM/qtgui/valslider.py, programs/CMakeLists.txt,
	  programs/e2projectmanager.py, programs/e2rct.py,
	  programs/spr.json, programs/tomo.json: Added project manager
	  config files

2011-09-13 09:53  zyang

	* sparx/libpy/applications.py: Trivial change.

2011-09-12 17:40  john

	* programs/: spr.json, tomo.json: JSON files for
	  e2projectmanager.py

2011-09-12 14:09  fjia

	* sparx/bin/sxshftali.py: [no log message]

2011-09-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-12 11:50  fjia

	* sparx/bin/sxshftali.py: output shifts are ints

2011-09-12 11:15  john

	* libpyEM/qtgui/: emitem3d.py, emscene3d.py: Added grouping for SG

2011-09-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-10 18:14  ross

	* libpyEM/qtgui/emdataitem3d.py: Volume node related stuff... 3D
	  texture now stores density in the alpha channel, using it for
	  transparency. Also, translation, rotation, and scaling work
	  properly for a single layer, next step is to add multiple layers
	  to show volume cross sections.

2011-09-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-09 16:52  john

	* libpyEM/qtgui/emscene3d.py: SG bugfix

2011-09-09 16:38  john

	* libpyEM/qtgui/emscene3d.py: Added more SG hot keys

2011-09-09 15:41  john

	* libpyEM/qtgui/: emscene3d.py, valslider.py: SG hot keys

2011-09-09 15:30  gtang

	* programs/e2proc2d.py: use regional writing for --twod2threed and
	  --threed2threed option to minimize memory footprint

2011-09-09 15:29  stevel

	* libpyEM/qtgui/embrowser.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2ctf.py: Fix CTF so it doesn't throw old quality values
	  away when refitting. Also refitting pays attention to old defocus
	  values (by default in GUI)

2011-09-09 15:25  zyang

	* sparx/libpy/applications.py: Trivial change

2011-09-09 15:21  zyang

	* sparx/libpy/applications.py: Made a small change to the ISAC
	  program.

2011-09-09 15:17  gtang

	* libEM/mrcio.cpp: fix MRC region writing bug

2011-09-09 14:48  john

	* libpyEM/qtgui/: emdataitem3d.py, emitem3d.py, emscene3d.py,
	  emshapeitem3d.py, valslider.py: SG uopdates and bufix

2011-09-09 12:30  john

	* libpyEM/qtgui/emscene3d.py, libpyEM/qtgui/valslider.py,
	  programs/e2projectmanager.py: bugfix for SG

2011-09-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-08 18:10  john

	* libpyEM/qtgui/emscene3d.py, programs/e2projectmanager.py: SG
	  bugfix

2011-09-08 16:41  fjia

	* sparx/bin/sxshftali.py: fix bug for --oneDx option

2011-09-08 15:53  gtang

	* CMakeLists.txt: support Python 2.7 for MacOS X 10.7(Lion)

2011-09-08 15:20  fjia

	* sparx/bin/sxgui.py: add centering tab for helical refinement

2011-09-08 14:29  zyang

	* sparx/libpy/applications.py: Minor change to ISAC problem

2011-09-08 14:27  zyang

	* sparx/libpy/applications.py: Fix a small bug in ISAC

2011-09-08 14:03  fjia

	* sparx/bin/: sxshftali.py, sxgui.py: [no log message]

2011-09-08 13:57  john

	* libpyEM/qtgui/: emrctboxergui.py, emrctstrategy.py: RCTboxer
	  bugfix

2011-09-08 13:29  fjia

	* sparx/bin/sxshftali.py: add option to apply calculated centering
	  parameters and write to output file

2011-09-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-08 11:48  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-09-08 11:33  fjia

	* sparx/bin/sxshftali.py: [no log message]

2011-09-08 11:08  fjia

	* sparx/bin/: sxgui.py, sxshftali.py: [no log message]

2011-09-07 18:16  john

	* libpyEM/qtgui/emscene3d.py: SG documentation

2011-09-07 18:07  john

	* libpyEM/qtgui/emscene3d.py: SG code beautification

2011-09-07 17:31  gtang

	* libEM/: hdfio2.cpp, hdfio2.h: read the meta attributes in
	  /MDF/images and save them in each image's attribute dictionary

2011-09-07 17:28  john

	* libpyEM/qtgui/emitem3d.py, libpyEM/qtgui/emscene3d.py,
	  libpyEM/qtgui/emshapeitem3d.py, programs/e2tomoboxer.py: SG
	  updates

2011-09-07 17:03  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-09-07 16:59  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-09-07 16:44  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-09-07 16:39  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-09-07 16:33  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-09-07 16:28  fjia

	* sparx/bin/sxshftali.py: changed some of the help messages

2011-09-07 16:27  fjia

	* sparx/bin/sxgui.py: add tab for pre-centering in sxisac

2011-09-07 15:10  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-09-07 14:38  john

	* programs/e2tomoboxer.py: Documentation

2011-09-07 14:32  john

	* libEM/emdata.cpp, programs/e2tomoboxer.py: Bugfix for tomoboxer
	  helixboxer

2011-09-07 14:29  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-09-07 14:10  zyang

	* sparx/libpy/applications.py: Small change to the ISAC program

2011-09-07 13:49  fjia

	* sparx/bin/sxgui.py: added explanations for sxisac params on
	  advanced tab

2011-09-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-07 12:00  fjia

	* sparx/bin/sxgui.py: add explanation for sxgui parameters in main
	  panel

2011-09-07 11:49  john

	* libEM/emdata.cpp, libpyEM/qtgui/emdataitem3d.py,
	  libpyEM/qtgui/emitem3d.py, libpyEM/qtgui/emshapeitem3d.py,
	  programs/e2tomoboxer.py: Got helixboxer working and added databox
	  size to SG

2011-09-06 17:20  ross

	* libpyEM/qtgui/emdataitem3d.py: fixing EMVolumeItem3D when the
	  root node has a (non-identity) transformation. Changing bounding
	  rectangle color for EMSliceItem3D.

2011-09-06 17:03  fjia

	* sparx/bin/sxshftali.py: for shift only centering

2011-09-06 16:31  ross

	* libpyEM/qtgui/emdataitem3d.py: One layer of Volume node is
	  working, now add multiple layers. (EMVolumeItem3D)

2011-09-06 15:52  fjia

	* sparx/bin/sxgui.py: change default params for sxisac

2011-09-06 15:44  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-09-06 15:11  zyang

	* sparx/libpy/applications.py: Some small change to ISAC program.

2011-09-06 15:05  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-09-06 14:53  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-09-06 12:03  eman-vm

	* programs/e2version.py: new date stamp

2011-09-06 11:57  gtang

	* libpyEM/qtgui/emshapeitem3d.py: [no log message]

2011-09-06 11:46  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-09-06 11:15  gtang

	* libpyEM/qtgui/emshapeitem3d.py: add line slice/stack control to
	  3D line inspector

2011-09-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-04 22:20  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, fourierfilter.cpp,
	  util_sparx.cpp, util_sparx.h: rotated astigmatism by 90 degrees

2011-09-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-02 17:53  ppenczek

	* sparx/libpy/projection.py: [no log message]

2011-09-02 17:25  ppenczek

	* sparx/libpy/projection.py: [no log message]

2011-09-02 17:01  ppenczek

	* sparx/libpy/projection.py: [no log message]

2011-09-02 16:56  ppenczek

	* sparx/libpy/projection.py: [no log message]

2011-09-02 16:54  gtang

	* libpyEM/qtgui/emshapeitem3d.py: wider box

2011-09-02 16:53  ppenczek

	* sparx/libpy/projection.py: [no log message]

2011-09-02 16:51  gtang

	* libpyEM/qtgui/emdataitem3d.py: John's fix

2011-09-02 15:57  john

	* libpyEM/qtgui/: emdataitem3d.py, emscene3d.py: Enhanced data
	  selection

2011-09-02 15:56  ppenczek

	* sparx/libpy/projection.py: [no log message]

2011-09-02 15:49  ppenczek

	* sparx/libpy/utilities.py: [no log message]

2011-09-02 15:08  john

	* libpyEM/qtgui/: emdataitem3d.py, emshapeitem3d.py: enhaced data
	  inspector look

2011-09-02 15:02  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-09-02 14:37  gtao

	* sparx/libpy/applications.py: [no log message]

2011-09-02 14:27  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-09-02 13:29  john

	* libpyEM/qtgui/: emscene3d.py, emshapeitem3d.py: bugfixO

2011-09-02 13:15  john

	* libpyEM/qtgui/: emscene3d.py, emshapeitem3d.py, valslider.py: SG
	  updates

2011-09-02 12:23  gtang

	* libpyEM/qtgui/emdataitem3d.py: [no log message]

2011-09-02 12:22  gtang

	* libpyEM/qtgui/emshapeitem3d.py: move label to the middle

2011-09-02 12:22  gtao

	* sparx/libpy/: applications.py, reconstruction.py: [no log
	  message]

2011-09-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-02 11:58  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-09-02 11:23  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-09-01 16:04  gtang

	* libpyEM/qtgui/emshapeitem3d.py: [no log message]

2011-09-01 13:50  gtao

	* libEM/sparx/emdata_sparx.cpp: [no log message]

2011-09-01 12:29  gtang

	* libpyEM/qtgui/emshapeitem3d.py: finish 3D line inspector

2011-09-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-09-01 11:29  gtao

	* sparx/libpy/: applications.py, reconstruction.py: [no log
	  message]

2011-08-31 22:15  ross

	* libpyEM/qtgui/emdataitem3d.py: EMVolumeItem3D is really a slice
	  viewer using 3D textures. Transparency working! Copied its
	  rendering code to give EMSliceItem3D the ability to use a 3D
	  texture. Modified EMSliceInspector to look better and give an
	  option to use a 3D texture. EMSliceItem3D uses transparency (for
	  both 2D and 3D textures).

2011-08-31 17:38  gtang

	* libpyEM/qtgui/emshapeitem3d.py: [no log message]

2011-08-31 16:42  gtao

	* sparx/libpy/reconstruction.py: [no log message]

2011-08-31 16:36  gtao

	* sparx/libpy/applications.py, sparx/libpy/reconstruction.py,
	  libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h: [no log
	  message]

2011-08-31 12:20  john

	* libEM/emdata.cpp, libpyEM/qtgui/emdataitem3d.py,
	  libpyEM/qtgui/emscene3d.py, libpyEM/qtgui/valslider.py,
	  programs/e2tomoboxer.py: Added helixboxer to tomoboxer and added
	  force close of inspector when emscene3d is closed

2011-08-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-31 11:09  gtao

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  sparx/bin/sxrecons3d_n.py, sparx/libpy/applications.py,
	  sparx/libpy/reconstruction.py: [no log message]

2011-08-31 08:36  stevel

	* libpyEM/qtgui/: emimagemx.py, emshape.py: Fixed font display ?

2011-08-30 22:41  ross

	* libpyEM/qtgui/emdataitem3d.py: Volume node closer to correct

2011-08-30 20:35  ross

	* libpyEM/qtgui/emdataitem3d.py: volume node has test code that
	  isn't working properly yet... saving my work though

2011-08-30 17:31  gtang

	* rt/demo/scene3d_test.py: [no log message]

2011-08-30 17:30  gtang

	* libpyEM/qtgui/emshapeitem3d.py: 3DText inspector work

2011-08-30 17:12  zyang

	* sparx/libpy/applications.py: Fix a trivial bug

2011-08-30 16:24  zyang

	* sparx/: bin/sxfind_struct.py, libpy/applications.py,
	  libpy/projection.py: Add a MPI version command-line algorithm.

2011-08-30 14:45  stevel

	* libEM/glutil.cpp, libEM/processor.cpp, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/embrowser.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emshape.py, programs/e2bdb.py,
	  programs/e2eulerxplor.py: Fixing font display...

2011-08-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-30 10:39  john

	* libpyEM/qtgui/emrctboxergui.py, libpyEM/qtgui/emshape.py,
	  programs/e2RCTboxer.py: Bug fix for the EMShape label

2011-08-30 09:44  zyang

	* sparx/: bin/sxstability.py, libpy/pixel_error.py: Very trivial
	  change.

2011-08-29 15:23  john

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/qtgui/emdataitem3d.py, libpyEM/qtgui/emshape.py,
	  programs/e2tomoboxer.py: Added helix boxer to tomoboxer, and
	  fixed transform bug in SG

2011-08-29 14:56  gtang

	* programs/e2.py, sparx/bin/sparx: revert the ipython to version <
	  0.11

2011-08-29 14:27  gtang

	* sparx/bin/sparx: [no log message]

2011-08-29 12:28  gtang

	* programs/e2.py, sparx/bin/sparx: [no log message]

2011-08-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-29 11:57  gtang

	* programs/e2.py, sparx/bin/sparx: fix for ipython 0.11

2011-08-29 08:30  stevel

	* examples/mergeproject.py: Improved mergeproject

2011-08-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-27 20:24  ppenczek

	* sparx/libpy/applications.py: [no log message]

2011-08-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-26 17:56  ross

	* libpyEM/qtgui/emitem3d.py: EMItem3D's constructor parameter
	  transform defaults to identity transform instead of None. Its
	  render method uses Transform::is_identity() to see if
	  transformations need to be applied. If the node is selected, the
	  render method also calls EMItem3DInspector.updateItemControls().

2011-08-26 17:32  gtang

	* rt/demo/scene3d_test.py: [no log message]

2011-08-26 17:31  gtang

	* libpyEM/qtgui/emshapeitem3d.py: workign on inspector for 3DText,
	  line

2011-08-26 17:16  gtao

	* sparx/libpy/applications.py: [no log message]

2011-08-26 17:05  ppenczek

	* sparx/libpy/applications.py:	to fix ihrsr

2011-08-26 16:50  gtao

	* sparx/libpy/applications.py: [no log message]

2011-08-26 14:50  gtang

	* libpyEM/qtgui/emshapeitem3d.py: put the Transform construction in
	  default argument end up with same Transform object for different
	  shape item object.

2011-08-26 12:15  stevel

	* examples/mergeproject.py: Example program merges particles from
	  multiple projects into a single project

2011-08-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-25 22:31  ross

	* libpyEM/qtgui/: emitem3d.py, emscene3d.py:
	  EMItem3D.update_matrices() renamed to updateMatrices()

2011-08-25 18:02  ross

	* libpyEM/qtgui/emdataitem3d.py: adding xy, yz, and zx plane
	  constraints for slice viewer

2011-08-25 14:39  fjia

	* sparx/bin/sxgui.py: rearranged buttons according to logical order
	  in main window

2011-08-25 14:20  fjia

	* sparx/bin/sxgui.py: added button for iter isac

2011-08-25 13:46  gtang

	* libpyEM/qtgui/emshapeitem3d.py, rt/demo/scene3d_test.py: [no log
	  message]

2011-08-25 12:12  stevel

	* libEM/emdata_transform.cpp, programs/e2eotest.py: Fixed color
	  display of phases

2011-08-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-25 09:26  gtang

	* libEM/glutil.cpp: [no log message]

2011-08-24 13:57  fjia

	* sparx/bin/sxgui.py: remove extra window in sxmref_ali3d

2011-08-24 13:21  john

	* libpyEM/qtgui/emshapeitem3d.py: Bug fixes

2011-08-24 12:11  ross

	* examples/mouse_and_key_modifiers.py: small code comment for
	  documentation

2011-08-24 12:04  ross

	* examples/mouse_and_key_modifiers.py: Demo program to test how
	  mouse buttons and keyboard modifiers work with Qt on different
	  operating systems.

2011-08-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-24 11:38  john

	* libpyEM/qtgui/: emscene3d.py, emshapeitem3d.py: Added Text to SG

2011-08-24 10:50  ross

	* libpyEM/qtgui/emdataitem3d.py:
	  EMDataItem3D.getBoundingBoxDimensions(),
	  EMIsosurface.getBoundingBoxDimenstions(), and skeleton code (as
	  in just starting) for EMVolumeItem3D and EMVolumeInspector

2011-08-24 10:40  stevel

	* libpyEM/qtgui/emform.py, programs/e2eotest.py: Hack to deal with
	  deleted files in workflow.

2011-08-24 10:21  john

	* libEM/transform.cpp, libpyEM/qtgui/emitem3d.py,
	  libpyEM/qtgui/emscene3d.py, libpyEM/qtgui/emshapeitem3d.py,
	  rt/demo/scene3d_test.py: Fixed line trig when z=0

2011-08-23 17:44  fjia

	* sparx/bin/sxgui.py: added sxmref_ali3d

2011-08-23 17:24  john

	* libpyEM/qtgui/: emitem3d.py, emscene3d.py: Bug fix for SG

2011-08-23 15:52  john

	* libpyEM/qtgui/emdataitem3d.py, libpyEM/qtgui/emitem3d.py,
	  libpyEM/qtgui/emscene3d.py, programs/e2tomoboxer.py: Bug fix for
	  node insertion transformation

2011-08-23 15:25  fjia

	* sparx/bin/sxgui.py: added sxpca

2011-08-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-23 10:32  john

	* libpyEM/qtgui/emscene3d.py: Bugfix for SG

2011-08-23 10:17  john

	* libEM/aligner.h, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emscene3d.py: Added new 3d widget to e2dispaly

2011-08-22 17:49  john

	* libpyEM/qtgui/emdataitem3d.py, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emscene3d.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emshapeitem3d.py, programs/e2display.py: Added new
	  3d widget for e2display which can be turned on by using
	  --newwidget

2011-08-22 17:14  fjia

	* sparx/bin/sxgui.py: added sxpdb2em button

2011-08-22 16:10  eman-vm

	* programs/e2version.py: new date stamp

2011-08-22 15:52  gtang

	* rt/demo/scene3d_test.py: [no log message]

2011-08-22 15:51  gtang

	* libpyEM/qtgui/emshapeitem3d.py: 3D text shape item

2011-08-22 15:37  fjia

	* sparx/bin/sxgui.py: made advanced window into a tab in main
	  window for ali2d, kmeans and kmeansgroups

2011-08-22 15:00  fjia

	* sparx/bin/sxgui.py: made advanced parameters window into another
	  tab in main window for ali3d, also prompts user for file name for
	  save/repop parameters

2011-08-22 14:03  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-08-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-22 11:05  gtang

	* libpyEM/qtgui/emshapeitem3d.py: finish shape item 3D line

2011-08-22 10:52  fjia

	* sparx/bin/sxgui.py: adding window for k_means_groups

2011-08-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-20 11:33  ross

	* libpyEM/qtgui/emdataitem3d.py: EMSliceItem3D is working! It may
	  not be feature complete yet.

2011-08-20 10:35  ross

	* libpyEM/qtgui/emdataitem3d.py: EMSliceItem3D and EMSliceInspector

2011-08-19 17:54  john

	* libpyEM/qtgui/: emitem3d.py, emscene3d.py, emshapeitem3d.py,
	  valslider.py: Bug fixes for the SG

2011-08-19 16:46  fjia

	* sparx/bin/sxgui.py: added tabs for ali3d advanced window

2011-08-19 15:59  john

	* libpyEM/qtgui/: emscene3d.py, emshapeitem3d.py: Added cone and
	  line functionality

2011-08-19 14:46  gtang

	* libpyEM/qtgui/: emscene3d.py, valslider.py: Fixed camera bug

2011-08-19 13:35  stevel

	* programs/e2evalimage.py: Trivial

2011-08-19 12:51  gtang

	* libpyEM/qtgui/emshapeitem3d.py: chenge cylinder and cone's rotate
	  center to the middle

2011-08-19 12:25  john

	* libpyEM/qtgui/: emdataitem3d.py, emimageutil.py, emscene3d.py,
	  emshapeitem3d.py: updates

2011-08-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-19 11:59  gtang

	* libpyEM/qtgui/emshapeitem3d.py, rt/demo/scene3d_test.py: add
	  shape cone

2011-08-19 09:51  stevel

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emimage.py,
	  programs/e2ctf.py: Fixed autoupdate of images ... again

2011-08-18 20:06  ppenczek

	* sparx/bin/sxcpy.py: [no log message]

2011-08-18 15:55  gtang

	* libpyEM/typeconverter.h: Fix the memory leak when setting a list
	  as image attribute.

2011-08-18 15:32  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-08-18 15:23  gtang

	* rt/pyem/test_processor.py, libEM/omapio.cpp: [no log message]

2011-08-18 13:50  fjia

	* sparx/bin/sxgui.py: fixed the way repop works in ali2d

2011-08-18 13:20  ppenczek

	* sparx/libpy/fundamentals.py: resample

2011-08-18 12:39  john

	* libpyEM/qtgui/: emscene3d.py, emshapeitem3d.py: Added Data
	  insertion

2011-08-18 12:15  fjia

	* sparx/bin/sxgui.py: changed ctf and fourvar options to use
	  checkbox for ali2d and ali3d

2011-08-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-18 11:40  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-08-18 10:47  stevel

	* libEM/processor.cpp, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emplot2d.py, libpyEM/qtgui/emshape.py,
	  programs/e2ctf.py, programs/e2evalimage.py,
	  programs/e2filtertool.py: Improvements to filtertool and
	  imageval. Font rendering handled completely differently. GLUT no
	  longer used.

2011-08-18 09:37  john

	* libpyEM/qtgui/emscene3d.py: Added mouse functionality

2011-08-17 17:57  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-08-17 17:55  fjia

	* sparx/bin/sxgui.py: added sxk_means

2011-08-17 16:20  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-08-17 15:40  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-08-17 15:10  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-08-17 13:46  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-08-17 13:22  gtao

	* sparx/bin/: sxgui.py: [no log message]

2011-08-17 12:19  fjia

	* sparx/bin/sxgui.py: put ali2d and ali3d code back

2011-08-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-17 11:44  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-08-17 11:32  john

	* libpyEM/qtgui/: emdataitem3d.py, emitem3d.py, emscene3d.py,
	  emshapeitem3d.py, valslider.py: Bugfixes

2011-08-17 11:08  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-08-17 10:50  fjia

	* sparx/: bin/sxgui.py, libpy/gui_ali2d.py, libpy/gui_ali3d.py: [no
	  log message]

2011-08-17 10:00  fjia

	* sparx/bin/gui_ali3d.py: moving gui_ali3d to libpy

2011-08-17 10:00  fjia

	* sparx/bin/gui_ali2d.py: moving gui_ali2d to libpy directory

2011-08-17 09:59  fjia

	* sparx/libpy/gui_ali3d.py: gui related code for ali3d

2011-08-17 09:58  fjia

	* sparx/libpy/gui_ali2d.py: gui related code for ali2d

2011-08-17 05:55  ppenczek

	* sparx/libpy/fundamentals.py: [no log message]

2011-08-16 16:50  john

	* libpyEM/qtgui/: emdataitem3d.py, emimageutil.py, emitem3d.py,
	  emscene3d.py, emshapeitem3d.py, valslider.py: 3D widget updates
	  and fixes

2011-08-16 16:12  fjia

	* sparx/bin/sxgui.py: moved classes for ali3d popup gui to
	  gui_ali3d

2011-08-16 16:11  fjia

	* sparx/bin/gui_ali3d.py: all the classes for ali3d gui is in here

2011-08-16 16:05  fjia

	* sparx/bin/sxgui.py: moved classes Popuptwodali and
	  Popupadvparams_ali2d into gui_ali2d.py

2011-08-16 16:03  fjia

	* sparx/bin/gui_ali2d.py: file containing class for ali2d popup gui

2011-08-16 15:55  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-08-16 15:45  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-08-16 15:38  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-08-16 15:36  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-08-16 15:20  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-08-16 15:10  fjia

	* sparx/bin/sxgui.py: added newline after "generate command line"
	  button for sxali2d and sxali3d

2011-08-16 14:47  fjia

	* sparx/bin/: sxgui_ali3d.py: [no log message]

2011-08-16 14:30  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-08-16 13:25  ppenczek

	* sparx/bin/sxgui.py: some text corrections

2011-08-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-16 10:51  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-08-15 17:47  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-08-15 17:01  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-08-15 16:13  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-08-15 14:50  stevel

	* libEM/processor.cpp, libEM/processor.h, programs/e2evalimage.py:
	  New 2-D BG subtraction mode in e2evalimage

2011-08-15 14:24  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-08-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-15 11:12  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-08-15 11:10  fjia

	* sparx/bin/sxgui.py: added drop down dialog for setting/importing
	  parameter xform.align2d

2011-08-14 20:07  ppenczek

	* sparx/demo/3_bdb_ctf/run_through_example: [no log message]

2011-08-14 20:06  ppenczek

	* libEM/reconstructor.cpp, libEM/sparx/emdata_sparx.cpp,
	  libEM/sparx/fourierfilter.cpp, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h,
	  sparx/demo/3_bdb_ctf/run_through_example, sparx/libpy/filter.py,
	  sparx/libpy/morphology.py, sparx/libpy/utilities.py: astigmatism

2011-08-14 19:35  gtang

	* libEM/emobject.cpp, libEM/emobject.h, libpyEM/typeconverter.cpp,
	  libpyEM/typeconverter.h: revert my previous change. There are
	  more things to go through since this fix breaks many existing
	  code.

2011-08-14 19:22  gtang

	* libEM/emobject.cpp, libEM/emobject.h, libpyEM/typeconverter.cpp,
	  libpyEM/typeconverter.h: use shared_ptr for float list attribute
	  to fix the memory leak, also avoid two extra memory copies when
	  set and get float list attribute.

2011-08-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-13 22:29  stevel

	* programs/e2refine.py: Support the breaksym orientgen option in
	  e2refine

2011-08-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-13 11:25  gtang

	* rt/emdata/CMakeLists.txt: [no log message]

2011-08-12 16:47  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-08-12 16:31  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-08-12 16:10  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-08-12 16:03  fjia

	* sparx/bin/sxgui.py: added entry for external user function

2011-08-12 15:43  gtang

	* rt/emdata/mem_test.cpp: [no log message]

2011-08-12 15:34  stevel

	* libEM/processor.cpp, libEM/processor.h, libEM/symmetry.cpp,
	  libEM/symmetry.h, programs/e2filtertool.py: New symmetry breaking
	  option

2011-08-12 12:02  gtang

	* rt/emdata/mem_test.cpp: [no log message]

2011-08-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-11 17:22  gtang

	* rt/emdata/: CMakeLists.txt, mem_test.cpp: testing code

2011-08-11 16:04  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-08-11 14:11  fjia

	* sparx/bin/sxgui.py: using subprocess to spawn external process

2011-08-11 13:23  fjia

	* sparx/bin/icon.png: [no log message]

2011-08-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-11 11:55  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-08-11 11:53  fjia

	* images/macimages/sparxicon.png, images/sparxicon.png,
	  sparx/bin/sxgui.py: [no log message]

2011-08-11 11:18  gtao

	* sparx/bin/sxgui.py: [no log message]

2011-08-11 11:05  stevel

	* libEM/processor.cpp, libpyEM/qtgui/valslider.py,
	  programs/e2filtertool.py: Filtertool now much more capable

2011-08-11 11:03  fjia

	* sparx/bin/sxgui.py: added _ali2d suffix to popupadvparams class

2011-08-11 10:35  fjia

	* sparx/bin/sxgui.py: removed all carriage returns

2011-08-10 21:27  ppenczek

	* sparx/bin/: sxgui.py: corrected wrong character

2011-08-10 17:25  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-08-10 17:07  fjia

	* sparx/bin/sxgui.py: [no log message]

2011-08-10 16:52  fjia

	* sparx/bin/sxgui.py: changed color of run button

2011-08-10 16:35  zyang

	* sparx/libpy/pixel_error.py: Trivial change.

2011-08-10 13:46  zyang

	* sparx/libpy/utilities.py: Fix a trivial bug.

2011-08-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-10 11:41  fjia

	* sparx/bin/sxgui.py: sparx gui

2011-08-10 11:41  fjia

	* sparx/bin/icon.png: icon for use in sparx gui (sx.py)

2011-08-09 13:29  stevel

	* programs/e2montecarlorecon.py: Fixes for montecarlorefine. Really
	  needs to be parallelized

2011-08-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-08 10:08  stevel

	* libEM/transform.cpp, programs/e2proc3d.py: Fixed 5 -> 2 fold
	  icosahedral rotation and added e2proc3d.py option to perform it.
	  Uses ViperDB convention.

2011-08-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-05 19:40  jgalaz

	* programs/e2tomoallvsall.py: Had accidentally commited an older
	  version. Still halfways developed.

2011-08-05 17:30  gtang

	* libEM/imagicio2.cpp: fix the first header's image count
	  field(should be nimg-1)

2011-08-05 16:33  jgalaz

	* programs/e2classaverage3d.py: Fixed typo

2011-08-05 16:16  jgalaz

	* programs/e2classaverage3d.py: Error fixed for sorting the best
	  peaks, The list of results  was previously sorted based on the
	  'coarse' key in the dictionaries for each alignment, instead of
	  the 'score' key.

2011-08-05 12:07  ross

	* libpyEM/qtgui/: emdataitem3d.py, emitem3d.py: Added
	  drawBoundingBox() function. It is used when EMIsosurface node is
	  selected.

2011-08-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-04 18:41  jgalaz

	* programs/e2classaverage3d.py: Added option to separte data in
	  sets based on correlation to a single reference

2011-08-04 18:39  jgalaz

	* programs/e2tomoallvsall.py: Self descriptive program name. Not
	  finished

2011-08-04 15:47  zyang

	* sparx/: bin/sxisac.py, libpy/pixel_error.py: Trivial change.

2011-08-04 13:10  ross

	* libpyEM/qtgui/emdataitem3d.py: changed the way updates happen in
	  data and isosurface nodes when new EMData is set for the data
	  node

2011-08-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-04 07:11  ppenczek

	* sparx/bin/sxfit_error.py: [no log message]

2011-08-03 16:55  ross

	* libpyEM/qtgui/emdataitem3d.py: Added EMDataItem3D.setData().
	  Removed commented-out isosurface rendering code (from before
	  outlining was used to indicate selection).

2011-08-03 15:38  zyang

	* sparx/libpy/pixel_error.py: Trivial change.

2011-08-03 13:19  zyang

	* sparx/libpy/: applications.py, pixel_error.py: Trivial change.

2011-08-03 12:55  gtang

	* libEM/imagicio2.cpp: pad the label and history with space

2011-08-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-03 11:52  stevel

	* programs/e2evalimage.py: evalimage is working well, thought could
	  use some additional feature enhancements

2011-08-03 11:41  john

	* libpyEM/qtgui/: emscene3d.py, valslider.py: Fixed lights bug

2011-08-03 11:19  stevel

	* programs/e2evalimage.py: trivial

2011-08-03 11:12  ross

	* libpyEM/qtgui/emdataitem3d.py: added sampling level; cleaning up
	  code

2011-08-03 11:09  stevel

	* libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py, programs/e2ctf.py,
	  programs/e2evalimage.py: Improved evalimage. Also made 2-D view
	  in e2ctf look much better (removed intensity conversion)

2011-08-03 09:48  zyang

	* sparx/bin/sxstability.py: Trivial change.

2011-08-02 17:31  john

	* libpyEM/qtgui/: emitem3d.py, emscene3d.py, emshapeitem3d.py,
	  valslider.py: Added toolbar functionality

2011-08-02 15:55  ross

	* libpyEM/qtgui/emdataitem3d.py: added histogram widget

2011-08-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-02 11:55  stevel

	* libEM/dm3io.cpp, programs/e2evalimage.py: evalimage working. DM3
	  reading improved

2011-08-02 11:17  stevel

	* libEM/dm3io.cpp, programs/e2evalimage.py: evalimage beginning to
	  work. Improving dm3 reader

2011-08-01 22:53  gtang

	* libEM/pngio.cpp: make png I/O compatible with libpng 1.5 API

2011-08-01 18:11  john

	* libpyEM/qtgui/: emscene3d.py, valslider.py: Removed several
	  irritating SG bugs

2011-08-01 15:10  stevel

	* libpyEM/EMAN2db.py, programs/e2evalimage.py: Work on evalimage.
	  Still not quite there.

2011-08-01 14:51  gtang

	* libEM/randnum.h: correct comment

2011-08-01 14:47  gtang

	* libEM/randnum.h: [no log message]

2011-08-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-08-01 11:38  gtang

	* libEM/imagicio2.cpp: Fix an issue the EMAN2's imagic file can not
	  be processed by IMAGIC software. The header field IDAT1(11) RSIZE
	  is the pixel size but written as bytes in EMAN2.

2011-08-01 11:11  gtao

	* sparx/: bin/sxihrsr.py, libpy/applications.py: merge helical
	  chunk code into applications.

2011-08-01 10:48  zyang

	* sparx/bin/: sxisac.py, sxiter_isac.py: Change the file name

2011-08-01 10:11  john

	* libpyEM/qtgui/emscene3d.py: Added tool connections

2011-08-01 09:28  john

	* libpyEM/qtgui/: emscene3d.py, valslider.py: Toolbar update

2011-07-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-30 19:28  ross

	* libpyEM/qtgui/emitem3d.py: EMItem3D's self.children is now a list
	  instead of a set. Also converted remaining space indentation to
	  tabs.

2011-07-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-29 17:14  john

	* libpyEM/qtgui/: emitem3d.py, emscene3d.py: Added toolbar

2011-07-29 12:37  john

	* libpyEM/qtgui/emdataitem3d.py: added documentation

2011-07-29 12:33  john

	* libpyEM/qtgui/: emdataitem3d.py, emitem3d.py, emscene3d.py,
	  emshapeitem3d.py: Chnaged eminspector widget to a grid layout

2011-07-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-29 11:13  zyang

	* sparx/libpy/pixel_error.py: Add a printout.

2011-07-29 10:08  zyang

	* sparx/: bin/sxiter_isac.py, libpy/applications.py: Add ISAC
	  (Iterative Stable Alignment and Clustering) program to the
	  system.

2011-07-29 06:06  ppenczek

	* sparx/libpy/alignment.py: [no log message]

2011-07-29 05:59  ppenczek

	* sparx/libpy/applications.py: [no log message]

2011-07-28 17:25  john

	* libpyEM/qtgui/: emitem3d.py, emscene3d.py, valslider.py: Made sg
	  inspector a strick observer of the SG

2011-07-28 16:25  john

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, libpyEM/qtgui/emdataitem3d.py,
	  libpyEM/qtgui/emitem3d.py, libpyEM/qtgui/emscene3d.py,
	  libpyEM/qtgui/emshapeitem3d.py, libpyEM/qtgui/valslider.py: Fixed
	  transformation disortion in the scenegraph

2011-07-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-28 10:24  stevel

	* programs/: e2evalimage.py, e2refine.py: Still working on
	  evalimage

2011-07-27 17:32  john

	* libpyEM/qtgui/emscene3d.py: Bug fix for session loader

2011-07-27 17:13  john

	* libpyEM/qtgui/: emdataitem3d.py, emitem3d.py, emscene3d.py,
	  emshapeitem3d.py: Improved design of session laoder

2011-07-27 17:01  john

	* libpyEM/qtgui/: emdataitem3d.py, emitem3d.py, emscene3d.py,
	  emshapeitem3d.py, valslider.py: Added session saving

2011-07-27 11:01  ross

	* libpyEM/qtgui/emdataitem3d.py: Can now browse for a new volume
	  file, and the EMData for the data node will be changed, and its
	  isosurfaces will be updated.

2011-07-26 17:34  ross

	* libpyEM/qtgui/emitem3d.py: EMItem3D constructor, setParent(), and
	  setChildren() are now smarter at adding parent and child
	  references. EMItem3D.removeChild() bugfix. Added new methods
	  addParentReferences(), removeParentReferences(), and
	  displayTree() to EMItem3D.

2011-07-26 16:05  john

	* libpyEM/qtgui/: emdataitem3d.py, emscene3d.py, emshapeitem3d.py,
	  valslider.py: Added selection outlining

2011-07-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-26 11:36  gtang

	* libEM/: CMakeLists.txt, all_imageio.h, emutil.cpp, emutil.h,
	  situsio.cpp, situsio.h: implement situs file I/O

2011-07-25 13:16  zyang

	* sparx/libpy/pixel_error.py: Fix a small bug

2011-07-25 12:57  ross

	* libpyEM/qtgui/emitem3d.py: fixed getSelectedAncestorNodes()

2011-07-25 12:44  john

	* libpyEM/qtgui/emscene3d.py: Enabled data to opened by inspector

2011-07-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-25 11:16  john

	* libpyEM/qtgui/: emdataitem3d.py, emitem3d.py, emscene3d.py,
	  valslider.py: Added weakrefs for the inspectors

2011-07-25 09:43  john

	* libpyEM/qtgui/: emitem3d.py, valslider.py: added Ross's emscene3d
	  comments

2011-07-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-22 19:07  ross

	* libpyEM/qtgui/: emdataitem3d.py, emitem3d.py, emscene3d.py,
	  emshapeitem3d.py: changing EMItem3D.widget to
	  EMItem3D.item_inspector and EMItem3D.getSceneGui() to
	  EMItem3D.getItemInspector()

2011-07-22 18:34  ross

	* libpyEM/qtgui/: emdataitem3d.py, emitem3d.py, emshapeitem3d.py:
	  Added name class attribute to EMItem3D and its subclasses. It is
	  a short string that describes the class and could be used to set
	  the text for the tree widget items in the inspector.

	  Also, fixed EMIsosurface.renderNode() code for culling back
	  faces.

2011-07-22 17:19  ross

	* libpyEM/qtgui/emitem3d.py: EMItem3D.removeNode(self, node) also
	  removes all descendant nodes now

2011-07-22 17:16  zyang

	* sparx/libpy/pixel_error.py: Use C++ code instead of scipy to
	  reduce dependency

2011-07-22 17:04  john

	* libpyEM/qtgui/emscene3d.py: bugfix

2011-07-22 16:55  zyang

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: Fix a gigantic
	  warning.

2011-07-22 16:50  john

	* libpyEM/qtgui/emscene3d.py, libpyEM/qtgui/valslider.py,
	  programs/e2tiltvalidate.py: Added node addition and removal by
	  the inspector

2011-07-22 16:44  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Change the C++ code of calculating the
	  pixel error.

2011-07-22 15:48  eman-vm

	* programs/e2version.py: new date stamp

2011-07-22 12:20  ross

	* libpyEM/qtgui/emdataitem3d.py: cleaning up iso rendering code and
	  adding wireframe mode

2011-07-21 17:09  john

	* libpyEM/qtgui/: emdataitem3d.py, emitem3d.py, emscene3d.py,
	  valslider.py: emscene updates

2011-07-21 16:41  zyang

	* sparx/: bin/sxstability.py, libpy/pixel_error.py: Overhaul to
	  alignment stability program using the new pixel error formula

2011-07-21 15:50  ppenczek

	* sparx/libpy/applications.py: changed fscmask for  ali3d_MPI

2011-07-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-21 11:58  stevel

	* CMakeLists.txt, libEM/symmetry.cpp, libEM/symmetry.h: Changes how
	  helical symmetry works

2011-07-20 18:21  john

	* libpyEM/qtgui/emdataitem3d.py: [no log message]

2011-07-20 18:07  jgalaz

	* programs/e2classaverage3d.py:
	  The postprocessing operation should NOT be applied to the final
	  average (written to --output), It is applied to the average on
	  each iteration, saved to class_00.bdb,  but we still need a
	  version of the final average that is COMPLETELY RAW. The final
	  average WITH the postprocessing applied is the last particle
	  inside class_00.bdb.	Also reset the origin of all iteration and
	  final averages, as well as the particles, to 0. THis prevents
	  display issues in chimera.  Changed other small stuff (can't
	  remember what now).

2011-07-20 18:06  john

	* libpyEM/qtgui/emscene3d.py, programs/e2tiltvalidate.py: [no log
	  message]

2011-07-20 18:06  john

	* libEM/aligner.cpp, libpyEM/qtgui/emdataitem3d.py,
	  libpyEM/qtgui/emscene3d.py, libpyEM/qtgui/emshapeitem3d.py,
	  programs/e2projectmanager.py, programs/e2tiltvalidate.py: Added
	  per particle for tilt validate, and integrated isosurfaces

2011-07-20 14:02  ross

	* libpyEM/qtgui/emdataitem3d.py: isosurface updates

2011-07-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-20 10:53  gtao

	* sparx/bin/sxihrsr.py: [no log message]

2011-07-19 18:12  ross

	* libpyEM/qtgui/emdataitem3d.py: browse for data file in data node;
	  set isosurface in iso node

2011-07-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-19 10:08  zyang

	* sparx/bin/sxstability.py: Add a verbose option to print the
	  individual pixel errors and write textfiles that contain
	  alignment parameters.

2011-07-18 14:16  jkovacs

	* sparx/bin/sxfit_error.py: Program to estimate fitting precision
	  into 3D maps.

2011-07-18 13:28  gtao

	* sparx/bin/: sxali3d.py: [no log message]

2011-07-18 13:06  gtao

	* sparx/bin/sxali3d.py: [no log message]

2011-07-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-16 18:23  ross

	* libpyEM/qtgui/emdataitem3d.py: isosurface bug fixes

2011-07-16 16:03  ross

	* libpyEM/qtgui/emitem3d.py: moved EMDataItem3D, EMIsosurface, and
	  their inspector classes to emdataitem3d.py

2011-07-16 16:02  ross

	* libpyEM/qtgui/emdataitem3d.py: scene graph node to work with
	  EMData objects; currently putting isosurface node in this file,
	  also

2011-07-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-15 17:00  john

	* libEM/transform.cpp, libEM/transform.h, libEM/vec3.h,
	  libpyEM/libpyTransform2.cpp, libpyEM/qtgui/emitem3d.py,
	  libpyEM/qtgui/emscene3d.py, libpyEM/qtgui/valslider.py,
	  programs/e2tiltvalidate.py: 3D widget updates

2011-07-15 16:00  ross

	* libpyEM/qtgui/emitem3d.py: porting code from emimage3diso.py to
	  EMIsosurface

2011-07-15 12:26  gtang

	* programs/e2proc2d.py: [no log message]

2011-07-15 12:20  gtang

	* programs/e2proc2d.py: [no log message]

2011-07-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-14 15:31  gtao

	* sparx/bin/sxali3d.py: [no log message]

2011-07-14 15:27  gtao

	* sparx/libpy/applications.py: add code ihrsr to put projections
	  back into unique range of group symmetry after helical wrapping.

2011-07-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-13 14:42  gtang

	* programs/e2unwrap3d.py: fix the carriage return

2011-07-13 12:47  gtang

	* libpyEM/EMAN2db.py: keyword argument call in Python style for
	  read_image()

2011-07-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-12 15:50  gtang

	* rt/demo/scene3d_test.py: [no log message]

2011-07-12 13:14  gtang

	* programs/e2version.py: 2.0.3

2011-07-12 12:54  gtang

	* programs/e2ctf.py: show angstrom symbol in e2ctf plot

2011-07-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-12 11:59  stevel

	* libpyEM/qtgui/emimage3d.py, programs/e2filtertool.py: Filtertool
	  working, if a bit simplistic

2011-07-12 11:46  ross

	* libpyEM/qtgui/emimage3d.py: memory leak fix: removing tabs from
	  the inspector causes them to be marked for deletion now rather
	  than hidden

2011-07-12 08:03  stevel

	* libpyEM/qtgui/emsprworkflow.py, programs/e2filtertool.py: Fixed
	  emsprworkflow bug with deleting particles

2011-07-12 07:41  stevel

	* libpyEM/qtgui/valslider.py, programs/CMakeLists.txt,
	  programs/e2filtertool.py, programs/e2refine.py: Working on
	  filtertool. A few valslider fixes

2011-07-11 15:35  gtang

	* libpyEM/qtgui/emshapeitem3d.py: solid cylinder

2011-07-11 15:28  stevel

	* programs/: CMakeLists.txt, e2refine.py: Activate filtertool

2011-07-11 12:45  stevel

	* programs/e2bdb.py: extractplots option

2011-07-11 12:07  gtang

	* libpyEM/qtgui/emshapeitem3d.py: eliminate glut

2011-07-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-08 09:51  zyang

	* sparx/libpy/pixel_error.py: Add an option to print individual
	  pixel error.

2011-07-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-06 23:17  jgalaz

	* programs/e2tomoboxer.py: Fixes.  -

2011-07-06 20:49  jgalaz

	* programs/e2tomoboxer.py: File was completely messed up, not sure
	  why. Updated/fixed.  -

2011-07-06 19:54  jgalaz

	* programs/e2tomoboxer.py: [no log message]

2011-07-06 12:52  gtang

	* programs/e2proc2d.py: fix the option threed2threed and
	  twod2threed append by default

2011-07-06 12:21  eman-vm

	* programs/e2version.py: new date stamp

2011-07-06 10:38  john

	* libpyEM/qtgui/emrctboxergui.py, libpyEM/qtgui/emscene3d.py,
	  libpyEM/qtgui/emshapeitem3d.py, programs/e2RCTboxer.py,
	  programs/e2projectmanager.py, programs/e2tiltvalidate.py,
	  programs/e2workflow.py: RCT updates and scene

2011-07-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-05 07:16  stevel

	* libEM/processor.h, libEM/sparx/processor_sparx.h,
	  programs/e2tomoboxer.py: flip -> mirror

2011-07-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-03 23:58  jgalaz

	* programs/e2tomoboxer.py: Got rid of the aberrant sheet coming up
	  in the sub-volumes resulting from flipping operations prior to
	  normalizing.	Fix a bug with contrast reversal (files were not
	  saved with contrast reversed, even if the option was selected).

2011-07-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-02 15:10  jgalaz

	* programs/e2tomoboxer.py: Had accidentally broken boxing from
	  disk. Fixed it.  Boxing from binned tomograms was enabled only
	  for boxing from memory. Enabled it from disk now too. Same thing
	  for contrast reversal.

2011-07-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-07-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-30 20:24  gtang

	* libpyEM/typeconverter.cpp: in numpy2e, copy the numpy array to
	  avoid memory leak.

2011-06-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-30 11:52  gtao

	* sparx/libpy/alignment.py: [no log message]

2011-06-30 11:39  gtao

	* libpyEM/libpyUtils2.cpp: python boost to handle new add function
	  for --an of ihrsr.

2011-06-30 11:38  gtao

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: to handel --an option
	  for ihrsr.

2011-06-30 11:37  gtao

	* sparx/libpy/: alignment.py, applications.py: add code to handle
	  --an option for ihrsr

2011-06-30 09:12  ross

	* libpyEM/qtgui/emitem3d.py: starting EMDataItem3D and EMIsosurface

2011-06-30 02:50  jgalaz

	* programs/e2tomoboxer.py:
	  Commented X,Y,Z coordinate buttons/displays out, since they were
	  not functional.  Restored the functionality of the
	  Limt_Side_Boxes option.

2011-06-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-28 16:12  ross

	* libpyEM/qtgui/: emitem3d.py, emscene3d.py: rename
	  EMInspectorControlBasic to EMItem3DInspector

2011-06-28 16:09  ross

	* rt/demo/scene3d_test.py: fix: underscore to CamelCase notation

2011-06-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-28 09:58  zyang

	* sparx/libpy/utilities.py: Fix a bug in ce_fit()

2011-06-27 21:39  jgalaz

	* programs/e2tomoboxer.py: Got rid of the Limit_side_boxes option
	  in the GUI, because it makes no sense to have it.  The boxes in
	  the sideviews should ALWAYS be limitted to the vicinity of the
	  current selected box, by default.  [Who would choose to crowd the
	  sideviews?].	Added X, Y and Z coordinate boxes to the GUI, so
	  the user can know where he/she is in the tomogram (I'm surprised
	  I didn't notice this lack before).  BUT they don't work yet
	  (don't know how to make them work, but will find out).  Changed
	  the boxes so that they're displayed in the XY view only within
	  boxsize/2 from their central coordinate in Z (otherwise they
	  disappear).  Fixed writting out the coordinate file correctly to
	  account for newly implemented binning options (the coordinates
	  file will always be written containing the UNBINNED coordinates,
	  in X,Y,Z format; added a 'yzswap' option, whenever the tomgogram
	  and the coordinates files don't agree regarding the order of Y
	  and Z; note that this is different from --yshort, because
	  swapping the coordinates file might not be necessary if the user
	  produced it already swapped, with IMOD or manually).	Other minor
	  changes.

2011-06-27 20:34  ross

	* rt/demo/scene3d_test.py: trivial

2011-06-27 20:30  ross

	* libpyEM/qtgui/: emitem3d.py, emscene3d.py: changing self.sgnode
	  to self.item3d and making similar changes to our naming
	  convention for the scene graph

2011-06-27 13:22  ross

	* libpyEM/qtgui/emitem3d.py: adding missing imports

2011-06-27 13:21  ross

	* libpyEM/qtgui/: emscene3d.py, valslider.py: fixing bugs with PyQt
	  signals, mostly QColor instead of Qcolor

2011-06-27 12:46  gtang

	* rt/demo/scene3d_test.py: [no log message]

2011-06-27 12:26  ross

	* libpyEM/qtgui/: emrctstrategy.py, emscene3d.py: spelling fix:
	  toggle instead of toogle

2011-06-27 12:24  ross

	* libpyEM/qtgui/: emitem3d.py, emscene3d.py: moving
	  EMInspectorControlBasic from emscene3d.py to emitem3d.py;
	  procesSelection() -> processSelection() spelling fix

2011-06-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-23 17:00  john

	* programs/e2projectmanager.py: New Workflow

2011-06-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-23 11:58  fjia

	* sparx/libpy/statistics.py: removed unnecessary memory allocation
	  in k_means_stab_bbenum and k_means_match_bbenum

2011-06-23 11:22  john

	* libpyEM/qtgui/: emitem3d.py, emscene3d.py, valslider.py:
	  Inspector updates

2011-06-23 03:01  jgalaz

	* programs/e2tomoboxer.py:
	  I have enabled boxing (finding particles) in a binned tomogram
	  but extracting them from the UNBINNED tomogram, using the GUI in
	  e2tomoboxer.py

2011-06-22 18:00  john

	* libpyEM/qtgui/emscene3d.py, libpyEM/qtgui/emshapeitem3d.py,
	  libpyEM/qtgui/valslider.py, programs/e2unwrap3d.py: 3D widget
	  update

2011-06-22 16:07  ppenczek

	* sparx/libpy/projection.py: [no log message]

2011-06-22 15:26  john

	* programs/e2unwrap3d.py: Program to unwrap 3D maps into
	  cylindrical coords

2011-06-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-22 03:13  jgalaz

	* programs/e2tomoboxer.py: Enabled binning the tomogram before
	  opening it with e2tomoboxer.py

2011-06-22 02:47  jgalaz

	* programs/e2tomoboxer.py:
	  Included several options for e2tomoboxer; for example, contrast
	  reversal (from the commandline) so the tomogram is in the proper
	  "white protein convention" from start.  Also included binning
	  options (but they do nothing for now), because NOBODY can
	  actually use the tomoboxer on tomograms that have not been binned
	  (so boxing in the binned tomogram but extracting particles from
	  its unbinned version SHOULD be enabled ASAP if anyone is ever
	  going to seriously use e2tomoboxer); very few people have
	  monstruous amounts of memory.  Added full command-line boxing
	  capabilities (so you don't have to open the tomogram at all if
	  you already have a coordinates file).

2011-06-21 22:48  zyang

	* libEM/sparx/util_sparx.cpp: Find two more sources of memory leak
	  in the matching algorithm, all leaks should be plugged now.

2011-06-21 18:19  ppenczek

	* sparx/libpy/projection.py: [no log message]

2011-06-21 18:19  ross

	* libpyEM/qtgui/: emitem3d.py, emscene3d.py: creating accessor
	  methods for EMItem3D and using them outside the class

2011-06-21 17:03  zyang

	* libEM/sparx/util_sparx.cpp: A little optimization in the matching
	  algorithm and more style-changing

2011-06-21 16:16  john

	* libpyEM/qtgui/: emitem3d.py, emscene3d.py, valslider.py:
	  Inspector updates

2011-06-21 15:20  zyang

	* libEM/sparx/util_sparx.cpp: Just change the code-styling from
	  dereference(*) to [] in the matching algorithm.

2011-06-21 13:50  zyang

	* sparx/bin/sxreproducibility.py: Improve some functionality.

2011-06-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-21 10:26  ppenczek

	* sparx/libpy/projection.py: [no log message]

2011-06-21 09:56  john

	* libpyEM/qtgui/: emrctstrategy.py, emscene3d.py, valslider.py:
	  Inspector updates

2011-06-20 18:49  zyang

	* libEM/sparx/util_sparx.cpp: Fix the memory-leak in the matching
	  algorithm

2011-06-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-17 16:30  ppenczek

	* sparx/libpy/projection.py: new version od cmlGA

2011-06-17 16:18  gtang

	* libEM/: mrcio.cpp, omapio.cpp: fix for windows compilation

2011-06-17 15:35  gtao

	* libEM/sparx/emdata_sparx.cpp: clean warnings.

2011-06-17 14:38  gtao

	* libEM/sparx/emdata_sparx.cpp: change helicise code.

2011-06-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-16 14:56  fjia

	* sparx/libpy/statistics.py: [no log message]

2011-06-16 12:36  stevel

	* libEM/ctf.cpp: Fix for ctf autotuning

2011-06-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-15 20:51  zyang

	* libEM/sparx/util_sparx.cpp, sparx/libpy/pixel_error.py: Trivial
	  change

2011-06-15 20:01  zyang

	* sparx/bin/sxreproducibility.py: Trivial change.

2011-06-15 15:57  ross

	* libpyEM/qtgui/: emscene3d.py, valslider.py: bug fix: replacing
	  Qcolor with QColor

2011-06-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-15 11:44  zyang

	* sparx/bin/sxreproducibility.py: Fix a bug, it should be fully
	  functional now.

2011-06-15 11:42  john

	* libpyEM/qtgui/: emitem3d.py, emscene3d.py, emsprworkflow.py:
	  Bugfixes

2011-06-15 10:49  zyang

	* sparx/bin/sxreproducibility.py: Improve the program such that it
	  can handle reproducibility of multiple partitions

2011-06-15 10:23  ppenczek

	* sparx/libpy/applications.py: [no log message]

2011-06-14 17:24  stevel

	* programs/e2evalparticles.py: trivial

2011-06-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-13 18:51  ross

	* libpyEM/qtgui/emitem3d.py: getSceneGui() was defined twice...
	  removing one definition

2011-06-13 16:41  zyang

	* sparx/bin/sxreproducibility.py: Trivial change

2011-06-13 13:35  john

	* programs/: e2align3d.py, e2rct.py, e2tiltvalidate.py: RCT updates

2011-06-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-13 11:58  john

	* programs/e2align3d.py: Bugfix

2011-06-13 11:54  john

	* programs/e2align3d.py: Aligner updates

2011-06-13 11:39  john

	* libEM/aligner.cpp, programs/e2align3d.py: Aligner updates

2011-06-13 10:30  gtang

	* rt/pyem/test_processor.py: [no log message]

2011-06-12 20:15  stevel

	* examples/redo_convergence.py: Redo convergence will work even
	  when comparisons haven't been computed already.

2011-06-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-10 17:12  john

	* libpyEM/qtgui/emsprworkflow.py, programs/e2workflow.py: Added
	  Steven's evaluate particles

2011-06-10 16:52  john

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/emdata_core.cpp,
	  libEM/emdata_cuda.cpp, libEM/emdata_metadata.cpp,
	  libEM/processor.cpp, libpyEM/qtgui/emscene3d.py,
	  programs/e2align3d.py, programs/e2montecarlorecon.py,
	  programs/e2project3d.py, programs/e2rct.py: CUDA and RCT updates

2011-06-10 16:03  gtang

	* libEM/emdata_metadata.cpp: fix the size_t problem.

2011-06-10 15:14  gtang

	* libEM/: CMakeLists.txt, all_imageio.h, emutil.cpp, emutil.h,
	  omapio.cpp, omapio.h: OMap I/O implementation. Not work yet.

2011-06-10 14:13  zyang

	* sparx/bin/sxreproducibility.py: [no log message]

2011-06-10 13:40  zyang

	* sparx/bin/sxreproducibility.py: Trivial change.

2011-06-10 13:37  stevel

	* examples/redo_convergence.py: Trivial

2011-06-10 12:43  stevel

	* programs/e2eotest.py: oops again

2011-06-10 12:32  stevel

	* programs/e2eotest.py: oops

2011-06-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-10 11:59  ross

	* .pydevproject: removing dependency on /home/john/EMAN2/

2011-06-10 11:44  zyang

	* sparx/bin/: sxreproducibility.py, sxstability.py: Check the
	  reproducibility between two averages.

2011-06-10 11:08  ross

	* libpyEM/qtgui/: emitem3d.py, emscene3d.py, emshapeitem3d.py:
	  changing from underscore to CamelCase. Added test code to
	  emitem3d.py

2011-06-10 10:45  stevel

	* programs/e2eotest.py: Fixed minor bug

2011-06-10 10:39  stevel

	* programs/: e2eotest.py, e2evalparticles.py: New eotest parms. Fix
	  for automask generation issue.

2011-06-10 10:30  john

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2pathwalker.py,
	  programs/e2rct.py: workflow bugfix

2011-06-09 15:03  zyang

	* sparx/bin/sxstability.py: Trivial change

2011-06-09 14:17  zyang

	* sparx/libpy/fundamentals.py: Add "from EMAN2 import xxx"

2011-06-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-09 10:57  stevel

	* libpyEM/EMAN2db.py, programs/e2evalparticles.py: All existing
	  features in evalparticles seem ok now

2011-06-09 10:18  john

	* libpyEM/qtgui/emscene3d.py: inspector updates

2011-06-09 08:55  stevel

	* libpyEM/: EMAN2PAR.py, qtgui/valslider.py: minor fix

2011-06-08 16:59  john

	* libpyEM/qtgui/emitem3d.py, libpyEM/qtgui/emscene3d.py,
	  libpyEM/qtgui/valslider.py, programs/e2tiltvalidate.py: Inspector
	  updates

2011-06-08 15:02  stevel

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/valslider.py, programs/e2bdb.py,
	  programs/e2evalparticles.py: evalparticles is now 90% complete
	  and is usable and tested

2011-06-08 13:32  gtao

	* sparx/libpy/applications.py: [no log message]

2011-06-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-08 10:24  gtao

	* sparx/libpy/applications.py: [no log message]

2011-06-07 16:43  john

	* libpyEM/qtgui/emscene3d.py, libpyEM/qtgui/valslider.py,
	  programs/e2tiltvalidate.py: inspector

2011-06-07 15:41  stevel

	* libpyEM/qtgui/emimagemx.py, programs/e2evalparticles.py:
	  evalparticles work

2011-06-07 15:16  john

	* libpyEM/qtgui/emscene3d.py, programs/e2tiltvalidate.py: inspector
	  updates

2011-06-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-07 10:24  john

	* libpyEM/qtgui/emscene3d.py, programs/e2tiltvalidate.py: inspector
	  updates

2011-06-06 14:34  stevel

	* libpyEM/qtgui/valslider.py, programs/e2evalparticles.py,
	  programs/e2filtertool.py: New evalparticles program not done yet

2011-06-06 13:20  zyang

	* sparx/bin/sxmontage.py: Attempted to add number on image
	  (unfinished)

2011-06-06 13:05  john

	* libpyEM/qtgui/emitem3d.py, libpyEM/qtgui/emscene3d.py,
	  libpyEM/qtgui/valslider.py, programs/e2tiltvalidate.py: inspector
	  updates

2011-06-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-06 11:14  john

	* libpyEM/qtgui/: emscene3d.py, emsprworkflow.py, valslider.py:
	  bugfix

2011-06-06 09:58  john

	* libpyEM/qtgui/emscene3d.py, programs/e2tiltvalidate.py: Inspector
	  updates

2011-06-05 14:22  zyang

	* sparx/libpy/fundamentals.py: Minor change

2011-06-05 14:08  zyang

	* sparx/libpy/fundamentals.py: Fix a small bug.

2011-06-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-03 17:01  gtao

	* libpyEM/libpyEMData2.cpp: python boost for griding based helicise

2011-06-03 16:59  gtao

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: add helicis
	  function using gridding interpolation

2011-06-03 13:48  zyang

	* sparx/bin/sxmontage.py: This program is to generate montage image
	  file.

2011-06-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-01 16:59  john

	* libpyEM/qtgui/emscene3d.py, programs/e2tiltvalidate.py: Worked on
	  inspector

2011-06-01 16:18  gtang

	* rt/demo/scene3d_test.py: [no log message]

2011-06-01 16:08  stevel

	* libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emsprworkflow.py,
	  libpyEM/qtgui/valslider.py, programs/e2filtertool.py: Filtertool
	  almost functional

2011-06-01 15:53  gtang

	* libEM/mrcio.cpp: default apix to 1.0 when read out an invalid
	  value from MRC file.

2011-06-01 14:23  gtang

	* libpyEM/qtgui/: emitem3d.py, emshapeitem3d.py: add inspector to
	  shapeitem3d

2011-06-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-06-01 10:30  gtang

	* libEM/isosurface.h: Isosurface has no ownership for the _emdata
	  pointer. Delete it will cause segfault when display another 3D
	  image without close the previous 3D window.

2011-06-01 10:12  john

	* libpyEM/qtgui/emscene3d.py, programs/e2tiltvalidate.py: Added
	  inspector

2011-05-31 17:15  zyang

	* sparx/libpy/: alignment.py, applications.py, fundamentals.py,
	  statistics.py: Change 'mirror' to 'xform.mirror'

2011-05-31 16:01  john

	* libpyEM/qtgui/emitem3d.py, libpyEM/qtgui/emscene3d.py,
	  programs/e2ctf.py, programs/e2tiltvalidate.py: SG updates

2011-05-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-30 22:28  stevel

	* libpyEM/qtgui/valslider.py, programs/e2filtertool.py: Work on
	  filtertool

2011-05-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-28 00:11  stevel

	* libEM/processor.cpp, libpyEM/qtgui/valslider.py,
	  programs/e2filtertool.py: Developments for filtertool

2011-05-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-27 07:13  stevel

	* mpi_eman/Makefile.linux2: New include file in makefile

2011-05-26 16:02  john

	* programs/e2tiltvalidate.py: bugfix

2011-05-26 15:38  john

	* libpyEM/qtgui/emscene3d.py, programs/e2rct.py,
	  programs/e2tiltvalidate.py: Updates

2011-05-26 12:16  gtang

	* libpyEM/qtgui/emshapeitem3d.py: [no log message]

2011-05-26 12:08  gtang

	* libpyEM/qtgui/emshapeitem3d.py: basic shapes for new 3D GUI

2011-05-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-26 09:52  john

	* libpyEM/qtgui/emscene3d.py: Fixed perspective selection

2011-05-25 18:48  john

	* libpyEM/qtgui/emscene3d.py: selection stuff

2011-05-25 18:31  john

	* libpyEM/qtgui/: emitem3d.py, emscene3d.py: Ehnaced the selection
	  mechanism

2011-05-25 12:37  john

	* libpyEM/qtgui/: emitem3d.py, emscene3d.py: Added Steve's
	  suggestions

2011-05-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-25 11:14  ross

	* libpyEM/qtgui/emitem3d.py: Added if __name__ == "__main__" test
	  code for the recursive get_*_selected_nodes() methods. Added the
	  add_children() method

2011-05-24 17:26  ross

	* libpyEM/qtgui/emitem3d.py: added methods to return all selected
	  nodes, selected nodes nearest the root node, or selected nodes
	  farthest from the root node

2011-05-24 17:23  john

	* libpyEM/qtgui/: emitem3d.py, emscene3d.py: Selection for 3d
	  widget

2011-05-24 13:37  john

	* libpyEM/qtgui/emscene3d.py: bugfix III

2011-05-24 13:37  john

	* libpyEM/qtgui/emscene3d.py: bugfix II

2011-05-24 13:35  john

	* libpyEM/qtgui/emscene3d.py: bugfix

2011-05-24 13:31  john

	* libpyEM/qtgui/emscene3d.py: update

2011-05-24 13:28  john

	* libpyEM/qtgui/emscene3d.py: [no log message]

2011-05-24 13:25  john

	* libpyEM/qtgui/: emscene3d.py, emwidget3d.py: Renamed SG

2011-05-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-24 11:47  john

	* .pydevproject, libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emrctboxergui.py, libpyEM/qtgui/emwidget3d.py,
	  programs/e2rct.py: renamed kernal to kernel and renamed the
	  convkenal processor: filter.convolution.kernel

2011-05-24 11:19  gtao

	* libEM/processor.cpp, sparx/libpy/fundamentals.py: change mirror
	  to xform.mirror.

2011-05-24 11:18  john

	* programs/e2tiltvalidate.py: program to validate a reconstruction
	  based on tilted vs untilted particles Yet to be fully tested

2011-05-24 10:53  stevel

	* libEM/processor.cpp, programs/e2filtertool.py,
	  programs/e2modeleval.py, programs/e2ssehunter.py,
	  rt/pyem/test_processor.py: Cleanup processors

2011-05-23 12:23  stevel

	* libpyEM/EMAN2PAR.py: Reorder ops to get more efficient MPI
	  processing ?

2011-05-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-22 20:42  stevel

	* libpyEM/EMAN2PAR.py, programs/e2project3d.py,
	  programs/e2refine.py: New MPI caching scheme working on 240 cores
	  !

2011-05-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-21 01:15  stevel

	* libpyEM/EMAN2PAR.py: MPI caching really working properly now I
	  think

2011-05-20 14:39  john

	* libpyEM/qtgui/emwidget3d.py: widget3d updates

2011-05-20 14:19  john

	* libpyEM/qtgui/emwidget3d.py: Enhanced perspective camera

2011-05-20 12:15  ppenczek

	* sparx/: bin/sxrecons3d_n.py, libpy/applications.py: correct list
	  in recons

2011-05-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-20 10:06  ppenczek

	* sparx/bin/sxrecons3d_f.py: [no log message]

2011-05-20 09:56  zyang

	* sparx/libpy/: pixel_error.py, utilities.py: Some minor changes

2011-05-20 09:07  ross

	* libpyEM/qtgui/emwidget3d.py: removed is_selected parameter from
	  render_node()

2011-05-19 21:57  ross

	* libpyEM/qtgui/emitem3d.py: removed is_selected parameter from
	  render_self()... meant to have that gone in the version I first
	  committed

2011-05-19 17:39  john

	* libEM/aligner.cpp, libEM/glutil.cpp, libEM/glutil.h,
	  libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyGLUtils2.cpp, libpyEM/libpyTransform2.cpp,
	  libpyEM/qtgui/emitem3d.py, libpyEM/qtgui/emwidget3d.py:
	  emwidget3d updates and debug for aligner

2011-05-19 15:39  ross

	* libpyEM/qtgui/emitem3d.py: EMItem3D is the parent node class for
	  the scene graph we are writing for an updated 3D viewer widget

2011-05-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-19 11:04  gtang

	* rt/pyem/test_imageio.py: [no log message]

2011-05-19 08:11  stevel

	* libpyEM/EMAN2db.py: MPI caching seems to be working !  Not
	  holding my breath though :^)

2011-05-19 08:06  stevel

	* libpyEM/: EMAN2PAR.py, EMAN2db.py: Just about working now

2011-05-18 20:31  gtang

	* programs/e2ctf2eman1.py: update by Benjamin Bammes

2011-05-18 15:32  stevel

	* libpyEM/EMAN2PAR.py: Just can't catch a break today

2011-05-18 15:31  stevel

	* libpyEM/EMAN2PAR.py: Getting closer...

2011-05-18 13:58  stevel

	* libpyEM/EMAN2PAR.py: uggh

2011-05-18 13:56  stevel

	* libpyEM/EMAN2PAR.py: oops

2011-05-18 13:49  stevel

	* libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py, mpi_eman/mpi_test.py,
	  programs/e2parallel.py: Experimental new broascast caching system
	  for MPI parallelism. Still debugging, should be debugged before
	  tomorrow's snapshot checkout.

2011-05-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-18 11:43  john

	* libEM/glutil.cpp, libEM/glutil.h, libpyEM/libpyGLUtils2.cpp:
	  renamed gl*TransposeMatrixFast to gl*Matrix

2011-05-18 11:18  john

	* libEM/glutil.cpp, libEM/glutil.h, libpyEM/libpyGLUtils2.cpp:
	  GLUtil updates

2011-05-17 16:10  john

	* libEM/transform.cpp: Comments

2011-05-17 16:07  john

	* libEM/transform.cpp: Bugfix fro incremnent_scale

2011-05-17 15:42  john

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp: Enhancements for the transfrom class

2011-05-17 14:51  gtang

	* libEM/mrcio.cpp: xform.align3d has no rotation, set the
	  translation parameter from (nxstart, nystart, nzstart).

2011-05-17 12:11  stevel

	* mpi_eman/: Makefile.linux2, pbs.example: PBS fixes

2011-05-17 12:09  stevel

	* programs/e2bdb.py: Read-only fix to e2bdb.py

2011-05-17 12:06  gtang

	* libEM/: mrcio.cpp, mrcio.h: Some 3D MRC map from EMDB is in axis
	  order y,x,z. Transpose it to x,y,z order when read into EMAN2.
	  Also adjust corresponding header attributes.

2011-05-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-16 15:40  stevel

	* libEM/mrcio.cpp, programs/e2parallel.py: trivial buffer overflow
	  fix

2011-05-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-13 23:34  zyang

	* sparx/libpy/applications.py: Fix a small bug

2011-05-13 16:20  ross

	* libpyEM/qtgui/emapplication.py: EMApp minor changes

2011-05-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-13 09:26  ppenczek

	* sparx/libpy/statistics.py: changed eigval in PCA

2011-05-12 19:43  gtang

	* programs/e2bdb.py: fix the broken --nocache option.

2011-05-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-11 17:02  gtang

	* libEM/mrcio.cpp: Take the (mapc, mapr, maps) info from previous
	  MRC source when writing a new MRC file.

2011-05-11 13:27  ppenczek

	* sparx/bin/sxgenbuf.py: [no log message]

2011-05-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-11 09:42  zyang

	* sparx/libpy/pixel_error.py: Fix a trivial bug.

2011-05-10 23:24  ppenczek

	* sparx/libpy/morphology.py: [no log message]

2011-05-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-10 10:29  zyang

	* sparx/bin/sxresample.py: Same as previous

2011-05-10 10:11  zyang

	* sparx/bin/sxresample.py: Change due to recent update on
	  Reconstructor

2011-05-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-06 15:58  gtang

	* libEM/tifio.cpp: tiff writing should be able to specify storage
	  type

2011-05-06 15:45  gtang

	* libEM/jpegio.cpp: flip image when read/write to solve the origin
	  conflict

2011-05-06 15:38  gtang

	* libEM/pngio.cpp: flip image when read/write to solve the origin
	  conflict

2011-05-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-06 11:58  john

	* libEM/: aligner.cpp, emdata_cuda.cpp: CUDA updates

2011-05-05 17:50  john

	* libEM/: aligner.cpp, aligner.h, cmp.cpp, emdata_cuda.cpp,
	  cuda/cuda_util.cu: CUDA updates

2011-05-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-05 10:56  john

	* libEM/: emdata.cpp, emdata_cuda.cpp, cuda/cuda_util.cu: CUDA
	  updates

2011-05-05 10:16  gtang

	* doc/eman2doc.h: install instruction link to wiki

2011-05-05 09:51  john

	* libEM/: emdata.cpp, emdata_cuda.cpp, emdata_transform.cpp,
	  processor.cpp: CUDA updates

2011-05-04 16:15  john

	* libEM/: emdata.cpp, emdata_cuda.cpp, emdata_transform.cpp,
	  processor.cpp: CUDA updates

2011-05-04 12:52  john

	* libEM/emdata.cpp, libEM/emdata_metadata.h,
	  libEM/cuda/cuda_cmp.cu, libEM/cuda/cuda_processor.cu,
	  libEM/cuda/cuda_reconstructor.cu, programs/e2simmx.py: CUDA
	  updates

2011-05-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-03 17:30  ross

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emboxerbase.py,
	  libpyEM/qtgui/emform.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emplot2d.py, libpyEM/qtgui/emselector.py,
	  programs/e2RCTboxer.py, programs/e2boxer.py,
	  programs/e2cmpxplor.py, programs/e2eulerxplor.py,
	  programs/e2helixboxer.py, programs/e2simmxxplor.py,
	  programs/e2workflow.py, sparx/bin/sxboxer.py: removed dektop_hint
	  attributes and get_desktop_hint() methods... these were remnants
	  from 3D desktop days

2011-05-03 17:15  ross

	* libpyEM/qtgui/emapplication.py: trivial

2011-05-03 17:14  ross

	* programs/e2eulerxplor.py: options.eulerdata is only available
	  when e2eulerexplorer is run as a top-level program; fixing
	  constructors to get file names as parameters rather than using
	  the options global variable

2011-05-03 17:12  ross

	* programs/e2ssehunter.py: making the algorithms more compatible
	  with ssehunter3.py in EMAN1

2011-05-03 14:42  john

	* libEM/emdata_cuda.cpp, programs/e2simmx.py: Reverted debugging
	  code

2011-05-03 14:25  john

	* libEM/emdata.cpp, libEM/emdata_cuda.cpp,
	  libEM/emdata_metadata.cpp, programs/e2rct.py,
	  programs/e2rctV2.py: CUDA updates and RCT updates

2011-05-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-03 11:19  gtang

	* doc/index.html: version update to 2.02

2011-05-03 09:58  gtang

	* libEM/isosurface.h: destructor implemented

2011-05-02 18:00  john

	* libEM/emdata_cuda.cpp: More CUDA updates

2011-05-02 17:49  john

	* libEM/emdata_cuda.cpp, libEM/emdata_transform.cpp,
	  libEM/projector.cpp, programs/e2refine.py, programs/e2simmx.py:
	  Cuda updates

2011-05-02 16:51  ross

	* programs/: e2eulerxplor.py, e2simmxxplor.py, e2workflow.py:
	  Removed self.under_qt_control attribute. It was a remnant from 3D
	  desktop days.

2011-05-02 16:46  ross

	* libpyEM/qtgui/: emapplication.py, emglobjects.py, emimage2d.py,
	  emimage3d.py, emimage3diso.py, emimage3dslice.py,
	  emimage3dsym.py, emimage3dvol.py, emimagemx.py, emlights.py,
	  empdbvaltool.py, emplot2d.py: removed self.under_qt_control which
	  was a remnant from 3D desktop days

2011-05-02 16:23  ross

	* programs/e2simmxxplor.py: bugfix

2011-05-02 16:21  ross

	* libpyEM/qtgui/emapplication.py: trivial

2011-05-02 15:25  ross

	* programs/e2simmxxplor.py: fixing display bugs probably existing
	  since the branch to remove the 3D desktop was merged into the
	  trunk

2011-05-02 12:26  gtang

	* programs/e2version.py: version 2.02

2011-05-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-05-02 10:31  gtao

	* sparx/libpy/applications.py: [no log message]

2011-05-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-29 17:54  john

	* libEM/aligner.cpp, libEM/processor.cpp,
	  libpyEM/qtgui/emimage3dsym.py, programs/e2RCTboxer.py,
	  programs/e2eulerxplor.py, programs/e2rctV2.py: RCT updates

2011-04-29 16:01  ross

	* libpyEM/qtgui/emboxerbase.py: shift + click in the particle
	  viewer now causes the particle to be deleted, when in "app" mode
	  (mouse modes are set with the inspector)

2011-04-29 15:12  stevel

	* programs/e2classifyligand.py: More work on ligand classifier

2011-04-29 14:53  zyang

	* sparx/bin/sxstability.py: Fix multiple bugs and changed the
	  program to MPI

2011-04-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-29 11:11  zyang

	* sparx/bin/sxstability.py: Due to the frequent need of this
	  program, I decided to add it as an sx program.  (not finished
	  yet)

2011-04-29 10:39  gtang

	* CMakeLists.txt: for freetype

2011-04-29 09:39  gtao

	* sparx/libpy/applications.py: [no log message]

2011-04-28 23:07  stevel

	* libpyEM/EMAN2.py, programs/e2classifyligand.py,
	  programs/e2display.py, programs/e2project3d.py: A few bugfixes.
	  Working on e2classifyligand, but not done yet

2011-04-28 20:12  ppenczek

	* sparx/libpy/applications.py: msg format in mref_ali2d

2011-04-28 17:09  gtang

	* CMakeLists.txt: [no log message]

2011-04-28 17:05  gtang

	* CMakeLists.txt: remove redundant code

2011-04-28 16:08  ppenczek

	* sparx/libpy/: alignment.py, utilities.py: cleaning

2011-04-28 15:15  ppenczek

	* sparx/libpy/: applications.py, projection.py: cleaning

2011-04-28 13:01  ppenczek

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/libpyEMData2.cpp: corrections of helicise

2011-04-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-28 11:04  john

	* libEM/aligner.cpp, libpyEM/qtgui/emimage3dsym.py,
	  libpyEM/qtgui/emrctboxergui.py, libpyEM/qtgui/emrctstrategy.py,
	  programs/e2RCTboxer.py, programs/e2align3d.py,
	  programs/e2eulerxplor.py, programs/e2rctV2.py,
	  programs/e2refine2d.py: Update e2RCTboxer, and added Ryan style
	  eulerfile capibility for e2eulerexplorer.py

2011-04-28 09:31  gtang

	* libEM/mrcio.cpp: fix the bug I introduced yesterday

2011-04-27 17:33  jkovacs

	* libEM/sparx/fourierfilter.cpp: fixed a bug in filt_gaussb

2011-04-27 16:11  zyang

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  sparx/libpy/applications.py, sparx/libpy/reconstruction.py: Fixed
	  the nnSSNR_reconstructor, they now works more or less similar to
	  all of the other reconstrucors.

2011-04-27 15:53  gtang

	* libEM/: mrcio.cpp, mrcio.h: FEI extended MRC format for
	  Tomography

2011-04-27 15:23  zyang

	* libpyEM/libpyUtils2.cpp: Fix an error

2011-04-27 14:48  gtao

	* sparx/libpy/alignment.py: [no log message]

2011-04-27 13:37  gtao

	* libpyEM/libpyUtils2.cpp: [no log message]

2011-04-27 13:26  gtao

	* sparx/libpy/alignment.py, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h: [no log message]

2011-04-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-27 11:57  gtao

	* sparx/libpy/fundamentals.py: [no log message]

2011-04-27 10:58  gtao

	* sparx/libpy/fundamentals.py: [no log message]

2011-04-27 10:48  zyang

	* sparx/libpy/reconstruction.py: Fix reconstructor problem due to
	  yesterday's change

2011-04-27 10:07  gtao

	* libEM/reconstructor.cpp: fix several warnings.

2011-04-26 16:35  zyang

	* sparx/libpy/reconstruction.py: Fix a minor bug

2011-04-26 16:17  zyang

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  sparx/libpy/reconstruction.py: An overhaul to the reconstruction
	  program such that: (1) no more copy is needed at the end of
	  reconstrction program; (2) the C++ code is same for non-MPI and
	  MPI program: now the reconstucted images are pass through
	  params["fftvol"], also, all finish() program will return a NULL
	  pointer.

2011-04-26 15:10  ppenczek

	* sparx/bin/sxfind_struct.py: cleaning

2011-04-26 12:31  gtao

	* libEM/reconstructor.cpp: [no log message]

2011-04-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-26 10:28  gtao

	* libEM/reconstructor.cpp: [no log message]

2011-04-26 10:17  zyang

	* sparx/libpy/applications.py: Add "from EMAN2db import
	  db_open_dict"

2011-04-26 10:10  ppenczek

	* sparx/: bin/sxheader.py, libpy/applications.py: [no log message]

2011-04-26 09:59  ppenczek

	* sparx/libpy/: fundamentals.py, statistics.py, utilities.py: added
	  import of periodogram

2011-04-25 17:26  gtang

	* libEM/mrcio.h: FEI extended MRC format for Tomography

2011-04-25 17:04  ppenczek

	* libEM/reconstructor.cpp: messed up version

2011-04-25 15:18  ppenczek

	* sparx/libpy/reconstruction.py: [no log message]

2011-04-25 15:11  ppenczek

	* sparx/libpy/reconstruction.py: added from EMNA2 import
	  Reconstructors

2011-04-25 15:09  zyang

	* sparx/libpy/reconstruction.py: Add "from EMAN2 import
	  Reconstructors"

2011-04-25 14:55  ppenczek

	* sparx/demo/1_bdb/run_through_example: [no log message]

2011-04-25 14:53  zyang

	* sparx/libpy/: alignment.py, applications.py, utilities.py: Add
	  "from EMAN2 import Vec3f"

2011-04-25 14:53  ppenczek

	* sparx/demo/1_bdb/run_through_example: deleted variance

2011-04-25 14:49  zyang

	* sparx/libpy/: alignment.py, applications.py, fundamentals.py,
	  projection.py, reconstruction.py, statistics.py, utilities.py:
	  Delete "from EMAN2 import Transform"

2011-04-25 14:49  ppenczek

	* sparx/libpy/global_def.py: added from EMNA2 import EMUtil

2011-04-25 14:41  ppenczek

	* sparx/libpy/: alignment.py, applications.py, projection.py,
	  statistics.py: added from EMAN2 import Processor

2011-04-25 14:34  ppenczek

	* sparx/libpy/filter.py: added from EMAN2 import Processor to
	  filter.py

2011-04-25 14:28  ppenczek

	* sparx/libpy/global_def.py: added import of EMData and Transform
	  to global_def

2011-04-25 14:23  zyang

	* sparx/: bin/sxali2d.py, libpy/alignment.py,
	  libpy/applications.py, libpy/filter.py, libpy/fundamentals.py,
	  libpy/projection.py, libpy/reconstruction.py,
	  libpy/statistics.py: Add from EMAN2 import xxx

2011-04-25 14:03  ppenczek

	* sparx/libpy/: applications.py, fundamentals.py, global_def.py,
	  statistics.py, utilities.py: rationalize imports

2011-04-25 12:25  ppenczek

	* libEM/sparx/fundamentals.h: [no log message]

2011-04-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-25 11:51  ppenczek

	* sparx/libpy/fundamentals.py: added transform to rot_shift3D

2011-04-25 10:17  gtao

	* libEM/reconstructor.cpp: [no log message]

2011-04-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-22 17:24  zyang

	* sparx/bin/sxiter_isac.py: Add generation parameters

2011-04-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-22 07:03  stevel

	* programs/e2classifyligand.py: uggh

2011-04-22 07:01  stevel

	* programs/e2classifyligand.py: trivial

2011-04-21 21:58  stevel

	* programs/: e2bdb.py, e2classifyligand.py: bdb problem

2011-04-21 17:57  john

	* libpyEM/qtgui/: emrctboxergui.py, emrctstrategy.py: Update for
	  RCTboxer

2011-04-21 13:47  zyang

	* programs/e2bdb.py: Add "from EMAN2 import xxx"

2011-04-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-21 11:45  zyang

	* sparx/libpy/: filter.py, fundamentals.py, morphology.py,
	  utilities.py: Add "from EMAN2 import xxx"

2011-04-21 09:51  john

	* libpyEM/qtgui/emrctboxergui.py, libpyEM/qtgui/emrctstrategy.py,
	  libpyEM/qtgui/emtprworkflow.py, programs/e2RCTboxer.py,
	  programs/e2rctV2.py: Fixed workflow for tomoboxing

2011-04-20 14:26  john

	* libpyEM/EMAN2.py, libpyEM/qtgui/emrctboxergui.py,
	  libpyEM/qtgui/emrctstrategy.py, programs/e2boxer.py: Bugfix and
	  rctboxer update

2011-04-20 13:03  gtang

	* libpyEM/qtgui/emselector.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2bdb.py: fix the mutual dependency between EMAN2.py and
	  EMAN2db.py

2011-04-20 12:59  gtang

	* libpyEM/: EMAN2.py, EMAN2db.py: fix the mutual dependency between
	  EMAN2.py and EMAN2db.py

2011-04-20 12:53  zyang

	* sparx/libpy/: filter.py, fundamentals.py, utilities.py: Add "from
	  EMAN2 import xxx"

2011-04-20 12:12  gtang

	* CMakeLists.txt: fix the boost include path issue on Mac

2011-04-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-20 11:13  gtang

	* programs/e2classaverage.py, programs/e2classifyligand.py,
	  programs/e2classptcl.py, programs/e2ctf.py, programs/e2eotest.py,
	  programs/e2eulerxplor.py, programs/e2evalrefine.py,
	  programs/e2history.py, programs/e2iminfo.py,
	  programs/e2initialmodel.py, programs/e2make3d.py,
	  programs/e2parallel.py, programs/e2preferences.py,
	  programs/e2project3d.py, programs/e2rct.py, programs/e2refine.py,
	  programs/e2refine2d.py, programs/e2refinefromfrealign.py,
	  programs/e2refinemulti.py, programs/e2resolution.py,
	  programs/e2simmx.py, programs/e2simmxxplor.py,
	  sparx/bin/sxboxer.py, sparx/bin/sxctf.py, examples/extractfsc.py,
	  examples/redo_convergence.py, examples/tasktest.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emrctboxergui.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emtprworkflow.py, programs/e2RCTboxer.py,
	  programs/e2bdb.py, programs/e2boxer.py, programs/e2classify.py,
	  programs/e2ctf2eman1.py, programs/e2proc2dmulti.py,
	  programs/e2rctV2.py, programs/e2refinetofrealign.py,
	  programs/e2scp.py, programs/e2tomohunter.py,
	  programs/e2workflow.py, pyemtbx/boxertools.py,
	  sparx/libpy/applications.py, sparx/libpy/statistics.py,
	  sparx/libpy/utilities.py: explicitly import name from EMAN2db

2011-04-20 10:22  stevel

	* mpi_eman/test.sge, programs/e2classifyligand.py,
	  programs/e2iminfo.py: SGE test script fix typo.

2011-04-20 10:20  gtang

	* sparx/libpy/utilities.py: EMAN2 name space issue

2011-04-19 19:52  gtang

	* libEM/marchingcubes.h: use free for realloc

2011-04-19 17:16  gtang

	* libpyEM/EMAN2db.py: [no log message]

2011-04-19 17:11  gtang

	* libpyEM/EMAN2db.py: [no log message]

2011-04-19 16:42  gtang

	* sparx/libpy/applications.py, libpyEM/EMAN2db.py: [no log message]

2011-04-19 16:19  gtang

	* sparx/libpy/global_def.py: [no log message]

2011-04-19 12:13  gtang

	* rt/pyem/test_transform.py: change TestSymmetry3D to TestSymmetry

2011-04-19 12:04  gtang

	* libpyEM/EMAN2db.py: [no log message]

2011-04-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-19 11:56  gtang

	* rt/pyem/test_transform.py: suppress two unit tests, which fails
	  on some platform and cause confusion for uers. need to be fixed
	  in the future.

2011-04-19 11:40  gtang

	* libEM/sspiderio.cpp: fix the single spider image swap endian bug.

2011-04-19 10:29  gtang

	* libpyEM/EMAN2db.py, programs/e2bdb.py: solve the duplicate
	  e2gethome() e2getcwd() issue in EMAN2.py and EMAN2db.py

2011-04-19 04:12  irees

	* programs/e2bdb.py: fixed typo: "system.exit" -> "sys.exit"

2011-04-18 16:51  john

	* libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/cuda/cuda_util.cu, libEM/cuda/cuda_util.h,
	  libpyEM/qtgui/emrctboxergui.py, libpyEM/qtgui/emshape.py,
	  programs/e2RCTboxer.py: Fail safe for CUDA

2011-04-18 16:03  gtang

	* libpyEM/EMAN2.py: update e2gethome() from e2bdb.py to handle a
	  winodws situation when HOMEPATH is set to \

2011-04-18 12:51  gtang

	* rt/pyem/test_reconstructor.py: enable unit test for
	  FourierReconstructor.

2011-04-18 12:50  gtang

	* libEM/reconstructor.h: register parameter "quiet" for
	  FourierReconstructor.

2011-04-18 12:38  gtang

	* libEM/reconstructor.cpp: in finish() function, give up the
	  ownership of the returned image. It's caller's responsibility to
	  handle it, i.e. Python.

2011-04-18 12:04  john

	* libEM/emdata.h, libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/reconstructor.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/qtgui/emrctboxergui.py, libpyEM/qtgui/emrctstrategy.py:
	  Update for e2RCTboxer.py

2011-04-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-18 11:00  gtang

	* libEM/marchingcubes.h: add destructor for CustomVector

2011-04-17 13:01  gtang

	* CMakeLists.txt: add option in debug mode to help tracing memory
	  leak.

2011-04-17 12:27  gtang

	* libEM/emdata_io.cpp, libEM/emdata_io.h, libEM/emutil.cpp,
	  libpyEM/libpyTypeConverter2.cpp: fix the memory leak in
	  EMData::read_images() function. It happens when this function get
	  called in Python.

2011-04-17 12:11  gtang

	* libEM/emdata_metadata.h: trivial

2011-04-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-16 22:15  gtang

	* libEM/reconstructor.cpp: add comment

2011-04-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-15 17:08  ppenczek

	* libEM/sparx/fourierfilter.cpp: corrected gaussb

2011-04-15 14:42  gtang

	* libpyEM/libpyReconstructor2.cpp: fix the memory leak in
	  reconstructor

2011-04-15 13:44  gtao

	* sparx/libpy/utilities.py, libEM/transform.cpp: [no log message]

2011-04-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-15 11:26  zyang

	* sparx/bin/sxiter_isac.py: Add an option

2011-04-14 17:11  gtao

	* libEM/: reconstructor.cpp, transform.cpp, transform.h: [no log
	  message]

2011-04-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-14 10:49  john

	* libpyEM/qtgui/: emrctboxergui.py, emrctstrategy.py: e2RCTboxer.py
	  update

2011-04-13 16:30  john

	* libEM/processor.cpp, libEM/processor.h,
	  rt/pyem/test_processor.py: Fix for threshold.binary.fourier test

2011-04-13 14:15  stevel

	* libEM/processor.cpp, programs/e2ctf.py: Trivial fix

2011-04-13 12:04  gtang

	* libpyEM/libpyEMData2.cpp: set_attr_python create memory leak. And
	  it seems running OK with set_attr as I tested.

2011-04-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-13 09:39  gtang

	* rt/pyem/test_processor.py: unit test update

2011-04-12 17:33  john

	* libpyEM/qtgui/emrctboxergui.py: [no log message]

2011-04-12 17:07  john

	* libpyEM/qtgui/emrctboxergui.py: RCTboxer update

2011-04-12 16:56  john

	* libpyEM/qtgui/emrctboxergui.py, libpyEM/qtgui/emrctstrategy.py,
	  libpyEM/qtgui/emshape.py, programs/e2RCTboxer.py: Enhanced
	  RCTbocer

2011-04-12 13:51  john

	* libpyEM/qtgui/emrctstrategy.py, libpyEM/qtgui/emshape.py,
	  programs/e2RCTboxer.py: Added a mask shape for use in RCTboxer

2011-04-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-12 11:57  john

	* libpyEM/qtgui/emboxerbase.py: fix

2011-04-12 11:56  john

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emboxerbase.py, libpyEM/qtgui/emrctboxergui.py,
	  libpyEM/qtgui/emrctstrategy.py, libpyEM/qtgui/emtprworkflow.py:
	  Update for e2RCTboxer.py

2011-04-12 10:18  gtang

	* libpyEM/qtgui/emboxerbase.py: fix broken script

2011-04-11 16:34  ppenczek

	* sparx/libpy/alignment.py: renamed Julio's ali_vol_func

2011-04-11 14:39  gtang

	* libEM/processor.cpp: fix for visual c++ compilation

2011-04-11 13:40  stevel

	* mpi_eman/mpi_test.py: Not sure why this got zapped. bug.

2011-04-11 13:06  stevel

	* mpi_eman/mpi_eman.c: Fix for use with makefile

2011-04-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-10 15:00  ppenczek

	* libpyEM/EMAN2.py: funky character removed

2011-04-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-08 19:43  ross

	* libpyEM/EMAN2.py: commenting out warning message when
	  get_3d_font_renderer() can't import EMFTGL (probably because FTGL
	  isn't installed)

2011-04-08 19:40  ross

	* libpyEM/qtgui/emimage3d.py: default isosurface values set in
	  EMIsosurfaceModel.set_data() instead of
	  EMImage3DWidget.set_data()

2011-04-08 19:37  ross

	* libpyEM/qtgui/emimage3diso.py: increasing default isosurface
	  threshold

2011-04-08 17:33  john

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emboxerbase.py, libpyEM/qtgui/emrctboxergui.py,
	  libpyEM/qtgui/emrctstrategy.py, programs/e2RCTboxer.py: Updates
	  fro the RCT boxer and I added a convolution filter to processor.x

2011-04-08 17:00  gtang

	* libpyEM/CMakeLists.txt: fix for windows

2011-04-08 14:46  stevel

	* libpyEM/EMAN2db.py: Oops

2011-04-08 12:55  stevel

	* libpyEM/EMAN2db.py: Fix bug in count update

2011-04-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-08 10:24  gtang

	* rt/pyem/test_processor.py: unit test update

2011-04-07 23:03  stevel

	* libEM/processor.cpp: Comment out broken processor

2011-04-07 16:37  john

	* programs/e2RCTboxer.py: bugfix

2011-04-07 15:35  stevel

	* libpyEM/EMAN2db.py, programs/e2bdb.py, programs/e2proc2dmulti.py:
	  This is a somewhat risky commit, as it uses a new caching
	  mechanism for counting the number of particles in a database.
	  However, when working on large data sets this provides a really
	  massive speedup, so I'm committing it before 2.02. Hopefully not
	  too many problems will arise as a result.

2011-04-07 15:12  john

	* programs/e2RCTboxer.py: BugFix for e2RCTboxer.py

2011-04-07 15:02  john

	* programs/e2RCTboxer.py: Completed phase 2 of e2RCTboxer.py

2011-04-07 13:17  zyang

	* sparx/bin/sxiter_isac.py: Add FL, FH as options.

2011-04-07 12:13  gtang

	* libpyEM/EMAN2PAR.py, programs/e2parallel.py: task file should be
	  opened in binary mode. Otherwise it cause EOFError on windows.

2011-04-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-07 07:18  stevel

	* programs/: e2iminfo.py, e2proc2d.py, e2proc2dmulti.py: Much
	  improved e2iminfo.py with ptcl_repr info.

2011-04-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-06 11:20  gtao

	* sparx/demo/7_mpi_bdb_ctf/run_through_example: [no log message]

2011-04-06 10:52  stevel

	* examples/extractfsc.py, libEM/emdata.cpp, libEM/processor.cpp,
	  libpyEM/EMAN2db.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2bdb.py,
	  programs/e2classaverage.py, programs/e2proc2dmulti.py,
	  programs/e2refine2d.py, programs/e2stacksort.py: Many
	  improvements to e2refine2d.py particularly for neg stain data.
	  New options in stacksort. Other fixes. First version of
	  e2proc2dmulti.py, but not complete yet.

2011-04-06 10:20  gtao

	* sparx/demo/5_mpi_bdb/run_through_example: [no log message]

2011-04-06 10:03  gtao

	* sparx/demo/: 1_bdb/run_through_example,
	  3_bdb_ctf/run_through_example: [no log message]

2011-04-06 09:56  gtang

	* libpyEM/EMAN2db.py: fix a windows path issue, convert "." to
	  e2getcwd()

2011-04-05 15:09  gtao

	* sparx/demo/7_mpi_bdb_ctf/run_through_example: [no log message]

2011-04-05 14:27  john

	* programs/e2RCTboxer.py: Bugfix for e2RCTboxer.py

2011-04-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-05 10:45  john

	* programs/e2RCTboxer.py: Updates to e2RCTboxer.py

2011-04-04 18:27  ross

	* libpyEM/EMAN2.py: get_3d_font_renderer() displays a more useful
	  message if EMFTGL can't be imported (such as if FTGL isn't
	  installed)

2011-04-04 17:26  john

	* programs/e2RCTboxer.py: New program for boxing tilit pair
	  particles.

2011-04-04 16:07  zyang

	* sparx/bin/sxiter_isac.py: [no log message]

2011-04-04 14:47  zyang

	* sparx/bin/sxiter_isac.py: Trivial change.

2011-04-04 13:45  gtao

	* sparx/libpy/utilities.py: [no log message]

2011-04-04 13:42  gtao

	* sparx/libpy/utilities.py: [no log message]

2011-04-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-03 13:57  ppenczek

	* libEM/sparx/emdata_sparx.cpp: cleaning

2011-04-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-02 10:58  ross

	* programs/e2ssehunter.py: fix: Eclipse spaces to tabs conversion
	  messed up PDB file writing

2011-04-01 17:06  gtao

	* libEM/sparx/emdata_sparx.cpp: [no log message]

2011-04-01 15:16  gtang

	* libpyEM/qtgui/emsprworkflow.py: clean up unnecessary file opening

2011-04-01 14:52  gtang

	* libpyEM/qtgui/emsprworkflow.py: tab issue

2011-04-01 14:14  gtang

	* libEM/: sparx/util_sparx.cpp, plugins/reconstructor_template.h:
	  fix warning in Visual C++ 2008(9.0)

2011-04-01 14:04  gtang

	* libpyEM/qtgui/: emsprworkflow.py, emtprworkflow.py: In windows,
	  when use 'pythonw' in sybprocess.Popen(), there is a 128
	  character length limit. Fix this issue by calling python script
	  directly and set shell=True

2011-04-01 13:49  zyang

	* libEM/sparx/util_sparx.cpp: Fix warnings.

2011-04-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-04-01 11:11  gtao

	* libEM/reconstructor.cpp: [no log message]

2011-04-01 09:48  stevel

	* libpyEM/EMAN2db.py, programs/e2bdb.py: More improvements to
	  database cleanup on interrupt and e2bdb.py.

2011-04-01 09:24  stevel

	* libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py,
	  programs/e2refinevariance.py: Fix problem with interrupted DB
	  calls not allowing program to exit.

2011-03-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-30 13:00  ross

	* programs/e2ssehunter.py: working on geometry_scores() function

2011-03-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-29 22:19  irees

	* programs/e2pathwalker.py: Added option to calculate RMSDs

2011-03-29 16:17  john

	* libEM/: aligner.cpp, emdata.cpp, cuda/cuda_processor.cu,
	  cuda/cuda_processor.h: Bugfix for using CUDA with e2boxer swarm
	  tool

2011-03-29 12:43  scmurray

	* programs/e2runfrealign.py: one last windows change

2011-03-29 12:05  john

	* libpyEM/qtgui/emboxerbase.py: Reverted emboxerbase

2011-03-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-29 11:23  stevel

	* libEM/ctf.cpp, programs/e2refinevariance.py: Major fix for
	  refinevariance

2011-03-28 16:47  gtang

	* programs/e2bdb.py: fix for windows

2011-03-28 16:46  gtang

	* rt/demo/reconstruction.py: fix the os.system('rm -rf ') call with
	  more general os.remove() for windows

2011-03-28 15:00  gtang

	* programs/e2classifykmeans.py: fix the os.system('rm -rf ') call
	  with more general os.remove() for windows

2011-03-28 14:33  gtang

	* libpyEM/EMAN2db.py: clean up database cache on windows

2011-03-28 14:19  scmurray

	* programs/e2runfrealign.py: fixing more windows stuff

2011-03-28 13:25  scmurray

	* programs/: e2refinetofrealign.py, e2runfrealign.py: Changes to
	  make FA module work with windows. shutil being used now

2011-03-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-26 20:43  zyang

	* libEM/sparx/util_sparx.cpp: An overhaul to the algorithm of
	  assign_groups(), which significantly improves the speed.

2011-03-26 12:11  zyang

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: An improvement to the
	  assign_groups() program

2011-03-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-25 16:56  gtang

	* rt/pyem/rt.py: fix for windows

2011-03-25 13:54  ppenczek

	* libEM/sparx/util_sparx.cpp, sparx/bin/sxiter_isac.py,
	  sparx/libpy/pixel_error.py: [no log message]

2011-03-25 12:09  eman-vm

	* programs/e2version.py: new date stamp

2011-03-24 21:37  zyang

	* libEM/sparx/lbfgsb.cpp: Add 'volatile' to avoid over-zealous
	  optimization.

2011-03-24 21:21  stevel

	* libpyEM/EMAN2PAR.py: Longer delays between server pings

2011-03-24 20:59  ppenczek

	* sparx/libpy/pixel_error.py: [no log message]

2011-03-24 17:03  gtang

	* libpyEM/EMAN2db.py: the fix for dealing with a bdb with bad
	  image(no meta data) in stack should go to c++ in hdfiio2.cpp

2011-03-24 17:01  gtang

	* libEM/hdfio2.cpp: enable blank image written. So no segfault when
	  deal with a no meta data image in a bdb.

2011-03-24 15:29  gtang

	* libpyEM/EMAN2db.py: revert the change I made yesterday. which
	  causes e2display.py --fullrange not functional.

2011-03-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-24 11:04  john

	* libpyEM/qtgui/emboxerbase.py, programs/e2rctV2.py: Improved
	  e2rctV2.py documentation

2011-03-23 17:03  gtang

	* libpyEM/EMAN2db.py: raise exception to avoid segfault when deal
	  with a no meta data image in a bdb

2011-03-23 14:40  john

	* programs/e2workflow.py: Removed degug info from the GUI

2011-03-23 12:21  gtang

	* libEM/processor.cpp: fix warnings

2011-03-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-22 17:13  john

	* programs/e2montecarlorecon.py: Added docs for e2montecarlo.py

2011-03-22 16:05  gtang

	* libpyEM/CMakeLists.txt: fix for Visual C++ compilation

2011-03-22 15:53  john

	* libEM/aligner.cpp, libEM/cmp.cpp, libEM/emdata_cuda.h,
	  libEM/processor.cpp, libEM/projector.cpp,
	  libEM/reconstructor.cpp, libpyEM/qtgui/emtprworkflow.py:
	  Privatized my CUDA members

2011-03-22 15:48  gtang

	* libEM/hdfio2.cpp: suppress a warning message

2011-03-22 14:17  gtang

	* CMakeLists.txt: fix enable_cuda

2011-03-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-22 10:12  gtang

	* libpyEM/: qtgui/emtprworkflow.py, EMAN2PAR.py: make the command a
	  string instead of a list when use 'shell=True'

2011-03-21 17:32  ppenczek

	* libEM/: processor.cpp: formatting

2011-03-21 16:37  scmurray

	* programs/: e2refinefromfrealign.py, e2refinetofrealign.py,
	  e2runfrealign.py: Changes suggested by Richard Henderson and
	  comply with new GUI

2011-03-21 15:55  john

	* libpyEM/qtgui/emsprworkflow.py, programs/e2refinetofrealign.py:
	  Repaired vandalism to the GUI

2011-03-21 15:20  gtang

	* CMakeLists.txt: minimum cmake version needs 2.4.4

2011-03-21 14:50  zyang

	* sparx/: bin/sxiter_isac.py, libpy/utilities.py: [no log message]

2011-03-21 14:27  john

	* libpyEM/qtgui/emsprworkflow.py: GUI update #2

2011-03-21 14:24  john

	* libpyEM/qtgui/emsprworkflow.py, programs/e2refinetofrealign.py:
	  GUI updates

2011-03-21 12:58  scmurray

	* programs/e2refinetofrealign.py: update for new gui

2011-03-21 12:15  gtang

	* CMakeLists.txt: put different optimization flags into
	  IF/ELSEIF/ELSE/ENDIF block.

2011-03-21 12:03  scmurray

	* programs/e2runfrealign.py: changing form os.system to call()

2011-03-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-21 11:15  zyang

	* sparx/bin/sxiter_isac.py: [no log message]

2011-03-21 10:56  scmurray

	* programs/e2refinetofrealign.py: removed certain options and
	  changed others as per Richard Hendersons suggestion

2011-03-21 08:13  stevel

	* programs/e2classaverage3d.py: Option name change

2011-03-21 07:53  stevel

	* examples/extracthelp.py: Minor improvements

2011-03-20 20:07  zyang

	* sparx/bin/sxiter_isac.py: Major improvement of this program

2011-03-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-18 15:43  gtao

	* sparx/libpy/statistics.py: [no log message]

2011-03-18 12:34  ppenczek

	* sparx/bin/sxiter_isac.py: change MPI default

2011-03-18 12:18  ppenczek

	* sparx/libpy/global_def.py: corrected global flags

2011-03-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-18 11:32  ppenczek

	* libEM/CMakeLists.txt, CMakeLists.txt: [no log message]

2011-03-18 10:40  zyang

	* sparx/libpy/utilities.py: [no log message]

2011-03-18 10:32  gtao

	* sparx/libpy/: global_def.py, statistics.py: [no log message]

2011-03-17 17:04  zyang

	* sparx/bin/sxiter_isac.py: [no log message]

2011-03-17 16:21  gtang

	* CMakeLists.txt: boost is required for EMAN2

2011-03-17 15:50  gtang

	* CMakeLists.txt: fix the broken mac compilation. Also add flag to
	  enforce C++ standard.

2011-03-17 15:35  zyang

	* sparx/libpy/utilities.py: [no log message]

2011-03-17 13:56  gtao

	* sparx/: bin/sxk_means.py, bin/sxk_means_groups.py,
	  bin/sxk_means_stable.py, libpy/applications.py,
	  libpy/statistics.py: [no log message]

2011-03-17 12:18  gtang

	* CMakeLists.txt, libEM/cuda/CMakeLists.txt,
	  libpyEM/CMakeLists.txt, libpyEM/qtgui/CMakeLists.txt,
	  rt/emdata/CMakeLists.txt, rt/imageio/CMakeLists.txt,
	  sparx/CMakeLists.txt, utils/CMakeLists.txt: replace deprecated
	  function calls in CMakeLists.txt and clean up

2011-03-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-17 10:50  gtao

	* sparx/libpy/statistics.py: [no log message]

2011-03-17 10:31  gtao

	* sparx/libpy/: applications.py, statistics.py: [no log message]

2011-03-16 17:18  zyang

	* sparx/libpy/utilities.py: Add gather_EMData() program (not
	  finished yet)

2011-03-16 14:45  gtao

	* sparx/: bin/sxk_means_stable.py, libpy/applications.py,
	  libpy/statistics.py: [no log message]

2011-03-16 13:19  gtang

	* libpyEM/: qtgui/emsprworkflow.py, qtgui/emtprworkflow.py,
	  EMAN2PAR.py: fix the problem to call python script on windows

2011-03-16 12:51  gtang

	* libpyEM/qtgui/emsprworkflow.py: fix the problem to call python
	  script on windows with os.system()

2011-03-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-14 21:31  scmurray

	* programs/e2runfrealign.py: fixed an import issue

2011-03-14 17:36  irees

	* programs/e2pathwalker.py: Resolved additional numbering issues

2011-03-14 17:26  ppenczek

	* sparx/bin/sxmref_ali2d.py: [no log message]

2011-03-14 12:12  irees

	* programs/e2pathwalker.py: Fixed problem with atom numbering of
	  TSP path vs. atom numbering of PDB

2011-03-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-14 10:40  gtao

	* libpyEM/libpyProcessor2.cpp, libEM/processor.cpp,
	  libEM/processor.h, libEM/sparx/cuda/cuda_mpi_kmeans.cu,
	  libEM/sparx/cuda/cuda_mpi_kmeans.h: [no log message]

2011-03-13 22:13  gtang

	* libEM/imagicio2.cpp: fix unused nz. It's for avoiding cases when
	  imagic images not fully abide by new Imagic4D standard (izlp not
	  set, leave as zero).

2011-03-13 17:20  irees

	* programs/e2pathwalker.py: Added license notice and --verbose
	  option for compliance with EMAN2 python style guide

2011-03-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-13 01:21  stevel

	* programs/: e2ctf.py, e2workflow.py: Tweak to CTF

2011-03-12 20:28  gtang

	* libEM/imagicio2.cpp: fix a bug when read 2D plane in 3D image of
	  Imagic4D image.

2011-03-12 19:38  gtang

	* rt/pyem/test_cmp.py: unit test update

2011-03-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-11 17:20  john

	* libEM/cuda/cuda_processor.cu, libpyEM/qtgui/emtprworkflow.py,
	  programs/e2workflow.py: GUI bugfix

2011-03-11 12:23  gtang

	* libEM/sparx/pca.cpp: These file should be opened in binary mode.
	  Otherwise it will generate error on windows.

2011-03-11 12:16  gtang

	* libEM/analyzer.cpp: fix for Windows platform

2011-03-11 12:10  gtang

	* libEM/emdata_transform.cpp: fix for Windows platform

2011-03-11 12:06  gtao

	* sparx/libpy/statistics.py: [no log message]

2011-03-11 12:03  gtang

	* libEM/analyzer.cpp: fix bug for Windows platform

2011-03-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-11 11:09  gtao

	* sparx/libpy/: applications.py, statistics.py: [no log message]

2011-03-10 22:15  gtang

	* programs/e2version.py: version 2.0.1

2011-03-10 21:24  gtang

	* libpyEM/EMAN2db.py: fix my fix. Oh, how dumb I am!

2011-03-10 20:46  gtang

	* libEM/sparx/util_sparx.cpp: quick fix for windows compilation

2011-03-10 19:06  ross

	* libpyEM/qtgui/emimage3d.py: using set_cam_z_from_fov_image() in
	  EMImage3DWidget.set_data() to prevent clipping plane problems

2011-03-10 19:04  gtang

	* libpyEM/EMAN2db.py: fix windows database path issue

2011-03-10 18:04  ppenczek

	* sparx/bin/sxmref_ali2d.py: [no log message]

2011-03-10 17:46  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, sparx/libpy/statistics.py: Add
	  multi-reference assignment C++ code:

2011-03-10 16:32  stevel

	* libpyEM/qtgui/emsprworkflow.py: trivial

2011-03-10 16:20  ross

	* libpyEM/qtgui/emimage3d.py: fixing a e2tomoboxer.py bug... if the
	  iso threshold was changed from default, clicking on a different
	  particle would result in a blank screen isosurface view

2011-03-10 15:50  stevel

	* programs/e2workflow.py: More tweaks to process display

2011-03-10 15:15  ppenczek

	* sparx/: bin/sxmref_ali2d.py, libpy/applications.py: [no log
	  message]

2011-03-10 14:55  gtang

	* programs/e2bdb.py: fix the path issue on windows

2011-03-10 14:54  ppenczek

	* sparx/libpy/applications.py: [no log message]

2011-03-10 14:42  stevel

	* libpyEM/EMAN2.py: process viewer working

2011-03-10 14:21  stevel

	* programs/e2workflow.py: Workflow fixed

2011-03-10 13:35  john

	* libEM/aligner.h: [no log message]

2011-03-10 12:42  john

	* libEM/aligner.cpp: Sym aligner update

2011-03-10 12:29  john

	* libEM/aligner.cpp: [no log message]

2011-03-10 12:14  john

	* libEM/: aligner.cpp, emdata_metadata.cpp: Bug fix for aligners

2011-03-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-10 11:44  john

	* libEM/: aligner.cpp, emdata_metadata.cpp, cuda/cuda_processor.cu:
	  Improved grid aligner

2011-03-10 11:42  scmurray

	* libpyEM/qtgui/emsprworkflow.py, programs/e2refinefromfrealign.py,
	  programs/e2refinetofrealign.py, programs/e2runfrealign.py: Made
	  frealign eman2 files formatted properly

2011-03-10 11:42  stevel

	* libpyEM/EMAN2.py, programs/e2workflow.py: Experimental workflow
	  task view

2011-03-10 11:26  gtang

	* rt/pyem/: test_imageio.py, test_utils.py: [no log message]

2011-03-10 11:05  gtang

	* rt/pyem/test_processor.py: unit test update

2011-03-10 10:46  gtang

	* libEM/testutil.cpp: clean up test print out

2011-03-09 22:47  stevel

	* programs/e2workflow.py: Starting work on process viewer in
	  workflow. Hope to finish by tomorrow.

2011-03-09 17:39  gtang

	* libpyEM/EMAN2db.py: fix path issue for windows system

2011-03-09 17:31  john

	* libEM/aligner.cpp: bugfix for sym alinger

2011-03-09 17:06  john

	* libEM/emdata_metadata.cpp: Subpixel prec

2011-03-09 16:01  john

	* libEM/: aligner.cpp, aligner.h, emdata_metadata.cpp: Added sym
	  aligner

2011-03-09 15:40  gtang

	* programs/e2version.py: version string update

2011-03-09 14:37  gtang

	* libEM/xydata.cpp: minor fix, nx needs to be declare earlier.

2011-03-09 13:48  stevel

	* libEM/xydata.cpp: Fix range problem in CTF

2011-03-09 13:28  scmurray

	* programs/e2runfrealign.py: fixed a minor issue

2011-03-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-09 10:15  john

	* libEM/: aligner.cpp, cuda/cuda_processor.cu,
	  cuda/cuda_processor.h, cuda/cuda_util.h: Subpixel for CUDA

2011-03-09 09:41  zyang

	* sparx/libpy/alignment.py: [no log message]

2011-03-08 17:51  john

	* libEM/aligner.cpp: bdebug statement

2011-03-08 17:48  john

	* libEM/: aligner.cpp, emdata_core.cpp, emdata_metadata.cpp:
	  Aligner stuff

2011-03-08 17:17  gtao

	* sparx/: libpy/applications.py, bin/sxk_means_stable.py: [no log
	  message]

2011-03-08 17:11  ppenczek

	* sparx/libpy/: applications.py, statistics.py: more changes in sse

2011-03-08 16:27  gtao

	* sparx/: bin/sxk_means.py, bin/sxk_means_groups.py,
	  bin/sxk_means_stable.py, libpy/statistics.py: [no log message]

2011-03-08 16:21  john

	* libEM/aligner.cpp: bugfiox

2011-03-08 15:48  john

	* libEM/: aligner.cpp, aligner.h: Bugfix for grid alinger

2011-03-08 15:45  john

	* libEM/: aligner.cpp, aligner.h: Bugfix for grid alinger

2011-03-08 14:45  zyang

	* sparx/libpy/alignment.py: [no log message]

2011-03-08 14:39  zyang

	* sparx/libpy/alignment.py: Delete two useless functions and add
	  one.

2011-03-08 14:33  john

	* libEM/cuda/cuda_processor.cu, libpyEM/qtgui/emsprworkflow.py: GUI
	  bug fix

2011-03-08 14:04  stevel

	* programs/e2ctf.py: trivial

2011-03-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-08 11:27  gtang

	* programs/e2parallel.py, libpyEM/EMAN2PAR.py: small fix

2011-03-07 19:24  ppenczek

	* sparx/libpy/applications.py: [no log message]

2011-03-07 18:04  john

	* libEM/: aligner.cpp, emdata_metadata.cpp, emdata_metadata.h,
	  cuda/cuda_processor.cu: subpixel prec for gridaligner

2011-03-07 16:33  fjia

	* sparx/libpy/statistics.py: [no log message]

2011-03-07 16:24  stevel

	* programs/CMakeLists.txt: Remove installation of some programs.

2011-03-07 15:41  stevel

	* libEM/emdata.cpp: More debugging

2011-03-07 15:30  stevel

	* CMakeLists.txt, libEM/emdata.cpp, libEM/emdata_metadata.cpp:
	  Better memory debugging

2011-03-07 14:44  scmurray

	* programs/: e2refinefromfrealign.py, e2refinetofrealign.py,
	  e2runfrealign.py: Final Changes. Runs several FA's

2011-03-07 14:32  john

	* libpyEM/qtgui/emsprworkflow.py, programs/e2workflow.py: GUI
	  changes

2011-03-07 14:30  fjia

	* sparx/libpy/statistics.py: [no log message]

2011-03-07 14:16  stevel

	* libpyEM/qtgui/emimagemx.py: Trivial typo

2011-03-07 13:13  stevel

	* programs/e2classaverage3d.py: Allows 1 particle when ref is
	  specified

2011-03-07 12:56  john

	* libpyEM/qtgui/emsprworkflow.py: Frealign update

2011-03-07 12:12  john

	* libEM/aligner.cpp: Sewt default options for refine grid aligner

2011-03-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-07 11:34  scmurray

	* programs/e2refinefromfrealign.py: Final FSC changes

2011-03-07 11:34  john

	* libEM/aligner.cpp: BugFix for gird aligner

2011-03-07 11:04  ppenczek

	* sparx/libpy/statistics.py: removed printout line 1747

2011-03-07 11:01  john

	* libEM/: aligner.cpp, aligner.h: Refine Grid Aligner update

2011-03-07 10:48  scmurray

	* programs/e2refinefromfrealign.py: FSC Change

2011-03-07 10:46  john

	* libEM/: aligner.cpp, aligner.h: Added refinegrid aligner

2011-03-07 10:13  scmurray

	* libpyEM/qtgui/emsprworkflow.py, programs/e2refinefromfrealign.py,
	  programs/e2runfrealign.py: FSC changes for FreAlign

2011-03-07 09:18  john

	* programs/e2workflow.py: Bugfix for the workflow

2011-03-07 09:09  ppenczek

	* sparx/libpy/: applications.py, statistics.py: [no log message]

2011-03-07 08:06  stevel

	* programs/e2tomoboxer.py: Trivial

2011-03-06 22:32  stevel

	* programs/: e2filtertool.py, e2tomoboxer.py, e2workflow.py:
	  Working on filtertool

2011-03-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-06 09:09  ppenczek

	* sparx/libpy/applications.py: [no log message]

2011-03-05 23:31  stevel

	* programs/e2simmx2stage.py: Fix for bizzare bug in database
	  writing by running with thread=1 instead of single-threaded.

2011-03-05 16:34  ross

	* programs/e2workflow.py: bugfix: the task manager can now kill
	  WorkFlowTask objects which have forms rather than GL display
	  widgets

2011-03-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-05 08:40  stevel

	* programs/e2bdb.py: Cache disable option

2011-03-05 08:20  stevel

	* examples/tomospeedtest.py, libEM/emdata_metadata.cpp,
	  libpyEM/EMAN2.py, libpyEM/EMAN2db.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2bdb.py,
	  programs/e2filtertool.py, programs/e2simmx2stage.py: Various
	  fixes

2011-03-05 07:24  stevel

	* CMakeLists.txt: Auto-find numpy on snow-leopard

2011-03-04 22:22  stevel

	* programs/e2classaverage3d.py: Minor fix

2011-03-04 22:08  stevel

	* programs/e2classaverage3d.py: minor bug

2011-03-04 22:06  stevel

	* programs/e2tomoboxer.py: Boxsize tweak

2011-03-04 17:42  ross

	* libpyEM/qtgui/: emform.py, emsprworkflow.py: EMForm close events
	  are propogated to the workflow (so the close button causes the
	  entry to be removed from running tasks).

2011-03-04 17:33  ross

	* libpyEM/qtgui/: emapplication.py, emimageutil.py: updated
	  documentation

2011-03-04 16:21  ppenczek

	* sparx/libpy/statistics.py: added ave

2011-03-04 14:00  ross

	* libpyEM/qtgui/emapplication.py: minor changes to EMGLWidget

2011-03-04 13:05  stevel

	* programs/: e2filtertool.py, e2simmx2stage.py: Working on new
	  program

2011-03-04 12:40  ppenczek

	* sparx/libpy/: applications.py, statistics.py: corrected SSE for
	  all clusterings

2011-03-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-04 11:53  irees

	* programs/e2pathwalker.py: Added e2pathwalker to EMAN2 cvs

2011-03-04 11:41  stevel

	* programs/: e2ctf.py, e2iminfo.py, e2simmx2stage.py,
	  e2tomoboxer.py: Tomoboxer shouldn't update box size unless it
	  changes

2011-03-04 10:45  gtang

	* libEM/: averager.cpp, processor.cpp, transform.cpp: fix Visual
	  C++ warnings

2011-03-04 07:49  stevel

	* libpyEM/qtgui/emsprworkflow.py: Trivial

2011-03-04 06:23  stevel

	* libEM/reconstructor.cpp, programs/e2classaverage3d.py: Remove
	  mask from final tomo average

2011-03-03 22:31  stevel

	* programs/e2make3d.py: Aack. The same in make3d fixed (sigma was
	  being computed incorrectly for class-average exclusion)

2011-03-03 22:14  stevel

	* programs/e2classaverage.py: Big whoops in class-averaging.
	  Regardless of keep with keepsig always threw away almost 1/2.
	  Uggh

2011-03-03 20:17  stevel

	* libpyEM/qtgui/emsprworkflow.py, programs/e2classaverage3d.py,
	  programs/e2proc3d.py: single parameter option for proc3d

2011-03-03 17:32  gtang

	* pyemtbx/CMakeLists.txt, rt/CMakeLists.txt,
	  rt/pyem/CMakeLists.txt, utils/CMakeLists.txt: update cmake to
	  remove deprecated commands

2011-03-03 17:23  gtang

	* doc/CMakeLists.txt, doc/latex/CMakeLists.txt,
	  doc/modular_class_html/CMakeLists.txt, examples/CMakeLists.txt,
	  fonts/CMakeLists.txt, images/CMakeLists.txt,
	  images/macimages/CMakeLists.txt, libEM/CMakeLists.txt,
	  libEM/gorgon/CMakeLists.txt, libEM/plugins/CMakeLists.txt,
	  libEM/sparx/CMakeLists.txt: update cmake to remove deprecated
	  commands

2011-03-03 17:14  ross

	* libpyEM/qtgui/emimage3d.py: if EMImage3DWidget.set_data() gets a
	  map with different dimensions than the previous one,
	  self.set_cam_z_from_fov_image() is called. This prevents display
	  problems, with some of the map being outside the OpenGL clipping
	  volume.

2011-03-03 17:01  scmurray

	* programs/: e2refinefromfrealign.py, e2runfrealign.py: More
	  changes to FA stuff

2011-03-03 16:55  john

	* programs/e2workflow.py: Bugfix for the GUI

2011-03-03 13:33  john

	* libpyEM/qtgui/emsprworkflow.py: FeAliogn updates

2011-03-03 13:19  john

	* libpyEM/: EMAN2.py, qtgui/emsprworkflow.py: GUI update for
	  reading frealign resolution

2011-03-03 12:40  john

	* libpyEM/qtgui/emsprworkflow.py: GUI update

2011-03-03 12:08  scmurray

	* programs/e2refinefromfrealign.py: Committed changes for FA stuff

2011-03-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-03 11:51  john

	* libpyEM/qtgui/emsprworkflow.py, programs/e2workflow.py: GUI
	  update

2011-03-03 11:48  ppenczek

	* sparx/libpy/applications.py: [no log message]

2011-03-03 11:41  ppenczek

	* sparx/libpy/statistics.py: SSE finished

2011-03-03 11:21  scmurray

	* programs/: e2refinefromfrealign.py, e2runfrealign.py: Added
	  FreAlign stuff

2011-03-03 11:18  gtang

	* programs/CMakeLists.txt: provide ways to exclude programs not
	  want to install into bin directory

2011-03-03 11:17  gtang

	* sparx/: bin/CMakeLists.txt, libpy/CMakeLists.txt: update cmake to
	  remove deprecated commands

2011-03-03 11:14  john

	* libpyEM/EMAN2.py, libpyEM/qtgui/emsprworkflow.py,
	  libpyEM/qtgui/emtprworkflow.py, programs/e2workflow.py: GUI
	  updates

2011-03-03 10:37  ross

	* libpyEM/qtgui/: emapplication.py, emglobjects.py, emimage3d.py:
	  Added self.busy to EMGLWidget and EM3DModel. It prevents
	  updateGL() from doing anything while it is true. Using it to
	  prevent mulitple GL refreshes during EMImage3DWidget.set_data().

2011-03-03 07:19  ppenczek

	* sparx/libpy/statistics.py: started fixing SSE

2011-03-02 19:56  ppenczek

	* sparx/libpy/statistics.py: started fixing SSE

2011-03-02 18:48  ross

	* libpyEM/qtgui/emimage3d.py: minimizing GL update flashes when
	  calling EMImage3DWidget.set_data()

2011-03-02 16:56  john

	* programs/e2refinetofrealign.py: Added to cvs

2011-03-02 16:32  gtang

	* programs/e2proc3d.py: fix the inplace writing for stack image.

2011-03-02 15:52  gtang

	* libEM/CMakeLists.txt, libEM/all_imageio.h, libEM/emutil.cpp,
	  libEM/imageio.h, libEM/imagicio.cpp, libEM/imagicio2.cpp,
	  libEM/imagicio2.h, rt/pyem/test_imageio.py: For IMGIC file I/O,
	  write with new Imagic4D format . Read both new and old IMAGIC
	  files.

2011-03-02 15:39  stevel

	* programs/e2classaverage3d.py: keep working (?)

2011-03-02 12:59  stevel

	* programs/: e2classaverage3d.py, e2refine.py, e2tomoboxer.py: More
	  improvements to e2classaverage3d.py. Masking fixed, and added for
	  intermediate models.

2011-03-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-02 11:50  gtao

	* libEM/processor.cpp, libEM/processor.h,
	  libEM/sparx/cuda/cuda_mpi_kmeans.cu,
	  libEM/sparx/cuda/cuda_mpi_kmeans.h, libpyEM/libpyProcessor2.cpp:
	  [no log message]

2011-03-02 11:47  gtao

	* sparx/libpy/: applications.py, statistics.py: kmeans-SSE cuda
	  python level update.

2011-03-02 11:25  zyang

	* sparx/libpy/applications.py: Split ali2d() into two programs
	  ali2d() and ali2d_data() such that ali2d_data() can take list of
	  EMData

2011-03-02 11:23  zyang

	* sparx/bin/: sxmref_alignment.py, sxrealignment.py: New
	  realignment program that get rid of intermediate hdf file.

2011-03-02 11:22  zyang

	* libEM/sparx/cuda/cuda_ccf.cu: Trival change

2011-03-02 11:22  zyang

	* libEM/aligner.cpp: Skipping seeting GPU when unnecessary.

2011-03-02 11:01  john

	* libpyEM/qtgui/: emform.py, emselector.py, emsprworkflow.py: GUI
	  updates

2011-03-02 11:01  zyang

	* sparx/libpy/pixel_error.py: Just edit some comments

2011-03-02 10:58  ppenczek

	* sparx/libpy/applications.py: applications.py

2011-03-02 10:38  ppenczek

	* sparx/: bin/sxisc.py, libpy/statistics.py: new version of isc

2011-03-02 09:10  stevel

	* libpyEM/EMAN2db.py, programs/e2classaverage3d.py: oops

2011-03-02 08:59  stevel

	* libpyEM/EMAN2db.py, programs/e2classaverage3d.py: Aack ! refine
	  aligns would always fail

2011-03-02 08:40  ppenczek

	* sparx/libpy/fundamentals.py: log option in rops

2011-03-02 07:12  stevel

	* programs/e2classaverage3d.py: Fixes for translation in alignment,
	  and error reporting.

2011-03-01 23:05  stevel

	* programs/e2classaverage3d.py: oops

2011-03-01 22:56  stevel

	* programs/e2classaverage3d.py: Revised e2classaverage3d to deal
	  with scaling translations

2011-03-01 17:33  john

	* libpyEM/qtgui/emsprworkflow.py: more GUI

2011-03-01 17:16  john

	* libpyEM/qtgui/emsprworkflow.py, libpyEM/qtgui/emtprworkflow.py,
	  programs/e2workflow.py: GUI stuff

2011-03-01 14:13  stevel

	* libEM/averager.cpp, libEM/averager.h,
	  programs/e2classaverage3d.py: New averager for tomography

2011-03-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-03-01 11:11  john

	* libpyEM/qtgui/emsprworkflow.py, libpyEM/qtgui/emtprworkflow.py,
	  programs/e2align3d.py, programs/e2workflow.py: tomo GUI stuff

2011-03-01 09:51  gtang

	* programs/e2proc3d.py: add --append option. default is inplace
	  writing.

2011-03-01 07:04  stevel

	* examples/simtomo.py, programs/e2classaverage3d.py: Reference free
	  classes in e2classaverage3d.py

2011-02-28 17:34  ross

	* programs/e2ssehunter.py: refactoring

2011-02-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-28 11:20  john

	* libEM/: aligner.cpp, aligner.h: Changed course aligner pars from
	  lxxx to xxx0 and uxxx to xxx1

2011-02-28 10:27  john

	* libEM/aligner.cpp, libpyEM/qtgui/emtprworkflow.py: Reverted the
	  'bug' in the refine aligner

2011-02-28 09:31  john

	* libEM/aligner.cpp: Bugfix for the refine aligner.

2011-02-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-26 02:13  stevel

	* programs/e2refinevariance.py: bugfix

2011-02-26 01:23  stevel

	* examples/simtomo.py, programs/e2classaverage3d.py:
	  e2classaverage3d working (?)

2011-02-25 17:51  ross

	* programs/e2ssehunter.py: refactoring...

2011-02-25 17:21  john

	* libpyEM/qtgui/emtprworkflow.py: Enabled the GUI to use the new
	  e2tomoboxer

2011-02-25 16:18  john

	* libEM/emdata_cuda.cpp, libEM/emdata_cuda.h, libpyEM/EMAN2db.py,
	  libpyEM/libpyEMData2.cpp: Renamed cuda_cleanup function

2011-02-25 16:15  ross

	* programs/e2ssehunter.py: fixing bugs and refactoring

2011-02-25 16:05  john

	* libEM/emdata_cuda.cpp, libpyEM/qtgui/emtprworkflow.py: Bug fix
	  for my system (Fixed issue from cudaThreadExit)

2011-02-25 14:43  john

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emtprworkflow.py, programs/e2workflow.py: Added
	  Some stuff for the aligning a recon to its sym axis, and worked
	  on the workflow

2011-02-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-25 11:55  zyang

	* sparx/bin/sxrealignment.py: [no log message]

2011-02-25 11:42  ppenczek

	* sparx/bin/: sxrealignment.py: [no log message]

2011-02-25 11:35  ppenczek

	* sparx/libpy/statistics.py: [no log message]

2011-02-25 10:35  stevel

	* libEM/aligner.cpp, libEM/emdata_cuda.cpp, libEM/symmetry.cpp,
	  libpyEM/libpyEMData2.cpp, programs/e2classaverage3d.py: Cuda
	  cleanup

2011-02-25 08:44  stevel

	* libEM/aligner.cpp, programs/e2classaverage3d.py,
	  programs/e2refinevariance.py: classaverage3d is functioning now,
	  but still incomplete

2011-02-24 18:33  ross

	* programs/e2helixboxer.py: updated Save dialog to be more logical
	  since we now have three particle image generation methods
	  "bilinear rotation", "gridding rotation", and "no rotation"

2011-02-24 17:42  ppenczek

	* sparx/libpy/statistics.py: [no log message]

2011-02-24 16:27  ppenczek

	* programs/e2proc2d.py, programs/e2proc3d.py,
	  sparx/demo/1_bdb/run_through_example,
	  sparx/demo/3_bdb_ctf/run_through_example,
	  sparx/demo/5_mpi_bdb/run_through_example,
	  sparx/demo/7_mpi_bdb_ctf/run_through_example: cleaned up e2procnd

2011-02-24 15:51  ross

	* programs/e2helixboxer.py: Simplified conditional logic in
	  get_unrotated_particles(). The title bar for the current helix
	  viewer now displays helix length and width.

2011-02-24 15:44  stevel

	* libEM/processor.cpp, libEM/processor.h, libpyEM/EMAN2.py,
	  libpyEM/EMAN2PAR.py, programs/e2classaverage3d.py: first testing
	  version of programs/e2classaverage3d.py

2011-02-24 14:53  ppenczek

	* programs/e2proc3d.py: removed filter option

2011-02-24 14:42  ppenczek

	* programs/e2proc2d.py, programs/e2proc3d.py,
	  sparx/libpy/statistics.py: changed e2proc3d and e2proc2d

2011-02-24 14:41  ppenczek

	* sparx/demo/: 3_bdb_ctf/run_through_example,
	  5_mpi_bdb/run_through_example, 7_mpi_bdb_ctf/run_through_example:
	  changed e2proc3d to process

2011-02-24 14:36  ppenczek

	* sparx/demo/1_bdb/run_through_example: [no log message]

2011-02-24 13:31  mingc

	* programs/e2helical_recons.py: helical reconstruction program

2011-02-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-23 17:01  john

	* programs/e2workflow.py: Remove the tomo garbage

2011-02-23 16:41  ross

	* libpyEM/qtgui/emimagemx.py: can now display the particles in a
	  set (double click in drag mode) without first closing the window
	  for last class average's particles--replaces what was displayed

2011-02-23 16:29  ppenczek

	* sparx/libpy/statistics.py: statistics.py

2011-02-23 14:38  stevel

	* libpyEM/qtgui/emshape.py, programs/e2classaverage3d.py,
	  programs/e2tomoboxer.py: tomoboxer improvement

2011-02-23 13:56  fjia

	* sparx/bin/sxk_means_stable.py: [no log message]

2011-02-23 13:15  gtao

	* sparx/libpy/applications.py: fix a bug for k_means_cuda.

2011-02-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-23 11:49  ppenczek

	* sparx/libpy/utilities.py: [no log message]

2011-02-23 07:33  stevel

	* programs/e2ctf.py: New fitting scheme working fairly well. Still
	  gives funny B-factors sometimes. Sigh.

2011-02-22 22:53  stevel

	* programs/e2ctf.py: More Ctf changes

2011-02-22 22:49  stevel

	* programs/e2ctf.py: Working on CTF. This version may not be
	  great... fix before noon tomorrow.

2011-02-22 21:35  stevel

	* libpyEM/EMAN2.py, programs/e2ctf.py: New ctf fitting does a much
	  better job with defocus

2011-02-22 19:54  ross

	* libpyEM/qtgui/emimagemx.py: removing print statements for the new
	  mouse handling functions

2011-02-22 18:21  ross

	* libpyEM/qtgui/emimage2d.py: trivial

2011-02-22 18:20  ross

	* libpyEM/qtgui/emimagemx.py: moving mouse event handling into
	  EMImageMXWidget rather than seperate classes for each mouse mode

2011-02-22 12:43  ppenczek

	* sparx/libpy/: global_def.py, user_functions.py: [no log message]

2011-02-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-22 09:45  gtang

	* rt/pyem/test_typeconverter.py: [no log message]

2011-02-21 16:22  john

	* libEM/cuda/cuda_util.cu: small mod to setcudadevice

2011-02-21 15:54  john

	* libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/cuda/cuda_emfft.cu, libEM/cuda/cuda_util.cu,
	  libpyEM/EMAN2.py, libpyEM/libpyEMData2.cpp: Code for mult cuda
	  devices

2011-02-21 15:13  ppenczek

	* libpyEM/EMAN2.py: changed printout in E2init

2011-02-21 14:09  ross

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emboxerbase.py,
	  libpyEM/qtgui/emform.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py, libpyEM/qtgui/emtprworkflow.py,
	  programs/e2eulerxplor.py, sparx/bin/sxboxer.py: moved
	  EMErrorMessageDisplay class and error() convenience function from
	  emsprworkflow.py to emapplication.py to simplify imports in
	  various places

2011-02-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-21 11:28  john

	* libEM/cuda/cuda_emfft.cu: Fix for CUDA FFT EXEC fail

2011-02-21 10:57  john

	* libEM/emdata_cuda.cpp, libpyEM/libpyEMData2.cpp: Bug fix for
	  previous commit

2011-02-21 10:11  john

	* libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/cuda/cuda_emfft.cu, libEM/cuda/cuda_emfft.h,
	  libpyEM/EMAN2db.py, libpyEM/libpyEMData2.cpp: Method to clean up
	  the cuda fft cache

2011-02-21 08:02  stevel

	* libpyEM/qtgui/emimagemx.py, programs/e2classaverage.py,
	  programs/e2evalrefine.py: Display excluded class-averages.
	  evalrefine fixes

2011-02-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-18 17:52  gtang

	* libEM/emobject.cpp, libEM/emobject.h, libEM/testutil.cpp,
	  libEM/testutil.h, libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyUtils2.cpp, libpyEM/typeconverter.cpp,
	  libpyEM/typeconverter.h, rt/emdata/CMakeLists.txt,
	  rt/emdata/transform.cpp, rt/pyem/test_typeconverter.py,
	  rt/pyem/testlib.py: support lists of Transform as header items

2011-02-18 17:00  john

	* libEM/aligner.cpp, programs/e2montecarlorecon.py: bug fix

2011-02-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-17 17:50  ross

	* programs/e2helixboxer.py: updated command-line option
	  descriptions

2011-02-17 16:04  gtang

	* programs/e2proc2d.py: fix 3D mrc output

2011-02-17 15:44  zyang

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/libpyProcessor2.cpp: Reverse John's change and put back
	  Julien's K-means CUDA program.

2011-02-17 15:43  stevel

	* programs/e2classaverage3d.py: Crasher

2011-02-17 15:23  gtang

	* programs/e2history.py: fix the --help option

2011-02-17 13:15  stevel

	* libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2tomoboxer.py: Many more tomoboxer fixes including
	  deletion.

2011-02-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-17 11:07  gtao

	* sparx/: libpy/statistics.py, bin/sxk_means_stable.py: [no log
	  message]

2011-02-17 10:59  gtao

	* sparx/libpy/morphology.py: [no log message]

2011-02-17 09:49  stevel

	* libEM/emdata_cuda.cpp, libpyEM/qtgui/emimage3d.py,
	  programs/e2tomoboxer.py: Cuda default on

2011-02-17 09:43  ross

	* programs/e2helixboxer.py: commandline option documentation
	  changes

2011-02-17 09:28  john

	* libEM/aligner.cpp: Added verbose info

2011-02-17 09:13  stevel

	* libpyEM/EMAN2PAR.py, programs/e2classaverage3d.py,
	  programs/e2refinemulti.py, programs/e2tomoboxer.py: Minor fixes
	  for tomoboxer. Still working on e2classaverage3d.py

2011-02-17 04:07  irees

	* programs/emen2client.py: Removing emen2client; it is now part of
	  the emen2 distribution, available via "easy_install emen2"

2011-02-16 22:38  ross

	* libpyEM/qtgui/: emapplication.py, emimage2d.py, emimage3d.py,
	  emimagemx.py: removing unused self.core_object, a QObject
	  instance which was once used by EM*Module classes to emit signals
	  (now use QWidget subclasses instead of EM*Module classes)

2011-02-16 18:41  gtang

	* programs/e2proc2d.py: add options for e2proc2d.py,
	  --threed2threed, --threed2twod, --twod2threed

2011-02-16 16:09  john

	* libEM/aligner.cpp: Bug fix for the grid aligner

2011-02-16 15:46  john

	* programs/e2montecarlorecon.py: progrma to generate ab initio via
	  Monte Carlo and simulated annealing methods

2011-02-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-16 10:20  gtang

	* libEM/sparx/emdata_sparx.cpp: fix big mem issue (size_t)

2011-02-15 17:32  john

	* libEM/aligner.cpp, libEM/aligner.h, libEM/cmp.cpp, libEM/cmp.h,
	  libEM/emdata_core.cpp, libEM/emdata_core.h,
	  libEM/cuda/cuda_cmp.cu, libEM/cuda/cuda_cmp.h,
	  programs/e2align3d.py: Updates to the 3D aligners

2011-02-15 16:00  gtang

	* libEM/sparx/: emdata_sparx.cpp, rsconvolution.cpp,
	  util_sparx.cpp, util_sparx.h: fix big mem issue (size_t)

2011-02-15 14:31  stevel

	* libEM/mrcio.cpp, libpyEM/qtgui/valslider.py,
	  programs/e2classaverage3d.py, programs/e2tomoboxer.py: Bug in MRC
	  reader with labels. New 3d class averaging program (incomplete).
	  Improvements (incomplete) to e2tomoboxer.

2011-02-15 12:41  ppenczek

	* sparx/bin/: sxbootstrap_bigdisk.py, sxbootstrap_calcwgts.py,
	  sxbootstrap_genbuf.py, sxbootstrap_run.py, sxbootstrap_smp.py:
	  [no log message]

2011-02-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-15 07:54  stevel

	* libEM/processor.cpp: Fixed update

2011-02-14 21:21  stevel

	* libEM/processor.cpp, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimage3diso.py,
	  programs/e2make3d.py, programs/e2tomoboxer.py: tomoboxer
	  additions. Gui fixes

2011-02-14 17:24  gtang

	* libEM/processor.cpp: fix the image center of odd size image for
	  CircularMaskProcessor

2011-02-14 16:53  gtang

	* rt/pyem/test_processor.py: unit test update

2011-02-14 16:48  gtang

	* libEM/: averager.cpp, cmp.cpp, emutil.cpp, projector.cpp: fix big
	  mem issue (size_t)

2011-02-14 16:22  john

	* libEM/aligner.cpp, libEM/cmp.cpp, libEM/emdata.cpp,
	  libEM/emdata_core.cpp, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libEM/cuda/cuda_util.cu,
	  libEM/cuda/cuda_util.h, libpyEM/libpyReconstructor2.cpp,
	  programs/e2rctV2.py: Bug fix for ccc.tomo

2011-02-14 15:59  gtang

	* libEM/: emdata.cpp, emdata_metadata.cpp, emdata_metadata.h,
	  emdata_transform.cpp, icosio.cpp, processor.cpp,
	  sparx/emdata_sparx.cpp: fix big mem issue (size_t)

2011-02-14 15:53  gtang

	* libEM/emdata_core.cpp: for warp around, use ptrdiff_t not size_t

2011-02-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-14 11:25  gtang

	* libEM/averager.cpp, libEM/emdata.cpp, libEM/emdata_metadata.cpp,
	  libEM/emdata_transform.cpp, libEM/mrcio.cpp,
	  libEM/pointarray.cpp, libEM/processor.cpp, libEM/vtkio.cpp,
	  libpyEM/sparx.cpp: fix big mem issue (size_t)

2011-02-14 10:00  zyang

	* libEM/processor.h: Small fix.

2011-02-13 22:48  stevel

	* libEM/: processor.cpp, processor.h: Prototype for symmetry
	  alignment processor.

2011-02-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-11 20:33  gtang

	* libEM/emdata.cpp: fix big mem issue (size_t)

2011-02-11 19:59  gtang

	* libEM/sparx/util_sparx.cpp: fix big mem issue (size_t)

2011-02-11 19:55  gtang

	* libEM/: aligner.cpp, amiraio.cpp, df3io.cpp, emdata_core.cpp,
	  emdata_core.h, emdata_metadata.cpp, emutil.cpp, fitsio.cpp,
	  hdfio2.cpp, reconstructor_tools.cpp: fix big mem issue (size_t)

2011-02-11 19:47  gtang

	* libEM/sparx/: emarray.h, emdata_sparx.cpp, fourierfilter.cpp,
	  fundamentals.cpp, util_sparx.cpp: fix big mem issue (size_t)

2011-02-11 15:27  fjia

	* sparx/libpy/statistics.py: added comments

2011-02-11 14:46  gtang

	* libEM/emdata.cpp: fix big mem issue (size_t)

2011-02-11 14:17  gtao

	* sparx/bin/sxk_means.py: [no log message]

2011-02-11 12:57  gtang

	* libEM/emdata.cpp: fix the xform.centerofmass crash

2011-02-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-11 11:39  gtao

	* sparx/bin/sxk_means.py: [no log message]

2011-02-11 10:03  gtang

	* libEM/processor.cpp: minor fix

2011-02-11 09:59  gtang

	* libEM/emdata.cpp: minor fix for type conversion warning

2011-02-11 07:41  stevel

	* libEM/emdata.cpp, libEM/processor.cpp,
	  libpyEM/qtgui/emimage2d.py, programs/e2tomoboxer.py: Big
	  tomographic reconstructions working!

2011-02-10 16:57  gtang

	* libEM/emdata_core.h, libEM/emdata_transform.cpp,
	  libpyEM/libpyEMData2.cpp, libEM/processor.cpp: fix the 8GB size
	  limit for do_fft_inplace. Use size_t instead of int for index.

2011-02-10 16:51  gtao

	* sparx/libpy/statistics.py: fix a bug for k_mean clustering.

2011-02-10 15:56  stevel

	* programs/e2tomoboxer.py: tomoboxer work

2011-02-10 15:53  stevel

	* libEM/reconstructor.cpp, libpyEM/qtgui/emimage2d.py,
	  programs/e2tomoboxer.py: Another big memory issue

2011-02-10 13:35  stevel

	* libEM/emdata.cpp, libpyEM/qtgui/emimage2d.py,
	  programs/e2tomoboxer.py: More large image issues.

2011-02-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-10 10:18  stevel

	* libEM/emdata.cpp, libEM/emdata_core.h, programs/e2proc3d_huge.py,
	  programs/e2tomoboxer.py: Additional fixes for large volumes

2011-02-09 15:43  gtao

	* programs/e2helixboxer.py: [no log message]

2011-02-09 14:38  stevel

	* programs/e2tomoboxer.py: More work on tomoboxer

2011-02-09 14:10  stevel

	* libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libEM/emdata_transform.cpp, libEM/reconstructor.cpp,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/valslider.py, programs/e2bdb.py,
	  programs/e2tomoboxer.py: Working on boxer. Fix some bugs with
	  >2Gpxl images

2011-02-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-09 11:11  john

	* libEM/: aligner.cpp, aligner.h, cmp.h, emdata.cpp, emdata.h,
	  emdata_transform.h, projector.h, reconstructor.h, util.cpp:
	  Bugfix to find_max Added CUDA documentation Added Pawel style
	  aligners(resample to polar in real space)

2011-02-09 10:18  zyang

	* libEM/aligner.cpp, libEM/aligner.h, sparx/libpy/applications.py,
	  libEM/sparx/cuda/cuda_ccf.cu, libEM/sparx/cuda/cuda_ccf.h,
	  libpyEM/libpyAligner2.cpp: An overhaul to the way of setting CUDA
	  device.

2011-02-08 17:42  gtang

	* programs/e2proc3d.py: bug fix for stack image processing

2011-02-08 17:07  gtang

	* libEM/processor.cpp: minor fix

2011-02-08 16:46  ppenczek

	* sparx/libpy/applications.py: [no log message]

2011-02-08 15:40  gtang

	* programs/e2proc3d.py: Bug fix. It failed before processing an
	  image stack with those options which can have multiple instanve
	  like processor.

2011-02-08 15:13  ppenczek

	* sparx/libpy/applications.py: returned to original 3D mref (for
	  demo)

2011-02-08 12:07  ppenczek

	* sparx/libpy/applications.py: [no log message]

2011-02-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-08 10:46  ppenczek

	* sparx/bin/: sxrecons3d_f.py, sxrecons3d_n.py, sxvar.py: [no log
	  message]

2011-02-07 17:13  gtang

	* libEM/: emdata.cpp, emdata_core.cpp, emdata_core.h: fix the 8GB
	  image creation and access bug. Use std::fill() instead of memset.
	  Use size_t instead of int for subscription index.

2011-02-07 15:21  ppenczek

	* sparx/libpy/applications.py: [no log message]

2011-02-07 12:42  ppenczek

	* sparx/libpy/statistics.py: [no log message]

2011-02-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-07 11:48  john

	* libEM/aligner.cpp, libEM/cmp.cpp, programs/e2align3d.py: Added
	  some bells and whistles to e2align3d.py

2011-02-07 10:58  john

	* libEM/aligner.cpp, libEM/aligner.h, libEM/processor.cpp,
	  programs/e2align3d.py: Enabled quaternion 3D refine aligner, and
	  updated thee2align3d.py to take advantage

2011-02-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-06 00:29  stevel

	* programs/: e2classaverage.py, e2make3d.py, e2project3d.py,
	  e2refinemulti.py: New program e2refinemulti, and changes to
	  others to support it.

2011-02-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-04 16:09  ross

	* programs/e2helixboxer.py: Fixing docstrings (@param x rather than
	  @x) and indentation (spaces only, not mixed tabs and spaces).

2011-02-04 13:09  ppenczek

	* sparx/bin/sxvar.py: [no log message]

2011-02-04 12:45  ppenczek

	* sparx/bin/sxresample.py: [no log message]

2011-02-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-04 09:38  gtang

	* libpyEM/libpyUtils2.cpp: add conditional compilation flag for
	  HDF5

2011-02-03 20:05  ross

	* libpyEM/qtgui/emimage3d.py: the first time
	  EMImage3DWidget.set_data() is called, the isosurface threshold is
	  set to mean + sigma, then subsequent calls make the normalized
	  isosurface value ([so_val-mean]/sigma) stay constant.

2011-02-03 18:22  ppenczek

	* sparx/libpy/applications.py: single proc variance

2011-02-03 17:02  ppenczek

	* libEM/reconstructor.cpp, sparx/bin/sxspliteigen.py: [no log
	  message]

2011-02-03 15:45  ppenczek

	* sparx/bin/sxbmask.py:  adaptive mask

2011-02-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-03 11:52  ppenczek

	* sparx/bin/sxresample.py: stratified resmapling

2011-02-03 11:49  gtang

	* libpyEM/libpyUtils2.cpp: add conditional compilation flag for
	  HDF5

2011-02-03 11:14  ppenczek

	* sparx/bin/sxgenbuf.py: generate disk buffer for resampling

2011-02-03 09:48  john

	* libEM/emdata_cuda.cpp: Bug fix for CUDA envvar

2011-02-02 16:52  john

	* libEM/emdata_cuda.cpp: Bug fix for CUDA

2011-02-02 16:46  john

	* libEM/: aligner.cpp, aligner.h, emdata_cuda.cpp, emdata_cuda.h,
	  reconstructor.cpp: Enabled 3D refine aligner, reconstructor, and
	  a bug fix

2011-02-02 13:35  zyang

	* sparx/bin/sxrealignment.py: [no log message]

2011-02-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-01 15:28  john

	* libEM/aligner.cpp, libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/reconstructor.cpp, libpyEM/libpyEMData2.cpp,
	  rt/emdata/ccf3.cpp: CUDA mem management bug fix, and automatic
	  enabling of CUDA recons

2011-02-01 12:33  john

	* libEM/emdata.cpp, libEM/emdata_cuda.cpp,
	  libEM/emdata_transform.cpp, libEM/processor.cpp,
	  libEM/cuda/cuda_cmp.cu, rt/emdata/ccf3.cpp: Bug fix for CUDA mem
	  management

2011-02-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-02-01 10:38  gtao

	* programs/e2helixboxer.py: Add an option for gridding
	  interpolation.

2011-02-01 08:06  ross

	* libpyEM/qtgui/: emimage3d.py, empdbvaltool.py: makeing
	  e2fhstat.py work correctly again, making
	  E2Image3DWidget.set_data() more robust

2011-02-01 00:52  stevel

	* examples/exhaustivealicmp.py: trivial

2011-01-31 23:04  stevel

	* examples/exhaustivealicmp.py, libpyEM/EMAN2.py,
	  programs/e2history.py: New logfile mechanism

2011-01-31 15:51  zyang

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/aligner.cpp,
	  libEM/cuda/FindCUDA.cmake, libEM/cuda/cuda_cmp.cu,
	  libpyEM/libpyAligner2.cpp, rt/emdata/ccf3.cpp: Major fix to CUDA

2011-01-31 13:20  gtang

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/aligner.cpp,
	  libEM/cmp.cpp, libEM/cmp.h, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emdata_core.cpp, libEM/emdata_core.h,
	  libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libEM/emdata_modular.h, libEM/emdata_transform.cpp,
	  libEM/emdata_transform.h, libEM/emutil.cpp, libEM/emutil.h,
	  libEM/processor.cpp, libEM/processor.h, libEM/projector.cpp,
	  libEM/projector.h, libEM/reconstructor.cpp,
	  libEM/cuda/CMakeLists.txt, libEM/cuda/FindCUDA.cmake,
	  libEM/cuda/cuda_cmp.cu, libEM/cuda/cuda_cmp.h,
	  libEM/cuda/cuda_emfft.cu, libEM/cuda/cuda_emfft.h,
	  libEM/cuda/cuda_processor.cu, libEM/cuda/cuda_processor.h,
	  libEM/cuda/cuda_projector.cu, libEM/cuda/cuda_projector.h,
	  libEM/cuda/cuda_util.cu, libEM/cuda/cuda_util.h,
	  libpyEM/libpyAligner2.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyProcessor2.cpp, rt/emdata/CMakeLists.txt,
	  rt/emdata/ccf3.cpp, utils/speedtest.cpp: [no log message]

2011-01-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-31 11:39  zyang

	* sparx/bin/sxlocal_ali3d.py: Fixed a small bug.

2011-01-31 11:39  zyang

	* sparx/libpy/: alignment.py, applications.py, filter.py,
	  fundamentals.py, morphology.py, pixel_error.py, projection.py,
	  reconstruction.py, sparx.py, statistics.py, user_functions.py,
	  utilities.py: Delete dependency on EMAN2_cppwrap

2011-01-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-28 15:45  gtang

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/aligner.cpp,
	  libEM/cmp.cpp, libEM/cmp.h, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emdata_core.cpp, libEM/emdata_core.h,
	  libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libEM/emdata_modular.h, libEM/emdata_transform.cpp,
	  libEM/emdata_transform.h, libEM/emutil.cpp, libEM/emutil.h,
	  libEM/processor.cpp, libEM/processor.h, libEM/projector.cpp,
	  libEM/projector.h, libEM/reconstructor.cpp,
	  libEM/cuda/CMakeLists.txt, libEM/cuda/FindCUDA.cmake,
	  libEM/cuda/cuda_cmp.cu, libEM/cuda/cuda_cmp.h,
	  libEM/cuda/cuda_emfft.cu, libEM/cuda/cuda_emfft.h,
	  libEM/cuda/cuda_processor.cu, libEM/cuda/cuda_processor.h,
	  libEM/cuda/cuda_projector.cu, libEM/cuda/cuda_projector.h,
	  libEM/cuda/cuda_util.cu, libEM/cuda/cuda_util.h,
	  libpyEM/libpyAligner2.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyProcessor2.cpp, rt/emdata/CMakeLists.txt,
	  rt/emdata/ccf3.cpp, utils/speedtest.cpp: Revert John's CUDA
	  change back to pre-Jan26th

2011-01-28 14:32  john

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/emdata_cuda.cpp,
	  libEM/emdata_cuda.h, libEM/projector.cpp,
	  libEM/reconstructor.cpp, libpyEM/libpyEMData2.cpp: Enabled
	  automatic CUDA

2011-01-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-27 16:46  gtang

	* CMakeLists.txt: Python 2.7 compilation support

2011-01-27 14:46  gtang

	* libEM/transform.cpp: check in Julio's fix for Transform::invert()

2011-01-27 13:39  john

	* CMakeLists.txt, libEM/emdata.cpp, libEM/emdata_transform.cpp,
	  libEM/transform.cpp, rt/pyem/test_aligner.py: Set CUDA default to
	  off, since its still in dev Reset some changes to the MCF that
	  causes test_align.py to fail

2011-01-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-26 19:35  ross

	* libpyEM/qtgui/emimage3dslice.py: commenting out (unused I think)
	  member variable related to the recently removed Transform3D class
	  (Transform3D constant was commented out in pyemtbx/imagetypes.py)

2011-01-26 19:07  ross

	* libpyEM/qtgui/emimage3d.py: keeps the rotation, translation, and
	  isosurface threshold (in terms of std dev above mean) when
	  calling EMImageWidget.set_data(), also keeps the zoom constant if
	  the new map has the same dimensions as the old one

2011-01-26 17:57  ppenczek

	* sparx/libpy/utilities.py: helical consistency

2011-01-26 16:26  john

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/aligner.cpp,
	  libEM/emdata_transform.cpp, libEM/emfft.cpp: Update Cmake to
	  remove CUDA_FFT flag

2011-01-26 14:18  john

	* rt/emdata/ccf3.cpp: Patch to enable comilation

2011-01-26 14:05  john

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/aligner.cpp,
	  libEM/cmp.cpp, libEM/cmp.h, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emdata_core.cpp, libEM/emdata_core.h,
	  libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libEM/emdata_modular.h, libEM/emdata_transform.cpp,
	  libEM/emdata_transform.h, libEM/emutil.cpp, libEM/emutil.h,
	  libEM/processor.cpp, libEM/processor.h, libEM/projector.cpp,
	  libEM/projector.h, libEM/reconstructor.cpp,
	  libEM/cuda/CMakeLists.txt, libEM/cuda/FindCUDA.cmake,
	  libEM/cuda/cuda_cmp.cu, libEM/cuda/cuda_cmp.h,
	  libEM/cuda/cuda_emfft.cu, libEM/cuda/cuda_emfft.h,
	  libEM/cuda/cuda_processor.cu, libEM/cuda/cuda_processor.h,
	  libEM/cuda/cuda_projector.cu, libEM/cuda/cuda_projector.h,
	  libEM/cuda/cuda_reconstructor.cu,
	  libEM/cuda/cuda_reconstructor.h, libEM/cuda/cuda_util.cu,
	  libEM/cuda/cuda_util.h, libpyEM/libpyAligner2.cpp,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyProcessor2.cpp,
	  rt/emdata/CMakeLists.txt, rt/emdata/ccf3.cpp,
	  utils/speedtest.cpp: Massive cuda related commit

2011-01-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-26 11:57  gtang

	* libEM/: CMakeLists.txt, SConscript, all_imageio.h, emimio.cpp,
	  emimio.h, emutil.cpp, pgmio.cpp, salio.cpp, tifio.cpp: eliminate
	  EmimIO, change the name for format specific flag

2011-01-26 11:29  gtao

	* sparx/libpy/utilities.py: [no log message]

2011-01-26 11:06  gtang

	* libEM/: transform.cpp, transform.h: eliminate Transform3D

2011-01-26 10:47  gtang

	* libEM/emdata.cpp, libEM/emdata.h, libEM/emobject.h,
	  libEM/hdfio.cpp, libEM/projector.cpp, libEM/reconstructor.h,
	  libEM/symmetry.h, libpyEM/EMAN2.py, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyTransform2.cpp, libpyEM/qtgui/em3Dfonts.py,
	  libpyEM/qtgui/em3Dhelloworld.py, programs/e2foldfitter.py,
	  pyemtbx/imagetypes.py, rt/pyem/test_aligner.py,
	  rt/pyem/test_reconstructor.py, rt/pyem/test_transform.py,
	  rt/pyem/test_vec.py, rt/timetests/test_times.py,
	  utils/proc2d.cpp: eliminate Transform3D

2011-01-26 09:58  gtang

	* libEM/pointarray.cpp, libEM/pointarray.h,
	  libpyEM/libpyPointArray2.cpp: eliminate Transform3D

2011-01-25 14:40  gtao

	* sparx/libpy/utilities.py: [no log message]

2011-01-25 14:13  ppenczek

	* sparx/libpy/: pixel_error.py, utilities.py: [no log message]

2011-01-25 14:03  gtao

	* sparx/libpy/utilities.py: [no log message]

2011-01-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-24 17:33  jkovacs

	* sparx/bin/sxpdb2em.py: added calculation of radius of gyration

2011-01-24 16:54  ross

	* libpyEM/qtgui/emimage3d.py: If tkhe new map has the same size as
	  the old one, set_data makes the isosurface threshold the same as
	  for the old data in terms of standard deviaif the new map has the
	  same size as the old one, EMImage3DWidget.set_data() makes the
	  isosurface threshold the same as for the old data in terms of
	  standard deviations above the mean.tions above the mean.

2011-01-24 13:25  ross

	* libpyEM/qtgui/emimage.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emselector.py, programs/e2workflow.py: changes to
	  EMImage3DWidget.set_data(): if parameter replace==True, all
	  viewables are cleared, a new isosurface renderer is created, then
	  the camera for that isosurface renderer is set the same as for
	  the old data, if the old and new data are the same size

2011-01-24 12:27  gtang

	* libEM/emdata_metadata.h,
	  libEM/plugins/reconstructor_template.cpp,
	  libEM/plugins/reconstructor_template.h,
	  libEM/sparx/emdata_sparx.h, libpyEM/libpyEMData2.cpp: eliminate
	  Transform3D

2011-01-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-24 09:57  zyang

	* sparx/bin/sxmref_alignment.py: [no log message]

2011-01-23 21:42  stevel

	* libEM/aligner.cpp: Fixes for scaling

2011-01-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-22 23:00  stevel

	* libEM/aligner.cpp, libEM/aligner.h, programs/e2simmx.py: scale
	  fixes

2011-01-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-22 00:49  stevel

	* libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py, programs/e2parallel.py:
	  Fixed a strange bug that occured a week or so ago.

2011-01-21 15:41  gtang

	* libEM/transform.cpp: fix compilation error on Visual C++ 2008

2011-01-21 12:31  ppenczek

	* sparx/libpy/: pixel_error.py, utilities.py: [no log message]

2011-01-21 12:05  gtao

	* sparx/libpy/utilities.py: [no log message]

2011-01-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-21 11:53  gtao

	* sparx/libpy/: utilities.py, pixel_error.py: add two function for
	  helical consistency checking.

2011-01-21 08:19  stevel

	* libpyEM/qtgui/emplot2d.py: Fixed problem with 8 lines

2011-01-20 16:33  jkovacs

	* libEM/transform.cpp: switched internal calculations to double
	  precision and cleaned up some rotation equations

2011-01-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-20 11:28  gtang

	* libEM/transform.h: minor fix for warnings

2011-01-19 22:22  stevel

	* libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py, programs/e2simmx.py:
	  Minor diagnostic tweaks

2011-01-19 21:54  stevel

	* programs/: e2classaverage.py, e2classify.py, e2simmx.py: Support
	  for scale in refinement. Only way to actually get it is with the
	  refine aligner.

2011-01-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-19 09:28  stevel

	* examples/testscaleali.py, libEM/aligner.cpp, libEM/aligner.h,
	  libEM/transform.cpp, libEM/transform.h: Scale added to refine
	  aligner (as option)

2011-01-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-18 09:27  stevel

	* examples/focalpairalign.py: Focal pair alignment example

2011-01-17 22:43  stevel

	* programs/e2ptcltrace.py: Begin reworking ptcltrace

2011-01-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-16 23:19  stevel

	* libpyEM/EMAN2PAR.py, programs/e2align2d.py: Oops. Bad commit

2011-01-16 13:47  ross

	* programs/e2fhstat.py: 2D plots are cleared before new data is
	  plotted when plot2d() is called repeatedly

2011-01-16 13:41  ross

	* libpyEM/qtgui/empdbvaltool.py: setting the maxiumum number of
	  transformations to 9999

2011-01-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-16 11:44  stevel

	* programs/e2history.py: trivial

2011-01-16 02:03  stevel

	* libpyEM/EMAN2PAR.py, libpyEM/qtgui/emimagemx.py,
	  mpi_eman/mpi_test.py: class average display improvement

2011-01-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-14 16:53  ross

	* libpyEM/qtgui/emfoldhunterstat.py, programs/e2fhstat.py: moving
	  plot2d() from emfoldhunterstat.py to e2fhstat.py

2011-01-14 14:59  ross

	* libpyEM/qtgui/emplot3d.py: EMPlot3DModel.draw_cube() bugfix

2011-01-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-13 09:46  stevel

	* programs/e2ctf.py: Ctf default structure factor fix

2011-01-12 16:43  gtao

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h, util_sparx.cpp:
	  fix the momory problem for Util.window by adding copy_empty_head
	  function.

2011-01-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-12 11:55  ppenczek

	* sparx/libpy/utilities.py: fixed mirror in rotate_3D_shift

2011-01-12 11:03  gtao

	* sparx/libpy/projection.py: [no log message]

2011-01-12 10:50  gtao

	* sparx/libpy/projection.py: add comments for prep_vol and prgs
	  since those codes can now handle the rectangular volume.

2011-01-12 10:20  jkovacs

	* sparx/libpy/alignment.py: now ali_vol_func_grid assumes rotation
	  params are in the xyz convention

2011-01-11 21:11  gtao

	* sparx/libpy/applications.py: fix a problem for helical wrapping.

2011-01-11 18:16  ross

	* programs/e2boxer.py: trivial: view_template_clicked() docstring
	  correction

2011-01-11 18:11  ross

	* programs/e2boxer.py: replacing EMImageMXModule with
	  EMImageMXWidget

2011-01-11 17:14  gtao

	* sparx/libpy/applications.py: fix bug for helical wrapping.

2011-01-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-10 20:48  ross

	* libpyEM/qtgui/: emapplication.py, emselector.py: trivial

2011-01-10 20:46  ross

	* libpyEM/qtgui/emimageutil.py: removing deprecated EMEventRerouter
	  class

2011-01-10 20:38  ross

	* programs/e2flick.py: commented out EMStandAloneApplication
	  import... that deprecated class was removed

2011-01-10 20:37  ross

	* libpyEM/qtgui/emapplication.py: removing deprecated classes
	  EMApplication, EMStandAloneApplication, EMGUIModule, and
	  EMQtWidgetModule

2011-01-10 20:27  ross

	* libpyEM/: CMakeLists.txt, qtgui/emborderdecoration.py,
	  qtgui/emfloatingwidgets.py: removing deprecated source files
	  emfloatingwidgets.py and emborderdecoration.py

2011-01-10 20:18  ross

	* libpyEM/CMakeLists.txt: removed emimagerotor.py

2011-01-10 20:16  ross

	* libpyEM/qtgui/emimagerotor.py: removing from CVS

2011-01-10 20:13  ross

	* sparx/bin/sxboxer.py: remove unused EMImageRotorModule code and
	  emimagerotor import

2011-01-10 15:57  ppenczek

	* sparx/libpy/: applications.py, projection.py, reconstruction.py,
	  utilities.py: [no log message]

2011-01-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-10 09:53  zyang

	* programs/e2bdb.py: [no log message]

2011-01-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-07 18:08  ross

	* programs/e2flick.py: importing os and sys to get to the printed
	  warning message when the program runs

2011-01-07 18:06  ross

	* programs/e2flick.py: program has been broken for a while...
	  removing import of deprecated emimagemxrotor.py which I just
	  removed from CVS so that the message that says the program is
	  broken will still display

2011-01-07 18:03  ross

	* libpyEM/CMakeLists.txt: removing emrotor.py and
	  emimagemxrotor.py; cleaning up duplicate installs of various *.py
	  files

2011-01-07 17:51  ross

	* libpyEM/qtgui/emimagemxrotor.py: removing from CVS

2011-01-07 17:46  ross

	* libpyEM/qtgui/emform.py, sparx/bin/sxboxer.py: removing unused
	  references to emimagemxrotor and EMQtWidgetModule

2011-01-07 17:44  ross

	* libpyEM/qtgui/emrotor.py: removing from CVS

2011-01-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-06 13:15  gtao

	* libEM/sparx/emdata_sparx.cpp: correct the spelling mistakes.

2011-01-06 12:50  gtang

	* CMakeLists.txt, mpi_eman/CMakeLists.txt: add mpi_eman directory

2011-01-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-06 11:26  ross

	* libpyEM/qtgui/emfoldhunterstat.py: added plot2d()

2011-01-05 16:31  gtang

	* libEM/emdata_modular.cpp: bug fix: revert last change

2011-01-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-04 17:03  gtang

	* libEM/emdata.h: bug fix

2011-01-04 16:21  ross

	* libpyEM/qtgui/emimage3d.py: made new models have the same scale,
	  orientation, and position as the first item in EMImage3DWidget's
	  self.viewables -- a bit of a hack to fix a bug

2011-01-04 16:11  ross

	* libpyEM/qtgui/emimage3dsym.py: bugfix

2011-01-04 15:45  zyang

	* sparx/libpy/statistics.py: Improve aves() function so that it
	  also take list of images

2011-01-04 15:01  zyang

	* sparx/bin/sxrealignment.py: [no log message]

2011-01-04 12:33  ppenczek

	* sparx/libpy/applications.py: [no log message]

2011-01-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2011-01-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-31 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-30 13:39  gtang

	* libEM/emutil.cpp: fix the bug, no extension spider file was
	  recognized as mrc file

2010-12-30 12:41  gtang

	* libEM/aligner.cpp, libEM/aligner.h, libEM/df3io.cpp,
	  libEM/emdata.h, libEM/emdata_metadata.h,
	  libEM/emdata_modular.cpp, libEM/fitsio.cpp, libEM/hdfio2.cpp,
	  libEM/imagicio.cpp, libEM/marchingcubes.h, libEM/pdbreader.cpp,
	  libEM/pointarray.cpp, libEM/processor.cpp, libEM/processor.h,
	  libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libEM/reconstructor_tools.cpp, libEM/symmetry.cpp,
	  libEM/gorgon/skeletonizer.cpp, libEM/gorgon/volume.cpp,
	  libEM/sparx/emdata_sparx.cpp, libEM/sparx/fourierfilter.cpp,
	  libEM/sparx/util_sparx.cpp, libpyEM/typeconverter.cpp,
	  libpyEM/typeconverter.h: fix warning message in gcc4(linux
	  x86_64)

2010-12-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-30 10:40  ross

	* libpyEM/qtgui/emfoldhunterstat.py: Muthu's changes for code
	  documentation and readability

2010-12-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-27 22:21  stevel

	* programs/e2ptcltrace.py: Restart work on ptcltrace

2010-12-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-23 14:00  zyang

	* sparx/bin/sxmulti_assign.py: Trivial change.

2010-12-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-22 11:05  ross

	* libpyEM/qtgui/empdbvaltool.py, libpyEM/qtgui/empdbviewer.py,
	  programs/e2fhstat.py: reworking GUI interface for e2fhstat.py

2010-12-21 14:10  jkovacs

	* libpyEM/libpyEMData2.cpp: modified defs to account for addition
	  of wrap argument to rot_scale_conv_new*_3D

2010-12-21 14:08  jkovacs

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: Added wrap
	  argument to rot_scale_conv_new*_3D to set pixel value to 0 if
	  outside of the map

2010-12-21 14:04  jkovacs

	* sparx/libpy/: alignment.py, applications.py, fundamentals.py:
	  Added wraparound option

2010-12-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-18 15:47  ppenczek

	* sparx/bin/sxfactcoords.py: [no log message]

2010-12-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-17 11:31  ppenczek

	* sparx/libpy/applications.py: fixed pca minor bug

2010-12-17 07:24  stevel

	* mpi_eman/: 0README, Makefile.linux, Makefile.linux2,
	  Makefile.osx, pbs.example, setup.py: Mpi support update

2010-12-17 06:34  stevel

	* mpi_eman/: Makefile.linux2, mpi_test_basic.py, pbs.example: new
	  makefile

2010-12-16 15:33  stevel

	* libpyEM/EMAN2PAR.py: Better MPI logging.

2010-12-16 14:55  stevel

	* programs/e2simmx.py: simmx fix for mpi

2010-12-16 14:51  stevel

	* programs/e2simmx.py: trivial

2010-12-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-16 09:58  zyang

	* sparx/bin/sxmulti_ali2d.py: Add a new command

2010-12-16 09:41  stevel

	* libpyEM/EMAN2PAR.py: trivial

2010-12-16 08:58  stevel

	* libpyEM/EMAN2PAR.py, programs/e2classaverage.py,
	  programs/e2simmx.py: Had to redo MPI parallelism without
	  fork()ing.

2010-12-15 22:48  stevel

	* mpi_eman/: mpi_test_basic.py, pbs.example: Some examples

2010-12-15 15:28  gtao

	* sparx/libpy/applications.py: change format of logfile for ihrsr

2010-12-15 13:29  stevel

	* libpyEM/EMAN2PAR.py: Fix for clusters

2010-12-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-14 16:50  gtang

	* programs/e2version.py: [no log message]

2010-12-14 13:07  stevel

	* libpyEM/EMAN2PAR.py: Make sure the main task sleeps when idle

2010-12-14 13:01  stevel

	* libpyEM/EMAN2PAR.py: oops

2010-12-14 13:00  stevel

	* libpyEM/EMAN2PAR.py: Bunch of MPI bugfixes

2010-12-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-14 11:27  stevel

	* libpyEM/EMAN2PAR.py: Debug tweak

2010-12-14 11:22  stevel

	* libpyEM/EMAN2PAR.py, programs/e2bdb.py: Debugging in mpi

2010-12-14 11:11  gtang

	* libEM/emutil.cpp: fix the bug the .map(mrc file) from
	  emdatabank.org is recognized as DF3.

2010-12-14 07:37  stevel

	* mpi_eman/: Makefile, Makefile.linux, Makefile.osx: Added initial
	  OSX makefile

2010-12-13 13:28  gtao

	* sparx/libpy/applications.py: cleaning memory for ihrsr_MPI

2010-12-13 13:20  stevel

	* libpyEM/EMAN2PAR.py, mpi_eman/mpi_eman.py,
	  programs/e2parallel.py: EMAN2 MPI subsystem working fully. Still
	  need to add some optimizations.

2010-12-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-13 12:00  gtang

	* libEM/: ctf.cpp, reconstructor.cpp, symmetry.cpp,
	  sparx/emdata_sparx.cpp: fix the unnecessary type conversion,
	  suppress the warning messages on VS2008

2010-12-13 10:33  gtao

	* sparx/libpy/applications.py: trivial change on sxihrsr

2010-12-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-10 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-09 14:52  zyang

	* sparx/bin/sxmulti_assign.py: Delete some parameters that no
	  longer in use.

2010-12-09 14:41  prb

	* libEM/symmetry.cpp:
	   introduced eps to overcome border issue 12/9/2010	PRB

2010-12-09 14:36  stevel

	* libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py, mpi_eman/mpi_eman.c,
	  mpi_eman/mpi_eman.py, programs/e2parallel.py,
	  programs/e2project3d.py: Working on mpi still

2010-12-09 13:25  zyang

	* libEM/aligner.cpp: Make some change to the multi-reference
	  assignment (CUDA version)

2010-12-09 12:17  ppenczek

	* sparx/libpy/statistics.py: added fit_ctf

2010-12-09 12:08  ppenczek

	* sparx/libpy/statistics.py: added fit_ctf

2010-12-09 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-08 17:16  zyang

	* libEM/: aligner.cpp, aligner.h: Fix small bugs.

2010-12-08 16:37  ross

	* programs/e2helixboxer.py: fixed "xform.projection" for unrotated
	  particles--a cylinder oriented along the z axis can use
	  "xform.projection" to be oriented along the direction of the
	  helix

2010-12-08 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-08 11:24  gtao

	* sparx/: bin/sxihrsr.py, libpy/alignment.py,
	  libpy/applications.py, libpy/utilities.py: add theta angles for
	  helical reconstrction.

2010-12-07 18:51  ross

	* libpyEM/qtgui/empdbvaltool.py: new EMPDBValWidget class

2010-12-07 18:50  ross

	* programs/e2helixboxer.py: changed xform.projection for unrotated
	  particles

2010-12-07 17:17  zyang

	* libEM/: aligner.cpp, sparx/cuda/cuda_ccf.cu: Fix one final bug in
	  the multi-reference assignment

2010-12-07 15:35  jkovacs

	* sparx/libpy/applications.py: changed the way parameters are input
	  to and output from ali_vol_grid

2010-12-07 13:46  gtang

	* libpyEM/libpyEMData2.cpp: comment out methods not necessary to
	  expose to Python. Too many methods in EMData class wrapped to
	  Python cause the "import libpyEMData2" segfault on Fedora
	  Core3/CentOS4 (gcc 3.4) 64 bit Linux system.

2010-12-07 13:37  zyang

	* sparx/libpy/pixel_error.py: [no log message]

2010-12-07 13:26  gtao

	* libEM/sparx/emdata_sparx.cpp: remove print out.

2010-12-07 13:22  gtao

	* libEM/sparx/: emdata_sparx.cpp, fundamentals.cpp: change the code
	  in order to handle rect image for rops_table.

2010-12-07 12:37  gtang

	* rt/pyem/test_emdata.py: comment out methods not necessary to
	  expose to Python. Too many methods in EMData class wrapped to
	  Python cause the "import libpyEMData2" segfault on Fedora
	  Core3/CentOS4 (gcc 3.4) 64 bit Linux system.

2010-12-07 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-07 11:40  gtang

	* libpyEM/libpyEMData2.cpp: comment out methods not necessary to
	  expose to Python. Too many methods in EMData class wrapped to
	  Python cause the "import libpyEMData2" segfault on Fedora
	  Core3/CentOS4 (gcc 3.4) 64 bit Linux system.

2010-12-07 07:24  stevel

	* mpi_eman/: mpi_eman.c, mpi_eman.py, mpi_test.py: Not completely
	  sure WHY, but this seems to have fixed the problem.

2010-12-06 18:00  zyang

	* libEM/: aligner.cpp, sparx/cuda/cuda_ccf.cu: Fix some bugs.
	  Almost correct now!

2010-12-06 16:05  stevel

	* libpyEM/EMAN2PAR.py, mpi_eman/mpi_eman.c, mpi_eman/mpi_eman.py,
	  mpi_eman/mpi_test.py, programs/e2parallel.py: Something a bit
	  wierd going on when broadcasting strings  :^(

2010-12-06 15:05  ross

	* libpyEM/qtgui/emapplication.py: EMGLWidget: closeEvent() calls
	  self.inspector.close(), if inspector is set

2010-12-06 12:48  stevel

	* mpi_eman/: mpi_eman.c, mpi_eman.py, mpi_test.py: mpi support
	  working on test machine (desktop)

2010-12-06 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-05 22:40  stevel

	* mpi_eman/mpi_eman.c, mpi_eman/mpi_eman.py, mpi_eman/mpi_test.py,
	  programs/e2ctf.py: mpi work

2010-12-05 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-04 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-03 20:24  ross

	* programs/e2helixboxer.py: setting xform.projection and
	  xform.align2d for helices and particles

2010-12-03 13:10  ross

	* libpyEM/qtgui/emselector.py: DataDisplayModule.item_action() fix
	  for Euler data display

2010-12-03 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-03 11:59  ross

	* libpyEM/qtgui/emselector.py: DataDisplayModule.item_action()
	  bugfix

2010-12-03 11:57  ross

	* libpyEM/qtgui/emglobjects.py: EM3DModel.show() calls
	  self.gl_widget().show()

2010-12-02 13:46  zyang

	* libEM/aligner.cpp: Restrore provious change

2010-12-02 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-01 14:12  john

	* libEM/aligner.cpp: Fixed mem leak

2010-12-01 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-12-01 07:54  stevel

	* libEM/aligner.cpp: Fix naming issue with iterative aligners.

2010-11-30 19:39  ross

	* libpyEM/qtgui/emapplication.py: removed a warning for
	  ModuleEventsManager and replaced with a #TODO comment

2010-11-30 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-11-30 10:50  stevel

	* mpi_eman/: mpi_eman.c, mpi_eman.py: A little more MPI work

2010-11-29 16:17  gtang

	* libEM/: hdfio2.cpp, processor.cpp, gorgon/skeletonizer.cpp,
	  gorgon/volume_data.cpp: fix for compilation Visual C++ 2005

2010-11-29 16:13  gtang

	* libEM/: aligner.cpp, emdata.cpp, sparx/processor_sparx.h: fix for
	  compilation Visual C++ 2005

2010-11-29 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-11-28 22:03  stevel

	* mpi_eman/: Makefile, mpi_eman.c, mpi_eman.py, mpi_test.py: More
	  MPI work

2010-11-28 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-11-27 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-11-26 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-11-25 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-11-24 16:57  zyang

	* libEM/sparx/util_sparx.cpp: Fix all of the warnings.

2010-11-24 16:49  zyang

	* sparx/bin/sxmulti_assign.py: Add simulated annealing as an
	  option.

2010-11-24 16:26  ppenczek

	* sparx/libpy/applications.py: binarize in mref

2010-11-24 13:46  zyang

	* libEM/sparx/util_sparx.cpp: [no log message]

2010-11-24 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-11-24 11:51  fjia

	* libEM/sparx/util_sparx.cpp: [no log message]

2010-11-24 11:23  stevel

	* mpi_eman/: Makefile, mpi_eman.c, mpi_test.py, setup.py: MPI work.
	  Having openmpi linking problems.

2010-11-24 10:33  fjia

	* libEM/sparx/util_sparx.cpp: [no log message]

2010-11-24 09:46  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2010-11-24 09:30  ppenczek

	* libEM/: emdata_metadata.cpp, transform.cpp: [no log message]

2010-11-24 09:23  ppenczek

	* libEM/averager.cpp: [no log message]

2010-11-24 06:34  stevel

	* mpi_eman/setup.py: initial version

2010-11-23 22:34  stevel

	* mpi_eman/mpi_eman.c: Working on mpi

2010-11-23 15:15  ppenczek

	* sparx/libpy/applications.py: corrected assignment for mref

2010-11-23 14:31  stevel

	* mpi_eman/mpi_eman.c, programs/e2ctf.py: Beginning mpi wrapper
	  implementation

2010-11-23 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-11-22 15:51  gtao

	* libEM/sparx/emdata_sparx.cpp: remove redundancy for nn4,nn4_ctf
	  reconstruction

2010-11-22 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-11-21 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-11-20 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-11-19 15:50  gtang

	* libEM/tifio.cpp: minor

2010-11-19 15:00  gtao

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h, util_sparx.cpp,
	  util_sparx.h: clean the code for rect recon and projection.

2010-11-19 14:56  gtao

	* libEM/: reconstructor.cpp, reconstructor.h: clean the code for
	  rect reconstruction.

2010-11-19 12:06  gtao

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: [no log message]

2010-11-19 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-11-18 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-11-18 11:06  ross

	* programs/e2eulerxplor.py: quick fix to
	  EMEulerExplorer.mouseReleaseEvent(self,event)

2010-11-17 16:16  john

	* libEM/aligner.cpp, libEM/processor.cpp, libEM/cuda/cuda_util.cu,
	  programs/e2align3d.py: Updated 3D aligners

2010-11-17 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-11-17 10:03  john

	* rt/emdata/ccf3.cpp: File for profiling

2010-11-17 08:02  stevel

	* libpyEM/qtgui/emplot2d.py, programs/e2ctf.py,
	  rt/emdata/CMakeLists.txt: More CTF work. Fixed compilation
	  problem in cmakelist

2010-11-16 17:30  john

	* examples/displaydemo.py, libEM/aligner.cpp, libEM/aligner.h,
	  libEM/emdata.h, libEM/emdata_cuda.cpp, libEM/emdata_metadata.cpp,
	  libEM/emfft.cpp, libEM/emfft.h, libEM/processor.cpp,
	  libEM/cuda/cuda_processor.cu, libEM/cuda/cuda_util.cu,
	  rt/emdata/CMakeLists.txt: Debugged aligner.cpp, and fixed some
	  CUDA bugs

2010-11-16 17:22  jkovacs

	* sparx/libpy/: alignment.py, applications.py, fundamentals.py: [no
	  log message]

2010-11-16 17:18  jkovacs

	* libEM/: sparx/emdata_sparx.cpp, sparx/emdata_sparx.h, cmp.cpp,
	  cmp.h: [no log message]

2010-11-16 17:14  jkovacs

	* libpyEM/libpyEMData2.cpp: [no log message]

2010-11-16 17:07  gtang

	* programs/e2make3d.py: bug fix, reported by Xiangan

2010-11-16 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-11-16 11:35  ppenczek

	* sparx/: libpy/applications.py, bin/sxmref_ali3d.py: added focuse
	  to 3D mref

2010-11-16 10:15  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-11-16 09:27  stevel

	* libpyEM/qtgui/emplot2d.py, programs/e2ctf.py: Added many useful
	  features to e2ctf.py including automatic filename detection and
	  new plotting modes.

2010-11-15 19:58  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-11-15 18:45  ppenczek

	* sparx/libpy/: applications.py, utilities.py: [no log message]

2010-11-15 16:16  fjia

	* libEM/sparx/emdata_sparx.cpp: Guozhi Tao---checked in.

2010-11-15 16:14  fjia

	* sparx/libpy/: alignment.py, applications.py: Guozhi Tao--checkin.
	  merge helical refinement code.

2010-11-15 16:12  fjia

	* sparx/bin/sxihrsr.py: Guozhi Tao checked in.

2010-11-15 15:02  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-11-15 14:30  zyang

	* libEM/sparx/emdata_sparx.cpp: Delete some redundant code

2010-11-15 13:54  ppenczek

	* sparx/libpy/: applications.py, utilities.py: balanced even mref

2010-11-15 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-11-14 20:53  stevel

	* libEM/cmp.cpp: Undo sqrt snrweight

2010-11-14 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-11-13 23:23  stevel

	* libEM/cmp.cpp: Sqrt weight frc comparator

2010-11-13 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-11-12 16:51  fjia

	* sparx/libpy/: applications.py, projection.py, reconstruction.py:
	  Guozhi Tao checked in. Merger projection and reconstruction code
	  at python level.

2010-11-12 16:49  fjia

	* sparx/bin/sxproject3d.py: Guozhi Tao checked in. Merge sxproejct
	  --rect and --cubic.

2010-11-12 15:32  stevel

	* programs/e2ctf.py: minor tweak to skip some files

2010-11-12 15:21  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-11-12 14:58  ppenczek

	* libEM/sparx/fundamentals.cpp: [no log message]

2010-11-12 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-11-12 10:00  gtang

	* CMakeLists.txt: for Python 2.7

2010-11-11 17:12  fjia

	* sparx/: bin/sxrecons3d_n.py, libpy/applications.py,
	  libpy/reconstruction.py: Guozhi Tao checked in Merge the
	  reconstruction code rect and cubic at python level.

2010-11-11 12:01  eman-vm

	* programs/e2version.py: new date stamp

2010-11-10 17:18  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Add a new version of multi-reference
	  alignment.

2010-11-10 15:00  eman-vm

	* programs/e2version.py: new date

2010-11-10 14:56  gtang

	* libpyEM/EMAN2.py, programs/e2version.py: keep time stamp in a
	  separate file, since we need check in this file every day to
	  refresh the time stamp.

2010-11-10 12:58  ppenczek

	* sparx/libpy/applications.py: new ali3dm

2010-11-10 12:31  gtang

	* sparx/libpy/global_def.py: [no log message]

2010-11-10 12:05  ross

	* libpyEM/qtgui/empdbvaltool.py, programs/e2fhstat.py: fixing PDB
	  validation tool to work with changes to EM3DModel

2010-11-10 11:42  fjia

	* sparx/bin/sxihrsr.py: Guozhi Tao added option for ihrsr symmetry
	  search.

2010-11-10 11:26  gtang

	* programs/e2version.py: [no log message]

2010-11-10 11:25  gtang

	* programs/e2help.py: add EMAN2 version and cvs date stamp for
	  'e2help.py version'

2010-11-10 11:24  gtang

	* libpyEM/EMAN2.py: add cvs date stamp

2010-11-10 11:02  gtang

	* programs/e2version.py: version and date stamp update by cvs
	  keyword substitution

2010-11-10 10:56  gtang

	* programs/e2version.py: [no log message]

2010-11-10 10:07  ross

	* programs/e2eulerxplor.py: EMImage2DModule -> EMImage2DWidget;
	  changing EMEulerWidget to work with the updated EMSymViewerWidget

2010-11-10 10:05  ross

	* libpyEM/qtgui/emimage3dsym.py: fixing EMSymViewerWidget so mouse
	  collisions work... made code much closer to what it was before
	  removing the 3D desktop

2010-11-10 08:03  ross

	* libpyEM/qtgui/emimage3dsym.py: EMViewportDepthTools2 object
	  created in EM3DSymModel constructor and saved in self.vdtools

2010-11-09 17:14  ross

	* libpyEM/qtgui/emimage3dsym.py: removing HSym as a choice: crashed
	  when renderering and Steve thought unneeded

2010-11-09 15:45  ross

	* programs/e2eulerxplor.py: EMEulerWidget no longer sets the
	  symmetry for EMSymViewerWidget

2010-11-08 11:24  fjia

	* sparx/libpy/applications.py: Guozhi Tao checked in

2010-11-06 13:59  stevel

	* libEM/cmp.cpp: Change default maxres due to improved SNR

2010-11-06 13:20  ross

	* programs/e2eulerxplor.py: bugfix & trying to get clicking on
	  Euler locations working again

2010-11-06 13:17  ross

	* libpyEM/qtgui/emimagerotor.py: added DeprecationWarning to module

2010-11-05 15:56  fjia

	* libEM/reconstructor.cpp: [no log message]

2010-11-05 14:14  gtao

	* libEM/reconstructor.cpp: [no log message]

2010-11-05 14:09  gtao

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: [no log message]

2010-11-05 12:19  fjia

	* sparx/libpy/applications.py: Guozhi Tao,change the output format
	  of ihrsr

2010-11-05 11:10  ppenczek

	* libEM/: reconstructor.cpp, sparx/emdata_sparx.cpp: [no log
	  message]

2010-11-05 09:55  zyang

	* libEM/aligner.cpp: Continue to work on multiref alignment

2010-11-05 09:51  zyang

	* libEM/sparx/cuda/cuda_ccf.cu: Continue to work on multiref
	  alignment

2010-11-04 18:21  ross

	* libpyEM/qtgui/emplot3d.py: trivial bugfix

2010-11-04 18:13  ross

	* libpyEM/qtgui/emlights.py: moving some GL commands back to
	  EMLightsDrawer.__init__() a QGLWidget should exist before this
	  constructor is called

2010-11-04 17:50  ross

	* libpyEM/qtgui/emselector.py: minor changes

2010-11-04 16:08  gtao

	* libEM/reconstructor.cpp: fix a bug

2010-11-04 13:35  stevel

	* programs/e2ctf.py: More tweaks in new e2ctf improvements

2010-11-04 08:55  stevel

	* programs/e2ctf.py: Remove high-pass filter from smoothed SNR

2010-11-03 22:00  stevel

	* libpyEM/qtgui/emselector.py: Quick bugfix

2010-11-03 19:01  stevel

	* programs/e2ctf.py: New CTF SNR smoothing and defocus refinement !
	  Seems to work so far. Still testing

2010-11-03 15:52  john

	* libEM/aligner.cpp: Fixed a bug

2010-11-03 15:47  fjia

	* sparx/libpy/applications.py: Guozhi Tao checked in

2010-11-03 15:27  ross

	* libpyEM/qtgui/: emapplication.py, emimage2d.py, emimagemx.py:
	  removing unneccesary EMGLWidget's self.supress_inspector;
	  replacing qt_context_parent with qt_parent

2010-11-03 15:18  ross

	* libpyEM/qtgui/em3Dfonts.py, libpyEM/qtgui/em3Dhelloworld.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emimage3dvol.py,
	  libpyEM/qtgui/emlights.py, libpyEM/qtgui/empdbvaltool.py,
	  libpyEM/qtgui/empdbviewer.py, libpyEM/qtgui/emplot3d.py,
	  libpyEM/qtgui/emselector.py, programs/e2cmpxplor.py,
	  programs/e2eulerxplor.py, programs/e2simmxxplor.py,
	  programs/e2workflow.py, libpyEM/qtgui/emimage3diso.py,
	  libpyEM/qtgui/emimage3dslice.py: changing the way EM3DModel and
	  EM3DGLWidget refer to each other

2010-11-03 14:37  john

	* libEM/aligner.cpp: Enhanced 3D alignment speed.

2010-11-03 10:48  fjia

	* sparx/libpy/applications.py: Guozhi Tao--remove print out for
	  ihrsr

2010-11-03 09:46  zyang

	* libEM/sparx/cuda/cuda_ccf.cu: Fix some bugs

2010-11-02 17:20  ppenczek

	* libEM/sparx/fundamentals.cpp: deleted printout

2010-11-02 16:57  john

	* libEM/aligner.cpp, programs/e2align3d.py, programs/e2rct.py,
	  programs/e2rctV2.py: Debugged rct to reflect changes in
	  e2align3d.py

2010-11-02 16:30  zyang

	* libEM/: aligner.cpp, sparx/cuda/cuda_ccf.cu: Make multiple
	  corrections of the CUDA code of multi-reference alignment

2010-11-02 16:29  fjia

	* sparx/libpy/applications.py: Guozhi Tao--fix a bug at helical
	  shift

2010-11-02 14:55  fjia

	* sparx/libpy/applications.py: parallize the helical
	  search.----Guozhi Tao

2010-11-02 14:54  fjia

	* sparx/libpy/alignment.py: trivial--Guozhi Tao

2010-11-02 14:43  stevel

	* libEM/ctf.cpp: New SNR smoothing routine. May need a little work
	  still.

2010-11-02 14:18  stevel

	* libEM/ctf.cpp, programs/e2align3d.py: trivial

2010-11-02 14:11  john

	* libEM/emdata_core.h, libEM/sparx/fundamentals.cpp,
	  programs/e2align3d.py: Reset the CCF to do cmplx mult uisng
	  complex.h Fixed tab issue with e2align3d.py

2010-11-02 13:04  stevel

	* CMakeLists.txt, libEM/ctf.cpp, programs/e2ctf.py: New cmake
	  option

2010-11-02 11:54  fjia

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: [no log message]

2010-11-02 11:43  zyang

	* libEM/: aligner.cpp, sparx/cuda/cuda_ccf.cu,
	  sparx/cuda/cuda_ccf.h: Fix some bugs.

2010-11-02 11:09  fjia

	* sparx/libpy/statistics.py, libEM/sparx/util_sparx.cpp: [no log
	  message]

2010-11-02 11:06  zyang

	* libEM/: aligner.cpp, sparx/cuda/cuda_ccf.cu,
	  sparx/cuda/cuda_ccf.h: Begin to add multiref CUDA function

2010-10-29 17:17  gtao

	* sparx/libpy/applications.py: fix a bug!

2010-10-29 10:10  john

	* rt/emdata/CMakeLists.txt: Fixed Cmake so that it does try to
	  build ccf.cpp, which doesn't exist on Blake

2010-10-29 10:01  gtao

	* libEM/reconstructor.cpp: fix a bug.

2010-10-29 09:52  john

	* libEM/aligner.cpp, libEM/aligner.h, libEM/emdata_metadata.cpp,
	  libpyEM/EMAN2.py, programs/e2align3d.py,
	  rt/emdata/CMakeLists.txt, rt/emdata/rotate_translate.cpp: Updated
	  3D aligners according toJesus's suggestions Enhanced e2align3d.py

2010-10-29 09:51  ppenczek

	* sparx/libpy/applications.py: corrections in ihrsr

2010-10-29 09:49  stevel

	* programs/e2simmx2stage.py: trivial

2010-10-28 18:46  ppenczek

	* sparx/libpy/: alignment.py, applications.py, utilities.py: [no
	  log message]

2010-10-28 18:19  ross

	* libpyEM/qtgui/emimage3d.py: change EMImage3DWidget.set_data() to
	  only reset window size and camera z-value if there was no
	  previous data

2010-10-28 16:15  zyang

	* libEM/sparx/cuda/cuda_ccf.cu: Trivial change.

2010-10-28 15:46  fjia

	* libEM/sparx/: util_sparx.h, util_sparx.cpp: [no log message]

2010-10-28 15:41  fjia

	* sparx/libpy/statistics.py: [no log message]

2010-10-28 15:38  fjia

	* libpyEM/libpyUtils2.cpp: [no log message]

2010-10-28 15:33  stevel

	* programs/e2simmx2stage.py: verbosity bugfix

2010-10-28 15:12  stevel

	* programs/e2classaverage.py: Playing with class averaging. Looks
	  like matchto filter in some cases can cause misalignment due to
	  low resolution terms. :^(

2010-10-28 12:55  stevel

	* libpyEM/qtgui/emimagemx.py: Fix crasher for matrices

2010-10-28 11:39  stevel

	* libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libEM/processor.cpp, libEM/processor.h, libpyEM/libpyEMData2.cpp,
	  programs/e2classaverage.py, programs/e2refine2d.py: Significant
	  improvements to e2refine2d.py.

2010-10-28 10:05  gtao

	* sparx/libpy/utilities.py: add function to print image slice along
	  all 3 directions.

2010-10-27 20:58  stevel

	* programs/e2align3d.py: Trivial

2010-10-27 17:24  ross

	* programs/: e2eulerxplor.py, e2workflow.py: fixing Euler Explorer

2010-10-27 17:00  ross

	* libpyEM/qtgui/emglobjects.py: EMGLWidget.target() weakref
	  replaced with EMGLWidget.model, model does not have to be set in
	  constructor, can be set later

2010-10-27 16:11  zyang

	* sparx/libpy/: applications.py, global_def.py: Reverse the
	  previous change that I accidentally checked in.

2010-10-27 16:06  zyang

	* libEM/aligner.cpp, sparx/libpy/applications.py,
	  sparx/libpy/global_def.py: Fix some bugs

2010-10-27 15:26  zyang

	* libEM/aligner.cpp, libEM/aligner.h, libpyEM/libpyAligner2.cpp,
	  sparx/libpy/applications.py: Add cuda code for multi-reference
	  alignment

2010-10-27 13:20  ross

	* programs/e2workflow.py: changes to
	  EMWorkFlowSelectorWidget.launch_lights_tool()

2010-10-27 13:14  ross

	* libpyEM/qtgui/emlights.py: getting EMLights and EMLightsDrawer to
	  work without providing a QGLWidget to their constructors... use
	  set_gl_context_parent() before renderering

2010-10-27 12:37  ross

	* libpyEM/qtgui/emglobjects.py: EM3DGLWidget constructor requires
	  an EM3DModel instance now

2010-10-27 12:29  ross

	* libpyEM/qtgui/emimage3dsym.py: fixed EMSymViewerWidget

2010-10-27 11:07  ross

	* programs/e2workflow.py: getting some of the 3D viewers working
	  again

2010-10-27 11:06  ross

	* libpyEM/qtgui/emform.py: bugfix

2010-10-26 17:14  zyang

	* libEM/reconstructor.cpp, sparx/bin/sxmulti_assign.py: Fix a bug

2010-10-26 11:35  john

	* libEM/processor.cpp, libEM/processor.h, programs/e2align3d.py:
	  Debugged proessor.h (a function that I wrote) and enhanced
	  e2align3d.py

2010-10-25 14:58  john

	* libEM/aligner.cpp, libEM/aligner.h, libEM/emdata_metadata.cpp,
	  libEM/emdata_metadata.h, libEM/emdata_modular.h,
	  libEM/processor.cpp, libEM/processor.h, libpyEM/libpyEMData2.cpp:
	  Fixed the default pars in the aligners Added a filter for preping
	  tomos before alignment

2010-10-25 10:19  fjia

	* libEM/sparx/emdata_sparx.cpp: Guozhi Tao checked in.

2010-10-24 16:13  ross

	* libpyEM/qtgui/emsprworkflow.py: added WorkFlowTask.close(self)

2010-10-23 13:46  stevel

	* programs/e2classaverage.py: Another refine2d related fix ?

2010-10-23 06:06  ppenczek

	* sparx/templates/import_SPIDER_refi.py: corrected amp contr

2010-10-22 22:52  stevel

	* libEM/emdata_modular.h: Fixed default aligner comparator.

2010-10-22 15:29  ross

	* libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2cmpxplor.py, programs/e2eulerxplor.py,
	  programs/e2simmxxplor.py, sparx/bin/sxboxer.py: expect signals
	  directly from QWidgets rather than from (module_object).emitter()

2010-10-22 15:25  ross

	* libpyEM/qtgui/emapplication.py: EMGLWidget.closeEvent() now emits
	  a "module_closed" signal like EMGUIModule and EMQtWidgetModule
	  did

2010-10-22 15:00  zyang

	* libEM/sparx/fourierfilter.cpp: Trivial change

2010-10-22 15:00  fjia

	* sparx/: bin/sxihrsr.py, libpy/applications.py,
	  libpy/alignment.py: By Guozhi Tao

2010-10-22 11:56  ross

	* sparx/bin/sparx: replaced EMStandAloneApplication with EMApp

2010-10-22 07:36  stevel

	* programs/e2classaverage.py: Fixed parallel e2refine2d.py

2010-10-22 07:09  stevel

	* libpyEM/EMAN2db.py: Debug parallelism issue

2010-10-21 22:40  stevel

	* programs/e2refine2d.py: Shrink bug in refine2d

2010-10-21 18:19  ross

	* sparx/bin/sxboxer.py: some Module -> Widget changes to get
	  sxboxer closer to working

2010-10-21 18:17  ross

	* libpyEM/qtgui/emimage2d.py: bugfix

2010-10-21 16:26  gtang

	* rt/pyem/test_imageio.py: [no log message]

2010-10-21 16:03  ross

	* libpyEM/qtgui/emboxerbase.py: bugfix

2010-10-21 15:53  fjia

	* libEM/sparx/: util_sparx.h, util_sparx.cpp: By Guozhi Tao

2010-10-21 15:52  gtang

	* libEM/emutil.cpp: check MRC is_valid() after Spider. Since let
	  the wrong size mrc image pass the is_valid() check will give
	  false positive signal to spider image.

2010-10-21 15:48  ppenczek

	* libEM/sparx/util_sparx.cpp: corrected code with doubles for
	  infomask

2010-10-21 15:46  fjia

	* libpyEM/libpyUtils2.cpp: By Guozhi Tao

2010-10-21 15:40  fjia

	* sparx/libpy/applications.py: By Guozhi Tao

2010-10-21 15:35  fjia

	* sparx/libpy/alignment.py: By Guozhi Tao

2010-10-21 15:33  fjia

	* sparx/bin/sxihrsr.py: remove --yr and add --ynumber By Guozhi Tao

2010-10-21 15:16  ross

	* libpyEM/qtgui/: emborderdecoration.py, emfloatingwidgets.py,
	  emimagemxrotor.py, emimageutil.py, emrotor.py: added
	  DeprecationWarning messages

2010-10-21 15:05  ross

	* libpyEM/CMakeLists.txt: removing qtgui/pyshed.py

2010-10-21 15:03  ross

	* libpyEM/qtgui/pyshed.py: removing--we use ipython via e2.py
	  instead

2010-10-21 14:32  ross

	* libpyEM/qtgui/emboxerbase.py: fixed the messed up merge... merged
	  1.25.2.2 with 1.28

2010-10-21 14:06  ross

	* examples/displaydemo.py, examples/e2fftsynth.py,
	  examples/tomotrackbox.py, libEM/processor.h,
	  libpyEM/CMakeLists.txt, libpyEM/EMAN2.py,
	  libpyEM/qtgui/em3Dfonts.py, libpyEM/qtgui/em3Dhelloworld.py,
	  libpyEM/qtgui/em3dmodule.py, libpyEM/qtgui/emanimationutil.py,
	  libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emboxerbase.py,
	  libpyEM/qtgui/embrowse.py, libpyEM/qtgui/emdesktop.py,
	  libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emfoldhunterstat.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emfximage.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emglplot.py, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emimage3dslice.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emimage3dvol.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimagemxrotor.py,
	  libpyEM/qtgui/emimagerotor.py, libpyEM/qtgui/emimageutil.py,
	  libpyEM/qtgui/emlights.py, libpyEM/qtgui/empdbvaltool.py,
	  libpyEM/qtgui/empdbviewer.py, libpyEM/qtgui/emplot2d.py,
	  libpyEM/qtgui/emplot3d.py, libpyEM/qtgui/emrotor.py,
	  libpyEM/qtgui/emsave.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emshape.py, libpyEM/qtgui/emsprworkflow.py,
	  libpyEM/qtgui/emtprworkflow.py, libpyEM/qtgui/valslider.py,
	  programs/e2.py, programs/e2boxer.py, programs/e2cmpxplor.py,
	  programs/e2ctf.py, programs/e2display.py,
	  programs/e2eulerxplor.py, programs/e2fhstat.py,
	  programs/e2helixboxer.py, programs/e2history.py,
	  programs/e2preferences.py, programs/e2simmxxplor.py,
	  programs/e2tomoboxer.py, programs/e2workflow.py,
	  sparx/bin/sxboxer.py, sparx/bin/sxctf.py: merged
	  removing_e2desktop_event_rerouting back into the trunk

	  I think I messed up the emboxerbase.py merge, by doing the wrong
	  thing in Eclipse. I will go back and check.

2010-10-21 11:40  john

	* libEM/aligner.cpp, libEM/aligner.h, libEM/cmp.cpp, libEM/cmp.h,
	  programs/e2align3d.py: Fixed a bug relating to the usage of
	  ccc.tomo with the refine.3d aligner enhanced e2align3d.py to
	  align tomos and enable greater accuracy

2010-10-21 09:43  zyang

	* sparx/libpy/applications.py: Trivial change.

2010-10-21 09:06  ross

	* libpyEM/qtgui/emimage3dsym.py: trivial

2010-10-20 17:26  ross

	* libpyEM/qtgui/: emimage.py, emselector.py: add isosurface
	  renderer by default when previewing 3D images

2010-10-20 16:41  ross

	* libpyEM/qtgui/: emimage2d.py, emimage3d.py, emimagemx.py,
	  emplot2d.py, emplot3d.py: EM*Module subclasses EM*Widget, and
	  EM*Module.__init__() issues a DeprecationWarning so developers
	  will modify code to use EM*Widget

2010-10-20 16:38  ross

	* libpyEM/qtgui/emapplication.py: changed warning message for
	  ModuleEventsManager constructor

2010-10-20 13:36  ross

	* programs/e2ctf.py: trivial

2010-10-20 13:36  ross

	* sparx/bin/sxctf.py: Module -> Widget changes

2010-10-20 11:53  zyang

	* sparx/libpy/applications.py: Fix a bug

2010-10-20 11:18  zyang

	* sparx/libpy/alignment.py: Trivial change

2010-10-20 11:03  john

	* libEM/aligner.cpp, libEM/aligner.h, libEM/cmp.cpp,
	  programs/e2align3d.py: Enabled the 3D refinealigner to report
	  back a score Enhanced e2align3d.py

2010-10-20 10:55  ross

	* libpyEM/qtgui/emimagerotor.py, programs/e2ctf.py,
	  sparx/bin/sxctf.py: removing unused emimage imports

2010-10-20 10:54  ross

	* libpyEM/qtgui/emform.py, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emimage3dsym.py, programs/e2display.py,
	  programs/e2workflow.py: Module -> Widget changes

2010-10-20 10:06  zyang

	* sparx/bin/sxmulti_assign.py: Some change to multi-assign program

2010-10-20 05:22  ppenczek

	* libEM/sparx/emdata_sparx.cpp:  corrected delete line #927

2010-10-19 11:42  john

	* libEM/aligner.cpp: aligner.cpp, enabled the 3D grid and sphere
	  aligners to use the Ccc.tomo cmp

2010-10-19 11:40  stevel

	* examples/e2fftsynth.py: More neat stuff in fftsynth

2010-10-19 08:28  ross

	* libpyEM/: EMAN2.py, qtgui/emapplication.py, qtgui/emform.py,
	  qtgui/emimagemx.py, qtgui/emplot2d.py: Module --> Widget changes

2010-10-19 06:39  stevel

	* examples/e2fftsynth.py, libpyEM/qtgui/emplot2d.py: A bit more
	  tweaking on fftsynth gui

2010-10-18 22:34  stevel

	* examples/e2fftsynth.py: New option

2010-10-18 21:47  stevel

	* examples/e2fftsynth.py: fftsynth complete and working

2010-10-18 17:30  john

	* libEM/: aligner.cpp, aligner.h, cmp.cpp, cmp.h: fixed the tomo
	  comparitor in cmp.cpp and cmp.h alter the 3D aligners in
	  aligner.cpp to use the new tomo cmp

2010-10-18 15:49  stevel

	* examples/e2fftsynth.py: Better fftsynth

2010-10-18 15:32  stevel

	* examples/e2fftsynth.py, libpyEM/qtgui/emplot2d.py: fftsynth is
	  working mostly. Normalization issue still.

2010-10-18 12:10  stevel

	* examples/e2fftsynth.py, libEM/processor.h,
	  libpyEM/qtgui/valslider.py: fftsynth mostly working

2010-10-18 06:18  stevel

	* libpyEM/qtgui/valslider.py: added valbox

2010-10-17 22:12  stevel

	* examples/e2fftsynth.py: New sample program for FFT teaching

2010-10-15 15:13  fjia

	* sparx/bin/sxboxer.py: [no log message]

2010-10-14 17:12  ross

	* libpyEM/qtgui/emboxerbase.py: trivial

2010-10-14 17:11  ross

	* libpyEM/qtgui/em3Dhelloworld.py: try, except block to fix bug in
	  update_rotations -- better fix probably exists

2010-10-13 16:51  fjia

	* libEM/sparx/emdata_sparx.cpp: guozhi tao checked in.

2010-10-13 16:40  fjia

	* sparx/bin/sxihrsr.py, libEM/reconstructor.cpp: Guozhi Tao checked
	  in.

2010-10-13 16:38  fjia

	* sparx/libpy/applications.py: GTao checked in.

2010-10-11 18:58  ross

	* libpyEM/qtgui/embrowse.py: trivial

2010-10-11 18:53  ross

	* libpyEM/qtgui/emselector.py: fix to get previews to show again
	  after they are closed (but objects still exists)

2010-10-11 18:11  ross

	* programs/e2workflow.py: removing 3D desktop stuff

2010-10-11 18:02  ross

	* programs/e2ctf.py, sparx/bin/sxctf.py: removing commented out
	  resizeEvent() code

2010-10-11 18:01  ross

	* libpyEM/qtgui/: em3Dfonts.py, emform.py, emglobjects.py,
	  emimage3diso.py, emimage3dslice.py, emimage3dsym.py,
	  emimage3dvol.py: resizeEvent() changed to resize() for objects
	  that are not QWidgets

2010-10-11 16:27  john

	* programs/: e2align3d.py, e2rctV2.py: Updated e2align3d.py
	  Enhanced e2rctV2.py, now aligns and averages all recons

2010-10-09 17:01  stevel

	* programs/e2proc2d.py: Add 1D pow spec comp to e2proc2d.py

2010-10-09 15:44  ross

	* libpyEM/qtgui/emglobjects.py: adding/removing print statements
	  for Camera2 and EM3DModel

2010-10-09 15:17  ross

	* libpyEM/qtgui/: emimagemxrotor.py, emimagerotor.py: trivial

2010-10-09 15:10  ross

	* programs/: e2cmpxplor.py, e2history.py, e2preferences.py,
	  e2simmxxplor.py: EMStandAloneApplication -> EMApp

2010-10-09 15:06  ross

	* programs/: e2boxer.py, e2eulerxplor.py, e2helixboxer.py,
	  e2history.py, e2preferences.py, e2tomoboxer.py, e2workflow.py:
	  *.closeEvent(None) replaced with *.close()

2010-10-09 15:03  ross

	* libpyEM/qtgui/: emform.py, emimagemx.py: trivial

2010-10-09 15:02  ross

	* libpyEM/qtgui/emfoldhunterstat.py: using EMApp; working with the
	  version of "normalize.toimage" processor that is in this branch
	  (will need to be changed back when the branch is merged back into
	  the trunk

2010-10-09 15:01  ross

	* libpyEM/qtgui/: emapplication.py, emimage3dsym.py, emselector.py,
	  emsprworkflow.py, emtprworkflow.py: *.closeEvent(None) ->
	  *.close() : fixes many bugs after EM*Modules have been replaced
	  with QWidgets

2010-10-09 14:31  ross

	* libpyEM/qtgui/emboxerbase.py: EMBoxerModule.done(self) bugfix

2010-10-09 14:29  ross

	* libpyEM/qtgui/emapplication.py: added EMGLWidget.closeEvent(self,
	  event) to ensure associated EMParentWin is closed

2010-10-09 13:51  ross

	* programs/e2tomoboxer.py: EMTomoBoxerModule.done(self) bugfix

2010-10-09 13:19  ross

	* libpyEM/qtgui/emform.py: commented out EMFormWidget.__del__(self)

2010-10-09 12:36  ross

	* libpyEM/qtgui/emapplication.py: trivial

2010-10-09 12:30  ross

	* programs/e2workflow.py: numerous changes to remove
	  EMQtWidgetModule dependence, and convert from EM*Module to
	  Widgets in general

2010-10-09 11:31  ross

	* programs/e2tomoboxer.py: removed EMTomoBoxerInspectorModule,
	  using EMTomoBoxerInspector in its place; EMImage2DModule ->
	  EMImage2DWidget

2010-10-09 11:10  ross

	* libpyEM/qtgui/emsprworkflow.py, programs/e2ctf.py: GUICtfModule
	  removed, GUIctf used instead

2010-10-09 07:28  stevel

	* libpyEM/qtgui/emplot2d.py: trivial fix

2010-10-09 06:45  stevel

	* libpyEM/: libpyUtils2.cpp, qtgui/emplot2d.py: Write data from 2d
	  plots to files

2010-10-08 17:39  ross

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emboxerbase.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emsprworkflow.py,
	  sparx/bin/sxboxer.py: EMProgressDialogModule -> EMProgressDialog,
	  removing EMProgressDialogModule

2010-10-08 16:56  ross

	* libpyEM/qtgui/emfximage.py: removing -- no longer used

2010-10-08 16:48  ross

	* libpyEM/qtgui/emform.py, libpyEM/qtgui/emsprworkflow.py,
	  libpyEM/qtgui/emtprworkflow.py, programs/e2history.py,
	  programs/e2preferences.py, programs/e2workflow.py,
	  sparx/bin/sxboxer.py: EMFormModule -> EMFormWidget,
	  EMTableFormModule -> EMTableFormWidget, deleting EMFormModule and
	  EMTableFormModule, thereby reducing dependency on
	  EMQtWidgetModule

2010-10-08 16:47  fjia

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/libpyEMData2.cpp, libEM/reconstructor.cpp: [no log
	  message]

2010-10-08 16:44  ross

	* libpyEM/qtgui/emselector.py: Module -> Widget changes

2010-10-08 16:43  ross

	* libpyEM/qtgui/emapplication.py: EMGLWidget: removing commented
	  out code

2010-10-08 16:39  john

	* programs/: e2rct.py, e2rctV2.py: Added e2rct.py to cvs

2010-10-08 16:29  john

	* libEM/aligner.h, programs/e2align3d.py: Rewrote the e2align3d.py
	  program

2010-10-08 14:03  john

	* libEM/: aligner.cpp, aligner.h: Updated doxygen docs

2010-10-08 10:18  john

	* libEM/aligner.cpp, libEM/aligner.h, libEM/emdata_modular.h,
	  libEM/mrcio.cpp, libpyEM/EMAN2db.py: Fixed 3D aligners in
	  aligner.h and aligner.cpp Changed some default behaviour in
	  emdata_modular.h Added a parameter called UCSF.chimera in
	  mrcio.cpp (this enables a sane map written out in mrc format to
	  read by Chimera)

2010-10-07 18:04  ross

	* examples/tomotrackbox.py: EMImage2DModule -> EMImage2DWidget,
	  using EMApp now

2010-10-07 18:00  ross

	* libpyEM/qtgui/emimage3d.py: minor changes

2010-10-07 17:59  ross

	* libpyEM/qtgui/: emform.py, emimagerotor.py, emrotor.py: trivial
	  changes

2010-10-07 17:57  ross

	* libpyEM/EMAN2.py, libpyEM/qtgui/embrowse.py,
	  libpyEM/qtgui/emsave.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2display.py,
	  programs/e2helixboxer.py, programs/e2workflow.py:
	  EMBrowserModule->EMBrowser, EMSelectorModule->EMSelectorDialog,
	  and removing the now unused EMBrowserModule & EMSelectorModule
	  classes

2010-10-07 10:06  ross

	* libpyEM/qtgui/emselector.py: trivial

2010-10-07 10:06  ross

	* libpyEM/qtgui/emapplication.py: removed unused EMModule class --
	  added DeprecationWarning to __init__ functions for
	  ModuleEventManager, EMGUIModule, EMApplication,
	  EMStandAloneApplication, and EMQtWidgetModule

2010-10-06 14:06  ppenczek

	* libEM/sparx/fourierfilter.cpp: [no log message]

2010-10-06 13:49  ross

	* libpyEM/qtgui/emform.py: using EMSelectorDialog instead of
	  EMSelectorModule

2010-10-06 13:49  ross

	* libpyEM/qtgui/emselector.py: changes to EMSelectorBase's and
	  EMSelectorDialog's cancel_button_clicked() and
	  ok_button_clicked() functions

2010-10-06 10:54  ross

	* libpyEM/qtgui/emselector.py: EMBrowser and EMSelectorDialog no
	  longer require EMBrowserModule and EMSelectorModule, thus
	  removing EMQtWidgetModule dependence.

2010-10-06 10:25  stevel

	* libEM/cmp.cpp: Try to fix crasher when using fsc in refine
	  aligner in some cases

2010-10-06 02:53  irees

	* programs/emen2client.py: [no log message]

2010-10-04 15:15  ppenczek

	* sparx/bin/sxfactcoords.py: restored

2010-10-04 14:33  ppenczek

	* sparx/libpy/applications.py: removed writing odd/even stat in
	  sxvar

2010-10-04 13:41  ppenczek

	* sparx/libpy/filter.py: [no log message]

2010-10-04 11:20  fjia

	* libEM/sparx/emdata_sparx.cpp: [no log message]

2010-10-04 10:29  stevel

	* programs/e2workflow.py: Fix bug due to desktop removal

2010-10-01 17:33  ross

	* sparx/bin/sxboxer.py: branch: making work with changes to
	  libpyEM/qtgui/*.py libraries

2010-10-01 17:30  ross

	* programs/: e2boxer.py, e2display.py: trivial

2010-10-01 17:28  ross

	* libpyEM/qtgui/emselector.py: organize imports

2010-10-01 17:27  ross

	* libpyEM/qtgui/: emboxerbase.py, emimage.py, emplot3d.py: trivial

2010-10-01 17:25  ross

	* libpyEM/qtgui/emapplication.py: hack to make ModuleEventsManager
	  work with QWidget objects temporarily

2010-10-01 14:36  ross

	* examples/tomotrackbox.py: trivial

2010-10-01 13:30  ross

	* programs/e2simmxxplor.py: removed unused InputEventsManager
	  import

2010-10-01 12:17  ross

	* libpyEM/qtgui/em3Dfonts.py: translation fix

2010-09-30 18:40  ross

	* libpyEM/qtgui/em3Dfonts.py: fixed mouse movements

2010-09-30 16:35  gtang

	* programs/: CMakeLists.txt, e2workflow.py: e2desktop.py removed
	  from EMAN2

2010-09-29 16:46  gtao

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/libpyEMData2.cpp, sparx/bin/sxproject3d.py: rectangular
	  projection coding work is done.

2010-09-29 07:51  stevel

	* libEM/averager.cpp, programs/e2refine2d.py: minor fixes

2010-09-28 17:03  zyang

	* libEM/: reconstructor.cpp, sparx/emdata_sparx.cpp,
	  sparx/util_sparx.cpp: Fix some codes such that it will compile
	  under Visual C++

2010-09-28 10:36  zyang

	* libEM/sparx/util_sparx.cpp, sparx/bin/sxali3d_em.py: Rewrite the
	  program such that it will compile for Visual C++

2010-09-27 10:34  gtao

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/libpyEMData2.cpp: [no log message]

2010-09-27 09:19  ross

	* libpyEM/qtgui/emimage.py: trivial

2010-09-26 23:23  stevel

	* programs/e2classaverage.py: refinevariance bugfix

2010-09-26 11:39  stevel

	* programs/e2evalrefine.py: Add new evalrefine option for comparing
	  2 refinements.

2010-09-26 00:33  stevel

	* libpyEM/: EMAN2db.py, qtgui/emimagemx.py: Revert change that
	  broke parallelism

2010-09-26 00:28  stevel

	* libpyEM/EMAN2db.py: Merge from 1.183

2010-09-25 17:18  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-09-25 15:09  ross

	* libpyEM/qtgui/emimage3dsym.py: trivial

2010-09-25 15:09  ross

	* libpyEM/qtgui/emimage.py: renaming "module" classes and variables
	  to "widget"

2010-09-25 15:06  ross

	* libpyEM/qtgui/emplot3d.py: fixed segmentation fault, added
	  EMPlot3DWidget(EMImage3DWidget) convenience class

2010-09-25 14:16  ross

	* libpyEM/qtgui/emplot2d.py: fixed segmentation fault in
	  EMPlot2DWidget.closeEvent(self,event)

2010-09-24 14:30  gtang

	* libEM/mrcio.cpp: [no log message]

2010-09-24 11:45  jkovacs

	* sparx/bin/sxpdb2em.py: removed a testing printout

2010-09-24 11:40  jkovacs

	* sparx/libpy/applications.py: in ali_vol_M, added options for
	  tight mask and for smallest-moving-sphere mask, to be used in
	  conjunction with ali_vol_func

2010-09-24 11:34  jkovacs

	* sparx/libpy/alignment.py: added options for tight mask and for
	  smallest-sphere mask, to be used in conjunction with ali_vol_M

2010-09-23 11:24  gtao

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: insert
	  rectangular slice into emdata class--- the emdata_sparx.cpp and
	  .h

2010-09-23 11:19  gtao

	* libEM/: reconstructor.cpp, reconstructor.h: nn4 ctf rectangular
	  reconstructor is tested.

2010-09-22 17:43  stevel

	* examples/extracthelp.py: New program to help making entries in
	  wiki

2010-09-22 15:12  irees

	* programs/e2boxer.py: Trivial change

2010-09-22 15:07  irees

	* libpyEM/qtgui/emboxerbase.py: Fixed an error that I caused

2010-09-22 14:10  john

	* examples/comparepairs.py, examples/sortsimilar.py,
	  libEM/averager.cpp, libEM/emdata.cpp, libEM/emdata_cuda.cpp,
	  libEM/pointarray.cpp, libEM/processor.cpp,
	  programs/e2classaverage.py, programs/e2tomogram.py,
	  utils/proc2d.cpp: [no log message]

2010-09-22 10:55  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-09-21 17:04  ross

	* programs/: e2helixboxer.py: command-line help-text changes

2010-09-21 16:53  john

	* libEM/: emdata.cpp, emobject.h, sparx/processor_sparx.h: [no log
	  message]

2010-09-21 16:52  ross

	* programs/: e2helixboxer.py: bugfix: --helix-width to specify
	  width with --db-add-hcoords and --db-set-hcoords fix

2010-09-21 16:41  ross

	* programs/e2helixboxer.py: added command line options to append
	  helix coordinates to the database or overwrite the current
	  database coordinates from a tab-delimited text file in EMAN1
	  *.box format

2010-09-21 16:39  ross

	* programs/e2helixboxer.py: trivial

2010-09-21 16:30  ross

	* programs/e2helixboxer.py: added command line options to append
	  helix coordinates to the database or overwrite the current
	  database coordinates from a tab-delimited text file in EMAN1
	  *.box format

2010-09-21 11:52  john

	* libEM/sparx/processor_sparx.h: [no log message]

2010-09-21 00:05  ross

	* programs/: e2helixboxer.py: trivial

2010-09-20 23:58  ross

	* programs/e2helixboxer.py: adding to branch, changes in trunk:
	  get_particles_from_helix() became get_rotated_particles() to
	  allow particles to be wider than the helix they came from

2010-09-20 23:53  ross

	* programs/e2helixboxer.py: adding changes to trunk from branch
	  version

2010-09-20 23:23  ross

	* programs/e2helixboxer.py: trivial bugfix &
	  get_particles_from_helix() became get_unrotated_particles() to
	  allow particles to be wider than the helices they come from

2010-09-20 16:56  john

	* libEM/processor.cpp, libEM/processor.h,
	  libEM/sparx/processor_sparx.h, rt/pyem/test_processor.py,
	  sparx/libpy/filter.py, sparx/test/main_example.py: [no log
	  message]

2010-09-20 14:12  ross

	* libpyEM/qtgui/: emrotor.py, emshape.py: trivial

2010-09-20 14:11  ross

	* libpyEM/qtgui/emapplication.py: removing unused/commented out
	  code

2010-09-20 14:10  ross

	* libpyEM/qtgui/emimageutil.py: EMEventRerouterToList isn't used
	  anywhere: removing

2010-09-20 14:10  ross

	* libpyEM/qtgui/emimage3dvol.py: EMVolumeWidget isn't being used:
	  removing it.

2010-09-17 17:42  ross

	* libpyEM/qtgui/: emglobjects.py, emimage3d.py: cleaning up imports

2010-09-17 17:32  ross

	* libpyEM/qtgui/: emfloatingwidgets.py, emglobjects.py,
	  emimage3d.py: removing EMImage3DGUIModule and
	  EMImage3DGeneralWidget

2010-09-17 17:17  ross

	* libpyEM/qtgui/em3Dhelloworld.py: EMImage3DGUIModule --> EM3DModel

2010-09-17 17:10  ross

	* libpyEM/qtgui/em3Dfonts.py: EMImage3DGUIModule --> EM3DModel,
	  EM3DFontWidget renamed to EM3DFontModel

2010-09-17 16:39  ross

	* programs/CMakeLists.txt: remving e2desktop.py

2010-09-17 16:38  ross

	* programs/e2desktop.py: removing: purpose of this branch is to
	  remove e2desktop and it's required libraries that make the
	  library code messy and hard to follow

2010-09-17 16:36  ross

	* libpyEM/qtgui/emdesktop.py: removing 3D desktop

2010-09-17 16:33  ross

	* libpyEM/qtgui/emfloatingwidgets.py: removing EMImage3DGUIModule

2010-09-17 15:43  gtao

	* libEM/reconstructor.cpp: [no log message]

2010-09-16 18:03  ross

	* programs/e2fhstat.py: changing app.show_specific() to app.show()
	  since only QWidgets can now be called with show_specific()

2010-09-16 18:01  ross

	* libpyEM/qtgui/emimage3d.py: EMImage3DWidget has no EM3DModel's by
	  default, though test code adds an Isosurface model -- use
	  add_model()

2010-09-16 17:59  ross

	* libpyEM/qtgui/empdbvaltool.py: changing tab order for the
	  inspector (still some display problems)

2010-09-16 17:34  ross

	* libpyEM/qtgui/: empdbvaltool.py, empdbviewer.py: simplifying
	  class hierarchy

2010-09-16 15:37  gtao

	* libEM/reconstructor.h, sparx/bin/sxrecons3d_n.py: [no log
	  message]

2010-09-16 15:37  gtao

	* libEM/reconstructor.cpp: direct inver fft reconstructin method
	  with rectangular windows is tested and cleaned

2010-09-16 15:17  ross

	* libpyEM/CMakeLists.txt: removed qtgui/em3dmodule.py

2010-09-16 10:17  ross

	* libpyEM/qtgui/: empdbvaltool.py, empdbviewer.py: removing
	  em3dmodule, no longer inherit from it

2010-09-16 10:16  ross

	* libpyEM/qtgui/em3dmodule.py: removing and collapsing inheritance,
	  so empdbviewer and empdbvaltool don't need em3dmodule

2010-09-16 10:07  stevel

	* libpyEM/: EMAN2.py, qtgui/emsprworkflow.py: examine refine_ dirs
	  without numbers

2010-09-16 09:45  prb

	* libEM/transform.cpp:
	  one line code change to definition of az in get_rotation

2010-09-15 17:46  jkovacs

	* sparx/libpy/applications.py: added a function, ali_vol_M, similar
	  to ali_vol_n but which takes a mask instead of just the radius of
	  a mask

2010-09-15 17:44  jkovacs

	* sparx/libpy/alignment.py: corrected data[3] to data[4] in
	  ali_vol_func

2010-09-15 11:53  ross

	* libpyEM/qtgui/empdbviewer.py: EMPDBModel has its own camera like
	  other EM3DModel objects (to be changed so only EMImage3DWidget
	  has a camera), zooming works

2010-09-15 11:34  ross

	* libpyEM/qtgui/empdbviewer.py: EMPDBModel subclasses EM3DModel
	  (previously, EMPDBViewer subclassed EM3DModule)

2010-09-15 11:16  ross

	* libpyEM/qtgui/emglobjects.py: NotImplementedException -->
	  NotImplementedError

2010-09-15 11:11  ross

	* libpyEM/qtgui/emimage3d.py: EMImage3DWidget.__add_module() -->
	  EMImage3DWidget.add_module()

2010-09-14 17:27  ross

	* libpyEM/qtgui/: emfoldhunterstat.py: Score 3 fix (processor
	  parameters changed names?)

2010-09-14 17:26  gtao

	* libEM/reconstructor.cpp: the rectangle fft inverse reconstrucotr
	  is now working

2010-09-14 16:42  irees

	* libpyEM/qtgui/emboxerbase.py, programs/e2boxer.py,
	  pyemtbx/boxertools.py: Changes to e2boxer base classes to work
	  better in non-GUI mode (e.g. EMEN2 autoboxing)

2010-09-14 15:41  irees

	* programs/emen2client.py: Adding emen2client.py to the EMAN2
	  distribution. It will be removed from the EMEN2 CVS.

2010-09-14 15:40  irees

	* libpyEM/EMAN2db.py: Small change to EMAN2db.py to play better
	  with EMEN2. The DB_Cleanup atexit and signal assignments are not
	  added until after DBEnv is created.

2010-09-14 14:51  stevel

	* examples/extracthelp.py: New program (not done) for doc
	  interrogation

2010-09-14 14:32  stevel

	* libpyEM/qtgui/emsprworkflow.py: Fixed particle import from
	  database problem.

2010-09-13 17:19  ross

	* programs/: e2cmpxplor.py, e2display.py, e2eulerxplor.py,
	  e2simmxxplor.py, e2workflow.py: renaming "renderer" to "model"
	  except for "font_renderer"

2010-09-13 16:37  jkovacs

	* sparx/bin/sxpdb2em.py: When quiet was set, centering was not
	  being done. Moved tr0 after centering, so as not to loose its
	  translation. Added a centering option to substract a given vector
	  from all PDB coordinates.

2010-09-13 08:03  ross

	* libpyEM/qtgui/: emimage3d.py, emimage3diso.py, emimage3dslice.py,
	  emimage3dsym.py, emimage3dvol.py, emlights.py, empdbvaltool.py,
	  emplot3d.py, emselector.py: renaming "renderer" to "model"
	  (except "font_renderer")

2010-09-11 18:48  ross

	* libpyEM/qtgui/: em3dmodule.py, empdbvaltool.py, empdbviewer.py:
	  removing EMImage3DGUIModule: fixing PDB validation

2010-09-10 18:11  ross

	* libpyEM/qtgui/: em3dmodule.py, emglobjects.py, emimage3diso.py,
	  emimage3dslice.py, emimage3dsym.py, emimage3dvol.py, emlights.py,
	  emplot3d.py: renaming EMRenderer3D to EM3DModel

2010-09-10 17:46  ross

	* libpyEM/qtgui/emfoldhunterstat.py, libpyEM/qtgui/empdbvaltool.py,
	  libpyEM/qtgui/empdbviewer.py, programs/e2fhstat.py: removing
	  EMImage3DGUIModule: fixing PDB validation

2010-09-10 17:45  ross

	* libpyEM/qtgui/emplot3d.py: trivial

2010-09-10 15:18  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-09-10 14:58  ross

	* libpyEM/CMakeLists.txt: removed qtgui/emglplot.py

2010-09-10 14:42  ppenczek

	* sparx/libpy/applications.py: working version of ihrsr

2010-09-10 14:40  gtang

	* libpyEM/typeconverter.h: to support empty list attribute in
	  Python: e = test_image() e['attr'] = []

2010-09-10 14:36  ross

	* libpyEM/qtgui/emglplot.py: no longer in use, emplot3d.py and
	  emplot2d.py provide plotting

2010-09-10 12:52  stevel

	* programs/e2classaverage.py: Fix for empty lists. Undo when C++
	  fixed.

2010-09-10 12:38  ross

	* libpyEM/qtgui/em3dmodule.py: converting to EMRenderer3D...
	  rendering is happening now in test code

2010-09-10 12:24  ppenczek

	* sparx/libpy/: alignment.py, applications.py: [no log message]

2010-09-10 11:54  ppenczek

	* sparx/libpy/: alignment.py, applications.py: [no log message]

2010-09-10 09:33  stevel

	* programs/e2classaverage.py: oneclass option added to class
	  average

2010-09-10 09:27  stevel

	* libpyEM/qtgui/emimage3dsym.py, programs/e2eulerxplor.py:
	  Eulerexpor now more tolerant of missing images

2010-09-10 08:01  stevel

	* programs/e2classaverage.py: oops

2010-09-10 07:57  stevel

	* programs/e2classaverage.py: Fix for div by zero

2010-09-10 07:48  stevel

	* programs/e2classaverage.py: Make class average interruptable

2010-09-10 07:27  stevel

	* programs/e2classaverage.py: Trivial

2010-09-10 07:22  stevel

	* programs/: e2classaverage.py, e2refine.py: Fixes for classiter=0

2010-09-09 21:57  stevel

	* libpyEM/qtgui/emimage3dsym.py, programs/e2eotest.py,
	  programs/e2eulerxplor.py: eotest fix for new options

2010-09-09 19:47  ross

	* libpyEM/qtgui/em3dmodule.py: converting to EMRenderer3D

2010-09-09 19:05  ross

	* libpyEM/qtgui/em3dmodule.py: converting to EMRenderer3D subclass

2010-09-09 19:04  ross

	* libpyEM/qtgui/emplot3d.py: get_qt_widget() added back (though it
	  does different things)

2010-09-09 19:02  ross

	* libpyEM/qtgui/: emimage.py, emimagemxrotor.py, emlights.py,
	  emplot2d.py, emfoldhunterstat.py: trivial

2010-09-09 19:00  ross

	* libpyEM/qtgui/emimage3dsym.py: trivial (comments)

2010-09-09 18:23  mingc

	* libEM/aligner.cpp: change FRM2d to frm2d

2010-09-09 18:18  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-09-09 17:24  gtao

	* libEM/reconstructor.cpp: [no log message]

2010-09-09 17:14  gtao

	* libEM/: reconstructor.h, reconstructor.cpp: [no log message]

2010-09-09 17:03  gtao

	* libEM/: reconstructor.h, reconstructor.cpp: [no log message]

2010-09-09 10:00  stevel

	* programs/e2classaverage.py: Fix for single image classes

2010-09-09 09:17  stevel

	* programs/e2classaverage.py: Fix for parallelism metadata.

2010-09-09 08:50  stevel

	* programs/e2classaverage.py: oops

2010-09-09 08:45  stevel

	* libpyEM/EMAN2db.py, programs/e2classaverage.py: Fix for
	  class-average metadata

2010-09-08 22:44  stevel

	* programs/e2classaverage.py: Orientation fix.

2010-09-08 22:22  stevel

	* programs/e2make3d.py: Fix for bad images

2010-09-08 22:02  stevel

	* programs/e2classaverage.py: Minor fix for classaverage

2010-09-08 17:15  gtao

	* libEM/reconstructor.h, libEM/reconstructor.cpp,
	  sparx/bin/sxrecons3d_n.py: [no log message]

2010-09-08 17:10  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-09-08 17:02  stevel

	* programs/e2refine.py: oops

2010-09-08 15:40  stevel

	* libpyEM/EMAN2PAR.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2classaverage.py, programs/e2parallel.py,
	  programs/e2refine.py: New e2classaverage. Rewritten from scratch.
	  New classautomask option in refine. Both only slightly testing.
	  Running thorough tests tonight.

2010-09-08 14:16  ppenczek

	* sparx/libpy/applications.py: corrections of ihrsr

2010-09-08 13:53  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-09-08 12:53  ppenczek

	* sparx/libpy/: alignment.py, applications.py: helical went back to
	  version 95, before Ryan's changes

2010-09-07 18:41  ross

	* libpyEM/qtgui/emplot3d.py: EMPlot3DRenderer subclasses
	  EMRenderer3D instead of being called EMPlot3DModule and
	  subclassing EMImage3DGUIModule

2010-09-07 17:17  zyang

	* sparx/bin/sxlocal_ali3dm.py: [no log message]

2010-09-07 13:35  ranlin

	* sparx/bin/sxali3d.py: add a option named --rantest for the
	  ali3d_MPI test

2010-09-07 11:40  gtang

	* libEM/emdata_io.cpp: [no log message]

2010-09-07 10:42  ranlin

	* sparx/bin/sxali3d_em.py: [no log message]

2010-09-07 10:38  fjia

	* sparx/libpy/applications.py: moved cml2_ori_collinearity here

2010-09-06 22:57  ranlin

	* sparx/bin/sxali3d_em.py: trivial change

2010-09-04 13:18  prb

	* libEM/transform.cpp:
	  Fixed again the small angle problem. Also fixed the problem with
	  e2eulerxplor.py

2010-09-03 22:28  ranlin

	* sparx/bin/sxali3d_em.py: local_ali3dm_MPI

2010-09-03 20:50  ppenczek

	* programs/e2bdb.py, sparx/libpy/applications.py: correction in
	  e2bdb.py

2010-09-03 17:10  gtang

	* libpyEM/libpyEMData2.cpp: this function seems not cause any daily
	  release compile problem any more

2010-09-03 16:12  gtao

	* libEM/: reconstructor.cpp, reconstructor.h: [no log message]

2010-09-03 15:25  zyang

	* sparx/: bin/sxali2d.py, libpy/applications.py: I have decided
	  that outdir should be able to take None as parameter, if the user
	  does not need an output directory.  This is particularly useful
	  in the ISAC program, nobody will care what is in the alignment
	  and realignment directory.  It takes a lot of disk space and time
	  to write these information. It may not be much for one iteration,
	  but will be enormous for several hundred iterations.

	  This change will not affect the normal usage.

2010-09-03 15:24  stevel

	* libEM/transform.cpp, programs/e2.py, programs/e2align3d.py,
	  programs/e2avg_ffts.py, programs/e2bdb.py, programs/e2boxer.py,
	  programs/e2classesbysim.py, programs/e2classify.py,
	  programs/e2classifykmeans.py, programs/e2cmmtomrc.py,
	  programs/e2ctf.py, programs/e2ctf2eman1.py,
	  programs/e2desktop.py, programs/e2display.py,
	  programs/e2eotest.py, programs/e2eulerxplor.py,
	  programs/e2evalrefine.py, programs/e2fileinfo.py,
	  programs/e2findsubunit.py, programs/e2flick.py,
	  programs/e2foldfitter.py, programs/e2helixboxer.py,
	  programs/e2history.py, programs/e2iminfo.py,
	  programs/e2make3d.py, programs/e2modeleval.py,
	  programs/e2parallel.py, programs/e2pdb2em.py,
	  programs/e2pdb2mrc.py, programs/e2proc2d.py,
	  programs/e2proc3d.py, programs/e2project3d.py,
	  programs/e2ptcltrace.py, programs/e2refine.py,
	  programs/e2refine2d.py, programs/e2refinemultinoali.py,
	  programs/e2refmerge.py, programs/e2resolution.py,
	  programs/e2scannereval.py, programs/e2scp.py,
	  programs/e2segment3d.py, programs/e2simmx.py,
	  programs/e2simmxxplor.py, programs/e2skelpath.py,
	  programs/e2speedtest.py, programs/e2ssehunter.py,
	  programs/e2ssematch.py, programs/e2stackanim.py,
	  programs/e2stacksort.py, programs/e2startcsym.py,
	  programs/e2symbest.py, programs/e2tilefile.py,
	  programs/e2tomoallvall.py, programs/e2tomoaverage.py,
	  programs/e2tomoboxer.py, programs/e2tomogram.py,
	  programs/e2tomohunter.py, programs/e2wx.py: Massive overhaul of
	  basic documentation, and removal of some old programs.

2010-09-03 14:33  ranlin

	* programs/e2bdb.py: --restore has been revised.  when data_source
	  and data_n will be kept in every "restore" if data_source is not
	  exist in the original stack, these parameters will be deleted in
	  the restore process.

2010-09-02 22:38  stevel

	* libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libpyEM/EMAN2.py, libpyEM/libpyEMData2.cpp: New EMData method to
	  search for specific values

2010-09-02 16:18  gtao

	* libEM/: reconstructor.cpp, reconstructor.h: [no log message]

2010-09-02 15:48  ranlin

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: delete max_search

2010-09-02 15:44  ranlin

	* libpyEM/libpyEMData2.cpp: delete max_search

2010-09-01 13:03  stevel

	* libEM/averager.cpp: A bit of work on averager, but still not
	  fixed.

2010-09-01 12:24  gtang

	* libEM/hdfio2.cpp: [no log message]

2010-09-01 10:36  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-09-01 10:33  ross

	* libpyEM/qtgui/emlights.py: trivial

2010-09-01 01:24  gtang

	* libEM/: hdfio2.cpp, hdfio2.h: HDF5 read_data will judge the data
	  type by dataset itself, not by header attribute 'datatype'. This
	  fixes the problem of the legacy hdf5 file may have inconsistent
	  'datatype' attribute with actual data storage type.

2010-08-31 18:01  ross

	* libpyEM/qtgui/emlights.py: refresh lights vector before drawing
	  the "lamps" that represent them

2010-08-31 17:35  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-08-31 17:20  gtang

	* libEM/hdfio2.cpp: HDF5 datatype default to float type.

2010-08-31 15:48  ppenczek

	* sparx/bin/sxali3d.py: [no log message]

2010-08-31 14:09  ranlin

	* sparx/libpy/applications.py: Changed the format that header
	  function import and export parameters.

2010-08-31 11:20  jkovacs

	* sparx/bin/sxpdb2em.py: Shift units in tr0 matrix are now Angstrom

2010-08-30 12:18  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-08-30 10:35  ross

	* libpyEM/qtgui/emimage3d.py: fixing mouse events for
	  EMImage3DWidget

2010-08-30 10:32  ross

	* libpyEM/qtgui/emlights.py: EMLights and EMLightsInspector mostly
	  working again

2010-08-29 22:57  stevel

	* libEM/averager.cpp: Again...

2010-08-29 22:53  stevel

	* libEM/averager.cpp: Another tweak

2010-08-29 22:49  stevel

	* libEM/averager.cpp: Mostly working. Little tweak.

2010-08-29 22:22  stevel

	* libEM/averager.cpp: I must be tired

2010-08-29 22:00  stevel

	* libEM/averager.cpp: One more try

2010-08-29 20:51  stevel

	* libEM/averager.cpp: oops

2010-08-29 20:05  stevel

	* libEM/averager.cpp: Fix averager so high freq zeroed

2010-08-28 23:02  stevel

	* libpyEM/qtgui/emsprworkflow.py: Quality in set making !

2010-08-27 23:55  stevel

	* libpyEM/qtgui/emsprworkflow.py, programs/CMakeLists.txt: Fix .box
	  file import

2010-08-27 20:29  ross

	* libpyEM/qtgui/emglobjects.py: EM3DGLWidget and EMRenderer3D
	  updates

2010-08-27 18:09  ppenczek

	* sparx/libpy/: applications.py, reconstruction.py: corrections of
	  npad

2010-08-27 15:08  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-08-27 13:34  ppenczek

	* sparx/libpy/: alignment.py, applications.py, user_functions.py:
	  [no log message]

2010-08-27 09:51  gtang

	* libEM/mrcio.cpp: bug fix for big endian mrc image file

2010-08-26 19:12  ross

	* libpyEM/qtgui/emimage3d.py: removing EMScene3DWidget

2010-08-26 18:08  ross

	* libpyEM/qtgui/emimage3d.py: EMImage3DWidget mostly functional
	  (not using signal rerouting anymore)

2010-08-26 18:05  ross

	* libpyEM/qtgui/emlights.py: EMLightsDrawer updated, EMLights,
	  EMLightsInspector commented out

2010-08-26 18:03  ross

	* libpyEM/qtgui/emapplication.py: EMGLWidget fixes

2010-08-26 13:33  stevel

	* libEM/transform.cpp: Merge from 1.186

2010-08-26 12:38  ranlin

	* programs/e2bdb.py: change the way to select image from --list

2010-08-26 10:42  ppenczek

	* sparx/: bin/sxrecons3d_f.py, bin/sxrecons3d_n.py,
	  libpy/applications.py: more npad

2010-08-26 10:19  ranlin

	* sparx/libpy/applications.py: set_attr('ctf_applied',0) in the
	  ali3d

2010-08-26 07:51  stevel

	* programs/e2parallel.py: trivial

2010-08-25 16:03  prb

	* libEM/transform.cpp:
	     Fixed get_rotate etc, because it didn't work so well for small
	  angles.

2010-08-25 15:05  ppenczek

	* sparx/: bin/sxlocal_ali3d.py, bin/sxmref_ali3d.py,
	  libpy/applications.py: more npad changes

2010-08-25 14:19  ranlin

	* sparx/libpy/applications.py: trivial changes

2010-08-25 11:44  ppenczek

	* sparx/: bin/sxali3d.py, libpy/alignment.py,
	  libpy/applications.py: additions to ali3d

2010-08-24 21:54  stevel

	* examples/tomotrackbox.py: Fix proj realign

2010-08-24 21:35  stevel

	* examples/tomotrackbox.py, programs/e2tomoboxer.py: Fix
	  compatibility issue in tomotrackbox

2010-08-24 15:29  ppenczek

	* sparx/libpy/applications.py: pixer from Ryan

2010-08-24 13:23  stevel

	* programs/: e2align2d.py, e2eulerxplor.py: New utility like eman1
	  align2d

2010-08-23 16:57  ranlin

	* programs/e2bdb.py: modify the "data_source" reference stack

2010-08-23 16:39  fjia

	* sparx/libpy/statistics.py: [no log message]

2010-08-23 15:24  zyang

	* sparx/libpy/applications.py: Fix a minor bug and some other
	  trivial change

2010-08-23 14:45  gtang

	* programs/e2proc2d.py: comment out the outdated gimme_fft()
	  function call.

2010-08-23 14:28  ranlin

	* sparx/libpy/applications.py: corrected an error in hdf write attr

2010-08-23 12:32  ranlin

	* sparx/libpy/applications.py: The header function has been changed
	  in the previous version. It is now setting attributes directly
	  rather than reading the whole stack before setting attributes.

2010-08-23 12:27  ranlin

	* programs/e2bdb.py: add a --restore option for write metadate in
	  derived virtual stack to the original stack.

2010-08-23 10:07  ranlin

	* sparx/libpy/applications.py: [no log message]

2010-08-23 09:36  stevel

	* libEM/analyzer.cpp: Improved speed when refine2d is making a lot
	  of classes

2010-08-22 11:52  stevel

	* programs/e2stacksort.py: Ooops messed up default

2010-08-22 01:32  stevel

	* programs/e2refine2d.py: oops

2010-08-22 01:22  stevel

	* programs/: e2refine2d.py, e2stacksort.py: permit 1 alignment ref
	  in refine2d

2010-08-21 12:18  gtang

	* rt/pyem/test_imageio.py: [no log message]

2010-08-21 12:15  gtang

	* libEM/hdfio2.cpp: when I fix the overwriting issue, forgot the
	  header only write situation. Now it's fixed.

2010-08-21 11:51  ranlin

	* sparx/libpy/applications.py: Trivial change

2010-08-21 02:16  stevel

	* programs/e2bdb.py: Fix for double dereferenced vstack

2010-08-21 02:11  stevel

	* programs/e2bdb.py: Modify vstack to include source file info

2010-08-20 17:55  jkovacs

	* sparx/libpy/applications.py: Added function ali_vol_n which
	  avoids composition of transformations, and does not apply input
	  transformations to the volumes.

2010-08-20 17:53  zyang

	* sparx/libpy/statistics.py: [no log message]

2010-08-20 11:52  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-08-20 10:29  stevel

	* programs/e2msa.py: trivial

2010-08-20 09:03  stevel

	* programs/e2msa.py: Few more msa tweaks

2010-08-20 08:48  stevel

	* programs/: e2msa.py, e2refine2d.py: Additional refine2d work

2010-08-20 08:03  stevel

	* programs/: e2msa.py, e2proc2d.py, e2proc3d.py: Major improvement
	  to e2refine2d.py by changing normalization in msa

2010-08-19 16:16  zyang

	* sparx/bin/sxk_means_stable.py: [no log message]

2010-08-19 16:11  gtang

	* libEM/hdfio2.cpp: bug fix for overwriting with same size image.

2010-08-19 14:43  zyang

	* sparx/libpy/statistics.py: Some test program

2010-08-19 14:13  ranlin

	* programs/e2bdb.py: add an option to import a file for virtual
	  stack generation reference

2010-08-19 10:22  fjia

	* sparx/libpy/statistics.py: [no log message]

2010-08-18 16:00  stevel

	* libEM/glutil.cpp, libpyEM/qtgui/emimage2d.py: Fix issue on
	  reading complex pixel values in left half of image fft

2010-08-18 15:33  gtang

	* libEM/emdata.cpp: bug fix. two EMData constructor not consistent.

2010-08-18 14:12  zyang

	* sparx/: bin/sxrealignment.py, libpy/pixel_error.py,
	  libpy/statistics.py: Change the way of checking multiple
	  alignment errors

2010-08-18 13:52  stevel

	* programs/e2proc2d.py: Fix sequential rotate/translate in e2proc2d

2010-08-18 10:43  fjia

	* sparx/libpy/statistics.py: [no log message]

2010-08-18 10:12  fjia

	* sparx/libpy/statistics.py: [no log message]

2010-08-18 09:58  zyang

	* libEM/sparx/util_sparx.cpp: Trivial change

2010-08-17 19:14  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Add function to calculate error of
	  multiple alignments

2010-08-17 17:51  ranlin

	* sparx/demo/1_bdb/run_through_example: [no log message]

2010-08-17 16:15  ranlin

	* sparx/demo/7_mpi_bdb_ctf/run_through_example: [no log message]

2010-08-17 15:20  ranlin

	* sparx/demo/5_mpi_bdb/run_through_example: [no log message]

2010-08-17 12:40  mingc

	* libEM/aligner.cpp: [no log message]

2010-08-17 12:20  gtang

	* libEM/emdata_transform.cpp: [no log message]

2010-08-17 12:18  mingc

	* libEM/: aligner.cpp, aligner.h, emdata.cpp, emdata.h,
	  emdata_transform.cpp, emfft.cpp, emfft.h: FRM2D aligner checked
	  in

2010-08-17 10:21  ppenczek

	* sparx/bin/sxali3d.py: [no log message]

2010-08-16 19:00  fjia

	* libEM/sparx/util_sparx.cpp: [no log message]

2010-08-16 18:47  fjia

	* sparx/libpy/statistics.py, libEM/sparx/util_sparx.h: [no log
	  message]

2010-08-16 18:44  fjia

	* libpyEM/libpyUtils2.cpp: [no log message]

2010-08-16 15:08  stevel

	* libpyEM/EMAN2db.py: Fixed problem with making a vstack from a
	  vstack

2010-08-16 14:56  gtang

	* programs/e2proc2d.py: some options like 'process', 'scale' etc.
	  can be called multiple times. make index_d dictionary inside
	  stack loop.

2010-08-16 12:28  ppenczek

	* sparx/libpy/applications.py, sparx/libpy/statistics.py,
	  libEM/sparx/util_sparx.cpp: [no log message]

2010-08-14 15:27  fjia

	* sparx/libpy/statistics.py: [no log message]

2010-08-13 16:28  gtang

	* rt/pyem/test_utils.py: unit test update

2010-08-13 16:28  gtang

	* libEM/emutil.cpp, libEM/emutil.h, libpyEM/libpyUtils2.cpp: delete
	  single attribute from HDF5 file

2010-08-13 14:17  ppenczek

	* sparx/libpy/: alignment.py, applications.py: [no log message]

2010-08-13 13:23  zyang

	* sparx/libpy/statistics.py: Fix a trivial bug

2010-08-13 13:17  zyang

	* sparx/libpy/applications.py: Trivial change

2010-08-13 13:13  ranlin

	* sparx/libpy/: statistics.py, applications.py: [no log message]

2010-08-13 11:59  ranlin

	* sparx/bin/sxk_means_groups.py: [no log message]

2010-08-13 11:42  ranlin

	* sparx/libpy/: applications.py, statistics.py: [no log message]

2010-08-13 11:15  zyang

	* sparx/libpy/applications.py: Reverse the last change

2010-08-13 11:07  ranlin

	* sparx/libpy/: applications.py, statistics.py: [no log message]

2010-08-12 18:02  ross

	* libpyEM/qtgui/emlights.py: removed mouse event classes and
	  integrated them into EMLightsDrawer

2010-08-12 16:39  zyang

	* sparx/libpy/pixel_error.py: Add function multi_align_stability()

2010-08-11 19:10  ppenczek

	* programs/e2bdb.py: corrected typos

2010-08-11 14:44  gtang

	* libEM/CMakeLists.txt, libEM/all_imageio.h, libEM/df3io.cpp,
	  libEM/df3io.h, libEM/emdata_io.cpp, libEM/emutil.cpp,
	  libEM/emutil.h, libpyEM/libpyUtils2.cpp, rt/pyem/test_imageio.py:
	  Support DF3 image format.

2010-08-11 09:36  ppenczek

	* sparx/libpy/applications.py: ::

2010-08-10 16:40  gtang

	* libEM/: hdfio2.cpp, mrcio.cpp: fix for 3D

2010-08-10 15:19  ranlin

	* sparx/bin/sxbootstrap_smp.py: [no log message]

2010-08-10 15:13  ranlin

	* sparx/bin/sxbootstrap_run.py: [no log message]

2010-08-10 15:09  ranlin

	* sparx/bin/sxk_means_groups.py: [no log message]

2010-08-10 15:05  ranlin

	* sparx/bin/: sxmulti_assign.py, sxrealignment.py: [no log message]

2010-08-10 14:59  ranlin

	* sparx/bin/sxmref_alignment.py: [no log message]

2010-08-10 14:58  stevel

	* programs/e2bdb.py: Remove debugging

2010-08-10 14:56  ranlin

	* sparx/bin/sxcopyfromtif.py: [no log message]

2010-08-10 14:51  ranlin

	* sparx/bin/sxihrsr.py: [no log message]

2010-08-10 14:46  stevel

	* examples/redo_convergence.py, programs/e2bdb.py,
	  programs/e2display.py, programs/e2proc3d.py: Major fix for
	  e2bdb.py in making vstacks...

2010-08-10 14:13  ranlin

	* sparx/bin/sxssnr3d.py: [no log message]

2010-08-10 14:09  ranlin

	* sparx/bin/sxmref_ali3d.py: [no log message]

2010-08-10 14:02  ranlin

	* sparx/bin/sxrecons3d_f.py: [no log message]

2010-08-09 17:06  ppenczek

	* sparx/libpy/utilities.py: [no log message]

2010-08-09 10:29  ppenczek

	* sparx/templates/: import_SPIDER_320.py, import_SPIDER_refi.py:
	  [no log message]

2010-08-07 19:56  stevel

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimage3d.py, programs/e2make3d.py,
	  programs/e2project3d.py, programs/e2tomoboxer.py: Starting new
	  version of tomoboxer

2010-08-06 18:21  jkovacs

	* sparx/libpy/alignment.py: Added function ali_vol_func_nopsi.
	  Changed ccc to data[4] in ali_vol_func.

2010-08-06 18:19  jkovacs

	* sparx/libpy/applications.py: removed application of initial
	  transformation from ali_vol_rotate and ali_vol_shift, since it is
	  applied in the corresponding func functions. Added function
	  ali_vol_nopsi to keep psi=0 during optimization

2010-08-06 17:37  ross

	* libpyEM/qtgui/emimage3d.py: merged EMImage3DModule and
	  EMImage3DWidget into a new EMImage3DWidget class

2010-08-06 14:51  ranlin

	* sparx/libpy/applications.py: [no log message]

2010-08-06 10:44  ppenczek

	* sparx/: libpy/applications.py, bin/sxvar.py: [no log message]

2010-08-06 10:43  zyang

	* sparx/libpy/applications.py: Trivial change

2010-08-05 20:49  ross

	* programs/e2eulerxplor.py: moved keyboard and mouse events into
	  EMEulerExplorer class (no separate event hanlder classes), using
	  EMApp

2010-08-05 18:10  ranlin

	* sparx/libpy/applications.py: changed some error logs

2010-08-05 16:31  jkovacs

	* sparx/bin/sxpdb2em.py: Added optional argument tr0. It's the name
	  of a file containing a 3x4 transformation matrix to apply to the
	  pdb prior to generating the EM map

2010-08-05 16:13  gtang

	* rt/pyem/test_imageio.py: add unit test for 16bit and 8bit HDF5
	  I/O

2010-08-05 16:12  gtang

	* rt/pyem/test_processor.py: unit test update

2010-08-05 16:07  gtang

	* libEM/emdata_io.cpp: [no log message]

2010-08-05 15:25  gtang

	* libEM/hdfio2.cpp: [no log message]

2010-08-05 14:39  ross

	* examples/displaydemo.py: using new EMImage2DWidget, EMApp

2010-08-05 14:32  ross

	* libpyEM/EMAN2.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emimage3dslice.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emimage3dvol.py,
	  libpyEM/qtgui/empdbvaltool.py, libpyEM/qtgui/emselector.py,
	  programs/e2cmpxplor.py, programs/e2eulerxplor.py,
	  programs/e2simmxxplor.py, programs/e2workflow.py:
	  EMIsosurfaceModule -> EMIsosurfaceRenderer, EMVolumeModule ->
	  EMVolumeRenderer, EM3DSliceViewerModule -> EM3DSliceRenderer,
	  EM3DSymViewerModule -> EM3DSymRenderer

2010-08-05 14:13  gtang

	* libEM/: emdata_io.cpp, hdfio2.cpp, hdfio2.h: support 16 bit and 8
	  bit HDF5 I/O

2010-08-05 14:13  ross

	* libpyEM/qtgui/emimage3dsym.py: removed event rerouting using
	  EMApp, EMRenderer3D, and EM3DGLWidget

2010-08-04 17:44  zyang

	* sparx/libpy/pixel_error.py: Just change some comments.

2010-08-03 19:30  ross

	* libpyEM/qtgui/emimageutil.py: trivial

2010-08-03 19:29  ross

	* libpyEM/qtgui/: em3Dfonts.py, em3dmodule.py, emanimationutil.py,
	  emapplication.py, emimage2d.py, emimagemx.py, empdbvaltool.py:
	  removing extraneous imports

2010-08-03 19:25  ross

	* libpyEM/qtgui/emglobjects.py: shifting responsibilities between
	  EMRenderer3D and EM3DGLWidget

2010-08-03 14:35  zyang

	* sparx/bin/sxrealignment.py: Merge sxmref_realignment.py and
	  sxisc_realignment.py into this file

2010-08-03 14:02  zyang

	* sparx/: bin/sxisc_realignment.py, libpy/statistics.py: Merge
	  isc_realignment() and mref_realignment() into one program

2010-08-02 15:42  ppenczek

	* libEM/: reconstructor.cpp, sparx/emdata_sparx.cpp: added
	  correction for the fall-off to NN reconstructor

2010-08-01 18:20  zyang

	* sparx/bin/sxmref_realignment.py: Merge sxmref_realignment and
	  sxisc_realignment.py into one program.

2010-07-30 16:51  zyang

	* sparx/libpy/pixel_error.py: Trivial change

2010-07-30 15:43  gtang

	* rt/pyem/test_utils.py: unit test for single attribute read/write
	  routine.

2010-07-30 15:10  gtang

	* libEM/emutil.cpp, libEM/emutil.h, libEM/hdfio2.h,
	  libpyEM/libpyUtils2.cpp: add utility functions to read/write
	  single attribute directly from/into HDF5 file.

2010-07-30 01:37  ross

	* libpyEM/qtgui/emglobjects.py: correction: added
	  EMRenderer3D.set_file_name() not
	  EM3DGLWidget.set_camera_defaults()

2010-07-30 01:35  ross

	* libpyEM/qtgui/emglobjects.py: EMRenderer3D.toggle_cube() and
	  EM3DGLWidget.set_camera_defaults() added

2010-07-30 01:33  ross

	* libpyEM/qtgui/: emimage3diso.py, emimage3dvol.py: set_data() test
	  for EM3DGLWidget in gl_context_parent rather than
	  EMImage3DGeneralWidget

2010-07-30 01:31  ross

	* libpyEM/qtgui/emimage3dslice.py: using EMRenderer3D instead of
	  EMImage3DGUIModule

2010-07-29 19:05  ross

	* libpyEM/qtgui/emimage3dvol.py: using EMRenderer3D instead of
	  EMImage3DGUIModule

2010-07-29 18:06  ppenczek

	* libEM/reconstructor.cpp: formatting

2010-07-29 15:53  jkovacs

	* sparx/libpy/applications.py: changed accuracy in various calls to
	  amoeba from 0.1 to 1e-4; added the application of the input
	  transformation to vol in functions ali_vol_rotate and
	  ali_vol_shift.

2010-07-29 13:41  zyang

	* sparx/libpy/utilities.py: Trivial change.

2010-07-29 11:06  ppenczek

	* sparx/bin/: sxbootstrap_bigdisk.py, sxbootstrap_calcwgts.py,
	  sxbootstrap_genbuf.py, sxbootstrap_run.py, sxbootstrap_smp.py,
	  sxheader.py, sximgstat.py, sxpca.py, sxrecons3d_n.py, sxvar.py,
	  sxvarimax.py: disclaimers updated

2010-07-29 11:03  ppenczek

	* sparx/bin/sxihrsr.py: [no log message]

2010-07-29 10:48  ppenczek

	* sparx/bin/sxihrsr.py: [no log message]

2010-07-29 10:45  ppenczek

	* sparx/libpy/applications.py: pixer in helical

2010-07-29 10:33  ppenczek

	* sparx/libpy/alignment.py: new version of proj_ali_helical

2010-07-29 10:27  gtang

	* libEM/: hdfio2.cpp, hdfio2.h: the write_header() does some job
	  which should be in write_data(). Just shift them into right
	  place. So the header only writing will not handle data writing
	  job.

2010-07-28 11:55  zyang

	* sparx/libpy/pixel_error.py: Just change some comments

2010-07-26 13:13  zyang

	* sparx/libpy/utilities.py: Trivial change

2010-07-26 08:03  stevel

	* libEM/processor.cpp: Minor fix for normalize processor

2010-07-24 23:43  stevel

	* libEM/: emdata_core.cpp, processor.cpp, processor.h: Fixed and
	  renamed normalization filter

2010-07-24 11:12  stevel

	* libpyEM/EMAN2db.py, programs/e2classaverage.py,
	  programs/e2proc2d.py, programs/e2refine.py: better refine2d

2010-07-23 17:23  zyang

	* libEM/sparx/emdata_sparx.cpp: Trivial change

2010-07-23 16:35  zyang

	* libpyEM/typeconverter.cpp: Fix a problem that cause deallocating
	  None

2010-07-23 13:19  zyang

	* libEM/sparx/emdata_sparx.cpp: Delete some curbersome code.

2010-07-23 13:15  stevel

	* libEM/transform.cpp: Fix display of Transforms when alt=180.

2010-07-23 10:06  stevel

	* programs/e2classaverage.py: Fix e2classaverage for threaded
	  parallelism

2010-07-23 09:21  ppenczek

	* sparx/libpy/projection.py: [no log message]

2010-07-23 08:16  stevel

	* libEM/analyzer.cpp, libEM/reconstructor.cpp,
	  programs/e2classaverage.py, programs/e2classifykmeans.py,
	  programs/e2proc2d.py, programs/e2refine2d.py,
	  programs/e2stacksort.py: Fixed problem with e2refine2d.py

2010-07-22 17:54  zyang

	* libEM/: emdata_metadata.cpp, sparx/emdata_sparx.cpp: Fix a memory
	  leak problem.

2010-07-22 17:31  ranlin

	* sparx/libpy/projection.py: [no log message]

2010-07-22 17:11  ranlin

	* sparx/libpy/projection.py: [no log message]

2010-07-22 16:17  ranlin

	* sparx/bin/sxihrsr.py: Trivial change

2010-07-22 12:11  ppenczek

	* sparx/libpy/: applications.py, reconstruction.py: [no log
	  message]

2010-07-22 05:44  ross

	* programs/e2helixboxer.py: more function documentation

2010-07-21 10:22  gtang

	* libEM/processor.h: parameter comment

2010-07-21 10:20  stevel

	* programs/e2simmx2stage.py: Fixed problem with twostage and
	  ralign=None

2010-07-21 10:01  stevel

	* libEM/util.cpp, libpyEM/EMAN2.py, libpyEM/qtgui/emimage2d.py: FFT
	  display issues fixed (again)

2010-07-21 09:01  ppenczek

	* sparx/libpy/fundamentals.py: fixed ;one 499

2010-07-20 12:49  ranlin

	* sparx/libpy/statistics.py: [no log message]

2010-07-20 11:15  ranlin

	* sparx/libpy/morphology.py: [no log message]

2010-07-20 10:58  ranlin

	* sparx/libpy/statistics.py: [no log message]

2010-07-20 08:14  stevel

	* libEM/glutil.cpp, libEM/glutil.h, libpyEM/qtgui/emimage2d.py:
	  Color rendering fixed.

2010-07-19 18:09  ranlin

	* sparx/libpy/morphology.py: [no log message]

2010-07-19 17:13  ranlin

	* sparx/libpy/reconstruction.py: trivial change

2010-07-19 10:48  stevel

	* libpyEM/EMAN2PAR.py, programs/e2make3d.py,
	  programs/e2simmx2stage.py: Improve twostage option. Better
	  distribution of first stage references should produce more
	  accurate classifications. Disbled debugging in DC parallelism.

2010-07-18 22:24  stevel

	* libpyEM/EMAN2db.py: Try to prevent unusual errors in DB update
	  process

2010-07-18 20:27  ppenczek

	* sparx/libpy/applications.py: corrected varmpi

2010-07-18 14:22  gtang

	* programs/e2bdb.py: database cleanup on windows. use 'force' mode.

2010-07-18 13:47  gtang

	* libEM/sparx/util_sparx.cpp: fix for Visual C++ compilation

2010-07-18 11:01  ppenczek

	* sparx/libpy/utilities.py: [no log message]

2010-07-18 01:54  ross

	* libpyEM/qtgui/emboxerbase.py: added auto-centering to manual
	  boxing

2010-07-17 21:12  ross

	* libpyEM/qtgui/emimage3diso.py: removing 3D destop signal
	  rerouting from EMIsosurfaceModule, changing its parent class

2010-07-17 20:53  ross

	* libpyEM/qtgui/emglobjects.py: EM3DGLWidget

2010-07-17 11:19  ranlin

	* sparx/libpy/statistics.py: [no log message]

2010-07-17 11:14  ranlin

	* sparx/libpy/statistics.py: Trivial change

2010-07-17 09:14  ppenczek

	* sparx/libpy/reconstruction.py: [no log message]

2010-07-16 17:56  ross

	* libpyEM/qtgui/emglobjects.py: Renderer3D class

2010-07-16 15:47  ranlin

	* sparx/libpy/fundamentals.py: [no log message]

2010-07-16 14:27  ranlin

	* sparx/libpy/morphology.py: [no log message]

2010-07-16 14:20  ranlin

	* sparx/libpy/morphology.py: [no log message]

2010-07-16 11:41  ppenczek

	* sparx/libpy/: applications.py, reconstruction.py: [no log
	  message]

2010-07-16 10:33  ranlin

	* sparx/libpy/statistics.py: Add center_of_gravity
	  phase_center_of_gravity

2010-07-16 10:30  ppenczek

	* sparx/libpy/__init__.py: [no log message]

2010-07-16 10:29  ranlin

	* sparx/libpy/applications.py: Trivial change.

2010-07-15 17:25  ranlin

	* sparx/libpy/fundamentals.py: [no log message]

2010-07-15 16:28  ranlin

	* sparx/libpy/fundamentals.py: [no log message]

2010-07-15 14:12  stevel

	* libEM/symmetry.cpp, libEM/symmetry.h, libpyEM/EMAN2PAR.py,
	  programs/e2classaverage.py, programs/e2parallel.py,
	  programs/e2project3d.py, programs/e2refine.py,
	  programs/e2refine2d.py, programs/e2simmx.py,
	  programs/e2tomoaverage.py: Threaded parallelism !!!

2010-07-15 12:16  gtang

	* rt/pyem/test_processor.py: [no log message]

2010-07-15 10:41  ranlin

	* sparx/libpy/: fundamentals.py: [no log message]

2010-07-15 10:14  ppenczek

	* sparx/templates/import_SPIDER_320.py: [no log message]

2010-07-15 10:09  ranlin

	* sparx/libpy/applications.py: [no log message]

2010-07-15 08:31  stevel

	* libEM/processor.cpp: Minor improvement

2010-07-15 08:17  stevel

	* libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libEM/processor.cpp, libEM/processor.h, libpyEM/EMAN2PAR.py,
	  programs/e2eulerxplor.py, programs/e2parallel.py: New
	  segmentation for Matt. Still working on new parallelism option,
	  but at least doesn't seem to crash.

2010-07-14 17:34  zyang

	* sparx/libpy/applications.py: Trivial change.

2010-07-14 12:03  ppenczek

	* sparx/libpy/applications.py: remove not needed code

2010-07-14 11:47  zyang

	* sparx/libpy/applications.py: Trivial change.

2010-07-14 10:59  ranlin

	* sparx/libpy/applications.py: [no log message]

2010-07-13 16:18  ross

	* programs/e2boxer.py: uses EMApp

2010-07-13 16:17  ross

	* libpyEM/qtgui/emapplication.py: EMApp.execute()

2010-07-13 16:16  ross

	* libpyEM/qtgui/emboxerbase.py: uses EMApp and new EMImage2DWidget

2010-07-13 14:25  ranlin

	* sparx/bin/sxpca.py: [no log message]

2010-07-13 13:54  ranlin

	* sparx/bin/sxk_means.py: [no log message]

2010-07-13 13:36  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2010-07-13 11:56  ranlin

	* sparx/bin/sxfind_struct.py: [no log message]

2010-07-13 10:51  gtang

	* examples/: clstoclsmx.py, sizes.py: [no log message]

2010-07-13 10:41  ranlin

	* sparx/bin/sxbootstrap_calcwgts.py: [no log message]

2010-07-13 10:31  ranlin

	* sparx/bin/sxbootstrap_bigdisk.py: [no log message]

2010-07-12 17:16  ranlin

	* sparx/bin/sxmref_ali3d.py: [no log message]

2010-07-12 16:11  ranlin

	* sparx/bin/sxali3d.py: [no log message]

2010-07-12 15:53  ppenczek

	* sparx/libpy/statistics.py: [no log message]

2010-07-12 15:49  ranlin

	* sparx/bin/sxali3d.py: [no log message]

2010-07-12 13:02  ppenczek

	* sparx/libpy/development.py: [no log message]

2010-07-12 11:56  ranlin

	* sparx/bin/sxali2d.py: [no log message]

2010-07-11 12:49  stevel

	* libEM/reconstructor.cpp: Working on reconstructing from Wiener
	  filtered averages

2010-07-09 13:49  zyang

	* sparx/libpy/: applications.py, pixel_error.py: Trivial change.

2010-07-09 12:11  gtang

	* libpyEM/libpyEMData2.cpp: revert the change, fix the memory leak
	  later.

2010-07-09 11:49  stevel

	* libEM/averager.cpp: Tweak snr cutoff in averager.

2010-07-09 11:34  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-07-09 10:35  stevel

	* libpyEM/EMAN2PAR.py: typo

2010-07-09 10:33  stevel

	* libpyEM/EMAN2PAR.py, programs/e2parallel.py, programs/e2simmx.py:
	  Oops. Need to keep client id's constant...

2010-07-09 09:50  stevel

	* libpyEM/qtgui/emsprworkflow.py: Add option for new reconstructor.

2010-07-09 09:19  stevel

	* libEM/: reconstructor.cpp, symmetry.cpp: New weiner_fourier
	  reconstructor seems to be working.

2010-07-09 08:35  stevel

	* programs/e2parallel.py: typo

2010-07-09 08:22  stevel

	* libEM/reconstructor.cpp, libEM/reconstructor.h, libEM/util.h,
	  libpyEM/EMAN2PAR.py, programs/e2parallel.py: Potential patch for
	  memory leak in client.

2010-07-08 23:00  stevel

	* libEM/: emobject.cpp, emobject.h: Memory debugging

2010-07-08 17:01  zyang

	* sparx/bin/sxali2d.py: Trivial change.

2010-07-08 15:38  ppenczek

	* sparx/libpy/: applications.py, reconstruction.py: added printout
	  of parameters to ihrsr

2010-07-08 15:00  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-07-08 14:31  gtang

	* rt/pyem/test_imageio.py: unit tests for HDF5 attributes I/O

2010-07-08 13:10  gtang

	* libEM/hdfio2.cpp: Support boolean attribute I/O for hdf5 file.

2010-07-08 12:00  stevel

	* programs/e2make3d.py: Lowmem fix

2010-07-08 09:58  stevel

	* libEM/averager.cpp: Fixes for new averager

2010-07-08 09:27  stevel

	* libEM/averager.cpp: Trivial

2010-07-08 09:19  stevel

	* libEM/: averager.cpp, averager.h: New averager for CTF correction
	  without Wiener filter. New header parameters for averagers.

2010-07-07 22:16  ppenczek

	* sparx/libpy/: statistics.py, user_functions.py: [no log message]

2010-07-07 18:18  gtang

	* libpyEM/libpyCmp2.cpp: overload XYData::get_yatx()

2010-07-07 14:44  stevel

	* libEM/: emobject.cpp, emobject.h: Adding some MEMDEBUG
	  capabilities

2010-07-07 13:25  gtang

	* libpyEM/libpyEMData2.cpp: use set_attr() to avoid memory leak.

2010-07-07 11:22  zyang

	* sparx/: bin/sxisc_realignment.py, libpy/applications.py: [no log
	  message]

2010-07-07 10:58  zyang

	* sparx/bin/sxrecons3d_n.py: [no log message]

2010-07-07 09:10  stevel

	* libEM/reconstructor.cpp, programs/e2iminfo.py,
	  programs/e2make3d.py: Significant fix to make3d normalization,
	  etc.	Still testing, but pretty sure it's improved.

2010-07-07 07:16  stevel

	* libEM/symmetry.cpp, libEM/symmetry.h, programs/e2iminfo.py,
	  programs/e2make3d.py: Major fix for make3d when keep !=1

2010-07-06 18:07  fjia

	* sparx/: libpy/applications.py, libpy/statistics.py,
	  bin/sxisc_realignment.py: [no log message]

2010-07-06 11:37  zyang

	* libEM/: aligner.cpp, sparx/rsconvolution.cpp: Clear up some
	  warnings

2010-07-06 11:15  zyang

	* libEM/: cmp.cpp, emdata_transform.cpp, hdfio2.cpp, processor.cpp,
	  reconstructor_tools.cpp, util.cpp, gorgon/skeletonizer.cpp,
	  gorgon/volume.cpp, sparx/util_sparx.cpp: Clean up all the
	  warnings

2010-07-05 18:53  ppenczek

	* sparx/libpy/: applications.py: [no log message]

2010-07-05 18:29  ppenczek

	* libEM/sparx/util_sparx.cpp, sparx/libpy/reconstruction.py,
	  sparx/libpy/statistics.py: [no log message]

2010-07-05 16:45  ppenczek

	* sparx/libpy/alignment.py: changed params in helicise

2010-07-02 22:48  stevel

	* programs/e2make3d.py: debug e2make3d

2010-07-02 16:59  ranlin

	* sparx/libpy/fundamentals.py: Add comments

2010-07-02 16:15  fjia

	* sparx/libpy/statistics.py: [no log message]

2010-07-02 15:13  zyang

	* sparx/: bin/sxali2d.py, bin/sxali2d_c.py, bin/sxali2d_e.py,
	  bin/sxali2d_m.py, bin/sxali3d.py, bin/sxali3d_d.py,
	  bin/sxali3d_e.py, bin/sxali3d_m.py, bin/sxlocal_ali2d.py,
	  bin/sxlocal_ali3d.py, bin/sxmref_ali2d.py, bin/sxmref_ali3d.py,
	  demo/1_bdb/run_through_example,
	  demo/3_bdb_ctf/run_through_example,
	  demo/5_mpi_bdb/run_through_example,
	  demo/7_mpi_bdb_ctf/run_through_example, libpy/applications.py,
	  libpy/statistics.py: Change names of all alignment programs

2010-07-02 14:39  ranlin

	* sparx/libpy/filter.py: Add comment

2010-07-02 11:45  zyang

	* sparx/bin/: sxrefvol.py, sxincpca.py, sxincvar.py, sxali_vol.py:
	  [no log message]

2010-07-02 11:43  zyang

	* sparx/bin/: sxali2d_a.py, sxali2d_b.py, sxali2d_cls_mref.py,
	  sxali2d_cross_res.py, sxali2d_ra.py, sxali2d_rac.py,
	  sxali2d_reduce.py, sxali2d_w.py, sxali2d_w_mf.py, sxali3d_b.py,
	  sxali3d_em.py, sxali3d_f.py, sxali_SSNR.py, sxali_vol.py,
	  sxaliunified.py, sxanghist.py, sxapply_ali_params.py,
	  sxauto_picking.py, sxcmlines_optall.py, sxdefocus_calc.py,
	  sxdefvar.py, sxdele_alist.py, sxfactcoords.py, sxnormal_prj.py,
	  sxpufit.py, sxra_cef.py, sxselect_even.py, sxstat_even.py,
	  sxtomo.py, sxwelch_psp.py, sxwelch_psp_tilt.py: Some old and
	  obselete command line programs, move them to
	  project_info/obselete, look there in case you need it.

2010-07-02 10:12  ranlin

	* sparx/libpy/filter.py: add help function

2010-07-02 00:04  stevel

	* programs/e2project3d.py: Doc update

2010-07-01 15:02  ranlin

	* sparx/libpy/applications.py:
	  change the way error called

2010-07-01 14:56  ranlin

	* sparx/bin/: sxrecons3d_n.py, sxssnr3d.py: Add MPI finalize

2010-07-01 14:53  ranlin

	* sparx/bin/sxrecons3d_f.py: Add MPI finalize

2010-07-01 14:46  ranlin

	* sparx/bin/sxpca.py: Add MPI finalize

2010-07-01 14:05  ranlin

	* sparx/bin/sxdefvar.py: Add MPI finalize

2010-07-01 13:50  ranlin

	* sparx/bin/sxauto_picking.py: Add MPI finalize

2010-07-01 11:47  ranlin

	* sparx/libpy/applications.py: Change the way error called

2010-07-01 11:34  ranlin

	* sparx/bin/sxk_means_stable.py: Add MPI finalize

2010-07-01 11:29  ranlin

	* sparx/bin/sxnormal_prj.py: Add MPI finalize

2010-07-01 11:21  ranlin

	* sparx/bin/sxali3d_m.py: Add MPI finalize

2010-07-01 11:10  ranlin

	* sparx/bin/sxvar.py: Add MPI finalize

2010-07-01 11:06  ranlin

	* sparx/bin/sxbootstrap_bigdisk.py: Add MPI finalize

2010-07-01 10:54  ranlin

	* sparx/bin/sxbootstrap_calcwgts.py: Add MPI finalize

2010-07-01 10:49  ranlin

	* sparx/bin/sxali3d_e.py: add MPI finalize

2010-07-01 10:44  ranlin

	* sparx/bin/sxparams_2D_to_3D.py: delete MPI finalize

2010-07-01 10:40  ranlin

	* sparx/bin/sxk_means.py: Add MPI finalize

2010-07-01 10:27  ranlin

	* sparx/bin/sxali3d_d.py: Add MPI finalize

2010-07-01 10:18  ranlin

	* sparx/bin/sxparams_2D_to_3D.py: Add MPI finalize

2010-07-01 10:12  ranlin

	* sparx/bin/sxrecons3d_n.py: add MPI finalize

2010-07-01 09:51  zyang

	* sparx/libpy/global_def.py: Trival change

2010-07-01 09:20  ppenczek

	* sparx/libpy/reconstruction.py: [no log message]

2010-07-01 08:56  ppenczek

	* sparx/libpy/reconstruction.py: [no log message]

2010-06-30 17:12  ranlin

	* sparx/bin/sxfind_struct.py: [no log message]

2010-06-30 17:04  ppenczek

	* sparx/libpy/: applications.py, reconstruction.py, utilities.py:
	  [no log message]

2010-06-30 16:56  ranlin

	* sparx/bin/sxali2d_m.py: [no log message]

2010-06-30 16:35  ranlin

	* sparx/bin/sxk_means.py: add MPI finalize()

2010-06-30 16:25  ranlin

	* sparx/bin/sxali2d_c.py: [no log message]

2010-06-30 15:56  zyang

	* sparx/: bin/sxali2d_c.py, libpy/applications.py,
	  libpy/global_def.py: MPI program exits on all nodes

2010-06-30 12:46  ppenczek

	* sparx/libpy/statistics.py: [no log message]

2010-06-30 10:07  ppenczek

	* sparx/libpy/reconstruction.py: unblock filt gaussl

2010-06-29 15:03  zyang

	* sparx/libpy/applications.py: [no log message]

2010-06-29 14:53  ppenczek

	* sparx/libpy/sparx.py: added development

2010-06-29 13:20  ppenczek

	* sparx/libpy/: reconstruction.py, statistics.py: [no log message]

2010-06-28 17:12  ppenczek

	* sparx/: bin/sxvar.py, libpy/applications.py: [no log message]

2010-06-26 07:06  ppenczek

	* sparx/: bin/sxvar.py, libpy/applications.py,
	  libpy/reconstruction.py: [no log message]

2010-06-25 15:55  zyang

	* sparx/: libpy/applications.py, bin/sxali2d_c.py,
	  bin/sxmref_alignment.py, bin/sxmref_realignment.py: Change the
	  way of setting GPU ID.

2010-06-24 17:17  ross

	* libpyEM/qtgui/emplot2d.py: removing 3D desktop: merged
	  EMPlot2DWidget and Module, using EMApp

2010-06-24 05:56  stevel

	* libEM/processor.cpp, libEM/xydata.cpp, libEM/xydata.h,
	  programs/e2classaverage.py, programs/e2ctf.py: New masking method
	  on class-average. CTF structure factor now includes sharp peak
	  near origin

2010-06-23 07:17  stevel

	* libpyEM/EMAN2db.py, programs/e2classifyligand.py,
	  programs/e2evalrefine.py, programs/e2make3d.py,
	  programs/e2proc3d.py, programs/e2refinevariance.py: Minor tweaks.
	  refinevariance improved, but still testing

2010-06-22 17:28  ross

	* libpyEM/qtgui/emimagemx.py: removing 3D desktop: EMImageMXWidget
	  and EMImageMXModule combined into EMImageMXWidget class, using
	  EMApp

2010-06-21 13:18  zyang

	* sparx/libpy/pixel_error.py: [no log message]

2010-06-21 11:18  zyang

	* sparx/libpy/pixel_error.py: Add function ali_stable_list()

2010-06-21 05:19  ppenczek

	* sparx/libpy/reconstruction.py, libEM/sparx/util_sparx.cpp: more
	  on pca

2010-06-19 05:07  ppenczek

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, sparx/libpy/applications.py,
	  sparx/libpy/reconstruction.py: work on pca

2010-06-17 20:11  ross

	* libpyEM/qtgui/emimage2d.py: trivial

2010-06-16 17:38  zyang

	* sparx/libpy/pixel_error.py: Add two new functions

2010-06-15 22:15  ross

	* libpyEM/qtgui/emimage2d.py: removed mouse handler classes and put
	  functionality in EMImage2DWidget

2010-06-15 17:38  stevel

	* programs/e2refinevariance.py: Fix for refinevariance

2010-06-15 15:49  ross

	* programs/e2.py: replacing EMStandAloneApplication with EMApp

2010-06-15 15:12  zyang

	* sparx/libpy/pixel_error.py: Add function align_diff_textfile()
	  and ave_ali_err_textfile()

2010-06-15 10:54  zyang

	* sparx/libpy/: applications.py, morphology.py, statistics.py,
	  utilities.py: Change read_txt_col() to read_text_row() (the name
	  is otherwise inconsistent with its contents), and change
	  write_text_rows() to write_text_row() to be more name consistent.

2010-06-15 08:40  stevel

	* programs/e2refinevariance.py: Fixed problem with shrinking
	  refinevariance

2010-06-14 18:23  zyang

	* sparx/libpy/: __init__.py, alignment.py, applications.py,
	  pixel_error.py, sparx.py, statistics.py, utilities.py: Move
	  everything relating to pixel error to a new file pixel_error.py.
	  Otherwise, they are scattered all over the place and cause a lot
	  of confusion and duplication.

2010-06-14 15:53  gtang

	* libEM/: processor.cpp, sparx/emdata_sparx.cpp: fix warnings on
	  Visual C++ 2008

2010-06-14 15:32  stevel

	* programs/e2refinevariance.py: New options for refinevariance

2010-06-14 15:04  gtang

	* libEM/sparx/: emdata_sparx.cpp, fourierfilter.cpp,
	  util_sparx.cpp: change _MIN =>_cpp_min,  _MAX=>_cpp_max to make
	  it compilable on visual c++ 2008.

2010-06-11 13:24  ppenczek

	* sparx/bin/sxvar.py: [no log message]

2010-06-11 11:37  ppenczek

	* sparx/: bin/sxvar.py, libpy/applications.py: [no log message]

2010-06-11 01:13  ross

	* libpyEM/qtgui/emimage2d.py: removed custom defined
	  EMImage2DWidget.setWindowTitle(), to use default PyQt one.

2010-06-11 01:08  ross

	* libpyEM/qtgui/emapplication.py: extend EMGLWidget.resize() to
	  modify its EMParentWin member's size also

2010-06-10 15:11  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, util_sparx.cpp: corrections of
	  wbp code

2010-06-09 12:11  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-06-08 20:01  ross

	* libpyEM/qtgui/emimage2d.py: removed old EMImage2DWidget, renamed
	  EMImage2DModule to EMImage2DWidget

2010-06-08 17:48  ross

	* libpyEM/qtgui/emimage2d.py: fixed display issue by using the
	  default height() and width() functions in EMImage2DModule.
	  Overriding them is no longer needed.

2010-06-08 17:42  ross

	* libpyEM/qtgui/emapplication.py: added EMApp.child_is_attached()

2010-06-08 09:12  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-06-05 10:12  stevel

	* libpyEM/qtgui/: emselector.py, emsprworkflow.py: Fix coordinate
	  import

2010-06-05 04:50  stevel

	* .project, libpyEM/qtgui/emselector.py: sort in browser

2010-06-04 19:29  ross

	* libpyEM/qtgui/emimage2d.py: basing EMImage2DModule on new
	  EMGLWidget class and bringing in EMImage2DWidget code to
	  EMImage2DModule

2010-06-04 19:26  ross

	* libpyEM/qtgui/emapplication.py: EMApp class and EMGLWidget class

2010-06-03 17:28  zyang

	* sparx/libpy/applications.py: [no log message]

2010-06-03 16:47  zyang

	* sparx/libpy/applications.py: [no log message]

2010-06-03 16:18  gtang

	* .cdtproject, .cproject, .project: [no log message]

2010-06-03 11:23  zyang

	* sparx/bin/: sxmref_alignment.py, sxmref_realignment.py: [no log
	  message]

2010-06-02 14:29  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-06-02 13:37  ppenczek

	* sparx/libpy/: alignment.py, applications.py: [no log message]

2010-06-02 13:22  zyang

	* sparx/bin/: sxmref_alignment.py, sxmref_realignment.py: [no log
	  message]

2010-06-01 13:45  zyang

	* libEM/sparx/cuda/cuda_ccf.cu, sparx/bin/sxmulti_assign.py: [no
	  log message]

2010-06-01 10:01  stevel

	* programs/: e2classaverage.py, e2refinevariance.py: One more tweak
	  on variance

2010-05-31 21:56  stevel

	* libpyEM/EMAN2db.py: Increase logging region size.

2010-05-31 20:48  stevel

	* programs/e2refinevariance.py: Ok, ready for final testing.

2010-05-31 00:37  stevel

	* libpyEM/qtgui/emsprworkflow.py, programs/e2refine.py,
	  programs/e2refinevariance.py: Working on variance maps

2010-05-30 00:58  stevel

	* libEM/reconstructor.h: doc fix

2010-05-27 17:04  mingc

	* libEM/symmetry.h: add "nstart"

2010-05-27 17:03  mingc

	* libEM/symmetry.cpp: add one parameter to helical symmetry

2010-05-27 16:11  stevel

	* programs/: e2initialmodel.py, e2refinevariance.py: First version
	  of new program to compute Penczek-style variance maps in eman2.

2010-05-27 15:14  zyang

	* sparx/: bin/sxali2d_c.py, bin/sxmref_alignment.py,
	  libpy/applications.py: [no log message]

2010-05-27 11:34  stevel

	* programs/e2classaverage.py: again

2010-05-27 11:22  stevel

	* programs/e2classaverage.py: Still working on resample

2010-05-27 09:54  stevel

	* programs/e2classaverage.py: another trivial fix

2010-05-27 09:42  stevel

	* programs/e2classaverage.py: oops

2010-05-27 09:39  stevel

	* programs/e2classaverage.py: New option for variance maps in
	  e2classaverage.py

2010-05-27 08:57  stevel

	* libpyEM/EMAN2db.py, programs/e2classaverage.py,
	  programs/e2eulerxplor.py: Nasty bug in reading virtual stacks.

2010-05-26 16:50  mingc

	* libEM/symmetry.cpp: helical symmetry

2010-05-26 10:37  stevel

	* programs/e2parallel.py: minor fix

2010-05-25 11:38  gtang

	* libpyEM/EMAN2.py: set_emdata_array(img, array) will set EMData's
	  data array with a list of float in Pyhton.

2010-05-25 10:54  ppenczek

	* sparx/libpy/statistics.py: [no log message]

2010-05-25 09:24  stevel

	* libpyEM/qtgui/emsprworkflow.py: More boxer output options

2010-05-24 22:32  ross

	* programs/e2boxer.py: made SwarmTool the default :
	  ----------------------------------------------------------------------

2010-05-24 19:12  gtang

	* programs/e2proc3d.py: fix "sym" option

2010-05-24 18:55  gtang

	* libEM/util.h: goodf() always fails for double on vc++. Fix it
	  with VC's function.

2010-05-24 15:19  zyang

	* sparx/bin/sxmref_alignment.py: [no log message]

2010-05-24 15:13  gtang

	* CMakeLists.txt: change the ENABLE_AUTODOC to a common option.

2010-05-24 14:21  gtang

	* libEM/symmetry.cpp: fix a bug for sym.gen_orientations(). It's
	  because the parameter in get_delimiters() are saved as doubles,
	  when withdraw them as float it returns 0.

2010-05-24 13:53  ppenczek

	* sparx/libpy/applications.py: restore ctf_applied in ihrsr

2010-05-24 12:15  stevel

	* programs/e2make3d.py: More fixes for 'bad' averages

2010-05-24 10:57  stevel

	* programs/e2make3d.py: Fix for make3d with bad class-averages

2010-05-24 10:30  stevel

	* libpyEM/qtgui/emsprworkflow.py: trivial

2010-05-24 10:29  stevel

	* libpyEM/qtgui/emsprworkflow.py, programs/e2ctf.py: Minor tweaks

2010-05-23 19:24  ppenczek

	* sparx/bin/sxali3d_d.py: [no log message]

2010-05-23 10:12  hauser

	* sparx/libpy/: applications.py, statistics.py, utilities.py:
	  Convert the rest of Numeric usages to numpy.

2010-05-21 15:40  ross

	* libpyEM/qtgui/emapplication.py: added EMGLWidget

2010-05-21 15:12  stevel

	* libEM/aligner.cpp, libpyEM/EMAN2.py: Prevent crash when refine
	  align operates on empty image

2010-05-21 14:34  ross

	* libpyEM/qtgui/emimageutil.py: test commit (added newline at end):
	  should only commit to remove_e2desktop_event_rerouting_branch

2010-05-21 14:21  ppenczek

	* sparx/libpy/: applications.py, utilities.py: [no log message]

2010-05-21 07:01  stevel

	* programs/e2simmx.py: Another issue causing problems in
	  e2refine2d.py

2010-05-20 14:44  zyang

	* sparx/bin/sxmref_alignment.py: [no log message]

2010-05-20 11:22  stevel

	* libEM/cmp.cpp, libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emimagemx.py, programs/e2classaverage.py,
	  programs/e2cmpxplor.py, programs/e2simmx.py,
	  programs/e2simmxxplor.py: Several major bugfixes. Refine2d.py
	  working again. --prefilt now working properly.  sqeuclidean
	  comparator without zeromask working better (maybe)

2010-05-20 11:04  mingc

	* libEM/symmetry.h: trivial

2010-05-20 10:01  ross

	* programs/e2helixboxer.py: EMWriteHelixFiles ->
	  EMWriteHelixFilesDialog, moved main() to be first function
	  defined, added some missing docstrings

2010-05-19 20:39  ppenczek

	* sparx/bin/sxvarimax.py: [no log message]

2010-05-19 13:12  stevel

	* libpyEM/EMAN2db.py, programs/e2bdb.py: Added --check option to
	  e2bdb.py to verify databases

2010-05-19 08:48  stevel

	* libpyEM/EMAN2.py, libpyEM/EMAN2db.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2classifyligand.py,
	  programs/e2simmxxplor.py: Make workflow output single-threaded.
	  Minor bugfixes.

2010-05-18 14:51  zyang

	* sparx/bin/sxmref_realignment.py: [no log message]

2010-05-18 14:38  gtang

	* libpyEM/EMAN2db.py: The key is not lower() in the database.

2010-05-17 16:09  ross

	* libpyEM/qtgui/emapplication.py: removed EventsEmittorAndReceiver

2010-05-17 16:08  ross

	* libpyEM/qtgui/emglobjects.py: removed EMEventsEmittorAndReceiver

2010-05-16 17:50  ppenczek

	* sparx/bin/: sxk_means.py, sxk_means_groups.py: [no log message]

2010-05-16 14:23  ross

	* libpyEM/qtgui/emimageutil.py: removed EventsEmitterAndReciever
	  class

2010-05-14 12:54  ppenczek

	* sparx/bin/: sxincpca.py, sxnormal_prj.py: [no log message]

2010-05-13 12:18  stevel

	* doc/index.html: doc fix

2010-05-12 09:32  stevel

	* libEM/cmp.cpp, programs/e2classaverage.py,
	  programs/e2classify.py: No infinities in sqeuclidean

2010-05-10 17:31  zyang

	* sparx/bin/: sxali2d_mref.py, sxisc_realignment.py: [no log
	  message]

2010-05-07 11:57  zyang

	* sparx/bin/sxmulti_assign.py: Trivial change

2010-05-06 07:48  stevel

	* programs/: e2classaverage.py, e2eotest.py, e2refine.py,
	  e2simmx.py: Fixed prefilt a bit

2010-05-05 18:08  zyang

	* sparx/bin/sxmulti_assign.py: Some adjustment

2010-05-04 17:07  zyang

	* sparx/bin/: sxali2d_mref.py, sxmulti_assign.py: Add two new
	  programs (not finished yet)

2010-05-04 13:56  zyang

	* sparx/bin/: sxali2d_c.py, sxali2d_cls_mref.py,
	  sxali2d_cross_res.py, sxali2d_e.py, sxali2d_m.py, sxali2d_ra.py,
	  sxali2d_rac.py, sxali2d_reduce.py, sxali2d_w.py, sxali2d_w_mf.py,
	  sxali3d_b.py, sxali3d_d.py, sxali3d_e.py, sxali3d_em.py,
	  sxali3d_f.py, sxali3d_m.py, sxali_SSNR.py, sxali_vol.py,
	  sxaliunified.py, sxapply_ali_params.py, sxauto_picking.py,
	  sxave_ali.py, sxboxer.py, sxcopyfromtif.py, sxcpy.py, sxctf.py,
	  sxdefocus_calc.py, sxdele_alist.py, sxfind_struct.py,
	  sxhac_averages.py, sxhac_clustering.py, sxihrsr.py, sxisc.py,
	  sxisc_realignment.py, sxk_means.py, sxk_means_groups.py,
	  sxk_means_stable.py, sxparams_2D_to_3D.py, sxparams_3D_to_2D.py,
	  sxpdb2em.py, sxplot_projs_distrib.py, sxprepare_2d_forPCA.py,
	  sxproject3d.py, sxpufit.py, sxra_cef.py, sxrecons3d_f.py,
	  sxrecons3d_n.py, sxrot_sym.py, sxssnr3d.py, sxtransform2d.py,
	  sxwelch_psp.py, sxwelch_psp_tilt.py: Trivial change.

2010-05-03 11:45  gtang

	* CMakeLists.txt: [no log message]

2010-05-02 20:49  gtang

	* libpyEM/EMAN2.py: fix a bug on windows, force num_cpus() return
	  an int instead of a string

2010-04-30 11:57  stevel

	* libpyEM/qtgui/: emsprworkflow.py, emtprworkflow.py: Doc updates

2010-04-30 09:53  stevel

	* programs/: e2cmpxplor.py, e2simmx.py: Include masking in prefilt

2010-04-30 09:37  stevel

	* libEM/processor.cpp, libpyEM/qtgui/emimage2d.py,
	  programs/e2cmpxplor.py: Fixed serious matched filter problem

2010-04-30 07:14  stevel

	* programs/e2classaverage.py: Sigh

2010-04-30 07:13  stevel

	* programs/e2classaverage.py: another oops

2010-04-30 07:11  stevel

	* programs/e2classaverage.py: oops

2010-04-30 07:07  stevel

	* programs/e2classaverage.py: Normalization fixes in
	  class-averaging

2010-04-30 06:36  stevel

	* libEM/cmp.cpp: Better normto option on sqeuclidean comparator

2010-04-29 13:42  stevel

	* libEM/emdata_metadata.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/qtgui/emimagemx.py: Change threshold for center of mass
	  calculation. A bit uneasy about this being called center of mass,
	  since it has never truly been this  :^(

2010-04-29 11:12  gtang

	* libEM/processor.cpp: print out in DEBUG mode

2010-04-29 11:12  gtang

	* rt/pyem/test_processor.py: minor fix

2010-04-28 16:46  zyang

	* sparx/libpy/applications.py: [no log message]

2010-04-28 16:03  stevel

	* libpyEM/EMAN2db.py, programs/e2bdb.py, programs/e2refine2d.py: A
	  few more tweaks.

2010-04-28 14:34  zyang

	* sparx/libpy/applications.py: Trivial

2010-04-28 14:31  zyang

	* sparx/libpy/alignment.py: trivial

2010-04-28 14:30  zyang

	* sparx/libpy/: alignment.py, applications.py, statistics.py: Add
	  delta to non-CUDA code. change aves_adw()

2010-04-28 13:39  stevel

	* libEM/processor.cpp, libEM/processor.h,
	  programs/e2classaverage.py, programs/e2initialmodel.py,
	  programs/e2refine2d.py: New automask 2d processor. Better
	  centering for e2refine2d and class averages for neg stain.

2010-04-27 22:23  stevel

	* libpyEM/qtgui/emimage2d.py: Fixed display of 2d images using NX.
	  Better contrast in power spectra.

2010-04-27 20:32  stevel

	* libpyEM/emdata_wrapitems.cpp, programs/e2ctf.py: Defocus range
	  fix

2010-04-27 14:13  zyang

	* libEM/cmp.cpp: Fix a small bug

2010-04-27 13:11  zyang

	* sparx/bin/sxali2d_a.py: [no log message]

2010-04-27 10:53  zyang

	* sparx/bin/sxali2d_a.py: [no log message]

2010-04-26 21:56  ross

	* libpyEM/qtgui/emimage2d.py: EMImage2DModule.scr_to_img() and
	  img_to_scr() updated to work with centering fix.

2010-04-26 14:56  zyang

	* sparx/libpy/applications.py: fix a small error

2010-04-26 13:38  fjia

	* sparx/bin/sxisc_realignment.py: [no log message]

2010-04-26 13:30  fjia

	* sparx/libpy/statistics.py: [no log message]

2010-04-26 13:20  zyang

	* sparx/libpy/applications.py: Switch back to old CTF corrrection,
	  but store different average image.

2010-04-26 13:18  zyang

	* sparx/bin/sxali2d_c.py: [no log message]

2010-04-24 21:58  stevel

	* libEM/cmp.cpp: Back to original method.

2010-04-23 22:10  stevel

	* libEM/cmp.cpp: Swap normto in sqeuclidean

2010-04-23 19:55  gtang

	* libEM/sparx/fourierfilter.cpp: quick fix

2010-04-23 16:37  ross

	* libpyEM/qtgui/emboxerbase.py: ComboBox to switch between boxing
	  tools, rather than tabs. Fixed a mode switching bug when clicking
	  on EMImageMX thumbnail of an added type, such as "Swarm".

2010-04-23 16:21  ppenczek

	* libEM/sparx/fourierfilter.cpp: [no log message]

2010-04-23 16:09  stevel

	* libEM/cmp.cpp, libEM/cmp.h, libEM/processor.h,
	  programs/e2simmx2stage.py: Additions to sqeuclidean processor.

2010-04-23 14:15  fjia

	* sparx/libpy/applications.py: [no log message]

2010-04-23 13:43  fjia

	* sparx/libpy/applications.py: [no log message]

2010-04-23 13:42  stevel

	* libEM/: cmp.cpp, cmp.h: New option for sqequclidean

2010-04-23 12:47  fjia

	* sparx/libpy/applications.py: [no log message]

2010-04-23 12:39  fjia

	* sparx/libpy/applications.py: [no log message]

2010-04-23 06:51  stevel

	* programs/: e2refine.py, e2simmx2stage.py: oops

2010-04-22 16:00  gtang

	* libEM/CMakeLists.txt: Fix a bug when ENABLE_OPENGL to OFF, should
	  not ask for installing libGLEM2 library.

2010-04-22 15:39  gtang

	* doc/CMakeLists.txt, rt/pyem/CMakeLists.txt: The MAKE_DIRECTORY
	  call seems redundant.

2010-04-22 15:15  stevel

	* examples/redo_convergence.py: Added command for recomputing
	  convergence plots properly

2010-04-21 14:57  stevel

	* libpyEM/qtgui/: emimage3d.py, emimagemx.py: Fix updating a bit
	  more. Still not 100% on matrix

2010-04-21 14:12  ppenczek

	* sparx/libpy/projection.py: [no log message]

2010-04-21 14:07  ppenczek

	* sparx/libpy/projection.py: [no log message]

2010-04-21 13:38  ppenczek

	* sparx/libpy/projection.py: [no log message]

2010-04-21 12:54  stevel

	* libpyEM/qtgui/: emimage.py, emimage2d.py, emimage3d.py,
	  emimagemx.py: Fixed updating in e2.py

2010-04-20 15:57  zyang

	* sparx/libpy/applications.py: Trivial change

2010-04-20 15:28  ppenczek

	* sparx/libpy/: applications.py, projection.py: [no log message]

2010-04-19 21:28  irees

	* programs/e2boxer.py: Fixed problem writing .box coord files;
	  "box_size" should have been "options.boxsize"

2010-04-19 16:35  gtang

	* libEM/: imagicio2.cpp, imagicio2.h: New IMAGIC-4D format I/O. Not
	  finished yet.

2010-04-16 16:04  zyang

	* sparx/bin/sxali2d_a.py: [no log message]

2010-04-16 11:27  zyang

	* sparx/libpy/applications.py: Minor change to the ali2d_c(_MPI)

2010-04-15 17:15  gtang

	* libpyEM/EMAN2db.py: advised by Alexander Heyne
	  <AHEYNE@fmp-berlin.de>. Use USERPROFILE on windows when HOMEPATH
	  point to c:\ drive.

2010-04-15 16:53  ross

	* libpyEM/qtgui/emimage2d.py: The image data doesn't really center
	  when you zoom in, which would take a lot to change. Instead, I
	  hacked the centering of EMShapes to behave the same way.

2010-04-15 10:17  stevel

	* libpyEM/: EMAN2db.py, qtgui/emsprworkflow.py: Better error
	  reporting for database issues.

2010-04-12 10:42  zyang

	* sparx/libpy/applications.py: Trivial change

2010-04-11 00:59  stevel

	* programs/e2refine.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2simmx.py, programs/e2simmx2stage.py: New prefilt
	  option

2010-04-10 18:21  ross

	* libpyEM/qtgui/emimage2d.py: EMImage2DModule.render_bitmap()
	  centering fix.

2010-04-10 14:34  fjia

	* sparx/libpy/statistics.py: [no log message]

2010-04-09 17:42  zyang

	* sparx/libpy/statistics.py: [no log message]

2010-04-09 17:36  zyang

	* sparx/: bin/sxali2d_c.py, libpy/applications.py: Add dst as a
	  parameter of ali2d_c(_MPI)

2010-04-09 17:08  fjia

	* sparx/libpy/applications.py: [no log message]

2010-04-09 16:19  zyang

	* sparx/libpy/: applications.py, statistics.py: Change the new CTF
	  correction

2010-04-08 15:00  fjia

	* sparx/libpy/applications.py: [no log message]

2010-04-04 02:06  stevel

	* libpyEM/qtgui/emsprworkflow.py: Default fix

2010-04-04 00:16  stevel

	* libEM/mrcio.cpp, libpyEM/qtgui/emsprworkflow.py: Bug in importing
	  images.

2010-04-02 14:06  zyang

	* sparx/libpy/: applications.py, user_functions.py: Trivial change

2010-04-02 14:02  zyang

	* libEM/aligner.cpp: Minor change to make the parameters more sense

2010-04-02 09:36  stevel

	* programs/e2evalrefine.py: New program for evaluating refinements

2010-04-01 23:08  stevel

	* libpyEM/EMAN2db.py: trivial

2010-04-01 22:53  stevel

	* libpyEM/EMAN2db.py: database version fix

2010-04-01 16:30  gtang

	* libpyEM/libpyEMData2.cpp: temporarily comment the
	  "calc_n_highest_locations" for nightly release

2010-04-01 16:29  gtang

	* libEM/emdata_metadata.h: [no log message]

2010-04-01 16:02  gtang

	* libpyEM/libpyEMData2.cpp: [no log message]

2010-04-01 13:40  zyang

	* sparx/libpy/applications.py: add delta to single processor
	  version of ali2d_c()

2010-04-01 11:09  zyang

	* libEM/aligner.cpp, libEM/aligner.h, sparx/libpy/applications.py:
	  Add delta as part of CUDA alignment

2010-04-01 09:25  stevel

	* libpyEM/qtgui/emsprworkflow.py: Default change in workflow

2010-03-31 16:34  ppenczek

	* sparx/libpy/: applications.py, user_functions.py: [no log
	  message]

2010-03-31 16:01  ppenczek

	* sparx/: libpy/applications.py, test/3DA/3dg.py: [no log message]

2010-03-31 13:37  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-03-31 13:36  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Add function Crosrng_ms_delta() and
	  multiref_ali_2d_delta()

2010-03-31 12:38  ppenczek

	* sparx/libpy/: applications.py, user_functions.py: [no log
	  message]

2010-03-31 11:55  ross

	* programs/e2ssehunter.py: porting SSEHunter from EMAN1 to EMAN2

2010-03-31 10:42  gtang

	* libEM/imagicio.cpp: small fix

2010-03-31 10:39  fjia

	* sparx/libpy/alignment.py: [no log message]

2010-03-31 10:20  ppenczek

	* sparx/libpy/applications.py: [no log message]

2010-03-31 08:27  stevel

	* libEM/processor.cpp, libpyEM/qtgui/emsprworkflow.py: Fixed
	  project file adding bug

2010-03-30 12:40  ppenczek

	* sparx/libpy/: statistics.py, utilities.py: [no log message]

2010-03-26 17:35  zyang

	* sparx/: bin/sxisc_realignment.py, libpy/statistics.py: Add
	  min_stab_class as a parameter of the realigment process of ISC

2010-03-26 16:26  zyang

	* sparx/libpy/applications.py: Fix a minor bug in ali2d_c()

2010-03-26 15:38  zyang

	* sparx/libpy/applications.py: Add CUDA and new filteration stuff
	  into ali2d_c(), we suddenly found out that non-MPI version may be
	  useful in some cases.

2010-03-26 14:43  stevel

	* libpyEM/EMAN2db.py: Big oops. Broke exclusion in set generation.

2010-03-26 13:03  stevel

	* libEM/processor.cpp: trivial

2010-03-26 12:55  mingc

	* libEM/emdata.cpp: calc_flcf function bug fixed, please check

2010-03-26 12:45  stevel

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2refine.py: Fixed autob
	  filter. Seems to be working now.

2010-03-26 11:57  zyang

	* libEM/sparx/cuda/cuda_ccf.cu: A major change. Add offset when
	  binding texture memory. Otherwise, it will only work for image
	  size 64*64 and 128*128.

2010-03-26 11:08  ppenczek

	* sparx/: bin/sxplot_projs_distrib.py, libpy/applications.py,
	  libpy/reconstruction.py: [no log message]

2010-03-26 08:34  stevel

	* libEM/: processor.cpp, processor.h: automask2 fixes

2010-03-25 23:10  stevel

	* libEM/: processor.cpp, processor.h: Minor tweaks to new
	  filters/masks

2010-03-25 16:54  ross

	* programs/e2helixboxer.py: error message if no micrograph is
	  specified in command-line version of the program

2010-03-25 16:12  gtang

	* rt/pyem/test_processor.py: unit test update

2010-03-25 16:10  gtang

	* libEM/: processor.cpp, processor.h: minor fix for compilation
	  error on asterix

2010-03-25 15:56  stevel

	* libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libEM/processor.cpp, libEM/processor.h, libpyEM/libpyEMData2.cpp:
	  Negative radius in automask for highest values. First draft of
	  henderson style B sharpening

2010-03-25 12:45  gtang

	* libEM/: aligner.cpp, aligner.h, emdata.cpp, emdata.h: minor fix

2010-03-25 12:30  mingc

	* libEM/: aligner.h, emdata.cpp, emdata.h: ming

2010-03-25 12:29  mingc

	* libEM/aligner.cpp: ming, test

2010-03-24 12:26  ross

	* programs/e2helixboxer.py: remove old coordinates from
	  self.helices_dict after modifying a helix box

2010-03-24 11:50  ross

	* libEM/: processor.cpp, processor.h: BinarySkeletonizerProcessor
	  now has option to mark surfaces with a value of 2.0 (whereas
	  curves still have a value of 1.0)

2010-03-24 11:27  ross

	* libEM/gorgon/: skeletonizer.cpp, skeletonizer.h: added
	  VolumeSkeletonizer::MarkSurfaces

2010-03-24 11:04  zyang

	* libEM/sparx/cuda/cuda_ccf.cu: Trivial change

2010-03-24 10:54  gtang

	* libEM/: aligner.cpp, aligner.h, emdata.cpp, emdata.h: revert
	  Ming's change

2010-03-24 10:32  mingc

	* libEM/emdata.h: come with emdata.cpp

2010-03-24 09:58  mingc

	* libEM/aligner.h: should come with aligner.cpp

2010-03-24 09:57  mingc

	* libEM/emdata.cpp: this should come with aligner.cpp

2010-03-23 17:24  mingc

	* libEM/aligner.cpp: ming add frm2d aligner

2010-03-23 11:01  ppenczek

	* sparx/libpy/reconstruction.py: [no log message]

2010-03-22 16:46  gtang

	* libEM/: mrcio.cpp, mrcio.h: update the min/max/mean/sigma when
	  writing mrc file as 8 bit or 16 bit

2010-03-22 16:17  zyang

	* libEM/sparx/cuda/cuda_ccf.cu: [no log message]

2010-03-22 14:47  gtang

	* libEM/: emutil.cpp, emutil.h, imageio.cpp, imageio.h, jpegio.cpp,
	  mrcio.cpp, pgmio.cpp, pngio.cpp, tifio.cpp: move
	  getRenderMinMax() to EMUtil to become a utility function.

2010-03-22 11:02  stevel

	* libpyEM/qtgui/emimage2d.py: Fix for viewing stack of images in
	  single viewer.

2010-03-19 17:01  zyang

	* libEM/sparx/cuda/cuda_ccf.cu: Fix a bug in cuda alignment

2010-03-19 15:19  zyang

	* libEM/sparx/emdata_sparx.cpp, sparx/libpy/fundamentals.py: Fix
	  the code for gridding-based interpolation, add mask in Fourier
	  space

2010-03-19 08:05  ppenczek

	* sparx/libpy/: fundamentals.py: [no log message]

2010-03-18 16:33  ppenczek

	* libEM/sparx/emdata_sparx.h: formatting

2010-03-18 12:24  fjia

	* sparx/libpy/statistics.py: [no log message]

2010-03-16 11:34  ppenczek

	* libEM/sparx/emdata_sparx.cpp: corrected minimum radius in
	  helicise

2010-03-15 12:37  majf

	* sparx/libpy/applications.py: [no log message]

2010-03-12 14:35  ppenczek

	* sparx/libpy/applications.py: Jean corrections of ihrsr

2010-03-12 13:03  stevel

	* libpyEM/EMAN2db.py, programs/e2bdb.py, programs/e2scp.py: vstacks
	  relative. Tested, but afraid something may break  :^S

2010-03-12 08:03  ppenczek

	* sparx/libpy/fundamentals.py: added error to resample

2010-03-12 07:01  ppenczek

	* sparx/libpy/fundamentals.py: added error to resample

2010-03-11 17:37  fjia

	* sparx/libpy/statistics.py: [no log message]

2010-03-11 16:45  gtang

	* libEM/vec3.h, libpyEM/libpyTransform2.cpp: We can construct list
	  or tuple with Vec3f, vec3i or Vec2f, i.e., they are iterable in
	  Python now.

2010-03-11 14:57  stevel

	* programs/e2scp.py: e2scp working ! (95% anyway)

2010-03-11 10:48  stevel

	* programs/e2scp.py: Almost there...

2010-03-11 10:04  stevel

	* programs/e2scp.py: progress on e2scp

2010-03-10 10:36  fjia

	* sparx/libpy/statistics.py: [no log message]

2010-03-09 07:00  stevel

	* libpyEM/EMAN2.py: Size bug

2010-03-08 15:11  stevel

	* programs/e2scp.py: trivial

2010-03-08 14:44  stevel

	* libEM/processor.cpp, libpyEM/EMAN2db.py, programs/e2project3d.py,
	  programs/e2scp.py: Added e2scp, still working on it. minor
	  bugfixes

2010-03-08 13:20  ppenczek

	* sparx/: bin/sxihrsr.py, libpy/applications.py, test/3DA/3dg.py:
	  updates of ihrsr

2010-03-08 11:38  ppenczek

	* sparx/libpy/applications.py: corrected finfo in rec3D_MPI

2010-03-08 10:24  ross

	* libEM/processor.cpp: BinarySkeletonizerProcessor::process()
	  change

2010-03-07 14:35  zyang

	* sparx/libpy/applications.py: Add freeze option ali2d_c_MPI()

2010-03-07 12:21  fjia

	* sparx/libpy/statistics.py: [no log message]

2010-03-07 12:08  fjia

	* libpyEM/libpyUtils2.cpp: [no log message]

2010-03-05 19:09  ross

	* programs/e2helixboxer.py: fixed the --helix-width option when
	  used with the --gui option

2010-03-05 19:04  ross

	* programs/e2helixboxer.py: added command line options to work
	  without a GUI on previously boxed helices

2010-03-05 16:29  zyang

	* sparx/libpy/utilities.py: add function ave_ali_err_params()

2010-03-05 16:28  zyang

	* sparx/libpy/applications.py: Trivial change

2010-03-05 15:50  ross

	* libEM/processor.cpp: minor changes to ModelEMCylinderProcessor
	  and ApplyPolynomialProfileToHelix

2010-03-05 15:49  ross

	* libEM/processor.h: updated descriptions for
	  ModelEMCylinderProcessor and ApplyPolynomialProfileToHelix

2010-03-05 14:12  fjia

	* libpyEM/libpyUtils2.cpp: [no log message]

2010-03-05 13:50  fjia

	* sparx/libpy/statistics.py: [no log message]

2010-03-05 10:33  zyang

	* sparx/bin/sxali2d_b.py: [no log message]

2010-03-05 10:03  zyang

	* sparx/bin/sxali2d_b.py: [no log message]

2010-03-04 15:50  gtang

	* libEM/: cmp.cpp, ctf.cpp, emdata.cpp, hdfio2.cpp, pdbreader.cpp,
	  processor.cpp, processor.h, reconstructor.cpp,
	  reconstructor_tools.cpp, symmetry.cpp, util.cpp, util.h,
	  sparx/emdata_sparx.cpp, sparx/util_sparx.cpp, sparx/util_sparx.h:
	  fix for Visual C++ 2005 compilation.

2010-03-03 20:52  ross

	* programs/e2helixboxer.py: particle coordinates to text files

2010-03-03 16:08  ppenczek

	* sparx/bin/sxfactcoords.py: [no log message]

2010-03-03 16:08  ppenczek

	* sparx/libpy/applications.py: added ctf to factcoords

2010-03-03 12:32  ross

	* programs/e2helixboxer.py: single save dialog for coords and
	  images

2010-03-03 08:00  ppenczek

	* sparx/bin/sxali3d_d.py: [no log message]

2010-03-02 11:04  ross

	* programs/e2helixboxer.py: added save unrotated particle images
	  option

2010-03-02 10:54  gtang

	* libEM/emdata.cpp, libEM/reconstructor.cpp,
	  libEM/reconstructor_tools.cpp, libEM/util.cpp, libEM/util.h,
	  libpyEM/libpyUtils2.cpp: fix for visual c++ 2005 compilation.

2010-03-01 17:55  fjia

	* sparx/libpy/statistics.py: [no log message]

2010-03-01 16:46  irees

	* programs/e2boxer.py: Added "--gui" option for backwards
	  compatibility.

2010-03-01 15:19  zyang

	* sparx/: bin/sxisc_realignment.py, libpy/utilities.py: Change
	  realignment such that it can do multiple times

2010-03-01 11:27  fjia

	* libEM/sparx/cuda/cuda_ccf.cu: [no log message]

2010-03-01 10:36  zyang

	* sparx/libpy/statistics.py: Trivial change

2010-02-26 15:04  fjia

	* sparx/: bin/sxisc_realignment.py, libpy/statistics.py: [no log
	  message]

2010-02-26 13:41  stevel

	* libEM/: emdata_core.cpp, emdata_core.h, projector.cpp: Fixed
	  projections on large volumes at certain angles.

2010-02-25 11:01  zyang

	* sparx/libpy/statistics.py: New aves_adw()

2010-02-24 18:56  ppenczek

	* sparx/libpy/: applications.py, fundamentals.py: changed resample,
	  added subsample

2010-02-24 17:12  gtang

	* libEM/: symmetry.h, transform.h: fix comment

2010-02-24 17:11  gtang

	* libpyEM/libpyTransform2.cpp: python docstring for Transform class

2010-02-24 14:42  gtang

	* libEM/: pointarray.cpp, pointarray.h: small change

2010-02-24 14:37  gtang

	* rt/pyem/test_reconstructor.py: update unit test, unit test for
	  reconstructor need revise

2010-02-24 14:26  stevel

	* examples/cudaspeedtest.py, libEM/aligner.cpp, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/processor.cpp, libEM/reconstructor.cpp,
	  libpyEM/qtgui/emtprworkflow.py, programs/e2boxer.py,
	  programs/e2classaverage.py, programs/e2classifyligand.py,
	  programs/e2simmx2stage.py, programs/e2tomoaverage.py,
	  programs/e2tomohunter.py, rt/pyem/test_aligner.py,
	  rt/pyem/test_processor.py: math.transform -> xform

2010-02-24 11:55  gtang

	* libEM/hdfio2.cpp: handle negative image_index

2010-02-24 11:51  gtang

	* libpyEM/qtgui/emsave.py: revert my previous change,
	  stack/non-stack image will handle negative image_index
	  differentially.

2010-02-24 11:49  gtang

	* libEM/emdata_io.cpp: Let each image format decide how to deal
	  with negative image_index

2010-02-24 11:46  gtang

	* libEM/pifio.cpp: for negative image_index

2010-02-24 11:42  gtang

	* libEM/imagicio.cpp: for negative image_index

2010-02-24 11:39  gtang

	* libEM/spiderio.cpp: for negative image_index

2010-02-24 11:38  gtang

	* programs/e2iminfo.py: fix a small bug for spider format info

2010-02-24 11:27  stevel

	* libEM/mrcio.cpp, libEM/processor.cpp, libEM/reconstructor.cpp,
	  programs/e2iminfo.py: RMSD fix in MRC header.

2010-02-23 17:34  ppenczek

	* sparx/libpy/statistics.py: corrected table_stat

2010-02-23 08:48  gtang

	* doc/: developer-guide.html, latex/misc-developers-guide.tex:
	  correct documentation for numpy2em

2010-02-20 10:20  gtang

	* libEM/: amiraio.cpp, dm3io.cpp, emimio.cpp, emio.cpp, icosio.cpp,
	  jpegio.cpp, mrcio.cpp, pgmio.cpp, pngio.cpp, tifio.cpp,
	  vtkio.cpp, xplorio.cpp: permit "-1" as image_index. It will
	  append image to stack for stack image format. It will overwrite
	  image for non-stack image format.

2010-02-19 20:13  gtang

	* libpyEM/qtgui/emsave.py: adjust to recent change -- "raise an
	  exception when giving non-zero image_index for writing non-stack
	  image format"

2010-02-19 17:43  zyang

	* sparx/bin/sxali2d_a.py: [no log message]

2010-02-19 16:49  zyang

	* sparx/libpy/applications.py: Fix a bug.

2010-02-19 16:34  gtang

	* libEM/: util.cpp, util.h, emutil.h, emio.cpp: organize comment

2010-02-19 16:33  gtang

	* rt/pyem/test_imageio.py: update

2010-02-19 16:33  gtang

	* libpyEM/libpyUtils2.cpp: Python documentation and keyword
	  argument for Util and EMutil module.

2010-02-19 16:20  gtang

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: organize comment

2010-02-19 16:10  gtang

	* libEM/: mrcio.cpp, pgmio.cpp, pngio.cpp, tifio.cpp, vtkio.cpp,
	  xplorio.cpp, jpegio.cpp, icosio.cpp, amiraio.cpp: small fix

2010-02-19 15:46  fjia

	* sparx/libpy/user_functions.py: [no log message]

2010-02-19 15:41  fjia

	* sparx/libpy/: global_def.py, user_functions.py: [no log message]

2010-02-19 14:52  ppenczek

	* sparx/libpy/projection.py:  deleted couple of unused functions

2010-02-19 13:22  zyang

	* sparx/libpy/applications.py: Fix a bug

2010-02-19 11:34  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, sparx/libpy/applications.py: Add
	  function add_img_abs()

2010-02-19 07:57  stevel

	* programs/e2simmx2stage.py: bugfix

2010-02-19 07:46  stevel

	* libpyEM/EMAN2db.py, programs/e2classaverage.py,
	  programs/e2classifyligand.py, programs/e2refine2d.py: New program
	  for ligand classification

2010-02-18 18:11  zyang

	* sparx/libpy/applications.py: Fix a small bug

2010-02-18 17:14  zyang

	* sparx/libpy/applications.py: Trivial change.

2010-02-18 15:51  zyang

	* sparx/libpy/applications.py: Fix some bugs

2010-02-18 15:29  zyang

	* sparx/: bin/sxali2d_c.py, libpy/applications.py: Add adw as an
	  option for ali2d_c_MPI()

2010-02-18 11:43  fjia

	* sparx/libpy/user_functions.py: [no log message]

2010-02-17 23:29  ross

	* programs/e2helixboxer.py: bug fix: File->Open Micrograph works
	  again if only one micrograph is selected

2010-02-17 23:12  ross

	* programs/e2helixboxer.py: set mag to 1 when creating helix
	  viewer, not when changing its data; update # of helices in table
	  when user adds or deletes a box

2010-02-17 22:30  ross

	* programs/e2helixboxer.py: single line edit for entire path for
	  helices and particles

2010-02-17 14:36  zyang

	* sparx/libpy/statistics.py: [no log message]

2010-02-17 14:31  zyang

	* sparx/bin/sxali2d_a.py: [no log message]

2010-02-17 12:12  zyang

	* sparx/bin/sxisc_realignment.py: [no log message]

2010-02-17 07:50  ppenczek

	* sparx/libpy/: alignment.py, applications.py: [no log message]

2010-02-16 14:53  zyang

	* sparx/libpy/: applications.py, statistics.py: Minor change

2010-02-16 10:20  fjia

	* sparx/bin/sxisc.py: import isc from development instead of
	  applications

2010-02-16 10:14  fjia

	* sparx/bin/sxk_means_stable.py: import k_means_stab code from
	  development instead of applications

2010-02-15 14:54  ross

	* programs/e2helixboxer.py: File->Open Micrographs uses
	  EMSelectorModule and can load multiple images

2010-02-15 14:02  ross

	* programs/e2helixboxer.py: command line supports box width option
	  and loads multiple images

2010-02-15 08:14  ppenczek

	* sparx/libpy/: morphology.py, reconstruction.py: [no log message]

2010-02-13 10:46  stevel

	* programs/e2refine2d.py: refine2d bugfix

2010-02-12 17:21  ross

	* programs/e2helixboxer.py: fix: "ptcl_source_coords" is now
	  "ptcl_source_coord"

2010-02-12 17:12  ross

	* programs/e2helixboxer.py: start numbering helices from 0 in
	  output files; save_particles(): catches RuntimeError not
	  ImageWriteException

2010-02-12 15:20  stevel

	* programs/e2bdb.py: New option to look inside dictionaries

2010-02-12 15:18  ross

	* programs/e2helixboxer.py: trivial: save_particles() catches
	  ImageWriteException, not all exceptions

2010-02-12 14:51  ppenczek

	* sparx/bin/sxali3d_d.py: ali3d_n

2010-02-12 14:45  gtang

	* libEM/: amiraio.cpp, emio.cpp, fitsio.cpp, gatan2io.cpp,
	  icosio.cpp, jpegio.cpp, mrcio.cpp, pgmio.cpp, pngio.cpp,
	  salio.cpp, tifio.cpp, v4l2io.cpp, vtkio.cpp, xplorio.cpp: raise
	  exception for stack access on non-stack image formats.

2010-02-12 13:48  ross

	* programs/e2helixboxer.py: changed metadata keys for helices and
	  particles, removed "As Stack" checkbox... attempts to write to a
	  stack file and writes individual files if that fails

2010-02-12 13:10  zyang

	* sparx/libpy/utilities.py: Trivial change

2010-02-12 13:01  zyang

	* sparx/libpy/utilities.py: Fix a small bug

2010-02-12 13:00  zyang

	* sparx/libpy/utilities.py: More changes to the previous change

2010-02-12 12:02  ross

	* programs/e2helixboxer.py: "As Stack" checkbox specifies whether
	  to save particles into a stack file or individual images

2010-02-12 11:46  ppenczek

	* sparx/libpy/utilities.py: [no log message]

2010-02-12 11:33  ross

	* programs/e2helixboxer.py: added back helix and particle metadata
	  I accidentally removed

2010-02-12 11:24  fjia

	* sparx/libpy/statistics.py: added function pixel_error_angle_sets
	  for computing max pixel errors between corresponding pairs of
	  angles in two lists of angles

2010-02-12 11:24  ppenczek

	* sparx/libpy/utilities.py: [no log message]

2010-02-12 10:27  zyang

	* sparx/libpy/utilities.py: Decompose ave_ali_err() into two
	  functions: align_diff() and ave_ali_err()

2010-02-11 22:06  ross

	* programs/e2helixboxer.py: file menu has two choices for saving
	  coordinates or images; the GUI for each option allows directories
	  and file names to be specified (helix number added before the
	  file extension automatically)

2010-02-11 17:04  gtang

	* libEM/mrcio.cpp: fix the bug which apix value not setup up. The
	  init() should be called at the beginning of read_header().

2010-02-11 15:35  stevel

	* programs/e2cmpxplor.py: added feature

2010-02-11 14:50  zyang

	* sparx/: bin/sxali2d_a.py, libpy/development.py: delete
	  development.py

2010-02-11 14:33  stevel

	* programs/e2cmpxplor.py: Few minor bugfixes

2010-02-11 14:21  fjia

	* sparx/libpy/development.py: moved k-means stability and isc code
	  from applications.py

2010-02-11 14:20  fjia

	* sparx/libpy/applications.py: moved k-means stability code and isc
	  code over to development.py

2010-02-11 13:48  zyang

	* sparx/libpy/: applications.py, development.py, statistics.py: Fix
	  a bug in ali2d_c_MPI()

2010-02-11 12:38  stevel

	* libpyEM/qtgui/emimage3dsym.py, programs/e2cmpxplor.py: cmpxplor
	  working mostly...

2010-02-11 12:03  zyang

	* sparx/libpy/applications.py: Fix a small bug in ali2d_c_MPI()

2010-02-10 17:20  gtang

	* programs/: e2basis.py, e2bdb.py, e2boxer.py, e2classaverage.py,
	  e2classifykmeans.py, e2classptcl.py, e2ctf.py, e2ctf2eman1.py,
	  e2display.py, e2eotest.py, e2eulerxplor.py, e2fileinfo.py,
	  e2findsubunit.py, e2flick.py, e2foldfitter.py, e2helixboxer.py,
	  e2help.py, e2history.py, e2iminfo.py, e2initialmodel.py,
	  e2make3d.py, e2modeleval.py, e2msa.py, e2parallel.py,
	  e2pdb2em.py, e2pdb2mrc.py, e2proc2d.py, e2proc3d.py,
	  e2project3d.py, e2ptcltrace.py, e2refine.py, e2refine2d.py,
	  e2refmerge.py, e2resolution.py, e2scannereval.py, e2segment3d.py,
	  e2simmx.py, e2simmx2stage.py, e2simmxxplor.py, e2skelpath.py,
	  e2speedtest.py, e2ssematch.py, e2stackanim.py, e2stacksort.py,
	  e2startcsym.py, e2symbest.py, e2tilefile.py, e2tomoallvall.py,
	  e2tomoaverage.py, e2tomoboxer.py, e2tomogram.py, e2tomohunter.py,
	  e2classify.py, e2refinemultinoali.py: for --verbose option.  "The
	  idea was that if you ran something like 'refine' with --verbose=2
	  it would pass --verbose=1 on to any programs that it ran, and if
	  they ran anything, they would have --verbose=0. This would be in
	  addition to the level of verboseness at the top level. --Steve"

2010-02-10 15:07  stevel

	* libpyEM/qtgui/emimage3dsym.py, programs/e2cmpxplor.py: cmpxplorer
	  working but not updating right

2010-02-10 12:22  ppenczek

	* sparx/libpy/: applications.py, statistics.py: [no log message]

2010-02-10 12:01  ppenczek

	* sparx/bin/sxk_means.py: typo

2010-02-09 16:23  zyang

	* sparx/libpy/statistics.py: Fix a small bug.

2010-02-08 22:17  ross

	* programs/e2helixboxer.py: added metadata to helices and
	  particles: the source micrograph file path and the coordinates on
	  that source micrograph of the helix or particle

2010-02-08 14:54  gtang

	* libEM/mrcio.cpp: raise exception when reading image from mrc file
	  with image_index not equal 0 or -1

2010-02-08 11:53  ross

	* programs/e2helixboxer.py: self.micrograph_table now lists the
	  micrographs that have been opened and the number of helices boxed
	  in each. Clicking on a different micrograph in the table makes
	  that micrograph be displayed.

2010-02-08 09:40  zyang

	* sparx/libpy/applications.py: Fix a small bug

2010-02-05 23:39  ross

	* programs/e2helixboxer.py: closing and re-opening micrograph and
	  helix viewer windows works; real-time updates to helix viewer
	  while drawing boxes; added table widget that will be used for
	  switching between micrographs

2010-02-05 16:10  stevel

	* libEM/cmp.cpp, libEM/cmp.h, programs/e2cmpxplor.py: Beginning of
	  new program. Added min/max to frc criterion.

2010-02-05 15:17  zyang

	* sparx/libpy/utilities.py: Trivial change

2010-02-05 12:15  fjia

	* sparx/libpy/applications.py: inserted code for the bounded
	  enumeration partition matching option in single processer and mpi
	  version

2010-02-05 12:06  fjia

	* libEM/sparx/util_sparx.cpp: added functions for bounded
	  enumeration partition matching algorithm

2010-02-05 12:05  fjia

	* libEM/sparx/util_sparx.h: added headers for functions for the
	  bounded enumeration partition matching algorithm

2010-02-05 12:04  fjia

	* libpyEM/libpyUtils2.cpp: added interface between python and c++
	  for bounded enumeration partition matching algorithm

2010-02-05 11:22  fjia

	* sparx/libpy/statistics.py: added helper functions
	  k_means_stab_bbenum, k_means_match_bbenum, k_means_stab_info for
	  bounded enumeration partition matching algorithm

2010-02-04 17:42  gtang

	* CMakeLists.txt, examples/CMakeLists.txt: add examples directory
	  for distribution

2010-02-04 13:14  zyang

	* sparx/libpy/applications.py: Fix a bug in ali2d_a_MPI()

2010-02-04 10:56  stevel

	* libEM/cmp.cpp: Bugfix in maxres in phase

2010-02-04 09:39  zyang

	* libEM/sparx/util_sparx.cpp: Trivial change

2010-02-04 09:30  zyang

	* libEM/sparx/util_sparx.cpp: Chnage to vector_mutation() and
	  list_mutation()

2010-02-04 09:29  stevel

	* libEM/cmp.cpp, libEM/cmp.h, programs/e2ctf.py: New option in
	  phase comparator, and better default behavior I hope.

2010-02-04 07:38  ppenczek

	* programs/e2ctf.py: corrected new addition by adding int

2010-02-03 16:47  zyang

	* sparx/libpy/applications.py: Fix a bug in ali2d_a()

2010-02-03 13:50  ross

	* programs/e2helixboxer.py: open micrographs from the file menu,
	  quit app from file menu

2010-02-03 11:07  ross

	* programs/e2helixboxer.py: load coordinates from text files added
	  to file menu, helix viewer has a default magnification of one

2010-02-03 10:55  stevel

	* libEM/processor.cpp, libEM/processor.h, libpyEM/qtgui/emform.py,
	  programs/e2ctf.py: New option in kmeans segmentation. ctf
	  background change

2010-02-03 00:10  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, sparx/libpy/applications.py: Change
	  list_mutation() from python to C++

2010-02-02 22:55  ross

	* programs/e2helixboxer.py: The save dialog is now modal.
	  EMHelixBoxerWidget.width_changed() doesn't update particle
	  dimensions, because they are now in a modal dialog.

2010-02-02 22:51  ross

	* programs/e2helixboxer.py: Added a menubar and a File menu with a
	  Save option. The options for saving files are now in a dialog.

2010-02-02 10:24  stevel

	* libEM/processor.cpp: Trivial

2010-02-02 10:20  stevel

	* libEM/processor.cpp, libEM/processor.h, libEM/symmetry.cpp,
	  libEM/sparx/util_sparx.cpp, programs/e2initialmodel.py,
	  programs/e2make3d.py, programs/e2segment3d.py,
	  programs/e2simmx.py, programs/e2simmx2stage.py: Segmentation.
	  make3d bugfix

2010-02-01 15:32  zyang

	* sparx/libpy/applications.py: Trivial change

2010-02-01 13:47  ross

	* libEM/: processor.cpp, gorgon/skeletonizer.cpp,
	  gorgon/skeletonizer.h: remove artifacts after running a binary
	  skeletonization algorithm

2010-02-01 12:12  zyang

	* sparx/libpy/applications.py: Trivial change

2010-02-01 11:40  ross

	* programs/e2helixboxer.py: removed *.hbox option from GUI

2010-02-01 11:33  zyang

	* sparx/libpy/applications.py: Block some unnecessary stuff to save
	  time in ali2d_c_MPI()

2010-02-01 11:26  ross

	* programs/e2helixboxer.py: 1. Change from frame->segment->particle
	  terminology to micrograph->helix->particle 2. Don't create
	  e2helixboxercache subdirectory for DB 3. Remove the new *.hbox
	  files completely -- (encourage DB use, and support old EMAN1 text
	  files) 4. Output file naming changes

2010-02-01 07:33  stevel

	* programs/: e2simmx.py, e2simmx2stage.py: Begin to change 2 stage
	  simmx strategy

2010-01-31 08:41  ppenczek

	* sparx/templates/import_SPIDER_refi.py: [no log message]

2010-01-30 10:51  gtang

	* programs/e2proc2d.py: apply regional reading to process 3D image
	  slice by slice

2010-01-30 09:45  gtang

	* rt/pyem/test_processor.py: [no log message]

2010-01-29 17:04  ross

	* programs/e2helixboxer.py: 1. reading from *.hbox file now uses
	  float coords, not int 2. bug fix: deleting a box removes it from
	  self.segments_dict 3. mouse click events give coordinates in
	  image pixels not angstroms --> documentation fix 4. added
	  docstrings

2010-01-29 16:16  ross

	* programs/e2helixboxer.py: db_get_segments_dict() bug fix; *.hbox
	  now the default coordinates file; *.hbox now uses floating point
	  coordinates (but integer box width); *.mrc removed as a particle
	  output file choice because it does not support stack files;

2010-01-29 15:04  ross

	* programs/e2helixboxer.py: os.path.relpath() was new in Python
	  2.6: test Python version before using to set self.frame_filepath
	  in EMHelixBoxerWidget; added option to use the normalize.edgemean
	  processor on particles that are saved to files

2010-01-29 14:32  stevel

	* libEM/processor.cpp, libEM/processor.h,
	  programs/e2classaverage.py, programs/e2simmx2stage.py: Precaching
	  works !!!  Minor fix to 2stage refinement. Beginning k-means
	  segmentation.

2010-01-29 13:50  ross

	* programs/e2helixboxer.py: The EMImage2DModule now gets a relative
	  path to the frame file rather than just the filename.

2010-01-29 13:27  ross

	* programs/e2helixboxer.py: Database dictionary keys are now
	  relative paths to the image file for the frame.

2010-01-29 12:30  zyang

	* sparx/libpy/applications.py: Some changes to ali2d_a_MPI()

2010-01-29 11:22  zyang

	* sparx/: bin/sxali2d_a.py, libpy/applications.py: Many changes to
	  ali2d_a_MPI()

2010-01-29 10:31  stevel

	* libpyEM/EMAN2PAR.py: Caching is 95% working !!!

2010-01-29 06:51  stevel

	* programs/e2bdb.py: e2bdb now has --delete

2010-01-28 15:29  stevel

	* libpyEM/EMAN2PAR.py: More trivial socket stuff.

2010-01-28 13:22  stevel

	* examples/tomotrackbox.py, libpyEM/EMAN2.py,
	  libpyEM/qtgui/emimage2d.py: Fixed metadata saving in
	  tomotrackbox. Saving stacks from single image viewer.

2010-01-28 11:46  stevel

	* examples/tomotrackbox.py: Draggng in frames

2010-01-28 09:45  zyang

	* sparx/libpy/statistics.py: Change aves_adw()

2010-01-28 08:31  stevel

	* libpyEM/EMAN2PAR.py: More minor changes

2010-01-28 08:20  stevel

	* libpyEM/EMAN2PAR.py: More tweaks on the chain sockets

2010-01-28 07:19  stevel

	* libpyEM/EMAN2PAR.py: Getting closer...

2010-01-28 07:15  stevel

	* libpyEM/EMAN2PAR.py: Another typo

2010-01-28 07:12  stevel

	* libpyEM/EMAN2PAR.py: typo

2010-01-28 07:09  stevel

	* libpyEM/EMAN2PAR.py: Tweak protocol to get actual client
	  addresses. DC protocol version change !

2010-01-27 21:59  ross

	* programs/e2helixboxer.py: image quality to/from db, color the box
	  for the current segment different from the others

2010-01-27 15:30  stevel

	* libpyEM/EMAN2PAR.py: Little tweaks to caching

2010-01-27 14:01  stevel

	* libpyEM/EMAN2PAR.py: oops

2010-01-27 13:49  stevel

	* libpyEM/EMAN2PAR.py: New test version of parallelism caching.

2010-01-26 17:20  gtang

	* libEM/hdfio2.cpp: HDF5 image regional I/O finished. support out
	  of bounds region. semantically equivalent as EMData::get_clip().

2010-01-26 17:15  gtang

	* rt/pyem/test_imageio.py: [no log message]

2010-01-26 17:04  gtang

	* rt/pyem/test_imageio.py: [no log message]

2010-01-25 19:56  ross

	* programs/e2helixboxer.py: can now load boxes from *.box or *.hbox
	  files to the database and the screen fixed a bug where
	  zero-length boxes were created when the user clicked on the image

2010-01-25 16:56  zyang

	* sparx/libpy/statistics.py: Change function aves_adw()

2010-01-25 11:37  ross

	* programs/e2helixboxer.py: segment viewer bugfix & code to display
	  segment moved to EMHelixBoxerWidget.display_segment()

2010-01-25 10:32  ross

	* programs/e2helixboxer.py: added docstrings for most of the
	  functions

2010-01-22 17:51  ross

	* programs/e2helixboxer.py: changing the box width spin box updates
	  the widths of all the boxes

2010-01-22 16:36  ross

	* programs/e2helixboxer.py: *.box file coordinates now the same as
	  in EMAN1

2010-01-22 16:06  jbert

	* sparx/libpy/applications.py: fix type error in cml

2010-01-22 13:33  jbert

	* sparx/: bin/sxisc.py, bin/sxisc_realignment.py,
	  libpy/applications.py, libpy/statistics.py: fix couple of things
	  to ISC

2010-01-22 13:12  stevel

	* examples/tomotrackbox.py, libEM/aligner.cpp, libEM/aligner.h,
	  libEM/emdata.cpp, libEM/processor.cpp, libpyEM/EMAN2.py,
	  libpyEM/qtgui/emimage2d.py: Improvements in tomoboxer. New
	  animation generation and saving for emimage2d

2010-01-22 02:10  ross

	* programs/e2helixboxer.py: directories created/used that display
	  the box width and coords/segments/particles

2010-01-21 08:44  stevel

	* libpyEM/qtgui/emshape.py: Fixed bugs

2010-01-20 23:37  ross

	* programs/e2helixboxer.py: supports writing particles to file

2010-01-20 19:18  ross

	* libpyEM/qtgui/emshape.py: mostly changes for code clarity

2010-01-20 17:14  jbert

	* sparx/libpy/applications.py: fix type

2010-01-20 16:15  jbert

	* sparx/libpy/applications.py: comment to Jia

2010-01-20 12:03  ross

	* programs/e2helixboxer.py: segment file i/o and further db
	  integration

2010-01-19 23:00  stevel

	* examples/tomotrackbox.py: Minor tomotrackbox improvement

2010-01-19 17:31  ppenczek

	* sparx/libpy/: statistics.py, user_functions.py: [no log message]

2010-01-19 17:03  ppenczek

	* libEM/sparx/fourierfilter.cpp: corrected filtration by table

2010-01-19 07:36  stevel

	* libEM/util.cpp, libpyEM/EMAN2PAR.py: More work on precaching.
	  Still a bit flakey

2010-01-18 18:35  ppenczek

	* sparx/libpy/statistics.py: aves_adw

2010-01-18 12:50  jbert

	* sparx/: bin/sxisc_realignment.py, libpy/applications.py: wrote
	  new MPI realignment code to fix pb in ali2d_a

2010-01-18 11:14  gtang

	* libEM/hdfio2.cpp: [no log message]

2010-01-16 16:58  stevel

	* libEM/util.cpp, libpyEM/EMAN2PAR.py: More caching work. Sigh

2010-01-16 14:18  stevel

	* libEM/util.cpp: turn of debugging

2010-01-16 14:16  stevel

	* libpyEM/EMAN2PAR.py: bugfix for precaching

2010-01-15 18:32  gtang

	* rt/pyem/test_imageio.py, libEM/imageio.h, libEM/hdfio2.cpp: [no
	  log message]

2010-01-15 16:20  stevel

	* libEM/util.cpp: Minor fixes. recv_broadcast still acting odd

2010-01-15 10:25  stevel

	* libEM/util.cpp: bugfix in recv_

2010-01-14 19:56  stevel

	* libEM/util.cpp: Oops

2010-01-14 19:39  stevel

	* libEM/util.cpp, libEM/util.h, libpyEM/EMAN2PAR.py,
	  libpyEM/libpyUtils2.cpp: Experimental new C++ broadcast receiver

2010-01-14 17:21  jbert

	* sparx/libpy/utilities.py: estimate_stability, fix wrong import

2010-01-14 17:21  jbert

	* sparx/: bin/sxisc.py, bin/sxisc_realignment.py,
	  libpy/applications.py, libpy/statistics.py: isc, add possibility
	  to use both data normal and decimated

2010-01-14 11:36  stevel

	* libpyEM/EMAN2PAR.py: Fixed case where files already cached

2010-01-14 11:19  stevel

	* libpyEM/EMAN2PAR.py: Fix ack

2010-01-14 10:28  stevel

	* libpyEM/EMAN2PAR.py: More fixes

2010-01-13 14:54  stevel

	* libpyEM/EMAN2PAR.py: Path error in caching

2010-01-13 14:23  stevel

	* libpyEM/EMAN2PAR.py: trivial

2010-01-13 13:47  stevel

	* libpyEM/EMAN2PAR.py, programs/e2classaverage.py,
	  programs/e2project3d.py, programs/e2simmx.py: Precaching
	  implementation for refinement

2010-01-13 10:50  stevel

	* libpyEM/EMAN2PAR.py: timing debugging on precaching

2010-01-13 10:15  ppenczek

	* sparx/libpy/filter.py: [no log message]

2010-01-13 10:07  ppenczek

	* libEM/sparx/fourierfilter.cpp: crrected binary CTF

2010-01-13 09:33  stevel

	* libpyEM/EMAN2PAR.py: Debug timing

2010-01-13 09:06  stevel

	* libpyEM/EMAN2PAR.py: Debug speed issues

2010-01-13 08:09  stevel

	* libpyEM/EMAN2PAR.py: bugfix

2010-01-13 07:34  stevel

	* libpyEM/EMAN2PAR.py: Better caching ?

2010-01-12 21:00  ppenczek

	* libEM/sparx/fourierfilter.cpp, sparx/libpy/filter.py: added
	  binary ctf

2010-01-12 16:47  ppenczek

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: switched off check of
	  both straight and mirror in local searches

2010-01-12 11:47  zyang

	* sparx/libpy/: development.py, utilities.py: Move ave_ali_err()
	  from development.py to utilities.py and blocked the old version.

2010-01-12 10:29  zyang

	* sparx/libpy/development.py: [no log message]

2010-01-11 18:43  zyang

	* sparx/libpy/development.py: [no log message]

2010-01-11 14:37  ppenczek

	* sparx/bin/sxali3d_d.py: [no log message]

2010-01-11 14:25  stevel

	* libpyEM/EMAN2PAR.py: Minor bugfix

2010-01-11 14:06  stevel

	* libpyEM/EMAN2PAR.py: Better locking

2010-01-11 13:29  stevel

	* libpyEM/EMAN2PAR.py: trivial

2010-01-11 13:24  stevel

	* libpyEM/EMAN2PAR.py: Better debugging

2010-01-11 13:17  stevel

	* libpyEM/: EMAN2PAR.py, EMAN2db.py: trivial

2010-01-11 13:06  stevel

	* libpyEM/EMAN2PAR.py: Client improvements

2010-01-11 12:49  stevel

	* libpyEM/EMAN2PAR.py: trivial

2010-01-11 12:47  stevel

	* libEM/transform.h, libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py,
	  programs/e2parallel.py, programs/e2refine.py: Working on caching
	  mechanism for parallelism

2010-01-11 12:30  ppenczek

	* sparx/libpy/: applications.py, reconstruction.py: [no log
	  message]

2010-01-10 22:54  stevel

	* libpyEM/EMAN2PAR.py: Working on cache improvements

2010-01-10 11:07  ppenczek

	* sparx/libpy/utilities.py: counter decreased in reduce emdata

2010-01-10 10:27  ppenczek

	* sparx/libpy/: utilities.py: counter increased in reduce emdata

2010-01-10 09:03  ppenczek

	* sparx/libpy/: reconstruction.py, statistics.py, utilities.py:
	  minor cleaning

2010-01-09 21:56  zyang

	* sparx/libpy/: alignment.py, applications.py, development.py,
	  projection.py, reconstruction.py, statistics.py, utilities.py:
	  Reverse the change on Thursday, but retain the numpy part

2010-01-09 01:04  stevel

	* examples/tomotrackbox.py, programs/e2refine.py: twostage added to
	  refine

2010-01-08 16:11  ppenczek

	* sparx/libpy/utilities.py: compose 2d done with transform object

2010-01-08 16:04  stevel

	* libpyEM/EMAN2db.py, programs/e2classify.py: Rewrote much of
	  e2classify. Wasn't working right in some cases

2010-01-08 15:13  ppenczek

	* sparx/libpy/utilities.py: corrected params 3d->2D

2010-01-08 15:06  jbert

	* sparx/: bin/sxk_means.py, bin/sxk_means_stable.py,
	  libpy/applications.py, libpy/statistics.py: add norm flag

2010-01-08 15:01  zyang

	* sparx/libpy/: applications.py, user_functions.py: Trivial change

2010-01-08 10:13  zyang

	* sparx/libpy/applications.py: Trivial change.

2010-01-08 07:32  stevel

	* programs/e2classaverage.py: reduce output

2010-01-07 15:32  ppenczek

	* sparx/libpy/: applications.py, utilities.py: applications.py

2010-01-06 18:30  gtang

	* rt/pyem/test_imageio.py: [no log message]

2010-01-06 15:23  jbert

	* sparx/libpy/: applications.py, projection.py: Find structure
	  check nb trials with nb of cpus

2010-01-06 14:53  jbert

	* sparx/libpy/statistics.py: fix minor bug k-means open im

2010-01-06 14:10  stevel

	* examples/speedprofile.py, programs/e2refine.py,
	  programs/e2speedtest.py: Bugfix and new profile program

2010-01-06 12:39  zyang

	* sparx/libpy/: alignment.py, applications.py, development.py,
	  projection.py, reconstruction.py, statistics.py, utilities.py: An
	  overhaul to mpi related functions. We deleted the dependency on
	  Numeric and assume that mpi always use numpy.  We changed the
	  function bcast_EMData_to_all(), reduce_EMData_to_root(),
	  send_EMData(), recv_EMData() to take advantage of the direct
	  conversion between EMData() and numpy array and thus eliminate
	  the middle variable.	We also changed the syntax of
	  bcast_EMData_to_all() and reduce_EMData_to_root() such that they
	  are consistent with mpi_bcast() and mpi_reduce(). Corresponding
	  change have been made to any function that use these two
	  fucntions.

2010-01-06 11:03  jbert

	* sparx/libpy/statistics.py: k_means change back norm

2010-01-05 16:13  jbert

	* sparx/libpy/applications.py: fix bugs to k-means CUDA

2010-01-05 15:29  jbert

	* sparx/libpy/: applications.py, development.py: move k-means stab
	  MPICUDA stream GROUP MPI from apli to dev

2010-01-05 15:00  jbert

	* sparx/libpy/: applications.py, development.py: move isc_dev from
	  appli to dev

2010-01-05 14:55  jbert

	* sparx/: bin/sxisc_realignment.py, libpy/applications.py: sxisc:
	  some change, some bug, put back ali2d_c

2010-01-05 14:05  gtang

	* sparx/libpy/utilities.py: change array from mpi to numpy, so we
	  can convert it to EMData without copying.

2010-01-05 13:56  gtang

	* libpyEM/libpyTransform2.cpp, libEM/emdata_metadata.h,
	  libEM/transform.h: change EMData::get_transform() to return
	  Transform instead of Transform3D.

2010-01-05 13:24  ppenczek

	* sparx/: bin/sxrecons3d_f.py, bin/sxrecons3d_n.py,
	  libpy/applications.py, test/3DA/3dg.py: list and group options
	  added to reconstruction applications

2010-01-04 17:45  fjia

	* sparx/libpy/statistics.py: put in the compare function for
	  Francisco (compare_fra)

2010-01-04 07:48  ppenczek

	* sparx/libpy/statistics.py: [no log message]

2010-01-03 10:08  ppenczek

	* libEM/hdfio2.cpp: Grant - I blicked the printout

2010-01-02 20:05  ppenczek

	* sparx/bin/: sxali3d_e.py, sxihrsr.py: changed Fourvar to fourvar

2010-01-02 17:49  ppenczek

	* sparx/libpy/: applications.py, user_functions.py: [no log
	  message]

2010-01-02 10:02  ppenczek

	* sparx/bin/sxrecons3d_n.py: [no log message]

2010-01-01 16:10  gtang

	* libEM/hdfio2.cpp: [no log message]

2010-01-01 15:41  ppenczek

	* sparx/libpy/alignment.py: [no log message]

2010-01-01 10:17  ppenczek

	* sparx/libpy/filter.py:  defsult for filt_median is BLOCK

2010-01-01 09:25  ppenczek

	* sparx/libpy/filter.py:  defsult for filt_median is BLOCK

2009-12-31 19:10  ppenczek

	* sparx/libpy/: applications.py, statistics.py, user_functions.py:
	  fourvar in ali2d_c corrected

2009-12-31 16:11  gtang

	* libEM/hdfio2.cpp: fix a bug for 2D region I/O

2009-12-31 12:51  ppenczek

	* sparx/libpy/development.py: ceommented out ali2d_a moved here

2009-12-30 10:25  zyang

	* sparx/libpy/statistics.py: Slightly change add_ave_varf() and
	  add_ave_varf_MPI()

2009-12-29 18:03  ppenczek

	* sparx/: bin/sxali2d_c.py, libpy/statistics.py,
	  libpy/user_functions.py, libpy/utilities.py: [no log message]

2009-12-29 16:13  ppenczek

	* sparx/libpy/: utilities.py, applications.py: [no log message]

2009-12-29 14:35  ppenczek

	* sparx/bin/sxali_param_2d_to_3d.py: [no log message]

2009-12-28 09:35  zyang

	* sparx/libpy/applications.py: Fix a small bug.

2009-12-25 07:04  ppenczek

	* libEM/sparx/util_sparx.cpp, sparx/libpy/statistics.py: [no log
	  message]

2009-12-23 10:45  zyang

	* sparx/libpy/applications.py: Use gray code for the encoding in
	  the genetic algorithm

2009-12-22 10:31  zyang

	* libpyEM/libpyEMData2.cpp: Fix a trivial bug.

2009-12-22 09:13  ppenczek

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyUtils2.cpp,
	  sparx/bin/sxali3d_d.py, sparx/bin/sxihrsr.py,
	  sparx/libpy/alignment.py, sparx/libpy/applications.py,
	  sparx/libpy/reconstruction.py, sparx/libpy/user_functions.py:
	  helices

2009-12-21 17:47  gtang

	* libEM/hdfio2.cpp: HDF5 region write done.

2009-12-21 15:58  zyang

	* sparx/: bin/sxali2d_a.py, libpy/applications.py: Many changes to
	  ali2d_a_MPI()

2009-12-20 14:47  zyang

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/libpyEMData2.cpp,
	  sparx/libpy/alignment.py: Move max_3D_pixel_error() to C++

2009-12-18 03:03  ppenczek

	* sparx/libpy/: alignment.py, applications.py:	max pixel error

2009-12-17 14:58  stevel

	* libpyEM/qtgui/emsprworkflow.py, programs/e2refine.py,
	  programs/e2simmx.py, programs/e2simmx2stage.py: Multistage
	  classification getting there...

2009-12-17 13:32  ross

	* programs/e2helixboxer.py: Adding top-level functions to clip
	  sections and particles from the image Changing some variable
	  names to use frame, segment, and particle terminology

2009-12-17 07:39  stevel

	* libpyEM/EMAN2db.py, programs/e2simmx.py,
	  programs/e2simmx2stage.py: Still working on multistage
	  classification

2009-12-17 04:56  ppenczek

	* sparx/: bin/sxrecons3d_f.py, libpy/alignment.py,
	  libpy/applications.py, libpy/development.py, libpy/utilities.py,
	  test/3DA/3dg.py: [no log message]

2009-12-16 14:53  zyang

	* sparx/libpy/applications.py: Trivial change.

2009-12-16 10:01  stevel

	* programs/e2simmx.py: another oops

2009-12-16 09:35  stevel

	* libpyEM/EMAN2PAR.py: oops

2009-12-16 09:31  stevel

	* libpyEM/EMAN2PAR.py, programs/e2simmx.py: Minor bugfixes

2009-12-16 09:23  jbert

	* sparx/libpy/applications.py: missing import k_means_stable MPI no
	  CUDA version

2009-12-16 09:06  stevel

	* libEM/processor.cpp, libEM/processor.h, libpyEM/EMAN2PAR.py,
	  programs/e2simmx.py, programs/e2simmx2stage.py: Working on 2
	  stage parallelism still. Not quite there yet, but getting close

2009-12-15 19:31  ross

	* libpyEM/qtgui/emshape.py: assert that endpoints don't coincide
	  for draw() with "rectline" shapes

2009-12-15 18:57  ross

	* programs/e2helixboxer.py: GUI mock-up for writing coordinate,
	  segment, and particles to files

2009-12-15 15:42  zyang

	* sparx/: bin/sxbootstrap_bigdisk.py, libpy/applications.py: Some
	  improvement to ali2d_a_MPI()

2009-12-15 11:28  zyang

	* sparx/libpy/applications.py: Fix a small bug

2009-12-15 07:31  stevel

	* programs/e2simmx.py: oops

2009-12-14 17:06  jbert

	* sparx/libpy/statistics.py: fix bug k_means_MPI_CUDA

2009-12-14 15:28  ross

	* programs/e2helixboxer.py: box coordinates and widths are saved to
	  the database and restored from the database when the program
	  opens

2009-12-11 20:13  ross

	* programs/e2helixboxer.py: major revision, most notably: using
	  fewer classes and using the collision detection that was added to
	  emshape.py

2009-12-11 16:22  jbert

	* sparx/bin/sxisc_realignment.py: fix type

2009-12-11 16:14  jbert

	* sparx/: bin/sxisc_realignment.py, libpy/applications.py,
	  libpy/statistics.py: still working on ISC

2009-12-11 15:07  stevel

	* examples/diffractsim.py, libEM/processor.cpp,
	  programs/e2simmx.py, programs/e2simmx2stage.py: fillzero in simmx
	  and work on simmx2stage. Don't think I broke anything...

2009-12-11 13:16  jbert

	* sparx/bin/sxk_means_stable.py: add missing import

2009-12-10 17:11  jbert

	* sparx/: bin/sxisc.py, bin/sxk_means_stable.py,
	  libpy/applications.py, libpy/statistics.py: add ISC procedure

2009-12-10 10:20  ross

	* libEM/gorgon/volume_data.cpp: some code documentation

2009-12-10 10:18  ross

	* libEM/gorgon/skeletonizer.cpp: skeletnizer constructor

2009-12-10 10:09  ross

	* libEM/gorgon/skeletonizer.h: declaring member functions static
	  and adding member variables

2009-12-09 16:10  ross

	* libEM/processor.cpp: BinarySkeletonizerProcessor - minor changes

2009-12-09 15:56  ross

	* libpyEM/qtgui/emshape.py: adding collision detection

2009-12-08 15:25  stevel

	* libEM/: reconstructor.cpp, reconstructor.h: Experimental option
	  in Fourier reconstructor.

2009-12-08 10:29  jbert

	* sparx/libpy/statistics.py: fix CTF in k_means_SSE_MPI

2009-12-07 18:13  zyang

	* sparx/demo/5_mpi_bdb/run_through_example: Trivial change.

2009-12-07 17:24  zyang

	* sparx/bin/sxboxer.py: Fix a small bug

2009-12-07 17:22  zyang

	* sparx/demo/: 1_bdb/run_through_example,
	  3_bdb_ctf/run_through_example, 5_mpi_bdb/run_through_example: Fix
	  run through examples using new sxboxer.

2009-12-07 15:52  jbert

	* sparx/libpy/statistics.py: fix bug k-means stable MPI and CTF

2009-12-07 15:51  jbert

	* sparx/demo/7_mpi_bdb_ctf/run_through_example: change params

2009-12-07 13:47  jbert

	* sparx/libpy/statistics.py: k-means trivial change

2009-12-07 11:28  jbert

	* sparx/libpy/statistics.py: k_means_headlog change a parameter

2009-12-07 11:27  stevel

	* libEM/util.cpp: Fixed phase comparator

2009-12-07 09:41  stevel

	* libEM/: util.cpp, util.h: fast_acos added for use in phase
	  comparator

2009-12-07 08:58  stevel

	* libEM/: cmp.cpp, cmp.h, util.h: New phase comparator options and
	  code

2009-12-05 19:15  gtang

	* sparx/test/bootstrap/mympimodule.c: revert to version 1.1

2009-12-05 18:50  gtang

	* sparx/libpy/utilities.py: revert it back to what Wei did

2009-12-04 16:24  gtang

	* rt/pyem/test_typeconverter.py: update the unit test since the
	  interface of numpy2em has changed.

2009-12-04 16:23  gtang

	* libpyEM/typeconverter.h: update comment

2009-12-04 16:22  gtang

	* libpyEM/typeconverter.cpp: increase the reference count for the
	  numpy array. EMData could take ownership of this data.

2009-12-04 16:19  gtang

	* sparx/test/bootstrap/mympimodule.c: Ooops, revert my change. The
	  Py_INCREF should not be called here.

2009-12-04 15:44  gtang

	* doc/: developer-guide.html, latex/misc-developers-guide.tex:
	  numpy2em interface changed

2009-12-04 15:41  gtang

	* sparx/test/bootstrap/mympimodule.c: increase the reference count
	  for the numpy array returned by mpi_recv. So at the receive end,
	  EMData could take ownership of this data.

2009-12-04 15:38  gtang

	* sparx/libpy/utilities.py: make use of the numpy2em to construct
	  an EMData object from the data received by mpi_recv(). No memory
	  copying involved.

2009-12-04 15:35  gtang

	* libpyEM/: libpyTypeConverter2.cpp, typeconverter.cpp,
	  typeconverter.h: modify numpy2em(). It now takes a numpy array,
	  return a EMData object. EMData will take the ownership of the
	  numpy array data. If the numpy array other data type than 32bit
	  float, a type conversion will be done.

2009-12-04 13:56  zyang

	* sparx/libpy/utilities.py: Add function estimate_stability

2009-12-04 12:15  jbert

	* sparx/bin/sxisc.py: add sxisc.py

2009-12-04 10:22  stevel

	* programs/e2simmx2stage.py: First stage simmx finished

2009-12-03 15:10  stevel

	* programs/: e2simmx.py, e2simmx2stage.py: 2 stage classification
	  making progress.

2009-12-03 11:46  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-12-03 10:34  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-12-02 16:00  stevel

	* programs/: e2simmx.py, e2simmx2stage.py: Working on 2 stage simmx

2009-12-02 12:23  ppenczek

	* sparx/libpy/statistics.py:  select_kmeans cleaned

2009-12-02 12:13  ppenczek

	* sparx/bin/sxbootstrap_bigdisk.py: new bigdisk

2009-12-02 11:23  stevel

	* libEM/projector.cpp, programs/e2initialmodel.py,
	  programs/e2simmx2stage.py: initial model generation fixed. oops

2009-12-01 14:21  stevel

	* programs/: e2ctf.py, e2eulerxplor.py, e2make3d.py,
	  e2simmx2stage.py: 2 stage refinement initial program outline

2009-12-01 11:47  zyang

	* sparx/libpy/applications.py: Fix a bug

2009-12-01 11:44  zyang

	* sparx/libpy/applications.py: Trivial change

2009-12-01 11:30  zyang

	* sparx/bin/sxali2d_a.py: Trivial change

2009-12-01 11:23  zyang

	* sparx/: bin/sxali2d_a.py, libpy/applications.py: Fix a bug

2009-12-01 10:32  ppenczek

	* sparx/libpy/development.py: [no log message]

2009-11-30 13:47  jbert

	* sparx/libpy/applications.py: open only header to
	  sx_plot_angles_distrib

2009-11-30 12:46  ppenczek

	* sparx/libpy/utilities.py: [no log message]

2009-11-30 12:26  ppenczek

	* sparx/libpy/utilities.py: correct pixel size handling

2009-11-30 12:22  ppenczek

	* sparx/libpy/: applications.py, development.py, fundamentals.py,
	  morphology.py, statistics.py, utilities.py: correct pixel size
	  handling

2009-11-30 10:46  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-11-29 15:34  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-11-29 05:13  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-11-28 16:39  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-11-28 14:19  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-11-28 07:01  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-11-27 21:13  ppenczek

	* sparx/libpy/reconstruction.py: [no log message]

2009-11-27 20:16  ppenczek

	* sparx/libpy/: applications.py, reconstruction.py:  more changes
	  in ali3d_em

2009-11-27 17:36  ppenczek

	* libpyEM/: typeconverter.cpp, typeconverter.h: [no log message]

2009-11-27 09:02  ppenczek

	* sparx/bin/: sxbootstrap_bigdisk.py, sxbootstrap_smp.py: added
	  true to sxbootstrap, not certain it is required

2009-11-26 16:10  ppenczek

	* sparx/libpy/: applications.py, development.py, reconstruction.py:
	  finish(True) added

2009-11-26 15:39  ppenczek

	* sparx/libpy/reconstruction.py:  corrected memory on rec3D

2009-11-26 15:37  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-11-25 17:12  zyang

	* libEM/aligner.cpp, libEM/aligner.h, libpyEM/libpyAligner2.cpp,
	  sparx/libpy/applications.py: Signification change to the program
	  such that we simply use C++ code to do combine_params2() and
	  inverse_transform2()

2009-11-25 16:16  ppenczek

	* sparx/libpy/reconstruction.py: change in tmp file

2009-11-25 15:49  ppenczek

	* sparx/libpy/: applications.py, reconstruction.py: change in tmp
	  file

2009-11-25 15:11  gtang

	* libEM/emdata.cpp: copy changecount in EMData's copy constructor

2009-11-25 14:32  stevel

	* CMakeLists.txt, doc/index.html, examples/tomotrackbox.py,
	  libEM/CMakeLists.txt, libEM/aligner.cpp, libEM/aligner.h,
	  libEM/analyzer.cpp, libEM/analyzer.h, libEM/averager.cpp,
	  libEM/averager.h, libEM/cmp.cpp, libEM/cmp.h, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/emdata_core.cpp, libEM/emdata_core.h,
	  libEM/emdata_cuda.cpp, libEM/emdata_metadata.cpp,
	  libEM/emdata_metadata.h, libEM/emobject.cpp, libEM/emobject.h,
	  libEM/processor.cpp, libEM/processor.h, libEM/projector.cpp,
	  libEM/projector.h, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libEM/reconstructor_tools.cpp,
	  libEM/reconstructor_tools.h, libEM/symmetry.cpp, libEM/util.cpp,
	  libEM/util.h, libEM/plugins/CMakeLists.txt,
	  libEM/plugins/aligner_template.cpp,
	  libEM/plugins/aligner_template.h,
	  libEM/plugins/averager_template.cpp,
	  libEM/plugins/averager_template.h,
	  libEM/plugins/cmp_template.cpp, libEM/plugins/cmp_template.h,
	  libEM/plugins/io_template.cpp, libEM/plugins/io_template.h,
	  libEM/plugins/processor_template.cpp,
	  libEM/plugins/processor_template.h,
	  libEM/plugins/projector_template.cpp,
	  libEM/plugins/projector_template.h,
	  libEM/plugins/reconstructor_template.cpp,
	  libEM/plugins/reconstructor_template.h,
	  libEM/sparx/analyzer_sparx.h, libEM/sparx/processor_sparx.h,
	  libEM/sparx/temp/Makefile, libpyEM/CMakeLists.txt,
	  libpyEM/EMAN2.py, libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py,
	  libpyEM/SConscript, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyReconstructor2.cpp, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emsprworkflow.py, libpyEM/qtgui/valslider.py,
	  plugins/CMakeLists.txt, plugins/aligner_template.cpp,
	  plugins/aligner_template.h, plugins/averager_template.cpp,
	  plugins/averager_template.h, plugins/cmp_template.cpp,
	  plugins/cmp_template.h, plugins/io_template.cpp,
	  plugins/io_template.h, plugins/processor_template.cpp,
	  plugins/processor_template.h, plugins/projector_template.cpp,
	  plugins/projector_template.h, plugins/reconstructor_template.cpp,
	  plugins/reconstructor_template.h, programs/e2ctf.py,
	  programs/e2eotest.py, programs/e2initialmodel.py,
	  programs/e2make3d.py, programs/e2parallel.py,
	  programs/e2proc2d.py, programs/e2speedtest.py: Merge
	  reconstructor branch

2009-11-25 13:53  stevel

	* examples/tomotrackbox.py: Everything seems to be working as it
	  should. Still need to consider normalization...

2009-11-25 12:42  stevel

	* examples/tomotrackbox.py, libEM/reconstructor.cpp,
	  libEM/reconstructor_tools.cpp, programs/e2make3d.py: Fixed

2009-11-25 11:40  zyang

	* sparx/libpy/applications.py: Fix a small bug

2009-11-25 10:38  zyang

	* sparx/libpy/applications.py: some change to CUDA alignment

2009-11-25 09:36  zyang

	* sparx/libpy/applications.py: some further change about CUDA
	  alignment

2009-11-25 08:45  stevel

	* examples/tomotrackbox.py, libEM/emobject.h,
	  libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libEM/reconstructor_tools.cpp, libpyEM/libpyReconstructor2.cpp:
	  Minor tweaks, but trying to debug an attribute related crash.

2009-11-24 17:18  zyang

	* sparx/libpy/statistics.py: Trivial change

2009-11-24 16:09  stevel

	* libEM/reconstructor.cpp, libpyEM/EMAN2db.py: Bugfix

2009-11-24 11:33  ppenczek

	* sparx/bin/sxrecons3d_n.py: option group added

2009-11-24 09:14  stevel

	* examples/tomotrackbox.py, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py,
	  programs/e2make3d.py, programs/e2parallel.py: Parallelism fix.
	  Fixing tomotrackbox for new reconstructors

2009-11-23 15:37  stevel

	* libEM/reconstructor.cpp, libpyEM/qtgui/emapplication.py,
	  programs/e2make3d.py: Relative quality for class-average
	  exclusion, good first try. Basically functional. GUI bugfix

2009-11-22 23:02  stevel

	* libEM/reconstructor.cpp, programs/e2make3d.py: Quality working,
	  but inverted weight

2009-11-21 23:14  stevel

	* libEM/reconstructor.cpp, programs/e2make3d.py: Make3d particle
	  exclusion working

2009-11-21 14:24  ppenczek

	* sparx/: bin/sxk_means_stable.py, libpy/applications.py,
	  libpy/statistics.py: corrected randomnes in clustering programs

2009-11-21 01:35  stevel

	* libEM/: reconstructor_tools.cpp, reconstructor_tools.h: Got
	  pretty well optimized parameters for the weighting kernels

2009-11-20 15:48  stevel

	* libEM/reconstructor.cpp, libEM/reconstructor_tools.cpp,
	  programs/e2make3d.py: Still tweaking.

2009-11-20 13:57  jbert

	* sparx/libpy/applications.py: change the logfile end k-means

2009-11-20 13:56  jbert

	* sparx/libpy/applications.py: change logfile k-means

2009-11-20 13:52  jbert

	* sparx/libpy/: applications.py, statistics.py: change some name
	  k-means

2009-11-20 12:55  jbert

	* sparx/bin/sxk_means_stable.py: add info to logfile K-means CUDA
	  stable

2009-11-20 12:26  jbert

	* sparx/libpy/statistics.py: change export name to stable
	  partitions (text format)

2009-11-20 12:09  jbert

	* sparx/libpy/statistics.py: fix bug

2009-11-20 09:53  ppenczek

	* sparx/bin/sxbootstrap_bigdisk.py: corrected reading mpi

2009-11-19 22:58  stevel

	* libEM/: emdata_core.cpp, emdata_core.h, reconstructor.cpp,
	  reconstructor.h: Working and now 2-3x faster than the old
	  reconstructor. Still needs a bit of tweaking (no particle pruning
	  yet, consider different interpolation schemes).

2009-11-19 21:18  ppenczek

	* sparx/libpy/utilities.py: [no log message]

2009-11-19 21:12  ppenczek

	* sparx/bin/sxbootstrap_bigdisk.py: new reading in bigdisk

2009-11-19 16:18  stevel

	* doc/index.html, libEM/emdata_core.cpp, libEM/emdata_core.h,
	  libEM/reconstructor.cpp, libEM/reconstructor_tools.cpp,
	  libEM/reconstructor_tools.h: Optimizing reconstructor

2009-11-19 14:56  zyang

	* libEM/sparx/cuda/cuda_ccf.h: Add image filteration and summation
	  funtion for 2d alignment

2009-11-19 14:56  zyang

	* libEM/aligner.cpp, libEM/aligner.h, libEM/sparx/cuda/cuda_ccf.cu,
	  sparx/libpy/applications.py: Fix some bugs relating to the CUDA
	  alignment program.

2009-11-19 05:41  stevel

	* CMakeLists.txt, libEM/emdata_core.cpp, libEM/processor.cpp,
	  libEM/projector.cpp, libEM/reconstructor.cpp,
	  libEM/reconstructor_tools.cpp, libEM/util.h: Improvements. Nasty
	  bugfix in hypot3 use.

2009-11-18 18:18  zyang

	* libEM/sparx/cuda/cuda_ccf.cu: Attempts to improve the performance
	  of CUDA code, but appearantly doesn't help much :(

2009-11-18 16:42  ppenczek

	* sparx/libpy/global_def.py: ooops, cache flag

2009-11-18 16:42  ppenczek

	* sparx/libpy/: applications.py, global_def.py, utilities.py:
	  corrected ID assignment for MPI

2009-11-18 16:13  stevel

	* libEM/emdata_core.cpp, libEM/reconstructor.cpp,
	  programs/e2make3d.py: Mostly working again. Needs some
	  optimization.

2009-11-18 11:58  loerke

	* sparx/libpy/user_functions.py: fixed user function bug.

2009-11-17 18:16  ppenczek

	* libpyEM/EMAN2db.py: slight change of syntax in EMAN2db

2009-11-17 15:56  zyang

	* libEM/sparx/cuda/cuda_ccf.cu: Trivial change.

2009-11-17 13:54  stevel

	* libEM/emdata.cpp, libEM/emdata.h, libEM/emdata_core.cpp,
	  libEM/emdata_core.h, libEM/emdata_cuda.cpp,
	  libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libEM/reconstructor.cpp, libEM/reconstructor_tools.cpp,
	  libEM/util.cpp, libEM/util.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyReconstructor2.cpp, programs/e2make3d.py: Working on
	  speed, but broke something too...

2009-11-17 11:55  zyang

	* libEM/sparx/cuda/cuda_ccf.cu: Trival change.

2009-11-17 10:45  zyang

	* libEM/aligner.cpp, libEM/aligner.h, libEM/sparx/cuda/cuda_ccf.cu,
	  libEM/sparx/cuda/cuda_ccf.h, libpyEM/libpyAligner2.cpp,
	  sparx/libpy/applications.py: Many changes to the ali2d_c_MPI()
	  and related programs such that it can use CUDA to do all of the
	  following things: (1) CTF filtration; (2) rotate, shift and
	  mirror the images; (3) sum of a stack of images

2009-11-16 23:16  stevel

	* libEM/reconstructor_tools.cpp: Fixed one bug in reconstructor
	  anyway...

2009-11-16 19:39  gtang

	* libEM/hdfio2.cpp: [no log message]

2009-11-16 15:52  ross

	* libEM/emdata.h: doxygen fix: moved commented-out functions to the
	  bottom of the EMData class declaration

2009-11-15 23:14  stevel

	* libEM/emdata_core.cpp, libEM/reconstructor.cpp,
	  libEM/reconstructor_tools.cpp, libpyEM/qtgui/valslider.py,
	  programs/e2make3d.py: Fixed problem with high resolution noise.
	  Reconstructions working.

2009-11-13 15:31  stevel

	* libEM/: analyzer.h, emdata_core.cpp, reconstructor_tools.cpp:
	  reconstructor work

2009-11-13 11:50  gtang

	* libEM/: emobject.cpp, emobject.h: fix the EMObject::type_registry
	  map initialization problem

2009-11-13 11:29  ppenczek

	* sparx/demo/generate_projections.py: generate_projections.py

2009-11-13 11:26  ppenczek

	* sparx/: bin/sxbootstrap_bigdisk.py, libpy/applications.py,
	  libpy/utilities.py: [no log message]

2009-11-13 10:36  stevel

	* libEM/emdata_core.cpp, libEM/emdata_core.h,
	  libEM/reconstructor.cpp, libEM/reconstructor_tools.cpp,
	  libpyEM/libpyEMData2.cpp: compiles again

2009-11-12 23:15  stevel

	* libEM/: emdata_core.cpp, emdata_core.h, reconstructor.cpp: Still
	  working on it

2009-11-12 16:09  stevel

	* libEM/emdata_core.cpp, libEM/emdata_core.h,
	  libEM/reconstructor.cpp, libEM/reconstructor_tools.cpp,
	  libEM/reconstructor_tools.h, libpyEM/libpyEMData2.cpp: still
	  revising

2009-11-11 23:31  zyang

	* libEM/aligner.cpp, libEM/aligner.h, libEM/sparx/cuda/cuda_ccf.cu,
	  libEM/sparx/cuda/cuda_ccf.h, libpyEM/libpyAligner2.cpp,
	  sparx/libpy/applications.py, sparx/libpy/statistics.py: Many
	  changes such that CTF filtration can now be done in CUDA.

2009-11-11 23:27  stevel

	* libpyEM/libpyEMData2.cpp: Some broken overloads need fixing

2009-11-11 22:53  stevel

	* libEM/: emdata_core.cpp, emdata_core.h, reconstructor.cpp,
	  reconstructor_tools.cpp: Working on reconstructors

2009-11-11 10:56  gtang

	* CMakeLists.txt, plugins/CMakeLists.txt,
	  plugins/aligner_template.cpp, plugins/aligner_template.h,
	  plugins/averager_template.cpp, plugins/averager_template.h,
	  plugins/cmp_template.cpp, plugins/cmp_template.h,
	  plugins/io_template.cpp, plugins/io_template.h,
	  plugins/processor_template.cpp, plugins/processor_template.h,
	  plugins/projector_template.cpp, plugins/projector_template.h,
	  plugins/reconstructor_template.cpp,
	  plugins/reconstructor_template.h: [no log message]

2009-11-11 10:20  stevel

	* doc/index.html: Doc update

2009-11-10 20:10  gtang

	* libEM/CMakeLists.txt, libEM/aligner.cpp, libEM/aligner.h,
	  libEM/analyzer.cpp, libEM/analyzer.h, libEM/averager.cpp,
	  libEM/averager.h, libEM/cmp.cpp, libEM/cmp.h, libEM/emobject.h,
	  libEM/processor.cpp, libEM/processor.h, libEM/projector.cpp,
	  libEM/projector.h, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libEM/reconstructor_tools.cpp,
	  libEM/reconstructor_tools.h, libEM/symmetry.cpp,
	  libEM/plugins/CMakeLists.txt, libEM/plugins/aligner_template.cpp,
	  libEM/plugins/aligner_template.h,
	  libEM/plugins/averager_template.cpp,
	  libEM/plugins/averager_template.h,
	  libEM/plugins/cmp_template.cpp, libEM/plugins/cmp_template.h,
	  libEM/plugins/io_template.cpp, libEM/plugins/io_template.h,
	  libEM/plugins/processor_template.cpp,
	  libEM/plugins/processor_template.h,
	  libEM/plugins/projector_template.cpp,
	  libEM/plugins/projector_template.h,
	  libEM/plugins/reconstructor_template.cpp,
	  libEM/plugins/reconstructor_template.h,
	  libEM/sparx/analyzer_sparx.h, libEM/sparx/processor_sparx.h,
	  libEM/sparx/temp/Makefile, libpyEM/CMakeLists.txt,
	  libpyEM/SConscript: change the Factory class force_add() and
	  add()n functions. It impact all modular classes.

2009-11-10 15:47  gtang

	* libpyEM/: libpyEMData2.cpp: [no log message]

2009-11-10 15:31  gtang

	* libpyEM/: libpyEMData2.cpp, libpyTransform2.cpp, libpyUtils2.cpp:
	  change the way to wrap static data member of class EMData,
	  Transform and Util. The old way failed compilation for Python >
	  2.6.2.

2009-11-10 14:15  gtang

	* libpyEM/libpyEMData2.cpp: [no log message]

2009-11-10 13:36  gtang

	* libpyEM/: libpyEMData2.cpp, libpyTransform2.cpp, libpyUtils2.cpp:
	  change the way to wrap static data member of class EMData,
	  Transform and Util. The old way failed compilation for Python >
	  2.6.2.

2009-11-10 12:08  stevel

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  programs/e2make3d.py: reconstructor work

2009-11-10 08:59  stevel

	* programs/e2initialmodel.py: Save initial models

2009-11-09 14:54  jbert

	* sparx/: bin/sxk_means.py, libpy/applications.py,
	  libpy/statistics.py: add init method D2w

2009-11-08 16:31  ppenczek

	* sparx/bin/sxbootstrap_bigdisk.py: [no log message]

2009-11-06 16:03  stevel

	* CMakeLists.txt, libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libpyEM/libpyReconstructor2.cpp, programs/e2make3d.py:
	  Reconstructor running, almost working...

2009-11-06 15:02  zyang

	* sparx/libpy/applications.py: Fix a bug

2009-11-06 14:56  zyang

	* sparx/libpy/applications.py: Change tolist() to map(). tolist()
	  will cause memory leak.

2009-11-06 00:54  gtang

	* libpyEM/libpyUtils2.cpp: keyword expression and function comment.

2009-11-06 00:53  gtang

	* libEM/sparx/util_sparx.h: comment.

2009-11-05 17:47  ppenczek

	* sparx/libpy/: applications.py: varimax

2009-11-05 17:31  fjia

	* sparx/bin/sxboxer.py: loads and saves boxes from cache so user
	  can pick up where he leaves off. inserted code to prevent user
	  from opening multiple micrographs at a time.

2009-11-05 17:28  fjia

	* pyemtbx/boxertools.py: added some procedures to class Box to
	  enable saving boxes and particle images to cache

2009-11-05 15:59  stevel

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  programs/e2make3d.py: Yea ! Almost working (reconstructors)

2009-11-05 13:45  zyang

	* sparx/libpy/: applications.py, statistics.py: Fix two small bugs

2009-11-05 13:34  zyang

	* sparx/libpy/applications.py: Fix a small bug

2009-11-05 10:56  zyang

	* sparx/libpy/applications.py: Trival change

2009-11-05 10:29  jbert

	* sparx/libpy/user_functions.py: change back

2009-11-05 10:26  jbert

	* sparx/libpy/: applications.py, statistics.py, user_functions.py:
	  change .tolist() to map(type, array) in order to fix leak memory

2009-11-04 17:08  zyang

	* sparx/libpy/applications.py: Some further change about
	  ali2d_c_MPI() using CUDA

2009-11-04 15:47  stevel

	* libEM/reconstructor.cpp, programs/e2make3d.py: Reconstructor.
	  Make3d in progress now.

2009-11-04 15:31  zyang

	* sparx/libpy/: alignment.py, applications.py: some changes to
	  ali2d_c_MPI() to improve the performance

2009-11-04 13:17  zyang

	* libEM/sparx/cuda/cuda_ccf.cu: Just add a comment

2009-11-04 11:17  gtang

	* libpyEM/libpyTransform2.cpp: bug fix

2009-11-04 07:38  stevel

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  programs/e2speedtest.py: Fixed crasher in reconstructor. Few
	  other minor bugs

2009-11-04 03:28  gtang

	* libpyEM/: libpyAligner2.cpp, libpyBoxingTools2.cpp,
	  libpyCmp2.cpp, libpyEMObject2.cpp, libpyGLUtils2.cpp,
	  libpyGeometry2.cpp, libpyPointArray2.cpp, libpyTransform2.cpp,
	  libpyUtils2.cpp: keyword expression and function comment.

2009-11-04 03:27  gtang

	* libEM/: boxingtools.h, emobject.h: comment.

2009-11-04 01:59  gtang

	* libpyEM/libpyEMData2.cpp: keyword expression and function
	  comment.

2009-11-04 01:56  gtang

	* libEM/emdata.h: comment.

2009-11-03 17:45  gtang

	* libpyEM/libpyEMData2.cpp: keyword expression and comment

2009-11-03 17:07  fjia

	* sparx/bin/sxboxer.py: changed it so the boxed particle can be
	  deleted from the micrograph window

2009-11-03 15:56  stevel

	* libEM/: emdata_metadata.cpp, emdata_metadata.h,
	  reconstructor.cpp, reconstructor.h, reconstructor_tools.cpp:
	  Reconstructor compiles, now does it work ?

2009-11-03 15:46  zyang

	* sparx/libpy/applications.py: Trivial change

2009-11-03 15:34  gtang

	* libpyEM/libpyEMData2.cpp: keyword expression and comment

2009-11-03 15:33  gtang

	* libEM/: emdata.h, emdata_core.h, sparx/emdata_sparx.h: comment

2009-11-03 14:55  zyang

	* sparx/: bin/sxali2d_c.py, libpy/alignment.py,
	  libpy/applications.py: CUDA now works on mutiple GPU

2009-11-02 16:53  zyang

	* libEM/aligner.cpp, libEM/aligner.h, libEM/sparx/cuda/cuda_ccf.cu,
	  libEM/sparx/cuda/cuda_ccf.h, libpyEM/libpyAligner2.cpp,
	  sparx/libpy/alignment.py, sparx/libpy/applications.py: Many
	  changes so that we can use CUDA to run ali2d_c_MPI() now.

2009-11-02 15:37  stevel

	* libEM/: reconstructor.cpp, reconstructor.h,
	  reconstructor_tools.cpp, reconstructor_tools.h, util.h: More
	  reconstructor work

2009-11-02 14:41  zyang

	* sparx/libpy/applications.py: Trivial change

2009-11-02 02:44  woolford

	* programs/e2boxer.py: added a check to save a crash in e2boxer

2009-11-02 02:36  woolford

	* libpyEM/qtgui/: emimage3d.py, emimage3dslice.py: no normalization
	  in 3d display, slice viewer works a bit better

2009-11-02 01:18  gtang

	* libpyEM/libpyEMData2.cpp: keyword expression and function
	  comment.

2009-11-02 01:18  gtang

	* libEM/: emdata_core.h, emdata_cuda.h: comment.

2009-11-01 23:08  stevel

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  programs/e2eotest.py: Working on reconstructor. Naming issue for
	  eotest files

2009-11-01 07:11  gtang

	* libpyEM/libpyEMData2.cpp: keyword expression and function
	  comment.

2009-11-01 07:11  gtang

	* libEM/emdata_metadata.h: comment.

2009-10-30 19:02  gtang

	* libpyEM/libpyEMData2.cpp: keyword expression and comment

2009-10-30 19:01  gtang

	* libEM/emdata_metadata.h: comment

2009-10-30 18:34  gtang

	* libEM/: sparx/emdata_sparx.h, emdata_core.h, emdata.h: comment

2009-10-30 15:52  gtang

	* libEM/emdata.h: comment

2009-10-30 15:43  gtang

	* libEM/sparx/emdata_sparx.h: comment

2009-10-30 10:41  stevel

	* libEM/reconstructor.cpp, libEM/reconstructor.h, libpyEM/EMAN2.py,
	  programs/e2initialmodel.py: more work on reconstructor

2009-10-30 10:18  gtang

	* libEM/sparx/emdata_sparx.h: comment

2009-10-30 08:35  gtang

	* libEM/hdfio2.cpp: [no log message]

2009-10-29 17:17  eman

	* libEM/hdfio2.cpp: fix compilation error for 'water'.

2009-10-29 06:37  stevel

	* libpyEM/EMAN2db.py: Another bugfix. Prevents jobs from getting
	  'stuck'

2009-10-29 06:30  stevel

	* libpyEM/EMAN2db.py: bugfix

2009-10-28 23:10  gtang

	* libpyEM/libpyEMData2.cpp: keyword expression and function
	  comment.

2009-10-28 23:01  gtang

	* libpyEM/libpyEMData2.cpp: keyword expression and function
	  comment.

2009-10-28 23:00  gtang

	* libEM/: emdata_modular.cpp, emdata_modular.h: fix comment.

2009-10-28 22:01  gtang

	* libEM/emdata_modular.h: [no log message]

2009-10-28 21:47  gtang

	* libEM/hdfio2.cpp, rt/pyem/test_imageio.py: hdf5 region I/O

2009-10-28 11:03  zyang

	* libEM/: aligner.cpp, aligner.h, sparx/cuda/cuda_ccf.cu,
	  sparx/cuda/cuda_ccf.h: Trivial change.

2009-10-27 16:51  zyang

	* libEM/: aligner.cpp, aligner.h, sparx/cuda/cuda_ccf.cu,
	  sparx/cuda/cuda_ccf.h: Many correction and improvement to CUDA
	  alignment program.

2009-10-27 13:58  zyang

	* libEM/sparx/util_sparx.cpp: Correct an incorrect comment.

2009-10-27 00:25  gtang

	* libpyEM/libpyEMData2.cpp: keyword expression and function
	  comment. Just a start.

2009-10-26 23:56  gtang

	* libEM/emdata_metadata.h: correct comment.

2009-10-26 13:54  zyang

	* sparx/libpy/development.py: Trivial change

2009-10-25 23:09  stevel

	* libEM/reconstructor.cpp, libpyEM/qtgui/emsprworkflow.py:
	  Revamping reconstructor(s) still

2009-10-23 15:57  stevel

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libEM/reconstructor_tools.h, libpyEM/qtgui/emapplication.py,
	  programs/e2proc2d.py: Broken at the moment...

2009-10-23 11:41  zyang

	* sparx/libpy/development.py: Trivial change.

2009-10-23 08:38  gtang

	* programs/e2proc2d.py: fix the way to handle multiple processors

2009-10-22 16:08  stevel

	* examples/tomotrackbox.py, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py,
	  libpyEM/libpyReconstructor2.cpp, libpyEM/qtgui/emapplication.py,
	  plugins/reconstructor_template.cpp,
	  plugins/reconstructor_template.h, programs/e2ctf.py,
	  programs/e2make3d.py: Working on revamping reconstructors

2009-10-22 11:44  ross

	* libEM/processor.cpp: removed print statements from
	  BinarySkeletonizerProcessor::process()

2009-10-22 11:37  ross

	* libEM/gorgon/: volume_data.cpp, volume.cpp: removed print
	  statement in destructor

2009-10-22 11:34  ross

	* libEM/: processor.cpp, processor.h: Fixed bug in
	  BinarySkeletonizerProcessor

2009-10-21 23:16  stevel

	* programs/e2ctf.py: Add particle selecting option to e2ctf

2009-10-21 15:56  ross

	* libEM/gorgon/: volume_data.cpp, volume_data.h: The VolumeData
	  class no longer stores its own values for the origin, angstroms
	  per pixel, and dimensions. It accesses that information stored in
	  the EMData object.

2009-10-21 15:27  gtang

	* rt/pyem/test_processor.py: [no log message]

2009-10-21 15:05  zyang

	* pyemtbx/boxertools.py, sparx/bin/sxboxer.py,
	  sparx/libpy/morphology.py: Made many change to sxboxer.py to make
	  it more bug-free, reasonable and user-friendly.

2009-10-21 13:32  ross

	* libEM/: processor.cpp, processor.h: added
	  BinarySkeletonizerProcessor class which is used by SSEHunter

2009-10-21 13:25  ross

	* libEM/CMakeLists.txt: added new source files from the gorgon
	  subdirectory

2009-10-21 13:20  ross

	* libEM/gorgon/: volume.cpp, volume.h: updated to reflect changes
	  in Gorgon source (e.g. separating VolumeData class out of Volume
	  class)

2009-10-21 13:17  ross

	* libEM/gorgon/: grid_queue.cpp, grid_queue.h, grid_queue2.cpp,
	  grid_queue2.h, skeletonizer.cpp, skeletonizer.h, volume_data.cpp,
	  volume_data.h: [no log message]

2009-10-21 08:46  gtang

	* libEM/emdata.cpp: copy changecount in the copy() function

2009-10-20 17:39  stevel

	* programs/e2ctf.py: Undid recent changes to restore functionality.

2009-10-20 17:07  zyang

	* sparx/: bin/sxali2d_a.py, libpy/applications.py: Made multiple
	  changes to ali2d_a_MPI()

2009-10-20 17:02  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Add function image_mutation()

2009-10-20 14:18  stevel

	* programs/e2ctf.py: Turn off default autofit

2009-10-20 14:17  stevel

	* programs/e2ctf.py: tweak b-factor fit

2009-10-20 09:08  jbert

	* programs/e2ctf.py: trivial change

2009-10-19 15:52  jbert

	* sparx/libpy/applications.py: trivial change k-means

2009-10-19 14:48  jbert

	* sparx/libpy/statistics.py: trivial change k-means

2009-10-19 10:43  zyang

	* sparx/bin/sxboxer.py: Fix two bugs

2009-10-18 15:09  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-10-16 21:11  zyang

	* sparx/bin/sxboxer.py: More change

2009-10-16 20:46  zyang

	* pyemtbx/boxertools.py, sparx/bin/sxboxer.py: [no log message]

2009-10-16 17:16  fjia

	* sparx/bin/sxboxer.py: sxboxer.py

2009-10-16 15:57  fjia

	* sparx/bin/sxboxer.py: sxboxer.py

2009-10-16 15:45  stevel

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emplot2d.py,
	  libpyEM/qtgui/emplot3d.py, programs/e2ctf.py: Window placement
	  fixes

2009-10-16 15:36  fjia

	* sparx/libpy/morphology.py: changed ctf_1 to ctf_2 in defocus_gett

2009-10-16 15:10  jbert

	* programs/e2ctf.py: trivial change

2009-10-16 13:16  zyang

	* pyemtbx/boxertools.py, sparx/bin/sxboxer.py: Many change to boxer
	  program.

2009-10-16 13:01  jbert

	* programs/e2ctf.py: fix a bug

2009-10-16 12:13  jbert

	* programs/e2ctf.py: can start from given CTF

2009-10-16 11:37  zyang

	* sparx/: bin/sxboxer.py, libpy/morphology.py: Trivial change.

2009-10-16 11:14  fjia

	* sparx/bin/sxboxer.py: fixed the change for spacing tickmarks on
	  plot

2009-10-16 10:00  zyang

	* libEM/: aligner.cpp, aligner.h, sparx/cuda/cuda_ccf.cu,
	  sparx/cuda/cuda_ccf.h: A small change

2009-10-15 17:36  gtang

	* rt/emdata/CMakeLists.txt: [no log message]

2009-10-15 16:17  zyang

	* sparx/bin/sxboxer.py: Fix a small bug, also did some cosmetic
	  changes.

2009-10-15 16:15  zyang

	* sparx/libpy/morphology.py, pyemtbx/boxertools.py: Some cosmetic
	  change

2009-10-15 16:01  stevel

	* examples/tomotrackbox.py, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimageutil.py: Work on tomotrackbox. Also method
	  for windows to remember where they are on the screen.

2009-10-15 15:56  gtang

	* libEM/pointarray.cpp: compilation warning fix

2009-10-15 14:10  zyang

	* sparx/bin/sxboxer.py: Delete some unused buttons.

2009-10-15 13:45  fjia

	* sparx/bin/sxboxer.py: change related to CTF Inspector

2009-10-15 12:57  jbert

	* sparx/libpy/: applications.py, statistics.py: fix bug k-means
	  export stability

2009-10-15 11:55  fjia

	* sparx/bin/sxboxer.py: changed it so user can set gauss_width from
	  command line via the width option

2009-10-15 11:47  fjia

	* sparx/bin/sxboxer.py: accidentally overwrote yang's version. this
	  should be the same as version 1.8

2009-10-15 11:40  fjia

	* sparx/bin/sxboxer.py: changed it so user can set gauss_width from
	  command line via the option width

2009-10-15 11:28  jbert

	* programs/e2ctf.py: add option id_micrograph

2009-10-15 11:27  zyang

	* sparx/bin/sxboxer.py: When click on the 'Write the output file'
	  button, no longer pops up a new window, just directly write the
	  output files.

2009-10-15 11:09  fjia

	* sparx/bin/sxboxer.py: removed method option, so the method used
	  will always be Gauss, and can't be changed to swarms. switching
	  to swarms is blocked in the main window, so there is no longer a
	  swarms option in the drop down box. the --gui option will be true
	  by default.

2009-10-14 23:08  stevel

	* examples/tomotrackbox.py: tomo work

2009-10-14 22:49  stevel

	* examples/tomotrackbox.py, libEM/cmp.cpp, libEM/cmp.h: Mask option
	  in frc. Still needs testing

2009-10-14 19:02  stevel

	* examples/tomotrackbox.py, libEM/.cvsignore, libEM/aligner.cpp,
	  libEM/aligner.h, libEM/emdata_core.h, libpyEM/EMAN2PAR.py,
	  plugins/cmp_template.cpp, plugins/cmp_template.h: Tomography work

2009-10-14 18:04  fjia

	* sparx/bin/sxboxer.py: changed it so pixel_in and pixel_out can be
	  set from command line

2009-10-14 17:41  zyang

	* pyemtbx/boxertools.py, sparx/bin/sxboxer.py: Some further
	  improvement of sxboxer.py

2009-10-14 15:37  zyang

	* libEM/sparx/cuda/cuda_ccf.cu: Fix a small bug.

2009-10-14 12:57  ppenczek

	* libEM/processor.h, pyemtbx/boxertools.py, sparx/bin/sxboxer.py:
	  corrections in sxboxer

2009-10-14 11:53  fjia

	* sparx/bin/sxboxer.py: modified how the plot is shown when Inspect
	  CTF button is activated

2009-10-14 11:32  ppenczek

	* sparx/demo/7_mpi_bdb_ctf/run_through_example: boxer changes

2009-10-14 10:02  gtang

	* libpyEM/qtgui/emsprworkflow.py, programs/e2boxer.py:
	  e2boxer2->e2boxer

2009-10-14 09:41  jbert

	* sparx/demo/7_mpi_bdb_ctf/run_through_example: change ctf_fstop
	  1.0 to 0.5

2009-10-13 18:49  gtang

	* programs/: e2boxer.py, e2boxer2.py: rename e2boxer2.py as
	  e2boxer.py. The original e2boxer is taken over by Pawel Penczeck.

2009-10-13 17:39  zyang

	* libpyEM/qtgui/emsprworkflow.py, pyemtbx/boxertools.py,
	  sparx/bin/sxboxer.py: Fix multiple problems relating to boxer

2009-10-13 15:02  gtang

	* libEM/emdata_io.cpp: fix the HDF5 file writing issue. Because
	  some attribute nx,ny,and nz are taken out of attribute
	  dictionary.

2009-10-13 14:48  zyang

	* sparx/bin/sxboxer.py: Move the file to here

2009-10-13 14:46  zyang

	* programs/e2boxer.py: Move to sxboxer.py

2009-10-13 06:44  woolford

	* libEM/reconstructor.cpp, libpyEM/qtgui/emboxerbase.py,
	  programs/e2boxer2.py, programs/e2eulerxplor.py: boxer fixes

2009-10-12 22:05  stevel

	* programs/e2simmx.py: bugfix

2009-10-12 18:57  stevel

	* programs/e2refmerge.py: Initial incomplete version

2009-10-12 00:42  stevel

	* libEM/emdata_metadata.cpp: error with stats

2009-10-11 23:18  stevel

	* libEM/emdata_metadata.cpp, libpyEM/EMAN2PAR.py,
	  programs/e2simmx.py: Bugfix in new mask option

2009-10-11 22:26  zyang

	* libEM/sparx/cuda/cuda_ccf.cu: Fix some bugs in the program,
	  should works well right now.

2009-10-11 21:28  zyang

	* libEM/sparx/cuda/cuda_ccf.cu: Made many change to the CUDA
	  alignment program so that is adapts to the current video card

2009-10-11 16:21  ppenczek

	* programs/e2boxer.py, sparx/demo/generate_projections.py,
	  sparx/demo/7_mpi_bdb_ctf/run_through_example,
	  sparx/libpy/applications.py, sparx/libpy/morphology.py,
	  sparx/libpy/utilities.py: many corrections in e2boxer

2009-10-11 01:01  stevel

	* programs/: e2refine.py, e2simmx.py: mask option in similarity
	  matrix

2009-10-09 16:56  jbert

	* sparx/libpy/statistics.py: fix memory leak when list is convert
	  from array given by MPI

2009-10-09 15:03  stevel

	* libpyEM/: EMAN2PAR.py, qtgui/emapplication.py: requeue fix

2009-10-09 10:56  jbert

	* sparx/bin/sxk_means_stable.py: trivial change

2009-10-09 10:42  jbert

	* sparx/bin/sxk_means.py: trivial change

2009-10-08 17:24  jbert

	* sparx/libpy/: applications.py, statistics.py: start some change
	  to k_means_stable MPI

2009-10-08 16:45  jbert

	* sparx/bin/sxk_means_stable.py: change a flag k_means_stable

2009-10-08 15:33  jbert

	* libEM/processor.cpp, libEM/processor.h,
	  libEM/sparx/cuda/cuda_mpi_kmeans.cu,
	  libEM/sparx/cuda/cuda_mpi_kmeans.h,
	  sparx/bin/sxk_means_stable.py, sparx/libpy/statistics.py: wrap
	  code: k-means stable MPI CUDA

2009-10-08 14:08  stevel

	* examples/tomotrackbox.py, libEM/processor.cpp, libEM/processor.h,
	  programs/e2boxer2.py, pyemtbx/boxertools.py,
	  rt/pyem/test_processor.py, utils/proc2d.cpp: Improve
	  tomotrackbox.

2009-10-08 13:19  zyang

	* sparx/libpy/applications.py: Made some changes in ali2d_a_MPI()

2009-10-08 11:40  zyang

	* sparx/libpy/applications.py: Fix a trival bug

2009-10-08 11:35  zyang

	* sparx/libpy/applications.py: Change ali2d_a_MPI() back to last
	  week's version

2009-10-08 10:54  zyang

	* sparx/libpy/applications.py: For test

2009-10-07 16:20  ross

	* libEM/gorgon/: volume.cpp, volume.h: incorporated the member
	  functions I know I'll need for skeletonizing a density map

2009-10-07 16:14  stevel

	* examples/tomotrackbox.py: Minor fixes

2009-10-07 06:00  woolford

	* libpyEM/qtgui/: emimagemx.py, emsave.py: emimagemx save works for
	  deleted particles

2009-10-07 05:14  woolford

	* programs/: e2boxer2.py, e2classaverage.py: more helpful output
	  statements in e2boxer2

2009-10-06 23:23  stevel

	* examples/tomotrackbox.py: trivial

2009-10-06 23:20  stevel

	* examples/tomotrackbox.py, libpyEM/EMAN2PAR.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emshape.py: Fix shape
	  problem

2009-10-06 18:19  ross

	* libEM/gorgon/volume.cpp: utdated makefiles made me think this
	  compiled --> commenting out the broken code

2009-10-06 18:18  ross

	* libEM/gorgon/volume.h: outdated makefiles made me think this
	  compiled --> commenting out the broken code

2009-10-06 18:03  ross

	* libEM/gorgon/priority_queue.h: copied in all the code from
	  PriorityQueue.h in the Gorgon project with very minimal changes

2009-10-06 18:01  ross

	* libEM/gorgon/volume.h: copied in the code from the Gorgon project
	  that I know we'll use for skeletonization

2009-10-06 18:01  ross

	* libEM/gorgon/volume.cpp: copied in the code from the Gorgon
	  project that I know we will use for skeletonization

2009-10-06 16:58  ross

	* libEM/gorgon/: volume.cpp, volume.h, priority_que.h: [no log
	  message]

2009-10-06 16:54  ross

	* libEM/gorgon/priority_queue.h: [no log message]

2009-10-06 16:51  gtang

	* libEM/: gorgon/priority_que.h, CMakeLists.txt,
	  gorgon/CMakeLists.txt, gorgon/priority_que.cpp,
	  gorgon/volume.cpp, gorgon/volume.h: gorgon

2009-10-06 16:29  ross

	* libEM/gorgon/: priority_que.cpp, priority_que.h, volume.cpp,
	  volume.h: [no log message]

2009-10-06 16:20  stevel

	* examples/tomotrackbox.py, libEM/processor.cpp,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emshape.py, programs/e2eulerxplor.py: Working on
	  tomotrackbox. Does reconstructions ! Support flattening in Eueler
	  explorer

2009-10-06 16:09  gtang

	* libEM/gorgon/CMakeLists.txt: [no log message]

2009-10-06 16:00  ppenczek

	* sparx/bin/sxbootstrap_calcwgts.py: corrected reading, now much
	  faster

2009-10-06 15:59  gtang

	* libEM/CMakeLists.txt: gorgon

2009-10-06 15:00  zyang

	* sparx/libpy/statistics.py: Fix an outdated code.

2009-10-06 12:33  jbert

	* libEM/sparx/cuda/cuda_mpi_kmeans.cu, sparx/libpy/applications.py,
	  sparx/libpy/statistics.py: change the way to select GPU device

2009-10-06 11:36  jbert

	* sparx/libpy/statistics.py: masking image for text file missing

2009-10-06 10:42  jbert

	* sparx/libpy/: applications.py, statistics.py: change criterion to
	  stop k-means cuda SA

2009-10-05 14:57  stevel

	* examples/tomotrackbox.py, libpyEM/EMAN2db.py,
	  libpyEM/qtgui/emimage2d.py, programs/e2eotest.py: New program for
	  subtomogram extraction at the tilt-series level

2009-10-04 23:20  ppenczek

	* sparx/libpy/applications.py: Many change to ali2d_a_MPI()

2009-10-04 22:13  stevel

	* programs/e2initialmodel.py: Working on initial models

2009-10-03 23:21  stevel

	* programs/e2classaverage.py: Setsf fix

2009-10-03 22:16  stevel

	* programs/e2classaverage.py: Work on setsf

2009-10-03 13:47  stevel

	* programs/e2classaverage.py: try fixing apix

2009-10-03 10:40  stevel

	* libpyEM/EMAN2PAR.py: Minor fix

2009-10-03 07:52  ppenczek

	* sparx/libpy/applications.py: cleaning

2009-10-03 07:48  ppenczek

	* sparx/: bin/sxfactcoords.py, libpy/applications.py: sxfact mpi
	  corrected

2009-10-03 00:19  stevel

	* libEM/processor.cpp, libpyEM/qtgui/emshape.py,
	  programs/e2simmxxplor.py: Fix refine2d crasher

2009-10-02 19:44  ross

	* programs/e2helixboxer.py: picked particles now displayed in an
	  EMImageMX module, though a new particle is added even when moving
	  a box currently

2009-10-02 17:15  jbert

	* libEM/processor.cpp: fix a bug

2009-10-02 17:13  jbert

	* sparx/libpy/statistics.py: trivial change

2009-10-02 14:44  stevel

	* libEM/emdata.cpp: Fix clip routine again

2009-10-02 13:04  stevel

	* libEM/emdata.cpp, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2refine2d.py: get_rotated_clip works in 2d (I hope)

2009-10-02 10:31  zyang

	* programs/e2msa.py: Fix a trival bug

2009-10-02 10:23  zyang

	* programs/e2msa.py: Trival change

2009-10-02 08:39  stevel

	* libEM/symmetry.cpp, libpyEM/qtgui/emselector.py,
	  programs/e2classaverage.py, programs/e2iminfo.py: Change to
	  projection generation. Trivial fixes.

2009-10-01 13:48  zyang

	* sparx/libpy/applications.py: Trival change

2009-10-01 09:04  jbert

	* sparx/libpy/: applications.py, statistics.py: fix some bugs to
	  cuda mpi k-means

2009-09-30 12:02  ross

	* programs/e2helixboxer.py: Moving entire boxes or just an endpoint
	  of a box is supported, also EMHelixBoxerModule is now in use. For
	  some reason, creating an Img2DModEventsHandler in
	  EMHelixBoxerModule causes mouse bugs, so it is created in main().

2009-09-30 11:57  ross

	* libpyEM/qtgui/emshape.py: added assert statements to ensure that
	  self.shape[8] is a positive number for all the shapes that use it

2009-09-30 10:31  jbert

	* libEM/sparx/cuda/: cuda_mpi_kmeans.cu, cuda_mpi_kmeans.h: add a
	  function to compute criterion with CUDA

2009-09-29 18:27  ross

	* install-dependencies.py: updated the comment at the top of the
	  file to say when the library download URLs were valid

2009-09-29 18:17  ross

	* install-dependencies.py: only need to set OS = "MAC" or OS =
	  "LINUX" depending on your operating system rather than comment
	  and uncomment several lines

2009-09-29 17:48  ross

	* install-dependencies.py: updated some download URL's

2009-09-28 16:54  zyang

	* sparx/libpy/applications.py: Fix two small bugs

2009-09-28 12:45  fjia

	* sparx/libpy/alignment.py: delete python code normalize_rings and
	  replace it with calls to the c version Normalize_ring

2009-09-28 12:42  fjia

	* sparx/libpy/projection.py: made change to use C++ version of
	  Normalize_ring instead of the python version

2009-09-28 12:27  fjia

	* libpyEM/libpyUtils2.cpp: added def for Normalize_ring

2009-09-28 12:23  fjia

	* libpyEM/libpyEMData2.cpp: added functions
	  rot_scale_trans2D_background, rot_scale_trans_background,
	  rot_scale_conv_new_background

2009-09-28 12:17  fjia

	* sparx/libpy/fundamentals.py: added "mode" option to rot_shift3D
	  and rot_shift2D. mode defaults to "background" which removes
	  background artifacts.

2009-09-28 11:46  fjia

	* libEM/sparx/emdata_sparx.cpp: added new functions to deal with
	  background artifacts: rot_scale_trans_background,
	  rot_scale_trans2D_background, rot_scale_conv_new_background

2009-09-28 11:37  fjia

	* libEM/sparx/util_sparx.cpp: added two helper functions for
	  dealing with background artifacts: quadri_background and
	  get_pixel_conv_new_background. added trivial change to the
	  signature of Normalize_ring

2009-09-28 11:28  fjia

	* libEM/sparx/util_sparx.h: added headers for the helper functions
	  quadri_background, get_pixel_conv_new_background. added header
	  for Normalize_ring.

2009-09-28 11:18  fjia

	* libEM/sparx/emdata_sparx.h: added headers for new functionalities
	  to deal with background artificats

2009-09-28 11:04  fjia

	* libEM/sparx/rsconvolution.cpp: modified to deal with boundary
	  cases

2009-09-28 10:25  gtang

	* rt/pyem/test_processor.py: [no log message]

2009-09-27 11:01  ppenczek

	* sparx/libpy/: applications.py, statistics.py, user_functions.py:
	  [no log message]

2009-09-25 17:22  zyang

	* sparx/libpy/applications.py: Optimize ali2d_a_MPI()

2009-09-25 16:54  jbert

	* sparx/: bin/sxk_means_stable.py, libpy/applications.py,
	  libpy/statistics.py: update k-means stab code

2009-09-25 15:26  stevel

	* libpyEM/qtgui/emsprworkflow.py, programs/e2classaverage.py:
	  bugfix

2009-09-25 13:35  stevel

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2classaverage.py,
	  programs/e2eulerxplor.py, programs/e2refine.py: New- setsf in
	  class-averaging

2009-09-24 16:43  jbert

	* libEM/sparx/cuda/CMakeLists.txt: clean cuda code

2009-09-24 16:41  jbert

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/libpyProcessor2.cpp, sparx/libpy/applications.py,
	  sparx/libpy/development.py, sparx/libpy/statistics.py: k-means
	  cuda mpi cla sse groups: remove consistency, wrap new cuda code,
	  clean code, remove old cuda code (same code for mpi and non mpi)

2009-09-24 15:21  zyang

	* sparx/libpy/applications.py: Another trival change

2009-09-24 15:19  zyang

	* sparx/libpy/applications.py: Trival change.

2009-09-24 14:27  ross

	* libEM/emdata.h: commented out Doxygen-formatted comments to
	  functions that have been commented out to fix
	  EMData::get_clipDoxygen documentation

2009-09-24 14:07  gtang

	* libEM/emdata.h: comment out unused comment for doxygen

2009-09-24 10:26  zyang

	* sparx/libpy/development.py: Some development of ali3d_d_MPI()

2009-09-23 19:20  ross

	* programs/e2helixboxer.py: added mock-up for EMHelixBoxerModule
	  and other classes in the program

2009-09-23 16:10  ross

	* libpyEM/qtgui/emimage2d.py: EMImage2DModule.get_shapes() was
	  defined twice. I removed the second identical defintion.

2009-09-23 16:03  ross

	* libpyEM/qtgui/emboxerbase.py: fixed comment to refer to
	  emboxerbase.py rather than e2boxerbase.py

2009-09-23 16:02  ross

	* libpyEM/qtgui/emshape.py: "rotatebox" changed to "rectline" and a
	  line is now drawn between the two endpoints lengthwise

2009-09-23 16:01  ross

	* programs/e2helixboxer.py: moving boxes, moving endpoints, and
	  deleting boxes now supported CS:
	  ----------------------------------------------------------------------

2009-09-23 15:30  zyang

	* sparx/libpy/statistics.py: Add a new function
	  ave_oe_series_textfile()

2009-09-23 15:23  stevel

	* libpyEM/EMAN2.py, libpyEM/EMAN2db.py, programs/e2classaverage.py,
	  programs/e2parallel.py, programs/e2project3d.py,
	  programs/e2simmx.py: First functional version of parallelism
	  server monitor

2009-09-23 14:33  stevel

	* libpyEM/EMAN2PAR.py: oops

2009-09-23 14:29  stevel

	* libpyEM/EMAN2PAR.py, programs/e2classaverage.py,
	  programs/e2parallel.py, programs/e2project3d.py,
	  programs/e2simmx.py: New parallelism version. Working GUI task
	  monitor.

2009-09-23 09:50  zyang

	* sparx/libpy/statistics.py: Make change to hist_list() to make it
	  more reasonable.

2009-09-22 17:18  ross

	* programs/e2helixboxer.py: Drawing rectangles on the main image is
	  supported. First steps toward moving or rotating existing
	  rectangles are implemented.

2009-09-22 15:49  stevel

	* libpyEM/qtgui/emselector.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2classaverage.py, programs/e2simmxxplor.py: Working on
	  new refinement features

2009-09-22 12:13  jbert

	* libEM/processor.cpp, libEM/processor.h,
	  libEM/sparx/cuda/CMakeLists.txt,
	  libEM/sparx/cuda/cuda_mpi_kmeans.cu,
	  libEM/sparx/cuda/cuda_mpi_kmeans.h, libpyEM/libpyProcessor2.cpp:
	  add mpicuda k-means

2009-09-21 17:12  zyang

	* sparx/libpy/development.py: Add a temp function.

2009-09-21 17:12  zyang

	* sparx/libpy/applications.py: Fix a third bug in ali3d_d_MPI()

2009-09-21 16:53  jbert

	* libEM/sparx/native_fft.cpp: fix a bug

2009-09-21 16:52  zyang

	* sparx/libpy/applications.py: Fix another bug in ali3d_d_MPI()

2009-09-21 15:25  gtang

	* libEM/processor.cpp: fix for MSVC

2009-09-21 15:19  zyang

	* sparx/libpy/applications.py: Fix a bug in ali3d_d_MPI()

2009-09-21 14:57  ppenczek

	* sparx/: bin/sxproject3d.py,
	  demo/7_mpi_bdb_ctf/run_through_example, libpy/applications.py,
	  libpy/user_functions.py: ali3dm

2009-09-21 11:46  zyang

	* sparx/libpy/applications.py: Add hist_dist() in ali2d_c() and
	  ali2d_c_MPI() to obtain the distribution of pixel error between
	  each iteration.

2009-09-21 09:36  jbert

	* sparx/libpy/applications.py: prepare cuda mpi

2009-09-21 09:35  ppenczek

	* sparx/libpy/user_functions.py: ali3d_e corrected

2009-09-20 15:26  ppenczek

	* sparx/libpy/: alignment.py, applications.py, user_functions.py,
	  utilities.py: ali3d_e corrected

2009-09-18 22:53  stevel

	* examples/displaydemo.py: Demo showing how to use a module

2009-09-18 18:46  ppenczek

	* sparx/libpy/: applications.py, alignment.py, development.py:
	  ali3d_e broken

2009-09-18 16:52  ross

	* libpyEM/qtgui/emshape.py: added "rcirclepoint" shape for use in
	  e2helixboxer.py and added a few code comments elsewhere

2009-09-18 16:13  stevel

	* libpyEM/EMAN2db.py: Fix bug in progress on dead process

2009-09-18 15:53  ppenczek

	* sparx/libpy/alignment.py:  beginning

2009-09-18 15:36  stevel

	* libpyEM/qtgui/emglobjects.py, programs/e2classaverage.py,
	  programs/e2simmxxplor.py: Gui tweaks

2009-09-18 14:11  gtang

	* libEM/mrcio.cpp: bug fix

2009-09-18 10:47  zyang

	* sparx/libpy/applications.py: Use function hist_list() in
	  ali2d_c()

2009-09-18 10:46  zyang

	* sparx/libpy/statistics.py: Trival change

2009-09-18 08:03  stevel

	* libpyEM/EMAN2PAR.py, programs/e2simmx.py: another oops

2009-09-18 07:43  stevel

	* libpyEM/EMAN2PAR.py: oops

2009-09-18 07:32  stevel

	* libEM/averager.cpp, libpyEM/EMAN2PAR.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimage3dsym.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2classifykmeans.py,
	  programs/e2eotest.py, programs/e2refine.py, programs/e2simmx.py,
	  programs/e2simmxxplor.py: Bugfixes. Better job termination in
	  parallelism.

2009-09-16 16:27  zyang

	* sparx/libpy/applications.py: Improve ali2d_c() such that it will
	  output pixel error between each run.

2009-09-16 15:40  stevel

	* libEM/emdata.cpp, libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2eulerxplor.py,
	  programs/e2make3d.py, programs/e2proc3d.py, programs/e2refine.py,
	  programs/e2simmx.py, programs/e2simmxxplor.py: Many experimental
	  changes. Hopefully nothing will break. Fixed setsf in proc3d.
	  Setsf option in refinement.

2009-09-16 12:31  ppenczek

	* sparx/libpy/: applications.py: stopping in ali3d_d

2009-09-16 12:30  ppenczek

	* sparx/libpy/applications.py: ali3d_d

2009-09-16 11:43  ppenczek

	* sparx/libpy/applications.py: stopping in ali3d_d

2009-09-16 10:32  zyang

	* sparx/: bin/sxali2d_c.py, libpy/applications.py: [no log message]

2009-09-16 09:51  ppenczek

	* sparx/bin/sxfind_struct.py: comments

2009-09-16 09:47  zyang

	* sparx/libpy/user_functions.py: [no log message]

2009-09-16 09:43  ppenczek

	* sparx/libpy/: alignment.py, projection.py: comments

2009-09-16 09:39  gtang

	* rt/pyem/test_processor.py: [no log message]

2009-09-15 15:56  stevel

	* libEM/xydata.cpp, libEM/xydata.h, programs/e2ctf.py: Use good
	  structure factor in visual fitting. Undid some performance
	  killers more sensibly.

2009-09-15 14:24  ppenczek

	* sparx/libpy/utilities.py: rotation_between_anglesets corrected

2009-09-15 12:58  ppenczek

	* sparx/libpy/utilities.py: rotation_between_anglesets

2009-09-15 12:54  stevel

	* programs/e2eulerxplor.py: trivial

2009-09-15 12:20  ppenczek

	* sparx/bin/sxbootstrap_bigdisk.py: added setting to zero largest
	  weights in bootstrap

2009-09-15 11:06  stevel

	* examples/makebigfromseq.py, examples/shrinkbigimage.py,
	  examples/transalignavg.py, libEM/processor.cpp,
	  libEM/processor.h, libpyEM/qtgui/emimage3dsym.py,
	  programs/e2classaverage.py, programs/e2initialmodel.py,
	  programs/e2simmxxplor.py, rt/pyem/test_processor.py:
	  Normalization bugfix. Flattening in simmx explorer.

2009-09-15 07:33  stevel

	* libpyEM/EMAN2PAR.py, programs/e2simmx.py: again

2009-09-15 07:09  stevel

	* programs/e2iminfo.py: trivial

2009-09-15 06:59  stevel

	* libpyEM/EMAN2PAR.py: Tweak parallelism

2009-09-14 16:02  gtang

	* libEM/averager.cpp, libEM/cmp.cpp, libEM/emdata_metadata.cpp,
	  libEM/emutil.cpp, libEM/imagicio.cpp, libEM/processor.cpp,
	  libEM/reconstructor.cpp, utils/iminfo.cpp,
	  rt/emdata/imagic_ctf_test.cpp: memory leak fix

2009-09-14 15:56  gtang

	* libEM/sparx/emdata_sparx.cpp: memory leak fix

2009-09-14 15:30  stevel

	* libpyEM/EMAN2PAR.py: More parallelism tweaks.

2009-09-14 14:27  gtang

	* libEM/: aligner.cpp, imagicio.cpp, mrcio.cpp, processor.cpp,
	  projector.cpp, reconstructor.cpp, spiderio.cpp,
	  sparx/util_sparx.cpp, emdata_metadata.cpp: memory leak fix

2009-09-14 14:22  gtang

	* rt/emdata/: CMakeLists.txt, memtest.cpp, memtest2.cpp,
	  test_emobject.cpp: new testing code

2009-09-14 14:21  gtang

	* CMakeLists.txt: use ENABLE_DEBUG for memory check

2009-09-14 12:40  stevel

	* libpyEM/EMAN2PAR.py, programs/e2classaverage.py,
	  programs/e2initialmodel.py, programs/e2simmx.py: More tweaking of
	  parallelism

2009-09-14 11:03  stevel

	* programs/e2initialmodel.py: Serious alignment error !  Should
	  work much better.

2009-09-14 09:50  stevel

	* programs/e2initialmodel.py: oops

2009-09-14 09:46  stevel

	* libEM/cmp.cpp, libEM/cmp.h, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2initialmodel.py, programs/e2simmxxplor.py: Turn off
	  ampweight default in frc comparator. Better centering in initial
	  model generator.

2009-09-13 16:23  gtang

	* programs/e2speedtest.py: [no log message]

2009-09-13 13:34  stevel

	* programs/: e2make3d.py, e2parallel.py: Parallel fix

2009-09-12 11:01  stevel

	* programs/: e2classaverage.py, e2simmx.py: die when told to

2009-09-11 16:47  gtang

	* programs/e2speedtest.py: [no log message]

2009-09-11 16:26  gtang

	* libEM/cmp.cpp: add const for constant pointer

2009-09-11 16:08  gtang

	* libEM/processor.cpp: comment fix

2009-09-11 14:06  stevel

	* libEM/cmp.cpp, libEM/cmp.h, libpyEM/qtgui/emplot2d.py,
	  programs/e2simmxxplor.py: Fix to frc comparator

2009-09-11 10:42  stevel

	* libEM/cmp.cpp, programs/e2simmxxplor.py: 1 more try

2009-09-11 10:34  stevel

	* libEM/cmp.cpp, programs/e2simmxxplor.py: Test bugfix on fsc
	  comparator

2009-09-10 16:30  stevel

	* libpyEM/EMAN2PAR.py, programs/e2simmxxplor.py: New display
	  options in simmxplor

2009-09-10 09:01  stevel

	* programs/e2parallel.py: trivial

2009-09-10 08:49  stevel

	* libpyEM/EMAN2PAR.py, libpyEM/qtgui/emimage3dsym.py,
	  programs/e2classaverage.py, programs/e2parallel.py,
	  programs/e2simmxxplor.py: Tweaks to parallelism, trying to debug
	  memory usage. Bugfix for simmxplor

2009-09-09 13:02  stevel

	* libpyEM/EMAN2PAR.py: Parallelism work

2009-09-09 12:29  stevel

	* libpyEM/EMAN2PAR.py, programs/e2classaverage.py,
	  programs/e2simmx.py: better job launching

2009-09-09 11:17  jbert

	* libEM/sparx/cuda/: cuda_mpi_kmeans.cu, cuda_mpi_kmeans.h: still
	  working on cuda mpi kmeans

2009-09-09 10:34  stevel

	* utils/CMakeLists.txt: Get rid of broken e2iminfo

2009-09-09 10:33  stevel

	* libpyEM/EMAN2PAR.py, programs/e2iminfo.py: revamped e2iminfo.py

2009-09-09 09:50  gtang

	* rt/pyem/test_processor.py: unit test update

2009-09-09 09:28  jbert

	* CMakeLists.txt: Add a supplementary path to NUMPY_INCLUDE_PATH

2009-09-09 08:44  stevel

	* libEM/aligner.cpp, programs/e2classaverage.py,
	  programs/e2stacksort.py: Make iter=1 do something in
	  class-averaging

2009-09-09 06:42  ppenczek

	* sparx/libpy/applications.py: import incorrectly indeted in cml

2009-09-08 18:15  ross

	* libEM/: processor.cpp, processor.h: added ModelHelixProcessor and
	  ApplyPolynomialProfileToHelix

2009-09-08 16:43  jbert

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/libpyProcessor2.cpp: draft cuda mpi k-means

2009-09-08 14:54  stevel

	* libEM/processor.cpp, libpyEM/EMAN2PAR.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2classaverage.py,
	  programs/e2classptcl.py, programs/e2parallel.py,
	  programs/e2simmxxplor.py: Centering bug, new particle extraction
	  program

2009-09-08 08:58  ppenczek

	* sparx/: bin/sxproject3d.py, libpy/applications.py: full

2009-09-07 23:55  stevel

	* programs/: e2parallel.py, e2simmxxplor.py: New command in
	  parallel. Start mod on simmxplor

2009-09-07 09:14  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-09-07 08:20  ppenczek

	* sparx/libpy/utilities.py: [no log message]

2009-09-07 07:01  ppenczek

	* sparx/libpy/utilities.py: [no log message]

2009-09-07 06:47  ppenczek

	* sparx/: bin/sparx, bin/sxproject3d.py, libpy/applications.py: [no
	  log message]

2009-09-06 21:37  stevel

	* libpyEM/EMAN2PAR.py: trivial parallelism fix

2009-09-05 23:45  stevel

	* libpyEM/EMAN2db.py: Fix to requeue

2009-09-05 12:21  gtang

	* rt/pyem/test_processor.py: unit test update

2009-09-05 12:14  gtang

	* libEM/emdata_metadata.cpp: just comment out the extra realloc()
	  call

2009-09-04 15:27  stevel

	* libEM/processor.h, libEM/sparx/processor_sparx.h,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2ctf.py: New autohp
	  option in generate output in ctf seems to be working well.
	  Various minor bugfixes.

2009-09-04 09:41  ppenczek

	* sparx/libpy/: applications.py, global_def.py, user_functions.py:
	  ou integer in ali3d_em

2009-09-03 17:33  zyang

	* sparx/libpy/applications.py: Change the merge method in
	  ali2d_a_MPI()

2009-09-03 16:15  stevel

	* libEM/processor.cpp, libpyEM/EMAN2.py, libpyEM/qtgui/emplot2d.py,
	  programs/e2ctf.py: Working on ctfit

2009-09-03 15:55  stephenm

	* libEM/cuda/cuda_processor.cu: I changed an error where AP2RI
	  swapped the real and imaginary parts of pixels values improperly

2009-09-02 18:18  ross

	* libEM/: processor.cpp, processor.h: added
	  ModelEMCylinderProcessor known in Python as
	  "math.model_em_cylinder"

2009-09-02 17:01  jbert

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/libpyProcessor2.cpp: prepare K-means code to GPU cluster

2009-09-02 16:23  stevel

	* libpyEM/qtgui/emform.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2ctf.py: Fixed
	  tomoboxer gui issue. Improving CTF options.

2009-09-02 15:41  zyang

	* sparx/libpy/alignment.py: Trival change

2009-09-02 12:57  stevel

	* examples/cudaspeedtest.py: Revamped

2009-09-01 15:52  jbert

	* sparx/libpy/applications.py: fix bug to ali3d_m_MPI (variable
	  name)

2009-09-01 14:57  stevel

	* libpyEM/qtgui/: emimage2d.py, emimage3d.py, emimage3dvol.py,
	  emimagemx.py, emimagemxrotor.py, emimagerotor.py, emimageutil.py,
	  emplot2d.py: Fixes for current versions of pyqt

2009-09-01 10:43  zyang

	* sparx/libpy/applications.py: Fix a small bug.

2009-09-01 09:27  stevel

	* libpyEM/EMAN2PAR.py: Minor fix

2009-09-01 09:08  stevel

	* libpyEM/EMAN2.py, libpyEM/EMAN2PAR.py,
	  programs/e2classifykmeans.py, programs/e2refine2d.py: typo

2009-09-01 08:43  ppenczek

	* sparx/libpy/: global_def.py, utilities.py: further corrections of
	  cache logic

2009-09-01 05:58  ppenczek

	* libpyEM/EMAN2.py: changed MPIMODE to BDB_CACHE_DISABLE

2009-09-01 04:43  loerke

	* sparx/libpy/global_def.py: variable renaming bug

2009-09-01 04:34  loerke

	* sparx/bin/: sxali2d_a.py, sxali2d_b.py, sxali2d_c.py,
	  sxali2d_cls_mref.py, sxali2d_cross_res.py, sxali2d_e.py,
	  sxali2d_m.py, sxali2d_ra.py, sxali2d_rac.py, sxali2d_reduce.py,
	  sxali2d_w.py, sxali2d_w_mf.py, sxali3d_b.py, sxali3d_d.py,
	  sxali3d_e.py, sxali3d_em.py, sxali3d_f.py, sxali3d_m.py,
	  sxali_SSNR.py, sxali_param_2d_to_3d.py, sxali_vol.py,
	  sxaliunified.py, sxapply_ali_params.py, sxauto_picking.py,
	  sxave_ali.py, sxbootstrap_bigdisk.py, sxbootstrap_calcwgts.py,
	  sxbootstrap_genbuf.py, sxbootstrap_run.py, sxbootstrap_smp.py,
	  sxcmlines_optall.py, sxcopyfromtif.py, sxcpy.py, sxctf.py,
	  sxdefocus_calc.py, sxdefvar.py: updated bin to disable bdb
	  caching

2009-09-01 04:27  ppenczek

	* sparx/: bin/sxdele_alist.py, bin/sxfactcoords.py,
	  bin/sxfind_struct.py, bin/sxhac_averages.py,
	  bin/sxhac_clustering.py, bin/sxheader.py, bin/sxihrsr.py,
	  bin/sximgstat.py, bin/sxincpca.py, bin/sxincvar.py,
	  bin/sxk_means.py, bin/sxk_means_groups.py,
	  bin/sxk_means_stable.py, bin/sxnormal_prj.py,
	  bin/sxparams_2D_to_3D.py, bin/sxparams_3D_to_2D.py, bin/sxpca.py,
	  bin/sxpdb2em.py, bin/sxplot_projs_distrib.py,
	  bin/sxprepare_2d_forPCA.py, bin/sxproject3d.py, bin/sxpufit.py,
	  bin/sxra_cef.py, bin/sxrecons3d_f.py, bin/sxrecons3d_n.py,
	  bin/sxrefvol.py, bin/sxrot_sym.py, bin/sxselect_even.py,
	  bin/sxssnr3d.py, bin/sxstat_even.py, bin/sxtransform2d.py,
	  bin/sxvar.py, bin/sxvarimax.py, bin/sxwelch_psp.py,
	  bin/sxwelch_psp_tilt.py, libpy/user_functions.py: changed to make
	  it possible to disable bdb cache

2009-09-01 04:21  ppenczek

	* sparx/bin/sxtemp.py: [no log message]

2009-09-01 03:56  loerke

	* libpyEM/EMAN2db.py, programs/e2parallel.py, sparx/bin/sparx,
	  sparx/bin/sxali3d_m.py, sparx/libpy/global_def.py,
	  sparx/libpy/utilities.py: change of bdb_cache_disable for
	  clustering

2009-08-31 16:07  zyang

	* sparx/libpy/applications.py: Change ali2d_a_MPI() such that it
	  will also works smmothly for only one and two averages.

2009-08-31 15:51  jbert

	* sparx/libpy/statistics.py: fix bug cuda txt data

2009-08-31 15:01  jbert

	* sparx/: bin/sxk_means_groups.py, libpy/applications.py,
	  libpy/statistics.py: add txt support to k-means groups and clean
	  the code

2009-08-31 13:37  stevel

	* libpyEM/EMAN2PAR.py, programs/e2bdb.py,
	  programs/e2classifykmeans.py: Parallelism server improvement.
	  --cleanup option in e2bdb.py

2009-08-28 11:16  ppenczek

	* sparx/bin/sxrecons3d_n.py: [no log message]

2009-08-28 05:06  ppenczek

	* sparx/bin/sxpdb2em.py: default no center in sxpdb2em

2009-08-27 17:07  ppenczek

	* sparx/: bin/sxali_vol.py, libpy/alignment.py,
	  libpy/applications.py, libpy/user_functions.py, test/3DA/3dg.py:
	  alignment on 50S modified, ref_ali3dm_new changed per Ch wishes

2009-08-27 15:44  stevel

	* libpyEM/EMAN2db.py, programs/e2bdb.py, programs/e2simmx.py:
	  Better subdivision for e2simmx. Beginnings of bdb improvements.

2009-08-27 14:17  zyang

	* sparx/libpy/: applications.py, development.py, utilities.py:
	  Change function rotate_3D_shift() such that it uses Transform
	  object, also change the sign of the shift to make more sense.

2009-08-27 09:35  stevel

	* libpyEM/EMAN2PAR.py: Alarm fixes

2009-08-27 09:18  stevel

	* libpyEM/EMAN2PAR.py: Better thread control in DC

2009-08-27 07:50  ppenczek

	* sparx/bin/sxali3d_m.py: [no log message]

2009-08-26 14:47  zyang

	* sparx/libpy/: applications.py, statistics.py, user_functions.py:
	  Many changes to ali2d_a_MPI() to make it more reliable and
	  user-friendly.

2009-08-26 11:16  ppenczek

	* sparx/: bin/sximgstat.py, libpy/applications.py: furhter
	  corrections of ali3d_m

2009-08-26 07:21  loerke

	* sparx/libpy/applications.py: bugfix in project3d

2009-08-26 06:20  ppenczek

	* sparx/libpy/projection.py: format changed to real in prgq

2009-08-26 05:52  ppenczek

	* sparx/libpy/: applications.py, projection.py: changed 2D fft
	  order in ali3d_m_MPI

2009-08-25 16:41  ppenczek

	* sparx/libpy/: alignment.py, applications.py, projection.py:
	  modified ali3d_m, not working yet

2009-08-25 13:26  zyang

	* sparx/libpy/development.py: Fix a trival bug

2009-08-25 10:37  ppenczek

	* sparx/libpy/applications.py: working version of ali3d_m_MPI with
	  timings

2009-08-25 09:28  ppenczek

	* sparx/libpy/user_functions.py: [no log message]

2009-08-25 09:28  loerke

	* sparx/libpy/applications.py: bugfix in project3d

2009-08-25 08:08  loerke

	* sparx/: bin/sxproject3d.py, libpy/applications.py: updated
	  sxproject3d

2009-08-25 08:00  ppenczek

	* sparx/libpy/: alignment.py, applications.py, user_functions.py:
	  ali3d_m

2009-08-25 04:17  ppenczek

	* sparx/bin/sxbootstrap_calcwgts.py: [no log message]

2009-08-24 10:31  gtang

	* libEM/CMakeLists.txt: [no log message]

2009-08-24 06:31  ppenczek

	* sparx/libpy/: applications.py, projection.py, statistics.py:
	  plot_angles corrected

2009-08-22 14:39  ppenczek

	* sparx/bin/sxbootstrap_bigdisk.py: added multiplication by number
	  of proj to bigdisk

2009-08-22 13:41  ppenczek

	* sparx/libpy/applications.py: corrections in ali3d_d

2009-08-22 05:03  ppenczek

	* sparx/demo/7_mpi_bdb_ctf/run_through_example: corrected script

2009-08-22 04:06  ppenczek

	* sparx/demo/7_mpi_bdb_ctf/run_through_example: rever ali3d_d to
	  fast version PAP

2009-08-22 03:42  ppenczek

	* sparx/libpy/: applications.py, development.py, utilities.py:
	  rever ali3d_d to fast version PAP

2009-08-21 20:35  woolford

	* programs/: e2eotest.py, e2make3d.py: eotest stuff

2009-08-21 20:12  woolford

	* libpyEM/qtgui/emboxerbase.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2boxer2.py,
	  programs/e2eotest.py, programs/e2tomohunter.py: autoboxing is
	  back in workflow

2009-08-21 14:33  ppenczek

	* sparx/libpy/: alignment.py, applications.py, user_functions.py:
	  [no log message]

2009-08-21 10:27  ppenczek

	* sparx/libpy/utilities.py: corrected recv headers

2009-08-21 07:51  ppenczek

	* sparx/: bin/sxali3d_em.py, bin/sxali3d_m.py,
	  libpy/applications.py, libpy/development.py: pixel error in more
	  places

2009-08-20 22:49  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emboxerbase.py,
	  libpyEM/qtgui/emform.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emselector.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2boxer2.py, programs/e2desktop.py,
	  programs/e2workflow.py: workflow fixes

2009-08-20 16:20  woolford

	* libEM/cuda/FindCuda.cmake: [no log message]

2009-08-20 16:16  woolford

	* libEM/cuda/: FindCUDA.cmake, run_nvcc.cmake: cuda stuff

2009-08-20 16:06  woolford

	* libEM/cuda/FindCuda.cmake: [no log message]

2009-08-20 15:00  woolford

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/cuda/CMakeLists.txt,
	  libEM/cuda/CudaCMakeExample, libEM/cuda/FindCUDA.cmake,
	  libEM/cuda/FindCuda.cmake, libEM/cuda/make2cmake.cmake,
	  libEM/cuda/parse_cubin.cmake, libEM/sparx/cuda/CMakeLists.txt,
	  utils/CMakeLists.txt: cuda compilation bugs

2009-08-20 13:44  ppenczek

	* sparx/libpy/: alignment.py, applications.py: pixel error et al

2009-08-20 11:56  zyang

	* sparx/libpy/: alignment.py, development.py: Slightly change
	  max_3D_pixel_error() and move it to alignment.py

2009-08-20 09:10  loerke

	* libEM/CMakeLists.txt, sparx/libpy/alignment.py,
	  sparx/libpy/applications.py, sparx/libpy/development.py,
	  sparx/libpy/utilities.py: pixel error

2009-08-20 04:39  ppenczek

	* sparx/libpy/applications.py:	ali3d_m

2009-08-20 03:59  ppenczek

	* sparx/libpy/development.py:  cleaning pixel error

2009-08-19 22:44  woolford

	* libpyEM/qtgui/: emimagemx.py, emselector.py, emsprworkflow.py:
	  [no log message]

2009-08-19 18:39  woolford

	* libpyEM/qtgui/: emform.py, emimagemx.py, emselector.py: mx bug

2009-08-19 17:12  zyang

	* sparx/libpy/development.py: Fix a bug

2009-08-19 17:04  zyang

	* sparx/libpy/development.py: Add function max_3D_pixel_error()

2009-08-19 14:46  woolford

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emselector.py:
	  transform bug

2009-08-19 13:08  woolford

	* libpyEM/qtgui/emselector.py:
	  selector fixes

2009-08-19 13:02  woolford

	* libpyEM/qtgui/emselector.py: selector fixes

2009-08-18 22:51  woolford

	* libpyEM/qtgui/emselector.py, programs/e2eulerxplor.py: browser
	  updates

2009-08-18 22:29  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimage3dslice.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emplot2d.py, libpyEM/qtgui/emplot3d.py,
	  libpyEM/qtgui/emsave.py, libpyEM/qtgui/emselector.py,
	  programs/e2ctf.py, programs/e2eulerxplor.py, programs/e2simmx.py,
	  programs/e2simmxxplor.py, programs/e2workflow.py,
	  sparx/bin/sxctf.py: browser updates

2009-08-18 13:23  stevel

	* libpyEM/: EMAN2PAR.py, EMAN2db.py: Minor cleanup

2009-08-18 12:49  stevel

	* libpyEM/EMAN2db.py: Fix region reading. Database image reading
	  may have been broken in a few cases for the last few days.

2009-08-18 12:08  stevel

	* libpyEM/EMAN2db.py: debugging

2009-08-18 11:51  stevel

	* libpyEM/EMAN2PAR.py: oops

2009-08-18 11:43  stevel

	* libpyEM/EMAN2PAR.py: Work on parallelism reliability

2009-08-18 10:30  ppenczek

	* sparx/: bin/sxali3d_m.py, libpy/alignment.py,
	  libpy/applications.py: ali3dm percentage

2009-08-18 04:36  ppenczek

	* sparx/: bin/sxk_means_groups.py, libpy/applications.py,
	  libpy/morphology.py, libpy/user_functions.py: [no log message]

2009-08-18 02:17  ppenczek

	* sparx/libpy/applications.py: HAC corrected

2009-08-17 18:08  zyang

	* sparx/libpy/applications.py: Many change to make ali2d_a_MPI()
	  possible to restart in case of a crash

2009-08-17 18:07  zyang

	* sparx/bin/sxali2d_a.py: Add restart function

2009-08-17 12:21  stevel

	* programs/e2parallel.py: Trivial

2009-08-17 12:11  stevel

	* libpyEM/qtgui/emimage2d.py, programs/e2parallel.py: Debugging

2009-08-17 11:03  stevel

	* programs/e2parallel.py: trivial

2009-08-17 10:52  stevel

	* libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emshape.py,
	  programs/e2ctf.py: Trying to fix @#$@# shapes

2009-08-17 01:52  stevel

	* libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emshape.py,
	  programs/e2ctf.py: Working on e2ctf improvements

2009-08-16 17:29  ppenczek

	* sparx/libpy/statistics.py: remover print from groups

2009-08-16 17:24  ppenczek

	* sparx/libpy/statistics.py: groups

2009-08-16 16:03  ppenczek

	* sparx/libpy/applications.py: ???

2009-08-14 23:24  woolford

	* libpyEM/qtgui/emimage3dsym.py, programs/e2eulerxplor.py,
	  programs/e2simmxxplor.py: simmxxplore alpha

2009-08-14 20:56  woolford

	* programs/: e2eulerxplor.py, e2simmx.py, e2simmxxplor.py: simmx
	  xplore

2009-08-14 18:56  woolford

	* libpyEM/qtgui/emimage3dsym.py: [no log message]

2009-08-14 18:49  woolford

	* libEM/emdata_metadata.cpp, libpyEM/EMAN2db.py,
	  libpyEM/libpyEMData2.cpp, programs/e2eulerxplor.py,
	  programs/e2simmxxplor.py: e2simmxxplor

2009-08-14 16:55  woolford

	* libpyEM/EMAN2PAR.py, libpyEM/qtgui/emimage3dsym.py,
	  libpyEM/qtgui/emselector.py, programs/e2eulerxplor.py,
	  programs/e2project3d.py, programs/e2simmxxplor.py,
	  programs/e2tomoaverage.py, programs/e2tomohunter.py: tomo fix

2009-08-14 15:12  gtang

	* libEM/: hdfio.cpp, hdfio2.cpp: read CTF attribute(string) as
	  attribute of EMAN1Ctf/EMAN2Ctf object

2009-08-14 14:46  stevel

	* libpyEM/EMAN2PAR.py: quick fix

2009-08-14 14:35  woolford

	* libpyEM/qtgui/emsprworkflow.py: particle import bug

2009-08-14 14:26  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2classaverage.py:
	  particle import bug

2009-08-14 10:01  ppenczek

	* sparx/: bin/sxvarimax.py, libpy/applications.py: correct varimax

2009-08-14 08:41  stevel

	* libpyEM/libpyAligner2.cpp: Expose more parameters in EMAN1 ctf
	  object

2009-08-14 07:02  ppenczek

	* sparx/libpy/applications.py: corrected var_mpi

2009-08-14 04:34  ppenczek

	* sparx/libpy/: statistics.py, utilities.py: [no log message]

2009-08-13 16:23  woolford

	* programs/: e2eulerxplor.py, e2simmxxplor.py: [no log message]

2009-08-13 16:19  stevel

	* libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py, programs/e2boxer2.py,
	  programs/e2parallel.py, programs/e2simmx.py: Work on parallelism

2009-08-13 15:47  woolford

	* programs/e2boxer2.py: e2classaverage ref_mask

2009-08-13 15:37  woolford

	* libpyEM/qtgui/emboxerbase.py, programs/e2boxer2.py: boxer fixes

2009-08-13 15:27  zyang

	* libEM/: aligner.cpp, sparx/cuda/cuda_ccf.cu: Fix three bugs to
	  make the 2-D alignment finally correct on GPU!!!

2009-08-13 14:22  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimagemx.py, programs/e2classaverage.py,
	  programs/e2eulerxplor.py, programs/e2tomoaverage.py,
	  programs/e2workflow.py: e2classaverage ref_mask

2009-08-13 10:08  ppenczek

	* sparx/: bin/sxpca.py, libpy/statistics.py, libpy/utilities.py:
	  changed definition of get_im

2009-08-13 09:33  ppenczek

	* sparx/libpy/: applications.py, morphology.py: add invert

2009-08-13 08:12  stevel

	* libpyEM/EMAN2PAR.py: Tweaking threading

2009-08-13 02:15  ppenczek

	* sparx/libpy/applications.py: ???

2009-08-13 02:09  ppenczek

	* sparx/libpy/: applications.py, statistics.py: more corrections of
	  kmeans

2009-08-13 01:46  ppenczek

	* sparx/bin/sxk_means.py: cleaning

2009-08-12 19:01  woolford

	* libpyEM/qtgui/emselector.py, libpyEM/qtgui/emsprworkflow.py,
	  libpyEM/qtgui/emtprworkflow.py, programs/e2tomoaverage.py,
	  programs/e2tomohunter.py: browser updates

2009-08-12 15:50  stevel

	* libpyEM/EMAN2PAR.py: Try to avoid DB deadlock

2009-08-12 15:29  stevel

	* libpyEM/EMAN2PAR.py: Better client tracking

2009-08-12 15:23  woolford

	* programs/e2tomohunter.py: tomo

2009-08-12 15:22  woolford

	* programs/e2project3d.py, programs/e2tomoallvall.py,
	  programs/e2tomoaverage.py, programs/e2tomoboxer.py,
	  programs/e2tomohunter.py, libEM/aligner.h, libEM/cmp.cpp,
	  libEM/cmp.h, libEM/cuda/cuda_cmp.cu: tomo work

2009-08-12 15:00  stevel

	* libpyEM/EMAN2PAR.py: Signals to avoid network lockups

2009-08-12 10:37  stevel

	* libpyEM/EMAN2PAR.py: bug

2009-08-12 10:30  stevel

	* libpyEM/EMAN2PAR.py: Issues on gauss. trying to fix...

2009-08-12 10:19  stevel

	* libpyEM/EMAN2PAR.py: minor

2009-08-12 10:00  stevel

	* libpyEM/EMAN2PAR.py: Better client process control

2009-08-12 09:59  stevel

	* libpyEM/EMAN2PAR.py: Better debugging again

2009-08-12 09:41  stevel

	* libpyEM/: EMAN2PAR.py, EMAN2db.py: Minor bugfixes

2009-08-12 09:16  stevel

	* libpyEM/EMAN2PAR.py: Experimental changes to parallelism

2009-08-12 08:56  stevel

	* libpyEM/EMAN2PAR.py: Working on progress monitoring

2009-08-12 08:10  ppenczek

	* sparx/: bin/sxk_means_stable.py, libpy/applications.py,
	  libpy/statistics.py: comments on k_means

2009-08-11 17:30  zyang

	* libEM/sparx/util_sparx.cpp: Trival change.

2009-08-11 16:11  stevel

	* libpyEM/: EMAN2PAR.py, EMAN2db.py: More parallelism fixes

2009-08-11 13:49  woolford

	* programs/: e2project3d.py, e2tomoallvall.py, e2tomoaverage.py,
	  e2tomohunter.py: parallel fix

2009-08-11 13:39  stevel

	* libpyEM/EMAN2PAR.py: More parallelism work

2009-08-11 12:35  stevel

	* libpyEM/EMAN2db.py: Working on locking and parallelism

2009-08-11 11:44  gtang

	* libEM/aligner.cpp: small fix for windows

2009-08-11 11:17  stevel

	* libpyEM/EMAN2PAR.py, programs/e2parallel.py: client killing
	  capability

2009-08-11 10:47  stevel

	* libpyEM/EMAN2PAR.py, programs/e2project3d.py: Work on database

2009-08-11 08:39  stevel

	* libpyEM/EMAN2db.py: trivial

2009-08-11 08:33  stevel

	* libpyEM/EMAN2db.py: Ok, locking mostly fixed...

2009-08-11 08:18  stevel

	* libpyEM/EMAN2db.py: oops

2009-08-11 08:14  stevel

	* libpyEM/EMAN2db.py, programs/e2bdb.py: trivial

2009-08-11 08:11  stevel

	* libpyEM/: EMAN2PAR.py, EMAN2db.py: Better thread locking (I hope)

2009-08-10 15:36  muthu

	* libpyEM/qtgui/emfoldhunterstat.py: timer on muthus program

2009-08-09 15:13  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-08-09 11:36  ppenczek

	* sparx/libpy/applications.py: app

2009-08-08 16:20  gtang

	* programs/e2speedtest.py, utils/speedtest.cpp: no
	  speed.img/speed.hed file writing

2009-08-07 18:12  gtang

	* programs/e2speedtest.py: [no log message]

2009-08-07 15:36  muthu

	* libpyEM/qtgui/empdbvaltool.py: muthu empdbvaltool change

2009-08-07 13:19  zyang

	* libEM/sparx/cuda/cuda_ccf.cu: Trival change

2009-08-07 12:45  ppenczek

	* sparx/libpy/morphology.py: [no log message]

2009-08-07 12:38  gtang

	* programs/: e2fhstat.py, e2validatemed.py: [no log message]

2009-08-07 12:37  muthu

	* libpyEM/qtgui/: emfoldhunterstat.py, emplot3d.py: muthu added
	  percentiles to e2validatemed

2009-08-07 11:30  jbert

	* sparx/libpy/: applications.py, statistics.py: [no log message]

2009-08-07 10:57  zyang

	* libEM/sparx/util_sparx.cpp: Fix a critical bug in bilinear()

2009-08-07 09:20  jbert

	* sparx/libpy/applications.py: some change

2009-08-06 18:18  ppenczek

	* sparx/libpy/statistics.py: [no log message]

2009-08-06 16:51  gtang

	* libEM/: emdata_io.cpp, emdata_metadata.h: small fix

2009-08-06 16:26  jbert

	* sparx/libpy/statistics.py: fix bug from numpy array and 64bit
	  system

2009-08-06 14:47  jbert

	* sparx/libpy/statistics.py: [no log message]

2009-08-06 14:37  jbert

	* sparx/libpy/statistics.py: [no log message]

2009-08-06 14:27  jbert

	* sparx/libpy/statistics.py: fix bug

2009-08-06 14:15  jbert

	* sparx/libpy/applications.py: fix bug

2009-08-06 14:07  jbert

	* sparx/libpy/applications.py: fix bug

2009-08-06 13:48  jbert

	* sparx/libpy/applications.py: [no log message]

2009-08-06 12:33  jbert

	* sparx/libpy/statistics.py: new code to match partition

2009-08-05 22:06  woolford

	* libEM/aligner.cpp, libpyEM/qtgui/emboxerbase.py,
	  libpyEM/qtgui/emform.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emtprworkflow.py, programs/e2make3d.py: minor fixes

2009-08-05 10:43  muthu

	* libpyEM/qtgui/emfoldhunterstat.py, programs/e2validatemed.py:
	  muthu latest e2val

2009-08-05 09:14  ppenczek

	* sparx/libpy/statistics.py: ??

2009-08-04 22:34  woolford

	* libEM/aligner.cpp, libEM/aligner.h, libEM/cmp.cpp, libEM/cmp.h,
	  libpyEM/qtgui/emform.py, libpyEM/qtgui/emsprworkflow.py,
	  libpyEM/qtgui/emtprworkflow.py, programs/e2refine2d.py,
	  programs/e2tomoallvall.py, programs/e2tomoaverage.py,
	  programs/e2tomohunter.py, programs/e2workflow.py: tomo done?

2009-08-04 17:15  ppenczek

	* sparx/demo/7_mpi_bdb_ctf/run_through_example: correction

2009-08-04 16:51  muthu

	* libpyEM/qtgui/emfoldhunterstat.py: muthu more fixes

2009-08-04 16:39  zyang

	* sparx/libpy/: applications.py, statistics.py: Trival change.

2009-08-04 16:35  muthu

	* libEM/pdbreader.cpp, libpyEM/qtgui/emfoldhunterstat.py,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/empdbvaltool.py:
	  muthu bug fix

2009-08-04 16:02  muthu

	* libEM/pdbreader.cpp, libpyEM/qtgui/emfoldhunterstat.py,
	  libpyEM/qtgui/empdbviewer.py: muthu bug fixes emfoldhunter

2009-08-04 14:50  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-08-04 14:37  muthu

	* libpyEM/qtgui/: emfoldhunterstat.py, empdbviewer.py: muthu fixes
	  final

2009-08-04 14:17  muthu

	* libEM/: pdbreader.cpp, pdbreader.h: muthu bug fixes pdbviewer

2009-08-04 13:53  muthu

	* libEM/pdbreader.cpp, libEM/pdbreader.h,
	  libpyEM/qtgui/emfoldhunterstat.py: muthu bug fixes pdbreader

2009-08-04 13:09  ppenczek

	* sparx/: demo/5_mpi_bdb/run_through_example,
	  libpy/applications.py, libpy/filter.py: sxnorm corrected

2009-08-04 13:08  ppenczek

	* sparx/demo/7_mpi_bdb_ctf/run_through_example: Corrected

2009-08-04 13:03  ppenczek

	* sparx/demo/5_mpi_bdb/: run_through_example: [no log message]

2009-08-04 12:26  ppenczek

	* sparx/bin/: sxbootstrap_bigdisk.py, sxnormal_prj.py: normal

2009-08-04 12:26  ppenczek

	* sparx/bin/: sxnormal_prj_3.py, sxnormal_prj_4.py,
	  sxnormal_prj_5.py: [no log message]

2009-08-04 12:20  jbert

	* libEM/sparx/cuda/cuda_kmeans.cu: some change

2009-08-04 09:05  jbert

	* sparx/demo/5_mpi_bdb/run_through_example: change params

2009-08-03 22:50  woolford

	* programs/: e2refine.py, e2tomoallvall.py, e2tomoaverage.py: tomo
	  stuff

2009-08-03 17:41  muthu

	* libpyEM/qtgui/emfoldhunterstat.py: muthu program sphere
	  restrictions

2009-08-03 16:59  zyang

	* sparx/libpy/statistics.py: trival change

2009-08-03 16:52  muthu

	* libpyEM/qtgui/emfoldhunterstat.py: muthu further fixes

2009-08-03 16:44  muthu

	* libEM/pdbreader.cpp, libEM/pointarray.cpp,
	  libpyEM/qtgui/emfoldhunterstat.py, libpyEM/qtgui/empdbvaltool.py:
	  muthu program bug fixes

2009-08-03 16:12  jbert

	* sparx/: bin/sxk_means_stable.py, libpy/applications.py,
	  libpy/statistics.py: fix bugs

2009-08-03 15:18  jbert

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, sparx/libpy/statistics.py: change the
	  way to build contingency table to match partition to k-means

2009-08-03 15:15  jbert

	* sparx/demo/: 2_hdf_ctf/run_through_example,
	  4_mpi_hdf/run_through_example, 6_mpi_hdf_ctf/run_through_example:
	  remove obsolete demo with hdf

2009-08-03 14:47  jbert

	* sparx/demo/: 0_hdf/run_through_example,
	  3_bdb_ctf/run_through_example, 7_mpi_bdb_ctf/run_through_example:
	  [no log message]

2009-08-03 13:52  ppenczek

	* sparx/bin/sxbootstrap_bigdisk.py,
	  sparx/bin/sxbootstrap_calcwgts.py,
	  sparx/bin/sxbootstrap_genbuf.py, sparx/libpy/applications.py,
	  libEM/sparx/util_sparx.cpp: cleaning

2009-08-03 13:51  ppenczek

	* sparx/demo/5_mpi_bdb/: run_through_example:  BOOTSTRAP FIXED

2009-08-03 10:25  jbert

	* sparx/libpy/: statistics.py: remove print out

2009-08-03 10:00  jbert

	* sparx/libpy/: applications.py, statistics.py: reverse some
	  correction k-means

2009-08-02 21:20  zyang

	* sparx/libpy/applications.py: Fix a small but fatal bug

2009-08-02 07:47  ppenczek

	* sparx/bin/sxali3d_m.py: typos

2009-08-01 14:11  ppenczek

	* sparx/libpy/: applications.py, statistics.py: corrections k_means

2009-07-31 20:38  woolford

	* libEM/aligner.cpp, libpyEM/EMAN2.py, libpyEM/EMAN2PAR.py,
	  libpyEM/qtgui/emimagemx.py, programs/e2eulerxplor.py,
	  programs/e2tomoallvall.py, programs/e2tomoaverage.py,
	  programs/e2tomohunter.py: tomo work

2009-07-31 15:59  ppenczek

	* sparx/demo/5_mpi_bdb/run_through_example:  corrections to genbug
	  in boot

2009-07-31 15:33  zyang

	* sparx/libpy/applications.py: Fix a stupid bug

2009-07-31 14:56  ppenczek

	* sparx/demo/5_mpi_bdb/: run_through_example: [no log message]

2009-07-31 14:46  ppenczek

	* sparx/bin/sxbootstrap_bigdisk.py: [no log message]

2009-07-31 14:44  jbert

	* sparx/: libpy/applications.py, libpy/statistics.py,
	  bin/sxk_means_stable.py: use numpy to hierarchical Hungarian

2009-07-31 14:37  muthu

	* libEM/pdbreader.cpp, libpyEM/qtgui/emfoldhunterstat.py,
	  libpyEM/qtgui/empdbviewer.py: muthu e2validate med updates

2009-07-31 14:34  ppenczek

	* sparx/libpy/applications.py: del obsolete factcoords

2009-07-31 14:31  ppenczek

	* sparx/libpy/applications.py: type

2009-07-31 14:27  ppenczek

	* sparx/libpy/applications.py: del obsolete VAR

2009-07-31 12:02  ppenczek

	* sparx/libpy/applications.py: VAR

2009-07-31 11:32  jbert

	* sparx/libpy/: applications.py, statistics.py: more change

2009-07-31 11:23  jbert

	* sparx/libpy/: applications.py, statistics.py: more change

2009-07-31 11:05  jbert

	* sparx/libpy/: applications.py, statistics.py: more change

2009-07-31 11:00  ppenczek

	* sparx/bin/sxvar.py: typo

2009-07-31 10:38  jbert

	* sparx/libpy/: applications.py, statistics.py: fix bug to txt
	  support in k-means

2009-07-31 05:44  gtang

	* libpyEM/qtgui/: emform.py, emsprworkflow.py: Fix the e2.py screen
	  flush in Python2.4 issue.

2009-07-30 22:27  woolford

	* libpyEM/qtgui/emimagemx.py: [no log message]

2009-07-30 22:06  woolford

	* libpyEM/qtgui/emboxerbase.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2boxer.py, programs/e2eulerxplor.py,
	  pyemtbx/boxertools.py: woops

2009-07-30 21:58  woolford

	* libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emsave.py,
	  libpyEM/qtgui/emselector.py, programs/e2initialmodel.py:
	  mx sets infrastructure in good shape

2009-07-30 18:36  ppenczek

	* sparx/: bin/sxrecons3d_n.py, libpy/applications.py: recon

2009-07-30 15:24  ppenczek

	* sparx/: bin/sxvar.py, libpy/applications.py: VAR

2009-07-30 15:09  muthu

	* libEM/pdbreader.cpp, libEM/pdbreader.h,
	  libpyEM/qtgui/emfoldhunterstat.py, libpyEM/qtgui/empdbvaltool.py,
	  libpyEM/qtgui/empdbviewer.py, libpyEM/qtgui/emplot3d.py,
	  programs/e2validatemed.py: muthu documented code

2009-07-30 12:45  woolford

	* libpyEM/qtgui/emimage3dsym.py, programs/e2eulerxplor.py: euler
	  efficiency

2009-07-30 11:51  zyang

	* sparx/bin/sxali2d_a.py: [no log message]

2009-07-30 11:39  jbert

	* sparx/libpy/statistics.py: fix bug

2009-07-30 11:21  muthu

	* programs/e2validatemed.py: muthu program final

2009-07-30 11:16  gtang

	* libpyEM/CMakeLists.txt, libpyEM/qtgui/emfoldhunterstat.py,
	  programs/e2foldhunterstat.py: move e2foldhunter.py to qtgui as
	  emfoldhunterstat.py

2009-07-30 10:58  muthu

	* libpyEM/qtgui/empdbvaltool.py, libpyEM/qtgui/empdbviewer.py,
	  programs/e2foldhunterstat.py, programs/e2validatemed.py: latest
	  e2validatemed muthu

2009-07-30 10:04  jbert

	* sparx/libpy/: applications.py, statistics.py: add read text file
	  to k-means

2009-07-29 22:53  woolford

	* libpyEM/qtgui/emimage3dsym.py: euler efficiency

2009-07-29 22:48  ppenczek

	* sparx/libpy/: applications.py: somewhere theere

2009-07-29 22:30  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emimage3dsym.py,
	  libpyEM/qtgui/emimagemx.py, programs/e2eulerxplor.py: euler stuff

2009-07-29 21:40  stevel

	* programs/e2ctf.py: Trivial

2009-07-29 21:24  woolford

	* libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2eulerxplor.py: euler updates

2009-07-29 21:20  ppenczek

	* sparx/bin/sxvarimax.py: VAR

2009-07-29 19:49  woolford

	* libpyEM/qtgui/emimagemx.py, programs/e2eulerxplor.py: in the
	  middle of euler stuff

2009-07-29 18:21  woolford

	* libpyEM/qtgui/emplot3d.py, programs/e2validatemed.py: plot3d bug

2009-07-29 18:10  ppenczek

	* sparx/libpy/applications.py: var

2009-07-29 17:55  muthu

	* programs/e2validatemed.py: muthu changes

2009-07-29 17:34  ppenczek

	* sparx/bin/sxfactcoords.py: factor

2009-07-29 17:27  jbert

	* sparx/bin/: sxfind_struct.py, sxk_means_stability.py: remove
	  sxk_means_stability.py

2009-07-29 17:26  jbert

	* sparx/: bin/sxk_means_stable.py, libpy/applications.py,
	  libpy/development.py, libpy/statistics.py: some changes

2009-07-29 17:23  ppenczek

	* sparx/bin/sxfactcoords.py: factor

2009-07-29 17:15  ppenczek

	* sparx/libpy/applications.py: factor

2009-07-29 17:11  woolford

	* libpyEM/qtgui/emform.py, libpyEM/qtgui/emimage3diso.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/empdbviewer.py,
	  libpyEM/qtgui/emselector.py, programs/e2classaverage.py,
	  programs/e2eulerxplor.py, programs/e2preferences.py,
	  programs/e2validatemed.py: [no log message]

2009-07-29 17:03  ppenczek

	* sparx/libpy/applications.py: factor

2009-07-29 17:01  muthu

	* libpyEM/qtgui/empdbvaltool.py, libpyEM/qtgui/empdbviewer.py,
	  programs/e2validatemed.py: muthu e2fhstat

2009-07-29 16:45  ppenczek

	* sparx/: bin/sxfactcoords.py, libpy/applications.py: var

2009-07-29 16:41  jgalaz

	* libEM/: processor.cpp, processor.h: fixed math.transform.scale
	  processor

2009-07-29 16:32  gtang

	* programs/e2fhstat.py: [no log message]

2009-07-29 16:26  muthu

	* libpyEM/: CMakeLists.txt, qtgui/empdbvaltool.py,
	  qtgui/empdbviewer.py: muthu e2fhstat

2009-07-29 15:50  jbert

	* sparx/demo/5_mpi_bdb/run_through_example: more change

2009-07-29 15:47  ppenczek

	* sparx/libpy/applications.py: var

2009-07-29 15:47  jbert

	* sparx/demo/5_mpi_bdb/run_through_example: change parameters

2009-07-29 15:42  muthu

	* libpyEM/CMakeLists.txt, libpyEM/qtgui/empdbvaltool.py,
	  libpyEM/qtgui/empdbviewer.py, libpyEM/qtgui/emplot3d.py,
	  programs/e2foldhunterstat.py, programs/e2validatemed.py: muthu
	  e2fhstat changes

2009-07-29 14:37  ppenczek

	* libEM/sparx/emdata_sparx.cpp: formatting

2009-07-29 14:22  ppenczek

	* libEM/sparx/emdata_sparx.cpp: formatting

2009-07-29 13:52  ppenczek

	* sparx/libpy/applications.py:	gentle exit

2009-07-29 10:58  jbert

	* sparx/libpy/applications.py: some changes

2009-07-29 10:56  jbert

	* sparx/libpy/statistics.py: add function

2009-07-28 22:32  woolford

	* libEM/processor.cpp, libpyEM/qtgui/emboxerbase.py,
	  libpyEM/qtgui/emsprworkflow.py: efficiency improvements

2009-07-28 19:57  woolford

	* libEM/exception.h, libpyEM/EMAN2.py, programs/e2ctf.py: general
	  updates

2009-07-28 19:53  woolford

	* libpyEM/qtgui/: emimage.py, empdbvaltool.py, emplot2d.py,
	  emselector.py, emshape.py, emsprworkflow.py: workflow fix

2009-07-28 17:02  zyang

	* sparx/libpy/applications.py: Many changes to ali2d_a_MPI()

2009-07-28 16:51  gtang

	* libpyEM/CMakeLists.txt: name fix

2009-07-28 16:39  gtang

	* libEM/: xydata.cpp, xydata.h: call update() in get_miny(),
	  get_maxy() and get_yatx(). Otherwise the miny, maxy and
	  man_x_spacing values are not set.

2009-07-28 16:01  muthu

	* libpyEM/: CMakeLists.txt, qtgui/empdbvaltool.py: pdbval fix muthu

2009-07-28 16:00  gtang

	* programs/e2ctf.py: call update() in XYData() before get_yatx()

2009-07-28 15:58  muthu

	* programs/: e2foldhunterstat.py, e2validatemed.py: e2validatemed,
	  e2foldhunter, e2fhstat, valtool changes muthu

2009-07-28 14:57  muthu

	* programs/e2fhstat.py: e2fhstat muthu

2009-07-28 14:35  muthu

	* libpyEM/qtgui/: em3dmodule.py, emimage3diso.py, empdbvaltool.py,
	  empdbviewer.py: muthu pdbviewer, pdbvaltool, emimaged3diso
	  changes

2009-07-28 13:45  woolford

	* libpyEM/qtgui/: emimage3diso.py, empdbvaltool.py, emplot2d.py,
	  emselector.py: browse pdbval stuff

2009-07-28 13:23  zyang

	* sparx/libpy/utilities.py: Trival change.

2009-07-28 13:20  woolford

	* libpyEM/qtgui/emboxerbase.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2boxer2.py: [no log message]

2009-07-28 10:09  muthu

	* libpyEM/qtgui/empdbviewer.py: muthu pdbviewer update

2009-07-28 10:01  zyang

	* sparx/libpy/: applications.py, statistics.py: Many change
	  relating to ali2d_a()

2009-07-28 09:57  ppenczek

	* sparx/: bin/sxfactcoords.py, libpy/applications.py: fact

2009-07-28 00:03  woolford

	* libpyEM/qtgui/emboxerbase.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2boxer2.py: e2boxer2 overlap tools in

2009-07-27 22:56  woolford

	* libpyEM/qtgui/emboxerbase.py, programs/e2boxer2.py,
	  programs/e2ctf.py: proximity removal in boxer, etc

2009-07-27 17:17  woolford

	* libpyEM/qtgui/: em3dmodule.py, emglobjects.py, empdbvaltool.py,
	  empdbviewer.py: adding empdbvaltool.py

2009-07-27 15:48  muthu

	* libpyEM/qtgui/empdbviewer.py: muthu pdbviewr

2009-07-27 15:15  muthu

	* libpyEM/qtgui/empdbviewer.py: pdbviewr muthu

2009-07-27 14:30  woolford

	* libpyEM/qtgui/empdbviewer.py: pdb stuff

2009-07-27 14:16  woolford

	* libpyEM/qtgui/: empdbvaltool.py, empdbviewer.py: pdb stuff

2009-07-27 13:56  woolford

	* libpyEM/qtgui/: em3dmodule.py, emboxerbase.py, empdbviewer.py:
	  pdb viewer updates

2009-07-27 12:14  muthu

	* libpyEM/qtgui/empdbviewer.py: muthu pdbvewer updates

2009-07-26 20:14  ppenczek

	* sparx/: bin/sxvar.py, libpy/applications.py: var

2009-07-26 11:42  ppenczek

	* sparx/: bin/sxfactcoords.py, libpy/applications.py: var

2009-07-25 13:41  ppenczek

	* sparx/libpy/utilities.py: circumference

2009-07-25 12:05  ppenczek

	* sparx/: libpy/__init__.py, libpy/applications.py,
	  libpy/statistics.py, libpy/utilities.py, test/3DA/3dg.py: fact

2009-07-25 06:33  ppenczek

	* sparx/: bin/sxfactcoords.py, libpy/applications.py: [no log
	  message]

2009-07-24 20:58  woolford

	* libpyEM/qtgui/emboxerbase.py: [no log message]

2009-07-24 20:38  woolford

	* programs/: e2refine2d.py, e2workflow.py: [no log message]

2009-07-24 20:26  woolford

	* libpyEM/qtgui/emboxerbase.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2boxer.py,
	  programs/e2boxer2.py, programs/e2ctf.py,
	  programs/e2preferences.py, programs/e2tomoaverage.py,
	  programs/e2tomoboxer.py, pyemtbx/boxertools.py: e2boxer2 is in
	  the workflow

2009-07-24 16:08  jbert

	* sparx/: bin/sxk_means.py, libpy/applications.py,
	  libpy/statistics.py: change flag to k-means to normalize

2009-07-24 15:38  gtang

	* rt/pyem/test_xydata.py: unit test update

2009-07-24 15:37  gtang

	* libEM/xydata.cpp: trivial

2009-07-24 14:20  zyang

	* sparx/libpy/development.py: Some change to ali3d_e_G_DUD().

2009-07-24 14:11  jbert

	* sparx/libpy/applications.py: fix bug ali3d_d ctf

2009-07-24 12:19  jbert

	* sparx/demo/1_bdb/run_through_example: some changes

2009-07-24 11:54  ppenczek

	* libpyEM/libpyUtils2.cpp, sparx/bin/sxvar.py,
	  sparx/libpy/statistics.py: var

2009-07-24 10:59  jbert

	* sparx/libpy/applications.py: change printout

2009-07-24 10:45  jbert

	* sparx/libpy/user_functions.py: change params

2009-07-24 10:29  ppenczek

	* libpyEM/libpyUtils2.cpp: temporary printout

2009-07-23 22:46  woolford

	* libEM/aligner.cpp, libEM/aligner.h, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emtprworkflow.py, programs/e2tomohunter.py: tomo
	  stuff, aligners updated, workflow updated

2009-07-23 17:51  ppenczek

	* sparx/: libpy/applications.py, bin/sxvar.py: var

2009-07-23 16:55  gtang

	* libEM/tifio.cpp: fix a 32 bit tiff image writing bug

2009-07-23 16:42  muthu

	* libpyEM/qtgui/emplot3d.py: emplot3d muthu update

2009-07-23 14:47  muthu

	* libpyEM/qtgui/empdbviewer.py: latest pdbviewr muthu

2009-07-23 08:14  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-07-22 22:50  woolford

	* libEM/aligner.cpp, libEM/aligner.h, libpyEM/EMAN2.py,
	  libpyEM/qtgui/emanimationutil.py, programs/e2tomohunter.py: 3d
	  aligner and tomo work

2009-07-22 20:07  woolford

	* libEM/aligner.cpp, libEM/aligner.h, libEM/emdata_modular.cpp,
	  libEM/emdata_modular.h, libEM/transform.cpp, libEM/transform.h,
	  libEM/cuda/cuda_processor.h, libpyEM/libpyAligner2.cpp,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyTypeConverter2.cpp,
	  libpyEM/qtgui/em3dmodule.py: 3d aligners

2009-07-22 17:09  muthu

	* libpyEM/qtgui/empdbviewer.py: muthu pdb latest

2009-07-22 16:57  muthu

	* libpyEM/qtgui/empdbviewer.py: muthu pdb viewer

2009-07-22 16:46  gtang

	* utils/CMakeLists.txt: small fix

2009-07-22 16:28  muthu

	* libEM/CMakeLists.txt, libEM/pdbreader.cpp, libEM/pdbreader.h,
	  libEM/pointarray.cpp, libpyEM/CMakeLists.txt,
	  libpyEM/EMAN2_cppwrap.py, libpyEM/libpyPDBReader2.cpp,
	  libpyEM/qtgui/emplot3d.py, utils/CMakeLists.txt: PDB Viewer class
	  - Muthu

2009-07-22 15:00  ppenczek

	* sparx/: bin/sxvar.py, libpy/applications.py: bvar

2009-07-22 11:55  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-07-22 11:42  gtang

	* rt/pyem/test_xydata.py: add unit test for XYData

2009-07-22 11:17  ppenczek

	* sparx/: libpy/applications.py, bin/sxvar.py: [no log message]

2009-07-21 22:52  woolford

	* examples/cudaspeedtest.py, libEM/aligner.h, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/emdata_transform.cpp,
	  libEM/emdata_transform.h, libEM/glutil.cpp, libEM/processor.cpp,
	  libEM/processor.h, libEM/cuda/cuda_processor.cu,
	  libEM/cuda/cuda_processor.h, libpyEM/libpyEMData2.cpp,
	  programs/e2tomohunter.py, utils/speedtest.cpp: tomohunter fixes,
	  cuda updates

2009-07-21 17:03  zyang

	* sparx/libpy/development.py: Add function ali3d_e_G_DUD() and some
	  other changes.

2009-07-21 15:41  ppenczek

	* sparx/libpy/applications.py: var

2009-07-21 15:01  gtang

	* libEM/mrcio.cpp: small fix for non-existing key

2009-07-21 10:37  zyang

	* sparx/libpy/development.py: Many changes relating to ali3d

2009-07-20 22:51  woolford

	* examples/cudaspeedtest.py, libEM/emdata_transform.cpp,
	  libEM/processor.cpp, libEM/transform.cpp, libEM/transform.h,
	  libEM/cuda/cuda_processor.cu, libEM/cuda/cuda_processor.h,
	  libpyEM/libpyTransform2.cpp, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimage3dsym.py,
	  libpyEM/qtgui/emimageutil.py, libpyEM/qtgui/emplot3d.py,
	  programs/e2eulerxplor.py, programs/e2workflow.py: general fixes,
	  some cuda

2009-07-20 20:56  woolford

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp: transform stuff

2009-07-20 20:13  woolford

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp: transform icos_2_to_5

2009-07-20 15:39  zyang

	* libEM/sparx/util_sparx.cpp, sparx/libpy/development.py: Many
	  changes to 2D alignment and 2D to 3D alignment

2009-07-20 14:49  ppenczek

	* sparx/libpy/fundamentals.py: fdecimate

2009-07-20 11:55  jbert

	* sparx/demo/7_mpi_bdb_ctf/run_through_example: change params

2009-07-17 20:42  woolford

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, libpyEM/qtgui/emboxerbase.py,
	  libpyEM/qtgui/emimage3dsym.py, programs/e2eulerxplor.py:
	  e2eulerxplor

2009-07-17 16:59  woolford

	* libpyEM/qtgui/emform.py, libpyEM/qtgui/emplot3d.py,
	  programs/e2boxer.py: e2boxer form bug

2009-07-17 15:47  woolford

	* libpyEM/qtgui/emplot3d.py: plot fixes

2009-07-17 15:36  woolford

	* libpyEM/qtgui/emplot3d.py: emplot3d bug

2009-07-17 15:31  woolford

	* libpyEM/qtgui/: emimage3d.py, emplot3d.py: emplot3d bug

2009-07-17 14:49  muthu

	* libpyEM/qtgui/: emimage3d.py, emplot3d.py: emplot3d updates

2009-07-17 11:52  zweig

	* sparx/libpy/applications.py: fix factcoords_prj

2009-07-16 22:17  woolford

	* libpyEM/qtgui/em3Dfonts.py, libpyEM/qtgui/em3dmodule.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emlights.py, programs/e2simmx.py: em3dmodule

2009-07-16 18:32  woolford

	* libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimage3dsym.py,
	  programs/e2classaverage.py, programs/e2simmx.py: simmx, etc

2009-07-16 18:00  stevel

	* libpyEM/EMAN2PAR.py: trivial

2009-07-16 17:02  stevel

	* libpyEM/EMAN2PAR.py: trivial

2009-07-16 16:31  stevel

	* libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py, programs/e2ctf.py: Work
	  on parallel debugging

2009-07-16 15:04  zweig

	* sparx/demo/: 4_mpi_hdf/run_through_example,
	  5_mpi_bdb/run_through_example, 6_mpi_hdf_ctf/run_through_example,
	  7_mpi_bdb_ctf/run_through_example: program name change, etc.

2009-07-16 14:35  zweig

	* sparx/demo/3_bdb_ctf/run_through_example: program name change,
	  etc.

2009-07-16 14:20  zweig

	* sparx/demo/2_hdf_ctf/run_through_example: program name change,
	  etc.

2009-07-16 13:56  zweig

	* sparx/demo/: 1_bdb/run_through_example,
	  0_hdf/run_through_example: program name change, etc.

2009-07-16 10:38  ppenczek

	* libEM/sparx/rsconvolution.cpp: a bug in rsconvolution

2009-07-15 22:52  woolford

	* libpyEM/qtgui/emselector.py, programs/e2boxer2.py,
	  programs/e2classaverage.py, programs/e2tomoboxer.py: selector
	  bug, e2classaverage centers less

2009-07-15 22:42  woolford

	* programs/e2boxer2.py: e2boxer2

2009-07-15 22:24  woolford

	* libpyEM/qtgui/emboxerbase.py, libpyEM/qtgui/emimage3d.py,
	  programs/e2boxer2.py: e2boxer2

2009-07-15 21:30  stevel

	* libpyEM/EMAN2PAR.py, programs/e2parallel.py: Timeout option for
	  client added

2009-07-15 17:02  stevel

	* libpyEM/EMAN2PAR.py: Version change

2009-07-15 16:46  woolford

	* programs/e2tomoboxer.py: tomoboxer bug

2009-07-15 15:53  woolford

	* libpyEM/qtgui/emimage3dsym.py, programs/e2classaverage.py:
	  e2classaverage ref bug

2009-07-15 15:45  ppenczek

	* sparx/: bin/sxvar.py, libpy/applications.py, libpy/statistics.py:
	  sxvar corrections

2009-07-15 14:56  stevel

	* libpyEM/: EMAN2.py, EMAN2db.py: Add print functions for
	  transforms,etc

2009-07-15 13:37  gtang

	* libEM/emutil.cpp: support "ccp4" and "map" as MRC image file
	  extension

2009-07-15 13:20  stevel

	* libpyEM/EMAN2PAR.py: Get ready for failure handling

2009-07-15 02:22  stevel

	* libpyEM/EMAN2PAR.py, programs/e2ctf.py: Using structure factor in
	  CTF fitting if present (again). Seems a pretty well balanced
	  routine for now...

2009-07-14 23:25  woolford

	* libpyEM/qtgui/emboxerbase.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2boxer2.py: e2boxer2

2009-07-14 20:38  woolford

	* libEM/glutil.cpp, libEM/glutil.h, libpyEM/libpyGLUtils2.cpp,
	  libpyEM/qtgui/emboxerbase.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emshape.py,
	  programs/e2boxer2.py: e2boxer2

2009-07-14 15:45  stevel

	* libpyEM/EMAN2PAR.py: sigh

2009-07-14 15:33  stevel

	* libpyEM/EMAN2PAR.py: one more time

2009-07-14 15:20  stevel

	* libpyEM/EMAN2PAR.py: More debugging on server

2009-07-14 14:37  stevel

	* libpyEM/EMAN2PAR.py: logging bug

2009-07-14 14:31  stevel

	* libpyEM/EMAN2PAR.py: oops

2009-07-14 14:27  stevel

	* libpyEM/EMAN2PAR.py: parallel debugging

2009-07-14 13:54  stevel

	* libpyEM/EMAN2.py, libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py,
	  programs/e2ctf.py, programs/e2simmx.py: More work on CTF and
	  parallelism

2009-07-14 09:51  stevel

	* libpyEM/EMAN2PAR.py: oops

2009-07-14 09:48  stevel

	* libpyEM/EMAN2PAR.py, programs/e2simmx.py: Work on parallelism

2009-07-14 09:41  zyang

	* sparx/libpy/development.py: Add ormq_all()

2009-07-14 02:00  stevel

	* programs/e2ctf.py: Remove auomatic use of SF, Seemed to make auto
	  fit worse sometimes. Very odd...

2009-07-13 22:57  woolford

	* libpyEM/qtgui/emboxerbase.py, programs/e2boxer2.py,
	  pyemtbx/boxertools.py: e2boxer2

2009-07-13 14:33  stevel

	* programs/e2ctf.py: oops

2009-07-13 14:16  stevel

	* programs/e2ctf.py: CTF fitting improvement

2009-07-13 13:01  stevel

	* programs/e2ctf.py: Another try with CTF fitting. Getting there
	  now...

2009-07-13 12:58  gtang

	* doc/header_naming.html, libEM/amiraio.cpp, libEM/emdata.cpp,
	  libEM/mrcio.cpp, libEM/pifio.cpp, libEM/pointarray.cpp,
	  libEM/processor.cpp, libEM/vtkio.cpp,
	  libpyEM/qtgui/emimage3diso.py, programs/e2modeleval.py,
	  rt/pyem/test_emdata.py, rt/pyem/test_imageio.py,
	  rt/pyem/test_processor.py: image header parameter name change:
	  origin_row -> origin_x origin_col -> origin_y origin_sec ->
	  origin_z

2009-07-13 10:15  stevel

	* libpyEM/qtgui/emplot3d.py, programs/e2ctf.py: More CTF work.
	  Better defocuses in this version, but B-factors need work

2009-07-12 22:51  woolford

	* libpyEM/qtgui/emboxerbase.py, programs/e2boxer2.py,
	  pyemtbx/boxertools.py: e2boxer2

2009-07-12 18:32  woolford

	* programs/e2boxer2.py: e2boxer2

2009-07-12 17:45  woolford

	* programs/e2boxer2.py: e2boxer2

2009-07-11 23:27  woolford

	* libpyEM/qtgui/emboxerbase.py, programs/e2boxer.py,
	  programs/e2boxer2.py, pyemtbx/boxertools.py: e2boxer2 closer

2009-07-11 14:50  stevel

	* libpyEM/EMAN2db.py, programs/e2ctf.py: Fix minor DB issue when
	  opening non-existent DB read-only

2009-07-11 02:45  stevel

	* programs/e2ctf.py: oops switched the wrong way

2009-07-11 02:12  stevel

	* programs/e2ctf.py: This seems to take care of occasional misfits
	  with a structure factor

2009-07-10 22:54  woolford

	* libEM/boxingtools.cpp, libpyEM/qtgui/em3Dfonts.py,
	  libpyEM/qtgui/emboxerbase.py, libpyEM/qtgui/emsprworkflow.py,
	  libpyEM/qtgui/valslider.py, programs/e2boxer2.py,
	  programs/e2tomoboxer.py, pyemtbx/boxertools.py: e2boxer2

2009-07-10 17:04  gtang

	* libEM/: emobject.cpp, util.h: avoid NaN in EMObject

2009-07-10 12:06  gtang

	* rt/pyem/test_xydata.py: add unit test for XYData

2009-07-10 11:51  gtang

	* rt/pyem/test_xydata.py: add unit test for XYData

2009-07-10 11:17  ppenczek

	* programs/e2simmx.py: spelling corrected

2009-07-10 10:29  stevel

	* programs/e2ctf.py: Oops, broke the interactive CTF GUI.

2009-07-10 01:44  stevel

	* programs/e2ctf.py: Oops. Minor fix

2009-07-10 01:36  stevel

	* programs/e2ctf.py: Ok, ctf fitting seems to be working pretty
	  well now ?

2009-07-09 22:27  woolford

	* libpyEM/CMakeLists.txt, libpyEM/qtgui/emboxerbase.py,
	  programs/e2boxer2.py: boxer stuff

2009-07-09 21:28  woolford

	* examples/e2boxerbase.py, libpyEM/qtgui/emboxerbase.py:
	  rearranging :

2009-07-09 20:37  woolford

	* examples/e2boxerbase.py, libpyEM/EMAN2PAR.py,
	  programs/e2classaverage.py, programs/e2project3d.py,
	  programs/e2simmx.py: boxerbase, dc updates

2009-07-09 20:04  gtang

	* libEM/xydata.h: add some functions for XYData class

2009-07-09 17:48  woolford

	* examples/e2boxerbase.py, libpyEM/qtgui/emform.py: boxerbase work

2009-07-09 17:19  gtang

	* libEM/xydata.cpp, libpyEM/libpyCmp2.cpp: add some functions for
	  XYData class

2009-07-09 16:30  stevel

	* libpyEM/EMAN2PAR.py: fix imalive

2009-07-09 16:23  stevel

	* libpyEM/EMAN2PAR.py: imalive added

2009-07-09 16:16  stevel

	* libEM/xydata.h, programs/e2ctf.py: Continue to work on automatic
	  ctf fitting

2009-07-09 14:12  jbert

	* sparx/demo/5_mpi_bdb/run_through_example: fix bug

2009-07-09 13:47  jbert

	* sparx/demo/5_mpi_bdb/run_through_example: change params

2009-07-09 11:57  jbert

	* sparx/demo/3_bdb_ctf/run_through_example: change params to
	  sxfind_struct

2009-07-09 11:40  jbert

	* sparx/libpy/applications.py: fix bug

2009-07-09 10:51  stevel

	* libpyEM/EMAN2db.py: Hopefully safer db_remove_dict that actually
	  removes associated files.

2009-07-09 10:50  jbert

	* sparx/demo/1_bdb/run_through_example: change params to find
	  structure

2009-07-09 02:43  stevel

	* programs/e2ctf.py: Working on auto ctf fitting some more...

2009-07-08 23:24  woolford

	* libpyEM/qtgui/emsprworkflow.py: workflow updates

2009-07-08 22:48  woolford

	* examples/e2boxerbase.py, libEM/emdata_core.cpp,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3dsym.py,
	  libpyEM/qtgui/emimagemx.py, programs/e2boxer.py,
	  pyemtbx/boxertools.py: boxerbase updates

2009-07-08 17:41  gtang

	* sparx/demo/: 0_hdf/run_through_example,
	  1_bdb/run_through_example, 2_hdf_ctf/run_through_example,
	  3_bdb_ctf/run_through_example, 4_mpi_hdf/run_through_example,
	  5_mpi_bdb/run_through_example, 6_mpi_hdf_ctf/run_through_example,
	  7_mpi_bdb_ctf/run_through_example: cutoff_frequency -> cutoff_abs

2009-07-08 16:34  stevel

	* programs/e2ctf.py: another tweak to ctf

2009-07-08 16:23  stevel

	* libpyEM/Simplex.py, programs/e2ctf.py, sparx/bin/sxctf.py: Redid
	  automatic CTF fitting with simplex algorithm. Much more reliable.

2009-07-08 14:41  gtang

	* libEM/processor.h: fix the MSVC platform

2009-07-08 14:33  zyang

	* sparx/libpy/development.py: Delete many useless codes.

2009-07-08 13:39  gtang

	* libpyEM/CMakeLists.txt: install em3Dfonts.py to EMAN2/lib
	  directory

2009-07-08 13:13  zyang

	* libEM/emdata_core.cpp: Block an annoying output

2009-07-08 11:17  zyang

	* sparx/libpy/development.py: Many changes

2009-07-08 09:35  stevel

	* libpyEM/EMAN2PAR.py: tweak to DC

2009-07-08 02:34  stevel

	* libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2ctf.py: trivial

2009-07-07 22:54  woolford

	* examples/e2boxerbase.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emselector.py,
	  programs/e2boxer.py, programs/e2classaverage.py,
	  pyemtbx/boxertools.py: adding boxerbase

2009-07-07 17:16  zyang

	* sparx/libpy/development.py: Multiple change. The major one is to
	  change ormy2(), ormy2lbfgsb() and ormy3() such that its treatment
	  of mirror is consistant with ormq()

2009-07-07 17:10  zyang

	* sparx/libpy/applications.py: Change ali2d_c() and ali2d_c_MPI()
	  so they write the middle results to a stack instead of multiple
	  files.

2009-07-07 16:25  stevel

	* libEM/processor.h, libpyEM/EMAN2db.py, programs/e2ctf.py: Subtle
	  improvements to CTF. Still working on them...

2009-07-07 13:24  woolford

	* libpyEM/qtgui/: emimage3dsym.py, emselector.py, emsprworkflow.py:
	  [no log message]

2009-07-07 12:13  woolford

	* libpyEM/qtgui/emsprworkflow.py: workflow recovery ptcls_dict

2009-07-07 10:26  gtang

	* rt/pyem/test_processor.py: unit test update

2009-07-07 02:15  stevel

	* libEM/: processor.cpp, processor.h: Working on new evaluation
	  processor

2009-07-06 23:00  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3dsym.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emsprworkflow.py,
	  libpyEM/qtgui/emtprworkflow.py, programs/e2boxer.py,
	  programs/e2classaverage.py, programs/e2ctf.py,
	  programs/e2eulerxplor.py, programs/e2simmx.py,
	  programs/e2workflow.py, pyemtbx/boxertools.py: general workflow
	  fixes

2009-07-06 13:09  stevel

	* libpyEM/EMAN2db.py: Another locking issue

2009-07-06 13:00  stevel

	* libpyEM/EMAN2db.py: Wierd bug...

2009-07-06 12:55  stevel

	* libpyEM/EMAN2db.py: Db fix

2009-07-06 12:51  stevel

	* libpyEM/qtgui/emsprworkflow.py:
	  oops

2009-07-06 12:51  stevel

	* libpyEM/qtgui/emsprworkflow.py: oops

2009-07-06 12:41  stevel

	* libpyEM/EMAN2db.py: minor oops in db

2009-07-06 11:46  stevel

	* libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py, programs/e2ctf.py: DB
	  threadsafety. Tweak to ctf

2009-07-06 02:33  stevel

	* libEM/processor.cpp, libEM/processor.h, programs/e2proc3d.py: New
	  autopeak processor. Still working on it.

2009-07-03 19:28  woolford

	* libpyEM/qtgui/emform.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2eulerxplor.py, programs/e2workflow.py: sym viewer
	  complete and efficient

2009-07-03 15:26  woolford

	* libpyEM/qtgui/: emselector.py, emsprworkflow.py: ctf output
	  single task

2009-07-03 12:51  stevel

	* libpyEM/EMAN2db.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/valslider.py, programs/e2ctf.py: Fix problem
	  (hopefully) with mutex exhaustion in DB.  Many e2ctf
	  improvements, including pretty decent envelope generation.

2009-07-03 01:09  stevel

	* programs/e2ctf.py: New e2ctf features working. Still no
	  astigmatism.

2009-07-02 23:01  woolford

	* libpyEM/EMAN2db.py, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimage3dsym.py,
	  programs/e2eulerxplor.py: more sym work

2009-07-02 16:39  jbert

	* sparx/libpy/statistics.py: fix bug

2009-07-02 16:15  stevel

	* libpyEM/EMAN2PAR.py: Still working

2009-07-02 16:08  stevel

	* libpyEM/EMAN2db.py, libpyEM/qtgui/emsprworkflow.py,
	  libpyEM/qtgui/valslider.py, programs/e2ctf.py: Working on CTF and
	  debugging database mutex problems

2009-07-02 15:40  woolford

	* libpyEM/EMAN2db.py, libpyEM/qtgui/emimage3dsym.py,
	  programs/e2eulerxplor.py: debug

2009-07-02 14:30  woolford

	* libEM/processor.cpp, libpyEM/EMAN2db.py,
	  libpyEM/qtgui/emimage3dsym.py, programs/e2eulerxplor.py: minor
	  fixes

2009-07-02 12:57  gtang

	* programs/e2proc2d.py: small fix

2009-07-02 12:48  gtang

	* programs/e2proc2d.py: fix the outtype=spidersingle option to
	  output 2D single images rather than 2D stack.

2009-07-02 12:26  jbert

	* sparx/libpy/statistics.py: fix bug

2009-07-02 09:15  jbert

	* sparx/libpy/applications.py: fix bug

2009-07-01 23:22  woolford

	* libpyEM/qtgui/emsprworkflow.py: set bug

2009-07-01 22:59  woolford

	* programs/e2eulerxplor.py: [no log message]

2009-07-01 22:15  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2eulerxplor.py: eulerxplor improvements

2009-07-01 16:08  jbert

	* sparx/libpy/: applications.py, statistics.py: add new matching to
	  kmeans stab

2009-07-01 15:53  stevel

	* libpyEM/: EMAN2PAR.py, EMAN2db.py: Playing with database

2009-07-01 14:44  gtang

	* libpyEM/CMakeLists.txt: fix the MSVC platform

2009-07-01 14:21  woolford

	* libEM/emdata_core.cpp, libEM/processor.cpp, libEM/processor.h,
	  libpyEM/EMAN2.py, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimage3dsym.py,
	  libpyEM/qtgui/emsprworkflow.py: import bug

2009-07-01 13:44  stevel

	* libEM/emobject.cpp: oops

2009-07-01 13:43  stevel

	* libEM/: emdata.cpp, emobject.cpp: Fix problem with assigning
	  (float)nan to Dict key

2009-07-01 10:28  gtang

	* rt/pyem/: test_aligner.py, test_emdata.py: unit test update

2009-07-01 09:53  gtang

	* rt/pyem/test_processor.py: unit test update

2009-06-30 18:49  woolford

	* libEM/: processor.cpp, processor.h, util.h: processor work

2009-06-30 16:47  woolford

	* libEM/processor.cpp: goodf

2009-06-30 16:22  woolford

	* libEM/processor.cpp, libEM/util.h, programs/e2workflow.py: goodf
	  stuff

2009-06-30 15:13  woolford

	* libEM/emdata_core.cpp, libEM/processor.cpp,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2classaverage.py,
	  programs/e2eulerxplor.py, programs/e2workflow.py: testing

2009-06-30 11:35  woolford

	* programs/e2classaverage.py: e2classaverage bug

2009-06-30 11:18  zyang

	* libEM/sparx/emdata_sparx.cpp: Trival change

2009-06-30 11:17  woolford

	* programs/e2simmx.py: e2simmx bug

2009-06-30 11:15  zyang

	* sparx/libpy/development.py: Fix a mistake in ormy3g()

2009-06-29 22:22  woolford

	* libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimage3dsym.py,
	  libpyEM/qtgui/emplot3d.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2eulerxplor.py,
	  programs/e2make3d.py, programs/e2workflow.py: interface updates

2009-06-29 16:22  zyang

	* sparx/libpy/: development.py, fundamentals.py: Many non-essential
	  changes.

2009-06-29 13:35  zyang

	* sparx/libpy/: applications.py, development.py: To work on
	  ali2d_g() and ali2d_g_MPI() again.

2009-06-29 04:51  ppenczek

	* libEM/emdata_modular.h, libEM/projector.cpp, libEM/projector.h,
	  libEM/sparx/util_sparx.cpp, sparx/bin/sxvar.py,
	  sparx/libpy/applications.py, sparx/libpy/reconstruction.py,
	  sparx/libpy/statistics.py, sparx/test/3DA/3dg.py: wbp

2009-06-29 03:12  stevel

	* programs/e2ctf.py: Working on extracting structure factor from
	  CTF fitting

2009-06-26 19:44  woolford

	* libEM/processor.cpp, programs/e2boxer.py, pyemtbx/boxertools.py:
	  boxer bugs + import coords in workflow

2009-06-26 18:10  gtang

	* libEM/sparx/emdata_sparx.cpp: fix for Visual Studio 2005.

2009-06-26 17:31  woolford

	* libEM/pointarray.cpp, libEM/symmetry.h, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emsave.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2boxer.py,
	  programs/e2workflow.py, pyemtbx/boxertools.py: boxer bugs

2009-06-26 15:50  gtang

	* libEM/processor.cpp: fix for Visual Studio 2005.

2009-06-26 14:51  gtang

	* libEM/cmp.cpp: fix for Visual Studio 2005.

2009-06-26 14:46  gtang

	* libEM/averager.cpp: fix for Visual Studio 2005.

2009-06-26 14:36  gtang

	* libEM/: emdata.cpp, marchingcubes.cpp: fix for Visual Studio
	  2005.

2009-06-26 14:32  gtang

	* libEM/: aligner.cpp, emdata_transform.cpp: fix for Visual Studio
	  2005.

2009-06-26 14:31  gtang

	* rt/pyem/test_processor.py: [no log message]

2009-06-26 14:22  gtang

	* libEM/processor.h: fix for Visual Studio 2005.

2009-06-26 14:09  woolford

	* libpyEM/qtgui/emimage3d.py, programs/e2classaverage.py: class
	  aver bug

2009-06-26 13:57  stevel

	* libpyEM/EMAN2PAR.py, programs/e2proc3d.py: trivial

2009-06-26 13:14  woolford

	* libpyEM/qtgui/: emapplication.py, emglobjects.py, emimage3d.py,
	  emselector.py: widget delete bugs

2009-06-26 12:51  woolford

	* libpyEM/qtgui/: emform.py, emimage2d.py: widget delete bugs

2009-06-25 22:06  woolford

	* libpyEM/qtgui/: emapplication.py, emform.py, emsprworkflow.py:
	  minor fixes

2009-06-25 18:31  woolford

	* programs/e2classaverage.py: minor tweaks

2009-06-25 17:57  woolford

	* libEM/emdata_core.cpp, libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emplot3d.py, programs/e2classaverage.py: simmx fix

2009-06-25 16:39  woolford

	* libpyEM/qtgui/: emplot3d.py, emselector.py: plot 3d

2009-06-25 16:31  jbert

	* sparx/libpy/: applications.py, statistics.py: fix bug

2009-06-25 16:22  woolford

	* libpyEM/qtgui/: emapplication.py, emglobjects.py, emimage2d.py,
	  emimagemx.py, emimageutil.py, emplot2d.py, emselector.py: good
	  bye QtObject: Do not delete...

2009-06-25 15:52  woolford

	* programs/e2simmx.py: simmx uses math.finite

2009-06-25 15:25  woolford

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emsprworkflow.py: finite proc

2009-06-25 14:26  woolford

	* libEM/aligner.cpp, libEM/aligner.h, programs/e2simmx.py: aligner
	  fixes

2009-06-25 13:22  woolford

	* libpyEM/EMAN2db.py, programs/e2desktop.py, programs/e2simmx.py:
	  write bug

2009-06-25 12:15  woolford

	* libEM/hdfio2.cpp, libEM/pointarray.cpp, libEM/pointarray.h,
	  libpyEM/libpyPointArray2.cpp, programs/e2eulerxplor.py: minor
	  fixes

2009-06-25 10:07  jbert

	* sparx/libpy/: applications.py, statistics.py: some modification
	  to k-means cuda

2009-06-25 02:08  stevel

	* libpyEM/libpyAligner2.cpp, programs/e2ctf.py: Refit button in
	  e2ctf

2009-06-24 23:02  woolford

	* libEM/averager.h, libEM/emdata_io.cpp, libEM/emdata_metadata.cpp,
	  libEM/emdata_metadata.h, libEM/emutil.cpp, libEM/geometry.h,
	  libEM/hdfio2.cpp, libpyEM/EMAN2db.py, libpyEM/libpyEMData2.cpp,
	  libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emsprworkflow.py,
	  libpyEM/qtgui/emtprworkflow.py, programs/e2boxer.py,
	  programs/e2simmx.py, programs/e2tomoboxer.py,
	  programs/e2workflow.py: region writing, simmx parallel, 2.6
	  compat

2009-06-24 16:14  jbert

	* sparx/libpy/applications.py: fix bug

2009-06-24 16:09  jbert

	* sparx/bin/sxk_means_stable.py: fix bug

2009-06-24 14:13  jbert

	* sparx/libpy/applications.py: k means stable cuda stream

2009-06-24 14:12  jbert

	* sparx/bin/sxk_means_stable.py: k means stab cuda stream

2009-06-24 14:01  gtang

	* libpyEM/qtgui/emselector.py: small fix

2009-06-24 13:31  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emplot2d.py,
	  libpyEM/qtgui/emsprworkflow.py, libpyEM/qtgui/emtprworkflow.py,
	  programs/e2display.py, programs/e2workflow.py: working on
	  QtCore.QObject issue

2009-06-24 12:03  woolford

	* libpyEM/qtgui/emsprworkflow.py: workflow improvements

2009-06-24 11:45  stevel

	* libpyEM/EMAN2PAR.py: Work on parallelism debugging

2009-06-24 11:08  woolford

	* libpyEM/qtgui/emsprworkflow.py: recovery stuff

2009-06-24 10:36  gtang

	* rt/pyem/test_vec.py: [no log message]

2009-06-24 01:43  stevel

	* programs/e2ctf.py: New output options in e2ctf.py

2009-06-23 21:50  woolford

	* libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emsprworkflow.py,
	  libpyEM/qtgui/emtprworkflow.py, programs/e2boxer.py,
	  programs/e2classaverage.py, programs/e2eulerxplor.py,
	  programs/e2initialmodel.py, programs/e2make3d.py,
	  programs/e2refine2d.py, programs/e2tomoboxer.py,
	  programs/e2tomohunter.py, programs/e2workflow.py: db dictionary
	  updates for workflow

2009-06-23 16:51  jbert

	* sparx/libpy/statistics.py: add function to Hungarian algorithm

2009-06-23 15:34  woolford

	* programs/e2classaverage.py: ref ali in e2classverage: no
	  centering

2009-06-23 15:17  woolford

	* libEM/transform.cpp, programs/e2classaverage.py: Transform fixed

2009-06-23 13:11  stevel

	* libpyEM/EMAN2db.py: Another fix to db_remove_dict

2009-06-23 10:41  gtang

	* libEM/emdata_transform.cpp: explicitly convert atan2()'s argument
	  to float

2009-06-23 00:24  stevel

	* libpyEM/EMAN2db.py: Removal fixed...

2009-06-22 22:20  woolford

	* libEM/transform.h, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emsprworkflow.py, libpyEM/qtgui/emtprworkflow.py,
	  programs/e2boxer.py, programs/e2initialmodel.py,
	  programs/e2make3d.py, programs/e2refine2d.py,
	  programs/e2tomoboxer.py, programs/e2tomohunter.py,
	  programs/e2workflow.py: lists go to dicts in the workflow

2009-06-22 16:25  stevel

	* programs/e2initialmodel.py: Working to improve initial models

2009-06-22 15:11  stevel

	* programs/: e2ctf.py, e2initialmodel.py, e2msa.py, e2refine2d.py:
	  Beginning overhaul of e2ctf. new improvements to e2refine2d and
	  e2initialmodel

2009-06-22 13:23  woolford

	* libEM/: transform.cpp, transform.h: transform tweaks

2009-06-22 13:13  woolford

	* libEM/: transform.cpp, transform.h: Transform is strict about
	  params

2009-06-22 01:10  stevel

	* programs/: e2basis.py, e2msa.py: trivial

2009-06-22 00:21  stevel

	* libEM/ctf.cpp, libpyEM/EMAN2db.py, programs/e2basis.py,
	  programs/e2msa.py, programs/e2refine2d.py: Real fixes for
	  e2refine2d

2009-06-19 17:29  woolford

	* libpyEM/: EMAN2.py, qtgui/emglobjects.py, qtgui/emimagemx.py,
	  qtgui/emlights.py, qtgui/emplot2d.py, qtgui/emplot3d.py,
	  qtgui/emshape.py: glut updates

2009-06-19 16:54  woolford

	* libpyEM/: EMAN2db.py, qtgui/emsprworkflow.py: minor updates

2009-06-19 16:01  woolford

	* libpyEM/qtgui/emsprworkflow.py: tmp workaround for set cleaning

2009-06-18 09:41  zyang

	* libEM/sparx/util_sparx.cpp: Fix a small bug.

2009-06-17 21:36  woolford

	* libEM/: processor.cpp, processor.h: ctf weight proc

2009-06-17 19:11  woolford

	* libEM/: aligner.cpp, aligner.h: 3d refine aligner

2009-06-17 17:49  woolford

	* CMakeLists.txt, libEM/cuda/cuda_cmp.cu,
	  libEM/cuda/cuda_processor.cu, libEM/cuda/cuda_util.cu,
	  libpyEM/EMAN2db.py, libpyEM/qtgui/emanimationutil.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2eulerxplor.py: eulerxplor animates particle
	  trajectories

2009-06-16 20:45  gtang

	* programs/e2proc2d.py: use less memory when processing 3D image as
	  2D stack

2009-06-16 20:26  gtang

	* libEM/: emdata.h, emdata_metadata.h: argument comment update

2009-06-16 20:26  gtang

	* rt/pyem/test_processor.py: unit test update

2009-06-16 16:39  zyang

	* sparx/libpy/utilities.py: Reverse the previous two changes.

2009-06-16 16:32  gtang

	* libEM/processor.h: argument comment update

2009-06-16 16:05  zyang

	* sparx/libpy/: applications.py, development.py: Some change to the
	  gradient method.

2009-06-15 21:53  woolford

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2classaverage.py,
	  programs/e2ctf.py: more updates

2009-06-15 20:52  stevel

	* libEM/averager.cpp: Minor tweak

2009-06-15 20:39  stevel

	* libEM/averager.cpp, libEM/ctf.cpp, programs/e2ctf.py: Work on
	  ctfc.auto averager. Seems mostly working now, but some bfactor
	  questions.

2009-06-15 18:44  stevel

	* programs/: e2basis.py, e2msa.py: FINALLY fixed the refine2d
	  problem (I think) !!!

2009-06-15 18:30  woolford

	* libEM/processor.cpp, libEM/processor.h, programs/e2workflow.py:
	  bug fixes

2009-06-15 15:04  woolford

	* programs/e2make3d.py: eotest bug

2009-06-14 20:26  stevel

	* libEM/averager.cpp, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emshape.py: probing values in 2d images. CTF
	  corrected averager fixes

2009-06-14 18:32  woolford

	* libpyEM/qtgui/: emimagemx.py, emselector.py: minor tweaks

2009-06-14 17:33  woolford

	* libpyEM/qtgui/emsprworkflow.py: ctf flag for particle tables

2009-06-14 17:29  woolford

	* libpyEM/qtgui/emapplication.py: inspectors raised

2009-06-14 09:11  gtang

	* libEM/: amiraio.cpp, exception.h, geometry.cpp, imageio.cpp,
	  log.cpp, lstfastio.cpp, lstio.cpp, reconstructor.cpp, salio.cpp,
	  transform.h, vec3.h, xydata.cpp: fix compilation error for gcc
	  4.4. It does not include stdio by default.

2009-06-13 22:31  stevel

	* libEM/averager.cpp: bugfix

2009-06-13 22:30  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2ctf.py: update ctf snr
	  column

2009-06-13 22:23  stevel

	* libEM/: averager.cpp, averager.h, ctf.cpp, ctf.h: ctf averager
	  ... almost works....

2009-06-13 19:20  woolford

	* libpyEM/qtgui/emimagemx.py: stack fix

2009-06-13 19:14  stevel

	* libpyEM/EMAN2.py, programs/e2ctf.py: Improved CTF auto fitting,
	  may work with viruses now (???) though the B-factors are still a
	  problem when they aren't very gaussian

2009-06-13 18:54  woolford

	* libEM/glutil.cpp, libEM/glutil.h, libEM/marchingcubes.cpp,
	  libEM/marchingcubes.h, libpyEM/libpyGLUtils2.cpp,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emimage3dslice.py,
	  libpyEM/qtgui/emselector.py: 2d iso improvements

2009-06-12 22:32  woolford

	* libpyEM/qtgui/emplot2d.py, programs/e2ctf.py: ctf tweaks

2009-06-12 22:09  woolford

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3dslice.py,
	  libpyEM/qtgui/emimage3dvol.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emselector.py: display updates

2009-06-12 20:10  woolford

	* libEM/emdata.cpp, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimage3diso.py,
	  libpyEM/qtgui/emimage3dslice.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emselector.py: interface updates

2009-06-12 17:39  stevel

	* examples/sizes.py, programs/e2ctf.py: Work on ctf. New 'sizes'
	  example that will try to measure the size of circular particles.

2009-06-12 17:05  woolford

	* libpyEM/qtgui/: emimage2d.py, emimage3d.py, emimage3diso.py,
	  emimage3dslice.py, emimage3dvol.py, emimagemx.py, emselector.py:
	  browser tweaks

2009-06-12 15:02  woolford

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2classaverage.py: double click for classes, fft
	  resample

2009-06-11 20:13  woolford

	* libpyEM/qtgui/: emimage3diso.py, emimage3dslice.py,
	  emimage3dvol.py: interface updates

2009-06-11 19:42  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimage3diso.py,
	  libpyEM/qtgui/emimage3dslice.py, libpyEM/qtgui/emimage3dsym.py,
	  libpyEM/qtgui/emimage3dvol.py, programs/e2workflow.py: interface
	  updates, no leaks

2009-06-11 18:28  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emform.py, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emlights.py,
	  libpyEM/qtgui/emplot2d.py, libpyEM/qtgui/emplot3d.py,
	  libpyEM/qtgui/emselector.py, libpyEM/qtgui/emshape.py,
	  programs/e2ctf.py, programs/e2desktop.py, programs/e2display.py,
	  programs/e2workflow.py: interface updates

2009-06-11 18:21  gtang

	* libEM/processor.h: update processors' parameters comment

2009-06-11 18:16  gtang

	* libEM/processor.h: update processors' parameters comment

2009-06-11 17:36  gtang

	* libEM/averager.h: update averager's parameters comment

2009-06-11 17:29  gtang

	* libEM/analyzer.h: update analyzer's parameters comment

2009-06-11 17:23  gtang

	* libEM/aligner.h: update aligner's parameters comment

2009-06-11 17:11  gtang

	* libEM/projector.h: update projector's parameters comment

2009-06-11 17:07  gtang

	* libEM/: processor.cpp, processor.h: update processors' parameters
	  comment

2009-06-11 16:45  jbert

	* sparx/: bin/sxk_means_stability.py, libpy/applications.py:
	  changethe way to random seed

2009-06-11 15:07  gtang

	* libEM/processor.h: update processors' parameters comment

2009-06-11 14:39  gtang

	* libEM/: processor.cpp, sparx/processor_sparx.h: put parameter
	  "sigma" back for New Fourier Filter

2009-06-11 11:54  gtang

	* rt/pyem/: test_aligner.py, test_processor.py: unit test update

2009-06-11 10:47  woolford

	* programs/e2tomohunter.py: [no log message]

2009-06-10 23:35  woolford

	* programs/e2tomohunter.py: fixes

2009-06-10 23:25  woolford

	* libpyEM/qtgui/emsprworkflow.py, libpyEM/qtgui/emtprworkflow.py,
	  programs/e2tomohunter.py, programs/e2workflow.py: tomo fixes

2009-06-10 22:49  gtang

	* libEM/mrcio.cpp: add nsymbt to offset when reading mrc file

2009-06-10 21:33  woolford

	* libpyEM/qtgui/emsprworkflow.py, libpyEM/qtgui/emtprworkflow.py,
	  programs/e2tomohunter.py, programs/e2workflow.py: more tomo stuff

2009-06-10 19:37  gtang

	* programs/e2proc2d.py: --treat3das2d process 3D image as a stack
	  of 2D image

2009-06-10 18:44  woolford

	* libEM/processor.cpp, libpyEM/qtgui/emtprworkflow.py,
	  programs/e2workflow.py: tomo filter options

2009-06-10 17:00  gtang

	* examples/shrinkbigimage.py, examples/transalignavg.py,
	  libEM/sparx/fourierfilter.cpp, libEM/sparx/processor_sparx.h,
	  sparx/libpy/filter.py, sparx/test/main_example.py: change the
	  parameters "cutoff_frequency" and "sigma" to "cutoff_abs" in
	  Pawel's new fourier processor.

2009-06-10 16:27  gtang

	* libEM/: amiraio.cpp, analyzer.cpp, cmp.cpp, emdata_core.cpp,
	  emdata_metadata.cpp, emdata_transform.cpp, fitsio.cpp, mrcio.cpp,
	  pifio.cpp, pointarray.cpp, pointarray.h, processor.cpp,
	  reconstructor_tools.cpp, xplorio.cpp, averager.cpp, emdata.cpp,
	  emdata_metadata.h, emutil.cpp, hdfio2.cpp, imageio.cpp,
	  projector.cpp, reconstructor.cpp, testutil.cpp: use size_t for 3D
	  image pixel index to avoid the 2GB limit by using int as index.

2009-06-10 16:23  gtang

	* rt/pyem/test_processor.py: unit test update

2009-06-10 15:27  woolford

	* libEM/emdata_cuda.cpp, libEM/sparx/processor_sparx.h,
	  libpyEM/qtgui/emtprworkflow.py, programs/e2tomohunter.py,
	  programs/e2workflow.py: fixed processor stuff

2009-06-10 11:00  jbert

	* sparx/libpy/utilities.py: fix bug in recv_attr_dic

2009-06-09 20:33  stevel

	* programs/e2ctf.py: Working on ctf correction

2009-06-09 20:31  woolford

	* images/CMakeLists.txt, images/tomo_hunter.png,
	  images/macimages/CMakeLists.txt,
	  images/macimages/tomo_hunter.png, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emsprworkflow.py, libpyEM/qtgui/emtprworkflow.py,
	  programs/e2boxer.py, programs/e2tomoboxer.py,
	  programs/e2tomohunter.py, programs/e2workflow.py: tomo updates

2009-06-09 13:57  zyang

	* sparx/libpy/alignment.py: Add printouts.

2009-06-08 23:23  woolford

	* programs/: e2make3d.py, e2simmx.py: more fixes

2009-06-08 22:57  woolford

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emsprworkflow.py, libpyEM/qtgui/emtprworkflow.py,
	  programs/e2make3d.py: more fixes

2009-06-08 21:05  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2eotest.py: set related
	  bug fixes

2009-06-08 20:34  woolford

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/processor.cpp,
	  libEM/sparx/processor_sparx.h, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2eotest.py: parameter conversion updates

2009-06-08 19:53  woolford

	* libEM/: processor.cpp, processor.h, sparx/processor_sparx.h:
	  formula fixes

2009-06-08 19:28  stevel

	* programs/e2resolution.py: Playing with norm parameters to try for
	  improved results...

2009-06-08 18:37  gtang

	* libEM/sparx/processor_sparx.h: New fourier processor accept
	  cutoff_abs/cutoff_freq/cutoff_pixels as parameters, which could
	  be converted to cutoff_frequency/sigma.

2009-06-08 18:37  woolford

	* libEM/aligner.cpp, libEM/processor.cpp,
	  libpyEM/qtgui/emimage3dslice.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py, libpyEM/qtgui/emtprworkflow.py:
	  tweaks

2009-06-08 18:01  stevel

	* libEM/emdata.cpp: Fix problem for cutting slices from large
	  tomograms

2009-06-08 16:37  gtang

	* programs/e2proc3d.py, pyemtbx/options.py: change multiple
	  arguments handling

2009-06-08 16:19  zyang

	* sparx/: libpy/applications.py, test/3DA/3dg.py: Trival change

2009-06-08 15:39  ppenczek

	* sparx/libpy/alignment.py: Beautify the printouts.

2009-06-08 15:13  woolford

	* libEM/sparx/processor_sparx.h, libpyEM/EMAN2.py,
	  libpyEM/qtgui/emselector.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2refine.py: post process in e2make3d for e2refine form

2009-06-08 12:39  woolford

	* programs/: e2eulerxplor.py, e2refine.py: e2eulerxplor fix

2009-06-08 12:28  woolford

	* programs/: e2eulerxplor.py, e2refine.py: e2eulerxplor works from
	  workflow

2009-06-08 09:40  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Add two news functions
	  multiref_polar_ali_2d_local_psi() and Crosrng_sm_psi()

2009-06-08 00:13  woolford

	* libpyEM/qtgui/emsprworkflow.py: bug fixes

2009-06-07 17:41  stevel

	* libEM/ctf.cpp, programs/e2ctf.py: Minor bug in wiener filtration

2009-06-07 00:28  woolford

	* libEM/emdata.cpp, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emsprworkflow.py, libpyEM/qtgui/emtprworkflow.py,
	  programs/e2tomoboxer.py: tomo work

2009-06-05 21:14  woolford

	* libpyEM/qtgui/emselector.py: selector fix

2009-06-05 21:09  woolford

	* libEM/reconstructor.cpp, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emsave.py, libpyEM/qtgui/emshape.py,
	  libpyEM/qtgui/emsprworkflow.py, libpyEM/qtgui/emtprworkflow.py,
	  programs/e2make3d.py, programs/e2refine2d.py: tomo workflow stuff

2009-06-05 18:35  woolford

	* libEM/emdata.cpp, libEM/emutil.cpp, libEM/processor.cpp,
	  libEM/reconstructor.cpp, libpyEM/CMakeLists.txt,
	  libpyEM/qtgui/emform.py, libpyEM/qtgui/emsprworkflow.py,
	  libpyEM/qtgui/emtprworkflow.py, programs/e2make3d.py,
	  programs/e2refine.py, programs/e2workflow.py: float translate bug

2009-06-05 17:27  gtang

	* libEM/: emdata.cpp, emdata_metadata.cpp: e2iminfo.py does not
	  need read the image's data

2009-06-05 17:20  jbert

	* sparx/demo/7_mpi_bdb_ctf/run_through_example: change k-means and
	  cml

2009-06-05 16:59  gtang

	* libEM/emdata_metadata.cpp: correct a confusing error mesage

2009-06-05 16:36  stevel

	* libEM/ctf.cpp: oops

2009-06-05 16:35  stevel

	* libEM/ctf.cpp, libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py: Still
	  trying to fix the database 'file not found' bug

2009-06-05 16:33  jbert

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, sparx/bin/sxk_means_stability.py,
	  sparx/libpy/applications.py, sparx/libpy/projection.py,
	  sparx/libpy/statistics.py: some change to k-means and cml

2009-06-05 16:29  jbert

	* sparx/demo/5_mpi_bdb/run_through_example: uncomment first line

2009-06-05 16:24  jbert

	* sparx/demo/5_mpi_bdb/run_through_example: changing for k-means
	  and cml

2009-06-05 15:23  stevel

	* libpyEM/EMAN2PAR.py: trivial

2009-06-05 14:59  stevel

	* libpyEM/EMAN2PAR.py: oops

2009-06-05 14:52  stevel

	* libpyEM/: EMAN2PAR.py, EMAN2db.py: Fix the db again

2009-06-05 14:43  woolford

	* libpyEM/qtgui/emselector.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2project3d.py, programs/e2workflow.py: project3d debug
	  comments

2009-06-05 13:46  ppenczek

	* sparx/libpy/: applications.py, reconstruction.py: activated ihrsr
	  MPI

2009-06-05 13:46  stevel

	* libpyEM/EMAN2PAR.py: oops

2009-06-05 13:44  stevel

	* libpyEM/EMAN2PAR.py: Still debugging :^(

2009-06-05 13:15  stevel

	* libpyEM/: EMAN2PAR.py, EMAN2db.py: more work fixing db

2009-06-05 13:07  woolford

	* libEM/emutil.cpp, libpyEM/qtgui/emselector.py: minor fix

2009-06-05 11:12  woolford

	* libpyEM/EMAN2db.py: get rid of print stmts

2009-06-05 10:21  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-06-05 09:44  stevel

	* CMakeLists.txt, install-dependencies.py, libpyEM/EMAN2db.py:
	  Better error detection in DB functions

2009-06-04 23:18  woolford

	* programs/e2bdb.py: [no log message]

2009-06-04 19:58  woolford

	* images/CMakeLists.txt, images/classes.png,
	  images/macimages/CMakeLists.txt, images/macimages/classes.png,
	  libpyEM/EMAN2db.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2workflow.py: set
	  integration in workflow - beta

2009-06-04 17:12  woolford

	* libEM/processor.cpp, libpyEM/EMAN2db.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2bdb.py,
	  programs/e2workflow.py: particle sets

2009-06-04 15:47  stevel

	* libpyEM/EMAN2PAR.py: Work on cache debugging

2009-06-04 15:11  stevel

	* libpyEM/EMAN2db.py: Bit more work on DB debugging

2009-06-04 14:57  stevel

	* libpyEM/EMAN2db.py: oops

2009-06-04 14:50  stevel

	* libpyEM/EMAN2db.py: Threadsafe opens on DB

2009-06-04 13:47  stevel

	* programs/e2bdb.py: appendvstack

2009-06-04 13:34  stevel

	* libpyEM/EMAN2PAR.py: trivial

2009-06-04 12:49  stevel

	* CMakeLists.txt: Trivial

2009-06-04 11:11  ppenczek

	* sparx/: libpy/applications.py, libpy/reconstruction.py,
	  test/3DA/3dg.py: centering of data ofr ihrsr

2009-06-04 10:55  woolford

	* libpyEM/qtgui/emsprworkflow.py: minor fix

2009-06-04 10:33  zyang

	* sparx/libpy/alignment.py: Trival change.

2009-06-04 10:08  ppenczek

	* sparx/libpy/utilities.py:  changes from monster

2009-06-04 02:37  stevel

	* libEM/ctf.cpp: trivial

2009-06-04 02:09  stevel

	* CMakeLists.txt, examples/cmpspeedtest.py, libEM/cmp.cpp: Work on
	  optimization and testing of similarity metrics.

2009-06-03 22:51  woolford

	* libpyEM/qtgui/: emform.py, emsprworkflow.py: minor fixes

2009-06-03 19:13  woolford

	* libpyEM/qtgui/emform.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emselector.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2boxer.py, programs/e2workflow.py: working on sets in
	  workflow

2009-06-03 14:25  ppenczek

	* sparx/libpy/alignment.py: [no log message]

2009-06-03 14:08  ppenczek

	* sparx/libpy/utilities.py: corrected even_angles

2009-06-03 12:06  ppenczek

	* sparx/libpy/utilities.py: [no log message]

2009-06-03 12:06  ppenczek

	* sparx/libpy/reconstruction.py: removed unnecessary info from rec

2009-06-03 03:07  stevel

	* libEM/: cmp.cpp, util.cpp, util.h: Playing with frc cmp speedups.

2009-06-03 00:45  stevel

	* libpyEM/: EMAN2PAR.py, EMAN2db.py: New EMDC protocol. Now has
	  unique(ish) client identifier.

2009-06-02 21:42  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emselector.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2classaverage.py, programs/e2eulerxplor.py: general
	  fixes

2009-06-02 17:10  zyang

	* sparx/libpy/reconstruction.py: Delete test code.

2009-06-02 16:29  woolford

	* libpyEM/qtgui/emanimationutil.py, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2project3d.py,
	  programs/e2simmx.py: general fixes

2009-06-02 16:11  stevel

	* programs/e2parallel.py: Try to deal with corruption problem

2009-06-02 14:34  ppenczek

	* sparx/libpy/applications.py: the last and the best

2009-06-02 14:28  ppenczek

	* sparx/: bin/sxihrsr.py, libpy/alignment.py: the last and the best

2009-06-02 11:53  zyang

	* sparx/libpy/applications.py: Trival change

2009-06-02 11:41  zyang

	* sparx/libpy/: applications.py, reconstruction.py: Trival change

2009-06-02 02:54  stevel

	* libEM/emdata.cpp, libEM/util.cpp, libEM/util.h,
	  libpyEM/EMAN2PAR.py: Added hypot_fast, and made calc_radial_dist
	  use it

2009-06-01 18:27  woolford

	* libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3diso.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emplot2d.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2simmx.py,
	  programs/e2workflow.py, pyemtbx/boxertools.py: general updates

2009-06-01 16:19  ppenczek

	* sparx/libpy/reconstruction.py: more correction ihrsr

2009-06-01 15:21  zyang

	* libEM/emobject.cpp, sparx/test/3dg.py: Temporary solution for a
	  bug

2009-06-01 13:53  ppenczek

	* sparx/test/3DA/3dg.py: [no log message]

2009-06-01 13:09  ppenczek

	* sparx/libpy/applications.py: first working version of ihrsr, old
	  code removed

2009-06-01 12:54  ppenczek

	* sparx/: bin/sxihrsr.py, libpy/applications.py,
	  libpy/reconstruction.py: first working version of ihrsr, old code
	  removed

2009-06-01 10:10  zyang

	* sparx/libpy/development.py: Made an improvement in ave_ali_err()

2009-05-31 16:22  ppenczek

	* sparx/libpy/: alignment.py, applications.py, reconstruction.py,
	  utilities.py: corrections of ihrsr

2009-05-31 12:05  ppenczek

	* sparx/bin/sxihrsr.py: updated name

2009-05-30 23:57  stevel

	* libpyEM/EMAN2PAR.py: Oops. broke something

2009-05-30 23:22  stevel

	* libpyEM/EMAN2PAR.py: Work on parallelism

2009-05-30 16:20  ppenczek

	* sparx/bin/sparx: import EMAN2 before change EMAN2.Guimode.

2009-05-30 11:49  stevel

	* libpyEM/: EMAN2PAR.py, EMAN2db.py: improvements to parallelism

2009-05-30 00:37  stevel

	* libpyEM/EMAN2db.py: minor fix

2009-05-30 00:27  stevel

	* libpyEM/EMAN2db.py: trivial

2009-05-29 18:27  woolford

	* libpyEM/qtgui/: emselector.py, emsprworkflow.py: [no log message]

2009-05-29 18:16  woolford

	* programs/e2eotest.py, rt/pyem/test_processor.py: [no log message]

2009-05-29 16:44  woolford

	* libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2make3d.py,
	  programs/e2project3d.py: selector animates correctly

2009-05-29 15:33  zyang

	* sparx/libpy/: applications.py, development.py: Trival change

2009-05-29 15:20  jbert

	* sparx/libpy/applications.py: ali3d_m_MPI comment print out

2009-05-29 15:18  jbert

	* sparx/bin/sxali3d_m.py: change default params

2009-05-29 12:21  woolford

	* libEM/processor.cpp, libpyEM/EMAN2.py, rt/pyem/test_processor.py:
	  test updates

2009-05-29 11:26  jbert

	* sparx/: bin/sxali3d_m.py, libpy/applications.py: ali3d_m fix some
	  minor bugs

2009-05-29 10:48  woolford

	* libEM/processor.cpp: [no log message]

2009-05-28 23:45  woolford

	* libEM/aligner.cpp, libEM/processor.cpp,
	  libpyEM/qtgui/emselector.py, programs/e2proc2d.py,
	  rt/pyem/test_aligner.py, rt/pyem/test_processor.py: xflip bug,
	  etc

2009-05-28 19:56  woolford

	* libEM/aligner.cpp, libEM/aligner.h, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/emdata_metadata.cpp,
	  libEM/emdata_metadata.h, libpyEM/EMAN2PAR.py,
	  libpyEM/qtgui/emimage.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2classaverage.py,
	  programs/e2ctf.py, programs/e2proc2d.py, programs/e2project3d.py,
	  programs/e2simmx.py, rt/pyem/test_aligner.py: [no log message]

2009-05-28 18:19  prb

	* libEM/emdata_transform.h: [no log message]

2009-05-28 17:41  prb

	* libEM/emdata_transform.cpp:
	  patched bispec stuff

2009-05-28 17:37  jbert

	* sparx/libpy/applications.py: fix bug params3d_to2d

2009-05-28 17:00  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-05-28 16:35  zyang

	* sparx/libpy/: applications.py, development.py: Add gradient
	  method.

2009-05-28 15:30  stevel

	* libpyEM/EMAN2db.py: oops

2009-05-28 15:20  stevel

	* libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py, programs/e2parallel.py:
	  Group capabilities, and other fixes for dc parallelism

2009-05-28 15:04  zyang

	* sparx/: bin/sxali2d_reduce.py, libpy/applications.py: Fix a bug.

2009-05-28 14:33  zyang

	* sparx/libpy/applications.py: Fix some bugs.

2009-05-28 13:55  woolford

	* libpyEM/qtgui/emimage.py: workspace

2009-05-28 13:51  woolford

	* libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2simmx.py: par updates

2009-05-28 13:28  zyang

	* sparx/libpy/applications.py: Some change in ali2d_reduce()

2009-05-28 12:25  stevel

	* install-dependencies.py: More updates to install-dependencies

2009-05-28 12:00  stevel

	* install-dependencies.py: Updated install-dependencies

2009-05-28 11:32  zyang

	* sparx/: bin/sxali2d_reduce.py, libpy/applications.py: Add new
	  alignment program ali2d_reduce()

2009-05-28 09:49  zyang

	* sparx/libpy/: fundamentals.py, user_functions.py: Trival change.

2009-05-27 21:08  woolford

	* libEM/boxingtools.cpp, libEM/symmetry.cpp,
	  libpyEM/qtgui/em3Dfonts.py, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emplot2d.py, libpyEM/qtgui/emplot3d.py,
	  libpyEM/qtgui/emshape.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2boxer.py, programs/e2eulerxplor.py,
	  programs/e2workflow.py: general improvements

2009-05-27 17:47  gtang

	* rt/pyem/test_emdata.py: test Transform attribute pickling

2009-05-27 17:40  gtang

	* libEM/: emobject.cpp, emobject.h: Transform object to vactoe<int>
	  in EMObject, solve the Transform attribute pickling issue

2009-05-27 17:19  woolford

	* libEM/symmetry.cpp, libEM/transform.cpp,
	  libpyEM/qtgui/emimage.py, programs/e2.py: import fixing

2009-05-27 17:12  stevel

	* programs/e2proc2d.py: trivial

2009-05-27 02:10  stevel

	* programs/e2proc2d.py: Added randomize, though broken due to an
	  unrelated bug...

2009-05-26 20:10  woolford

	* examples/tasktest.py, libEM/aligner.cpp, libpyEM/EMAN2.py,
	  libpyEM/EMAN2PAR.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2ctf.py,
	  programs/e2make3d.py, programs/e2project3d.py,
	  programs/e2workflow.py, rt/pyem/test_emdata.py: parallel updates

2009-05-26 17:16  jbert

	* sparx/libpy/projection.py: cml change cml_prepare_line

2009-05-26 17:05  jbert

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, sparx/libpy/projection.py: cml add
	  set_line and prepare_line

2009-05-26 17:04  jbert

	* sparx/libpy/applications.py: HAC use 2d align parameters

2009-05-26 16:25  stevel

	* programs/e2parallel.py: trivial

2009-05-26 15:52  woolford

	* libEM/aligner.cpp, libEM/transform.cpp, libpyEM/EMAN2_cppwrap.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emshape.py, libpyEM/wxgui/wxemimage.py,
	  libpyEM/wxgui/wxemimageframe.py, programs/e2basis.py,
	  programs/e2classaverage.py, programs/e2eulerxplor.py,
	  programs/e2project3d.py, programs/e2refine2d.py,
	  programs/e2simmx.py, rt/pyem/test_emdata.py: parallel updates

2009-05-26 12:52  woolford

	* libpyEM/EMAN2.py: [no log message]

2009-05-26 12:03  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2classaverage.py: [no
	  log message]

2009-05-26 10:56  woolford

	* images/macimages/CMakeLists.txt, libpyEM/qtgui/emform.py: [no log
	  message]

2009-05-26 09:09  jbert

	* libpyEM/libpyUtils2.cpp: add set_line

2009-05-26 02:26  stevel

	* libEM/cmp.cpp, libEM/emdata.cpp, libEM/emdata.h,
	  libpyEM/EMAN2.py, libpyEM/EMAN2db.py, programs/e2parallel.py,
	  programs/e2proc2d.py, programs/e2refine2d.py,
	  programs/e2simmx.py: Work on footprints and parallelism.

2009-05-24 18:27  gtang

	* rt/pyem/test_processor.py: unit test update

2009-05-24 11:34  ppenczek

	* sparx/libpy/utilities.py: set seed

2009-05-23 10:42  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2classaverage.py,
	  programs/e2refine.py: workflow fixes

2009-05-23 10:36  gtang

	* libpyEM/CMakeLists.txt: [no log message]

2009-05-22 20:28  woolford

	* libEM/processor.cpp: processor stuff

2009-05-22 19:18  gtang

	* libEM/CMakeLists.txt, libEM/hdfio2.cpp, libpyEM/CMakeLists.txt,
	  libpyEM/libpyGLUtils2.cpp, libpyEM/libpyUtils2.cpp: assemble ftgl
	  into libpyGLUtils2.so, originally in libpyUtils2.so

2009-05-22 17:28  woolford

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emsprworkflow.py: processor for Phil

2009-05-22 17:07  gtang

	* utils/CMakeLists.txt, rt/emdata/CMakeLists.txt: to get around a
	  nightly build problem

2009-05-22 16:47  stevel

	* programs/e2refine2d.py: Minor fixes

2009-05-22 15:48  woolford

	* libEM/processor.cpp, libEM/processor.h,
	  programs/e2classaverage.py: [no log message]

2009-05-22 15:28  woolford

	* programs/e2classaverage.py: [no log message]

2009-05-22 15:21  woolford

	* libEM/transform.cpp, programs/e2classaverage.py: [no log message]

2009-05-22 14:36  jbert

	* libEM/sparx/: util_sparx.h: fix bugs cml

2009-05-22 14:35  jbert

	* libEM/sparx/util_sparx.cpp, sparx/libpy/applications.py,
	  sparx/libpy/projection.py: cml fix bugs

2009-05-22 14:20  stevel

	* libEM/cmp.cpp, programs/e2classaverage.py: Fixes for optvariance

2009-05-22 13:31  woolford

	* programs/: e2classaverage.py, e2project3d.py, e2refine.py,
	  e2refine2d.py, e2simmx.py: dc working for e2refine2d and e2refine

2009-05-21 23:08  woolford

	* libpyEM/EMAN2PAR.py, programs/e2project3d.py,
	  programs/e2refine.py, programs/e2simmx.py: parallelism, simmx,
	  project3d

2009-05-21 19:36  gtang

	* libEM/CMakeLists.txt, libEM/emdata_transform.cpp,
	  libEM/glutil.cpp, libEM/glutil.h, libEM/isosurface.h,
	  libEM/marchingcubes.cpp, libEM/marchingcubes.h,
	  libpyEM/CMakeLists.txt, libpyEM/libpyGLUtils2.cpp,
	  libpyEM/libpyMarchingCubes2.cpp, libpyEM/qtgui/emimage3diso.py:
	  put all opengl depend functions into GLUtil class

2009-05-21 19:06  woolford

	* libpyEM/EMAN2PAR.py, programs/e2classaverage.py,
	  programs/e2refine2d.py, programs/e2simmx.py: parallelism fixes

2009-05-21 16:44  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2classaverage.py,
	  programs/e2ctf.py, programs/e2refine.py, programs/e2refine2d.py,
	  programs/e2simmx.py: class average updates

2009-05-21 16:14  gtang

	* libEM/CMakeLists.txt, libEM/emdata.h, libEM/emdata_gl.cpp,
	  libEM/emdata_gl.h, libEM/emdata_transform.cpp, libEM/glutil.cpp,
	  libEM/glutil.h, libEM/util.cpp, libEM/util.h,
	  libpyEM/EMAN2_cppwrap.py, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyGLUtils2.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emshape.py, libpyEM/wxgui/wxemimage.py,
	  libpyEM/wxgui/wxemimageframe.py, programs/e2eulerxplor.py,
	  rt/pyem/test_emdata.py: put all opengl depend functions into
	  GLUtil class

2009-05-21 15:26  stevel

	* libpyEM/EMAN2PAR.py, programs/e2classaverage.py,
	  programs/e2parallel.py: bugfix in classaverage

2009-05-21 13:46  woolford

	* libEM/: aligner.cpp, cmp.cpp, cmp.h: removed errant statement

2009-05-21 11:27  zweig

	* sparx/libpy/alignment.py: comment out print outs

2009-05-21 11:27  zweig

	* sparx/libpy/user_functions.py: add ali on 50s to ref_ali3dm_new

2009-05-21 11:26  zweig

	* sparx/libpy/user_functions.py: fix a problem in ali_mask

2009-05-21 01:33  gtang

	* libEM/CMakeLists.txt, libEM/emdata.h, libEM/glutil.cpp,
	  libEM/glutil.h, libpyEM/CMakeLists.txt,
	  libpyEM/libpyGLUtils2.cpp: add GLUtil class to wrap all opengl
	  depend functions

2009-05-20 21:58  woolford

	* programs/: e2classaverage.py, e2simmx.py: minor updates

2009-05-20 19:11  woolford

	* libpyEM/EMAN2db.py, programs/e2classaverage.py,
	  programs/e2simmx.py: [no log message]

2009-05-20 17:10  zweig

	* sparx/libpy/applications.py: fix alivol

2009-05-20 17:10  zweig

	* sparx/libpy/alignment.py: fix alivol_func

2009-05-20 16:04  ppenczek

	* libpyEM/qtgui/emsave.py: type in eman2

2009-05-20 16:02  stevel

	* libEM/: emdata.cpp, imagicio.cpp: fix imagicio

2009-05-20 15:44  woolford

	* libEM/emutil.cpp, libEM/imagicio.cpp, libpyEM/EMAN2.py,
	  programs/e2classaverage.py: imagic bug, documentation

2009-05-20 12:37  zweig

	* sparx/libpy/user_functions.py: add function alivol_mask(), fix
	  error in ref_ali3dm_new

2009-05-20 12:00  gtang

	* libEM/emdata_transform.cpp: fix the missing is_fftodd attribute,
	  this	cause HDF5 file writing error

2009-05-20 09:52  zweig

	* sparx/libpy/user_functions.py: add new function ref_ali3dm_new

2009-05-19 22:32  woolford

	* libpyEM/EMAN2PAR.py, programs/e2classaverage.py: e2classaverage
	  cleaning

2009-05-19 20:38  woolford

	* libpyEM/EMAN2PAR.py, programs/e2classaverage.py: class
	  parallelism

2009-05-19 20:32  woolford

	* libpyEM/EMAN2PAR.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2classaverage.py, programs/e2eulerxplor.py,
	  programs/e2refine.py: class parallelism

2009-05-19 17:06  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2classaverage.py: [no
	  log message]

2009-05-19 16:20  woolford

	* programs/: e2classaverage.py, e2proc2d.py: [no log message]

2009-05-19 15:53  woolford

	* libEM/processor.cpp, libpyEM/qtgui/emselector.py,
	  programs/e2ali2img.py, programs/e2classaverage.py: bugs

2009-05-19 15:37  woolford

	* programs/e2classaverage.py: parallelism stuff

2009-05-19 10:27  ppenczek

	* sparx/libpy/: applications.py, user_functions.py: [no log
	  message]

2009-05-18 23:11  woolford

	* programs/e2classaverage.py: class average parallelism

2009-05-18 23:01  woolford

	* libpyEM/EMAN2.py, libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py,
	  programs/e2classaverage.py: class average parallelism

2009-05-18 13:41  woolford

	* libpyEM/qtgui/em3Dfonts.py, programs/e2classaverage.py: class
	  average

2009-05-18 11:44  zyang

	* sparx/libpy/fundamentals.py: Trival change

2009-05-18 09:53  prb

	* libEM/emdata_transform.cpp:
	    switched out the atan2 to discrete version

2009-05-18 09:45  zyang

	* libEM/sparx/util_sparx.cpp: Trival change

2009-05-18 01:25  stevel

	* libEM/emdata.cpp, programs/e2proc2d.py: More work on footprints
	  using bispectrum

2009-05-17 22:03  woolford

	* programs/e2classaverage.py: [no log message]

2009-05-17 22:03  woolford

	* examples/tasktest.py, libpyEM/EMAN2PAR.py,
	  programs/e2classaverage.py: classaverage parallelism in progress

2009-05-16 21:41  woolford

	* libEM/reconstructor.h, libEM/symmetry.h,
	  libpyEM/qtgui/em3Dfonts.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emimage3dvol.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2tomoboxer.py, programs/e2workflow.py: workflow updates

2009-05-16 09:55  woolford

	* programs/e2classaverage.py: e2classaverage.py bug

2009-05-15 23:25  woolford

	* programs/e2classaverage.py: fix an error

2009-05-15 23:23  woolford

	* libpyEM/EMAN2PAR.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2classaverage.py: workflow cleaning

2009-05-15 21:31  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2refine2d.py: user friendly worklow

2009-05-15 18:56  woolford

	* libEM/imagicio.cpp: imagic ctf header attribute bug

2009-05-15 18:40  woolford

	* libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimagerotor.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2classaverage.py,
	  programs/e2workflow.py: workflow updates

2009-05-15 18:30  gtang

	* libEM/: amiraio.cpp, amiraio.h: implement amira file reading, now
	  can read both Amiramesh 2.0 and 2.1 file, and write as Amiramesh
	  2.1

2009-05-15 12:53  jbert

	* sparx/libpy/projection.py: change flag cml

2009-05-15 11:50  jbert

	* sparx/libpy/applications.py: cml, display also disc without
	  weights

2009-05-15 10:51  ppenczek

	* sparx/libpy/statistics.py: mask gone from ccc

2009-05-15 02:46  stevel

	* libEM/emdata.cpp, programs/e2proc2d.py: More footprint trials

2009-05-14 15:48  zyang

	* libEM/sparx/emdata_sparx.cpp: add maximum value

2009-05-14 15:36  zyang

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/libpyEMData2.cpp: Add function max_search()

2009-05-14 14:58  stevel

	* libEM/emdata.cpp, libEM/emdata_core.h, libpyEM/EMAN2PAR.py:
	  Working on invariants.

2009-05-14 14:52  jbert

	* sparx/libpy/projection.py: change weights again cml

2009-05-14 13:48  jbert

	* sparx/libpy/: applications.py, projection.py: fix some bug cml

2009-05-14 13:47  jbert

	* sparx/libpy/development.py: fix some bug

2009-05-14 12:48  woolford

	* libpyEM/qtgui/em3Dfonts.py, programs/e2workflow.py: workflow
	  updates

2009-05-14 12:19  woolford

	* libpyEM/qtgui/: em3Dfonts.py, emapplication.py, emglobjects.py,
	  emimage3d.py, emimage3dslice.py: font tool fixed

2009-05-14 02:39  stevel

	* libEM/emdata.cpp, libEM/emdata.h, libEM/emdata_core.cpp,
	  libEM/emdata_core.h, libpyEM/libpyEMData2.cpp: more work on
	  invariants.

2009-05-13 23:38  woolford

	* libEM/symmetry.h: disallowing copy and assignment

2009-05-13 22:48  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2initialmodel.py,
	  programs/e2refine2d.py, programs/e2workflow.py: workflow user
	  friendly

2009-05-13 18:39  woolford

	* libpyEM/qtgui/emform.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2boxer.py,
	  programs/e2refine2d.py, programs/e2workflow.py: workflow more
	  dynamic

2009-05-13 17:19  jbert

	* sparx/demo/3_bdb_ctf/run_through_example: change kmeans add cml

2009-05-13 17:00  jbert

	* sparx/demo/7_mpi_bdb_ctf/run_through_example: change params cml

2009-05-13 16:50  jbert

	* sparx/demo/5_mpi_bdb/run_through_example: change params cml

2009-05-13 16:50  jbert

	* sparx/demo/1_bdb/run_through_example: [no log message]

2009-05-13 16:44  jbert

	* sparx/demo/1_bdb/run_through_example: change kmeans add cml

2009-05-13 16:35  jbert

	* sparx/bin/sxfind_struct.py: change flag

2009-05-13 16:19  jbert

	* sparx/libpy/projection.py: Cml, stretch weights by power of 2

2009-05-13 15:06  woolford

	* libpyEM/qtgui/emform.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2ctf.py, programs/e2workflow.py: workflow updates

2009-05-13 14:46  gtang

	* libEM/cmp.cpp: accept None as mask image

2009-05-13 14:33  jbert

	* sparx/demo/7_mpi_bdb_ctf/run_through_example: update script,
	  change kmeans and add cml

2009-05-13 14:13  jbert

	* sparx/demo/5_mpi_bdb/run_through_example: update the script for
	  kmeans and cml

2009-05-13 11:48  jbert

	* sparx/bin/sxfind_struct.py: cml working

2009-05-13 11:32  jbert

	* sparx/libpy/development.py: move old code cml

2009-05-13 11:30  jbert

	* sparx/libpy/applications.py: cml working

2009-05-12 17:12  jbert

	* sparx/libpy/: applications.py, projection.py: working cml MPI

2009-05-12 16:55  ppenczek

	* sparx/libpy/statistics.py: mask corrected in ali2d_c

2009-05-12 16:18  zweig

	* sparx/libpy/applications.py: fix ali3d_d()

2009-05-12 11:04  jbert

	* sparx/libpy/applications.py: comment print out

2009-05-12 02:13  stevel

	* libEM/emdata.cpp: Playing with new bispectrum code.

2009-05-11 16:50  ppenczek

	* sparx/libpy/applications.py:	subtract average in ali2dc

2009-05-11 16:34  woolford

	* libpyEM/qtgui/emform.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2ctf.py: workflow stuff

2009-05-11 15:46  gtang

	* rt/pyem/test_emdata.py: add unit test for odd-size image fft/ift

2009-05-11 13:42  ppenczek

	* sparx/libpy/: applications.py: ihrsr

2009-05-11 12:04  woolford

	* libpyEM/qtgui/emapplication.py, programs/e2boxer.py: bug fixes

2009-05-11 11:12  woolford

	* libpyEM/qtgui/emform.py: bug fix

2009-05-11 01:42  stevel

	* libEM/emdata.cpp, libEM/emdata.h, programs/e2proc2d.py,
	  pyemtbx/boxertools.py: Work on bispectrum

2009-05-10 22:07  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emselector.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2boxer.py: workflow updates

2009-05-10 18:05  gtang

	* libEM/: emdata.cpp, emdata.h, emdata_io.cpp, emdata_metadata.h:
	  change flag to attribute

2009-05-09 18:28  ppenczek

	* sparx/: bin/sxihrsr.py, libpy/applications.py: ihsr

2009-05-08 18:50  woolford

	* libpyEM/qtgui/emform.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2boxer.py, programs/e2workflow.py,
	  pyemtbx/boxertools.py: workflow updates

2009-05-08 17:23  jbert

	* sparx/: bin/sxfind_struct.py, libpy/development.py: working cml
	  ga, add function to get degree of collinearity of the solution
	  found

2009-05-08 03:58  prb

	* libEM/emdata_transform.cpp, libEM/emdata_transform.h,
	  libpyEM/libpyEMData2.cpp:
	   classification helper: still need to clean it up (remove
	  diagnostics)

2009-05-07 21:47  woolford

	* libpyEM/qtgui/emform.py: workflow memory management

2009-05-07 21:21  woolford

	* libpyEM/qtgui/emform.py, programs/e2classaverage.py,
	  programs/e2refine.py, programs/e2simmx.py: efficiency

2009-05-07 19:04  woolford

	* programs/e2classaverage.py: class average work

2009-05-07 17:17  woolford

	* libpyEM/EMAN2db.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emsave.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2classaverage.py: workflow updates

2009-05-07 13:30  jbert

	* sparx/libpy/development.py: working cml ga

2009-05-07 11:48  jbert

	* sparx/libpy/development.py: working cml ga

2009-05-07 11:43  jbert

	* libpyEM/EMAN2db.py: comment print "using emdata write" line 344

2009-05-06 17:24  woolford

	* libpyEM/qtgui/emform.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2workflow.py: workflow
	  updates

2009-05-06 13:30  jbert

	* sparx/: bin/sxfind_struct.py, libpy/development.py: working cml
	  GA

2009-05-06 12:34  woolford

	* libpyEM/: EMAN2.py, EMAN2db.py, qtgui/emsave.py,
	  qtgui/emselector.py: save as and bdb works

2009-05-06 11:45  jbert

	* sparx/libpy/applications.py: change flag active to k_means stab
	  MPI

2009-05-06 09:59  jbert

	* sparx/libpy/applications.py: k-means stab flag fix some big

2009-05-06 01:54  stevel

	* examples/tasktest.py, libpyEM/EMAN2PAR.py: New option for
	  estimate of number of CPUs available.

2009-05-06 01:18  stevel

	* libpyEM/EMAN2PAR.py: Parallelism working. Now we just need some
	  tasks...

2009-05-05 22:42  woolford

	* libEM/emdata_metadata.cpp, libEM/emobject.h, libEM/transform.h,
	  programs/e2classaverage.py, programs/e2refine.py: script updates

2009-05-05 20:04  woolford

	* libEM/averager.h, libEM/processor.cpp, libpyEM/EMAN2.py,
	  libpyEM/qtgui/emform.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py: workflow

2009-05-05 17:19  woolford

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emdata_cuda.cpp, libEM/emdata_metadata.cpp,
	  libEM/emdata_metadata.h, programs/e2display.py: memory leak fix

2009-05-05 16:13  zweig

	* sparx/libpy/alignment.py: fix some typo in proj_ali_incore

2009-05-05 16:12  zweig

	* sparx/bin/sxbootstrap_calcwgts.py: add call for init_mpi_bdb

2009-05-05 14:27  stevel

	* examples/tasktest.py, libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py:
	  Working on parallelism some more. Now have customer object.
	  Debugging.

2009-05-05 13:50  jbert

	* sparx/libpy/: applications.py, statistics.py: change the way the
	  flag active is used in k-means stab

2009-05-05 13:04  woolford

	* libpyEM/qtgui/: emform.py, emselector.py, emsprworkflow.py:
	  workflow updates

2009-05-05 11:56  jbert

	* sparx/libpy/applications.py: manage flag active for ali2dc non
	  MPI

2009-05-05 11:14  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-05-05 10:22  jbert

	* sparx/: bin/sxave_ali.py, libpy/applications.py,
	  libpy/statistics.py: add active flag to compute average with
	  sxave_ali

2009-05-05 09:56  jbert

	* sparx/libpy/: applications.py, statistics.py: manage flag active
	  for k-means and ali2dc_MPI

2009-05-04 20:56  woolford

	* libpyEM/qtgui/emform.py, libpyEM/qtgui/emimageutil.py,
	  libpyEM/qtgui/emsave.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2history.py,
	  programs/e2workflow.py: workflow updates

2009-05-04 15:08  gtang

	* rt/pyem/test_processor.py: unit test update

2009-05-04 15:06  gtang

	* CMakeLists.txt: python 2.6 compilation support

2009-05-04 13:13  ppenczek

	* sparx/libpy/: applications.py, statistics.py: ali2d_c working

2009-05-04 11:35  zweig

	* libEM/sparx/util_sparx.cpp: add normalize_ring after Polar2Dm

2009-05-02 18:59  zweig

	* sparx/bin/sxbootstrap_bigdisk.py: add call for init_mpi_bdbb,
	  release memory after one iteration

2009-05-01 19:53  woolford

	* examples/cudaspeedtest.py, libEM/emdata_core.cpp,
	  libEM/emdata_cuda.cpp, libEM/emdata_io.cpp,
	  libEM/emdata_metadata.cpp, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2workflow.py,
	  pyemtbx/boxertools.py: workflow related

2009-05-01 16:54  gtang

	* programs/e2workflow.py, libpyEM/qtgui/emsprworkflow.py:
	  tomography work in workflow

2009-05-01 10:42  jbert

	* sparx/libpy/statistics.py: fix norm k-means

2009-05-01 02:26  stevel

	* examples/tasktest.py, libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py:
	  Minor tweak

2009-05-01 02:15  stevel

	* examples/tasktest.py, libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py:
	  Parallelism working. Just need to add tasks and write customers.

2009-04-30 18:57  woolford

	* libEM/emutil.cpp, rt/pyem/test_imageio.py: [no log message]

2009-04-30 14:53  gtang

	* rt/pyem/test_imageio.py: fix for 3D imagic read

2009-04-30 14:29  gtang

	* libEM/imagicio.cpp: [no log message]

2009-04-30 13:08  woolford

	* libEM/emdata_transform.cpp, libEM/imagicio.cpp,
	  programs/e2boxer.py, programs/e2tomoboxer.py,
	  pyemtbx/boxertools.py, rt/pyem/test_imageio.py: boxer related
	  fixes

2009-04-30 12:58  gtang

	* libEM/xplorio.cpp: bug fix

2009-04-29 22:55  woolford

	* libEM/processor.cpp, libEM/processor.h, libpyEM/libpyEMData2.cpp,
	  programs/e2tomohunter.py, rt/pyem/test_processor.py: [no log
	  message]

2009-04-29 18:23  ppenczek

	* sparx/libpy/applications.py: corrected (again!) ali2d_c_mpi

2009-04-29 15:38  gtang

	* libEM/imagicio.cpp: fix the imagic 3D image reading problem

2009-04-29 12:32  ppenczek

	* sparx/libpy/: alignment.py, applications.py, user_functions.py:
	  ali2d_c Fourvar working!

2009-04-29 12:04  woolford

	* libEM/: emio.cpp, hdfio2.cpp, icosio.cpp, imageio.cpp, imageio.h,
	  mrcio.cpp, spiderio.cpp: imageio updates

2009-04-29 09:18  woolford

	* libEM/emutil.cpp, libEM/imagicio.cpp, libpyEM/qtgui/emimage.py,
	  programs/e2display.py, rt/pyem/test_imageio.py: io updates

2009-04-28 20:28  woolford

	* libEM/emutil.cpp, rt/pyem/test_imageio.py: test script update

2009-04-28 20:27  gtang

	* libpyEM/CMakeLists.txt: install the libpyxxx.dylib as libpyxxx.so
	  on MacOS

2009-04-28 20:24  gtang

	* libEM/emio.cpp: fix the EM file reading error for MacOS

2009-04-28 20:18  woolford

	* libEM/emdata.cpp: uncut slice bug

2009-04-28 20:17  woolford

	* libEM/emutil.cpp, libpyEM/EMAN2.py, rt/pyem/test_emdata.py,
	  rt/pyem/test_imageio.py: io region support more robust

2009-04-28 16:04  jbert

	* sparx/libpy/development.py: fix bug cml

2009-04-28 14:43  woolford

	* rt/pyem/test_imageio.py: pif testing

2009-04-28 14:40  ppenczek

	* sparx/libpy/: applications.py, statistics.py: ali2d_c

2009-04-28 14:31  woolford

	* libEM/transform.h, libpyEM/EMAN2.py, rt/pyem/test_imageio.py:
	  testing updates

2009-04-28 14:26  ppenczek

	* sparx/bin/sxcpy.py: sxcpy printouts removed

2009-04-28 12:05  woolford

	* libEM/processor.h, libEM/transform.h, rt/pyem/test_processor.py:
	  doc updates

2009-04-28 11:43  ppenczek

	* sparx/libpy/: applications.py, statistics.py: ali2d_c

2009-04-28 10:19  gtang

	* rt/pyem/test_processor.py: [no log message]

2009-04-27 22:07  woolford

	* libEM/cuda/FindCuda.cmake, programs/e2tomoboxer.py: tomoboxer
	  updates

2009-04-27 20:31  woolford

	* libEM/processor.cpp, libEM/processor.h, libEM/reconstructor.cpp,
	  libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emimage2d.py,
	  programs/e2proc3d.py, programs/e2tomoboxer.py,
	  pyemtbx/boxertools.py: tomoboxer ready for use

2009-04-27 18:43  ppenczek

	* sparx/libpy/statistics.py: ali2d_c

2009-04-27 18:06  ppenczek

	* sparx/libpy/: applications.py, statistics.py: ali2d_c no-mpi,
	  varf

2009-04-27 15:53  woolford

	* libEM/processor.cpp, libEM/processor.h, libpyEM/EMAN2db.py,
	  programs/e2tomoboxer.py: tomoboxer - massive files

2009-04-27 15:50  ppenczek

	* sparx/libpy/statistics.py: [no log message]

2009-04-27 15:49  ppenczek

	* sparx/libpy/: applications.py, morphology.py: ali2d_c no-mpi

2009-04-27 14:48  jbert

	* sparx/libpy/applications.py: add something to stop k-means cuda
	  properly

2009-04-27 14:29  jbert

	* sparx/libpy/statistics.py: fix bug to k_means_stable_cuda

2009-04-27 14:25  jbert

	* sparx/libpy/applications.py: fix bug to k_means_stab_CUDA

2009-04-27 13:15  ppenczek

	* sparx/: bin/sxali2d_c.py, libpy/applications.py: varf in ali2d_c
	  noMPI

2009-04-27 11:28  gtang

	* libpyEM/CMakeLists.txt: revert the change on Mac OS

2009-04-26 02:40  stevel

	* examples/tasktest.py, libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py:
	  Parallelism server progress. Not complete. Shouldn't crash
	  anything at least .

2009-04-24 20:03  woolford

	* pyemtbx/boxertools.py: boxer

2009-04-24 20:03  woolford

	* programs/e2tomoboxer.py, pyemtbx/boxertools.py: tomoboxer

2009-04-24 19:56  woolford

	* libEM/boxingtools.cpp, programs/e2boxer.py,
	  pyemtbx/boxertools.py, rt/pyem/test_imageio.py: boxer bugs

2009-04-24 17:35  gtang

	* libpyEM/CMakeLists.txt: install the libpyxxx.dylib as libpyxxx.so
	  on MacOS

2009-04-24 16:19  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emimage2d.py,
	  programs/e2tomoboxer.py: tomoboxer

2009-04-23 22:03  woolford

	* libEM/emdata_io.cpp, libEM/emdata_metadata.cpp,
	  libEM/emdata_metadata.h, libEM/emutil.cpp, libEM/emutil.h,
	  libEM/imageio.cpp, libEM/mrcio.cpp, libEM/xplorio.cpp,
	  libEM/cuda/FindCuda.cmake, libpyEM/EMAN2.py, libpyEM/EMAN2db.py,
	  libpyEM/libpyEMData2.cpp, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2tomoboxer.py: tomboxer

2009-04-23 17:01  jbert

	* sparx/libpy/development.py: add u2 in cml

2009-04-23 10:55  woolford

	* libEM/: emdata_metadata.cpp, emutil.cpp, geometry.h: read data
	  updates

2009-04-22 23:22  woolford

	* libpyEM/qtgui/emsave.py, programs/e2tomoboxer.py: tomoboxer work

2009-04-22 21:09  woolford

	* libpyEM/qtgui/emimagemx.py, programs/e2preferences.py,
	  programs/e2tomoboxer.py: typo

2009-04-22 17:52  woolford

	* programs/e2preferences.py: preferences

2009-04-22 17:49  woolford

	* libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2preferences.py,
	  programs/e2tomoboxer.py, programs/e2workflow.py: tomoboxer and
	  preferences

2009-04-21 17:54  woolford

	* programs/e2tomoboxer.py: tomo boxer

2009-04-21 17:26  jbert

	* sparx/libpy/statistics.py: change k_means_init_mpi even nb ims
	  per node

2009-04-21 16:07  ppenczek

	* sparx/libpy/applications.py: ali2d_a

2009-04-21 15:26  zweig

	* sparx/bin/: sxali3d_e.py, sxali3d_em.py: add option ts

2009-04-21 15:25  zweig

	* sparx/libpy/applications.py: fix error of ali3d e

2009-04-21 12:56  zweig

	* sparx/libpy/applications.py: add ts to ali3d_e

2009-04-21 12:47  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-04-21 10:48  zweig

	* libEM/: reconstructor.h, reconstructor.cpp: add option varsnr to
	  nn4_ctf reconstructor

2009-04-21 09:40  gtang

	* rt/pyem/test_processor.py: unit test update

2009-04-20 21:56  woolford

	* libEM/processor.cpp, libEM/processor.h, programs/e2tomoboxer.py:
	  tomo boxer updates

2009-04-20 19:15  woolford

	* libpyEM/qtgui/emimage2d.py, programs/e2tomoboxer.py: tomo boxer
	  updates

2009-04-20 17:53  woolford

	* libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emsave.py,
	  libpyEM/qtgui/emselector.py, programs/e2boxer.py,
	  programs/e2tomoboxer.py, pyemtbx/boxertools.py: tomoboxer work

2009-04-20 15:31  ppenczek

	* sparx/libpy/user_functions.py: corrections

2009-04-20 15:27  ppenczek

	* sparx/libpy/: alignment.py, applications.py: removed changes in
	  ali2d_c

2009-04-20 13:37  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-04-20 13:25  woolford

	* libpyEM/: CMakeLists.txt, qtgui/emimagemx.py, qtgui/emsave.py,
	  qtgui/emselector.py, qtgui/emsprworkflow.py: save stuff

2009-04-20 01:49  stevel

	* libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py, programs/e2parallel.py:
	  Parallelism work

2009-04-19 19:34  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-04-19 11:10  ppenczek

	* sparx/libpy/statistics.py: [no log message]

2009-04-17 18:05  woolford

	* programs/e2tomoboxer.py: minor change

2009-04-17 17:40  woolford

	* pyemtbx/boxertools.py: boxer updates

2009-04-17 14:42  woolford

	* libEM/emdata.cpp, libEM/emdata.h, libEM/processor.cpp,
	  libpyEM/libpyEMData2.cpp, programs/e2boxer.py,
	  programs/e2ctf2eman1.py, programs/e2tomoboxer.py,
	  pyemtbx/boxertools.py: boxer updates

2009-04-17 14:12  woolford

	* libpyEM/qtgui/: emimageutil.py, emplot2d.py: bug fix

2009-04-16 16:32  zweig

	* sparx/libpy/: alignment.py, applications.py: fix ali3d_d_MPI()

2009-04-16 13:43  zweig

	* sparx/libpy/applications.py: fix small errors in ali3d_d_MPI

2009-04-16 13:43  zweig

	* sparx/libpy/alignment.py: fix type in proj_ali_incore

2009-04-16 13:20  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emselector.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2ptcltrace.py: doc updates

2009-04-15 22:59  woolford

	* libpyEM/qtgui/: emform.py, emselector.py: bug

2009-04-15 22:52  woolford

	* libpyEM/: EMAN2.py, EMAN2db.py, qtgui/emselector.py,
	  qtgui/emsprworkflow.py: improved saving functionality

2009-04-15 21:07  woolford

	* libpyEM/qtgui/emselector.py: saving fixes

2009-04-15 16:44  woolford

	* libpyEM/qtgui/emselector.py: save related updates

2009-04-15 15:32  woolford

	* programs/e2ptcltrace.py: ptcltrace works better

2009-04-15 12:13  jbert

	* sparx/libpy/development.py: fix a minor bug in cml

2009-04-15 11:56  zweig

	* sparx/libpy/applications.py: fix ali3d_d()

2009-04-15 11:45  woolford

	* libpyEM/qtgui/: emapplication.py, emimage.py, emimage3d.py,
	  emimage3diso.py, emimage3dslice.py, emimage3dsym.py,
	  emimage3dvol.py, emplot3d.py: bugs:

2009-04-15 11:09  woolford

	* libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emplot2d.py,
	  programs/e2eulerxplor.py: bug fixes

2009-04-15 10:59  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emform.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emimage3dsym.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimagemxrotor.py,
	  libpyEM/qtgui/emimagerotor.py, libpyEM/qtgui/emimageutil.py,
	  libpyEM/qtgui/emplot2d.py, libpyEM/qtgui/emrotor.py,
	  libpyEM/qtgui/emselector.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2boxer.py, programs/e2ctf.py, programs/e2desktop.py,
	  programs/e2display.py, programs/e2eulerxplor.py,
	  programs/e2workflow.py, sparx/bin/sxctf.py: gui infrastructure
	  updates

2009-04-14 17:26  zweig

	* sparx/libpy/alignment.py: fix another typo

2009-04-14 17:23  zweig

	* sparx/libpy/alignment.py: fix a typo

2009-04-14 17:19  zweig

	* sparx/libpy/: alignment.py, applications.py: new ali3d_d

2009-04-14 16:00  woolford

	* libpyEM/qtgui/: emimagemx.py, emselector.py: save work

2009-04-14 14:20  jbert

	* sparx/libpy/development.py: add some functions to new cml

2009-04-14 13:22  ppenczek

	* sparx/libpy/: reconstruction.py, statistics.py: nothing

2009-04-14 12:09  zyang

	* sparx/libpy/: alignment.py, applications.py, statistics.py: Many
	  changes to make alignment program preserve partial alignment
	  results

2009-04-14 11:16  woolford

	* libpyEM/qtgui/emselector.py: saving bug

2009-04-14 09:59  zyang

	* sparx/libpy/: applications.py, statistics.py: Minor change

2009-04-13 22:53  woolford

	* libpyEM/: libpyEMData2.cpp, qtgui/emimagemx.py,
	  qtgui/emimageutil.py, qtgui/emselector.py: general saving
	  functionality

2009-04-13 19:56  woolford

	* libpyEM/: EMAN2.py, qtgui/emimageutil.py, qtgui/emselector.py:
	  rounded file saving approach

2009-04-13 17:39  zweig

	* sparx/libpy/: applications.py: fix ali3d_em

2009-04-13 17:16  ppenczek

	* sparx/libpy/: applications.py, reconstruction.py, statistics.py:
	  [no log message]

2009-04-13 16:16  jbert

	* sparx/bin/sxfind_struct.py: change some options

2009-04-13 15:58  jbert

	* sparx/libpy/utilities.py: Add function get_rotation_angles

2009-04-13 15:35  zyang

	* sparx/libpy/: applications.py, development.py: Change to
	  eqproj_cascaded_ccc() and a test program

2009-04-13 15:28  woolford

	* libpyEM/: EMAN2.py, qtgui/emimagemx.py, qtgui/emimageutil.py:
	  minor stuff

2009-04-13 14:57  zweig

	* sparx/libpy/applications.py: fix ali3d_m: use ccc as criterion

2009-04-13 14:37  ppenczek

	* sparx/test/3DA/3dg.py:  modernized

2009-04-13 12:21  ppenczek

	* sparx/test/3DA/3dg.py:  modernized

2009-04-13 01:59  stevel

	* libpyEM/EMAN2PAR.py: oops

2009-04-13 01:58  stevel

	* libpyEM/: EMAN2PAR.py, EMAN2db.py: Work on parallelism

2009-04-11 21:23  prb

	* libEM/emdata_transform.cpp:
	   minor changes to bispec

2009-04-11 12:35  prb

	* libpyEM/libpyEMData2.cpp:
	    forgot to commit this when I committed the bispec code
	  yesterday.

2009-04-10 16:10  prb

	* libEM/emdata_transform.h:
	   commit invariants of 2d images code

2009-04-10 16:10  prb

	* libEM/emdata_transform.cpp:

	   committed invariants code

2009-04-10 14:40  zyang

	* sparx/libpy/applications.py: Fix a bug

2009-04-10 13:52  zweig

	* libpyEM/libpyUtils2.cpp, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h: add function crosrng_msg_vec_p

2009-04-10 11:48  zyang

	* sparx/libpy/applications.py: Fix a minor bug.

2009-04-10 09:47  zyang

	* sparx/libpy/applications.py: Minor change

2009-04-10 09:00  stevel

	* programs/e2parallel.py: trivial

2009-04-09 23:27  woolford

	* libEM/emdata_metadata.cpp, programs/e2ptcltrace.py: ptcltrace
	  works for Rui

2009-04-09 20:26  woolford

	* programs/e2proc3d.py: minor stuff

2009-04-09 19:39  woolford

	* libEM/emdata_cuda.cpp, libpyEM/EMAN2.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimageutil.py,
	  libpyEM/qtgui/emsprworkflow.py, libpyEM/qtgui/valslider.py,
	  programs/e2boxer.py, programs/e2ptcltrace.py,
	  programs/e2workflow.py, pyemtbx/boxertools.py: interface and
	  boxer fixes

2009-04-09 12:37  jbert

	* sparx/libpy/applications.py: change ali2dm_mpi

2009-04-09 12:29  jbert

	* libEM/sparx/util_sparx.cpp: fix again voronoi, leak memory

2009-04-09 11:27  zyang

	* sparx/libpy/applications.py: Trival change

2009-04-09 11:27  woolford

	* libpyEM/qtgui/emimagemx.py, programs/e2boxer.py: boxer bug fix

2009-04-09 09:58  zyang

	* sparx/libpy/applications.py: Trival change

2009-04-08 22:29  woolford

	* examples/cudaspeedtest.py, libEM/aligner.cpp, libEM/cmp.cpp,
	  libEM/emdata_cuda.cpp, libEM/emdata_cuda.h, libEM/processor.cpp,
	  libEM/processor.h, libEM/cuda/cuda_cmp.cu,
	  libpyEM/qtgui/emselector.py, rt/pyem/test_emdata_cuda.py: cuda
	  work

2009-04-08 13:36  zyang

	* sparx/libpy/applications.py: Many minor changes

2009-04-08 13:33  zweig

	* sparx/libpy/user_functions.py: modify spruce_up_var_m

2009-04-08 12:32  woolford

	* examples/cudaspeedtest.py, libEM/cmp.cpp, libEM/emdata_cuda.cpp,
	  libEM/emdata_cuda.h, libEM/cuda/cuda_cmp.cu, libpyEM/EMAN2.py,
	  libpyEM/libpyEMData2.cpp, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimageutil.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2boxer.py,
	  pyemtbx/boxertools.py: general work

2009-04-08 09:52  zyang

	* sparx/bin/sxctf.py: Fix a bug

2009-04-07 22:44  stevel

	* libpyEM/EMAN2PAR.py, programs/e2parallel.py: Working on
	  parallelism

2009-04-07 16:23  jbert

	* sparx/bin/sxfind_struct.py: add some options

2009-04-07 16:18  jbert

	* sparx/libpy/development.py: working on cml mpi GA

2009-04-06 15:54  zyang

	* sparx/libpy/applications.py: Some test codes.

2009-04-06 09:12  jbert

	* libEM/sparx/util_sparx.cpp: change the function cml in 3d

2009-04-05 00:56  stevel

	* libpyEM/: EMAN2db.py, qtgui/emsprworkflow.py: Workflow import
	  fix.

2009-04-01 11:09  zyang

	* sparx/libpy/development.py: Some improvements

2009-03-31 22:43  woolford

	* libEM/cuda/cuda_cmp.cu: mac compilation fix

2009-03-31 22:39  woolford

	* doc/eman2doc.h, examples/cudaspeedtest.py, libEM/aligner.h,
	  libEM/cmp.cpp, libEM/cmp.h, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emdata_cuda.cpp, libEM/processor.cpp, libEM/processor.h,
	  libEM/cuda/CMakeLists.txt, libEM/cuda/cuda_cmp.cu,
	  libEM/cuda/cuda_cmp.h, libEM/cuda/cuda_processor.cu,
	  libEM/cuda/cuda_processor.h, programs/e2pdb2mrc.py: cuda cmp

2009-03-31 16:33  woolford

	* programs/e2pdb2mrc.py: minor alterations

2009-03-31 14:38  woolford

	* libpyEM/qtgui/emimage3diso.py, programs/e2pdb2mrc.py: minor
	  alterations

2009-03-31 13:32  woolford

	* programs/e2pdb2mrc.py: minor stuff

2009-03-31 13:32  woolford

	* libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimage3diso.py,
	  libpyEM/qtgui/emimage3dsym.py, programs/e2desktop.py,
	  programs/e2ptcltrace.py: gui updates

2009-03-31 09:44  jbert

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Add new function for common-lines

2009-03-30 11:17  zweig

	* sparx/libpy/applications.py: fix a bug: the argument of
	  estimate_3D_center_MPI must be the total nimage number

2009-03-29 18:06  woolford

	* libpyEM/qtgui/emimage3dsym.py, programs/e2ptcltrace.py: [no log
	  message]

2009-03-27 17:07  jbert

	* sparx/libpy/development.py: Work on Cml

2009-03-27 14:54  zyang

	* sparx/libpy/statistics.py: Minor change

2009-03-27 11:42  zweig

	* sparx/libpy/applications.py: change ali3d_em tolerance

2009-03-27 09:11  jbert

	* sparx/libpy/utilities.py: Grant fix bug to png, change back
	  drop_png_image

2009-03-26 19:59  gtang

	* libEM/pngio.cpp: fix binary image writing bug

2009-03-26 16:46  zyang

	* sparx/libpy/applications.py: Just try something new.

2009-03-26 16:08  woolford

	* programs/e2boxer.py: boxer bug fix

2009-03-26 15:31  jbert

	* sparx/libpy/development.py: Draft of Common-lines, the new
	  version

2009-03-26 14:07  jbert

	* sparx/libpy/development.py: Clean old code of k-means stab and
	  Cml

2009-03-26 10:38  zweig

	* sparx/bin/sxali3d_em.py: init_mpi_bdb

2009-03-26 10:08  gtang

	* rt/pyem/test_processor.py: unit test update.

2009-03-25 22:57  woolford

	* examples/cudaspeedtest.py, libEM/aligner.cpp, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/processor.cpp, libEM/processor.h,
	  libEM/vec3.h, libEM/cuda/cuda_processor.cu: translate done with
	  clip, works partially with cuda, processor added

2009-03-25 17:32  gtang

	* libEM/pngio.cpp: minor fix

2009-03-25 16:46  gtang

	* libEM/hdfio2.cpp: bug fix. init_test() should open hdf5 file read
	  only.

2009-03-25 16:42  zweig

	* sparx/libpy/applications.py: fix ali3d_em: use
	  eqproj_cascaded_ccc for measurement

2009-03-25 16:20  zyang

	* sparx/libpy/: applications.py, development.py: Fix a bug.

2009-03-25 14:31  gtang

	* CMakeLists.txt, libEM/emftgl.h: solve the ftgl.h/FTGL.h issue

2009-03-25 14:29  woolford

	* libEM/: emdata_cuda.cpp, emdata_metadata.cpp, processor.cpp,
	  cuda/cuda_processor.cu: transform works on cuda

2009-03-25 13:25  zweig

	* sparx/libpy/applications.py: fix ali3d_em

2009-03-25 13:25  zweig

	* sparx/libpy/alignment.py: add function eqprojDot

2009-03-25 13:07  woolford

	* libEM/aligner.cpp: aligner fix

2009-03-25 12:58  zyang

	* sparx/libpy/applications.py: Fix a bug

2009-03-25 11:07  zyang

	* sparx/libpy/applications.py: [no log message]

2009-03-25 10:56  zyang

	* sparx/libpy/applications.py: Change the alignment target from avg
	  to SSNR

2009-03-25 10:31  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2009-03-25 03:09  stevel

	* libpyEM/qtgui/emimage2d.py: More work...

2009-03-25 02:48  stevel

	* .pydevproject, libEM/imageio.cpp, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemx.py: Fixed GUI brightness/contrast issues
	  (hopefully) and 8 bit file writing

2009-03-24 22:55  woolford

	* examples/cudaspeedtest.py, libEM/aligner.cpp,
	  libEM/emdata_cuda.h, libEM/processor.cpp, libEM/processor.h,
	  libEM/cuda/cuda_processor.cu, libEM/cuda/cuda_processor.h,
	  libEM/cuda/cuda_util.cu: cuda updates

2009-03-24 22:09  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2boxer.py,
	  pyemtbx/boxertools.py: invert in boxer

2009-03-24 17:23  woolford

	* libpyEM/qtgui/emimagemxrotor.py, programs/e2classify.py:
	  e2classify bug

2009-03-24 16:48  gtang

	* programs/CMakeLists.txt: install extra .pyw version python GUI
	  program for windows

2009-03-24 16:27  gtang

	* libpyEM/CMakeLists.txt: change the .dll to .pyd for win32

2009-03-24 15:49  zweig

	* sparx/: libpy/applications.py, bin/sxali3d_m.py: add new
	  centering

2009-03-24 15:49  zweig

	* sparx/libpy/reconstruction.py: remove debug info

2009-03-24 15:40  zyang

	* sparx/libpy/applications.py: Add CTF processing in ali2d_a_MPI()

2009-03-24 15:02  zyang

	* sparx/libpy/statistics.py: Just change some name to make it
	  consistent with what it means

2009-03-24 14:03  zweig

	* sparx/: libpy/applications.py, bin/sxali3d_m.py: remove the
	  cccmake for ali3d_m

2009-03-24 13:09  woolford

	* libpyEM/qtgui/: emapplication.py, emlights.py, emselector.py:
	  glut lighting problem

2009-03-24 12:48  zweig

	* sparx/libpy/applications.py: change the way dot was calculated:
	  ctf was applied to reference projection after normalization

2009-03-24 12:48  zweig

	* sparx/libpy/alignment.py: change the way ccf was cacluated:
	  nomralization was applied to img before ctf

2009-03-24 12:13  woolford

	* programs/e2eulerxplor.py: minor alterations

2009-03-24 11:01  gtang

	* programs/e2display.py: revert zyang's change to make display()
	  works in Python prompt

2009-03-23 22:30  woolford

	* examples/cudaspeedtest.py, programs/e2classaverage.py,
	  programs/e2eulerxplor.py: general updates

2009-03-23 20:58  woolford

	* libEM/util.h, libpyEM/EMAN2.py: add browse() to e2.py

2009-03-23 14:12  zweig

	* sparx/libpy/applications.py: add import model_blank for
	  ali3d_em_MPI

2009-03-23 11:56  jbert

	* sparx/libpy/projection.py: clean cml code

2009-03-23 10:59  jbert

	* sparx/libpy/utilities.py: change drop_png_image

2009-03-23 09:33  jbert

	* sparx/libpy/utilities.py: Add function, drop_png_image

2009-03-20 20:51  woolford

	* examples/cudaspeedtest.py, libEM/emdata.cpp,
	  libEM/emdata_cuda.cpp, libEM/emdata_transform.cpp,
	  libEM/emdata_transform.h, libEM/geometry.cpp, libEM/geometry.h,
	  rt/pyem/test_emdata.py: cuda updates

2009-03-20 17:10  zweig

	* sparx/: libpy/applications.py, bin/sxali3d_em.py: fix ali3d_em

2009-03-20 14:03  jbert

	* sparx/libpy/applications.py: k_means_stab fix minor bug

2009-03-20 13:50  ppenczek

	* sparx/bin/sxpdb2em.py: printout blocked

2009-03-20 13:16  jbert

	* sparx/libpy/applications.py: split the function stability
	  streamline in severals part (in order to manage the re-alignment)

2009-03-20 13:09  woolford

	* examples/cudaspeedtest.py, libEM/emdata_cuda.cpp,
	  libEM/emdata_cuda.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/qtgui/emimage.py, libpyEM/qtgui/emsprworkflow.py,
	  utils/speedtest.cpp: cuda fixes

2009-03-19 23:06  woolford

	* examples/cudaspeedtest.py, libEM/emdata.cpp,
	  libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/emdata_metadata.cpp, libEM/cuda/cuda_processor.cu,
	  libEM/cuda/cuda_processor.h, libpyEM/libpyEMData2.cpp,
	  utils/speedtest.cpp: cuda nasty bug fix

2009-03-19 16:52  zweig

	* sparx/libpy/applications.py: minor change on ali3d_d, use a
	  spherical mask to calculate fsc

2009-03-19 16:40  gtang

	* programs/e2tomohunter.py: David convert this script to work with
	  EMAN2

2009-03-19 15:41  gtang

	* libEM/: cmp.cpp, emdata_metadata.cpp, reconstructor.cpp: fix
	  issue for win32

2009-03-19 15:30  gtang

	* libEM/analyzer.cpp: minor

2009-03-19 15:09  gtang

	* libEM/: sparx/emdata_sparx.cpp, analyzer.cpp: fix issue for win32

2009-03-19 14:23  stevel

	* programs/e2proc2d.py: trivial

2009-03-19 14:21  stevel

	* programs/e2proc2d.py: Trivial fix

2009-03-19 10:54  jbert

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h, sparx/libpy/applications.py,
	  sparx/libpy/projection.py: fix find_structure

2009-03-19 10:16  zyang

	* sparx/libpy/development.py: Fix a small bug.

2009-03-18 21:41  woolford

	* examples/cudaspeedtest.py, libEM/emdata_cuda.cpp: cuda bug fix

2009-03-18 15:32  zyang

	* sparx/libpy/development.py: Fix a small bug

2009-03-18 15:22  zyang

	* sparx/libpy/development.py: Consider mirror in my ali_SSNR()
	  program

2009-03-18 15:19  zyang

	* sparx/libpy/statistics.py: Delete some unnecessary code.

2009-03-18 13:54  woolford

	* libEM/emdata_cuda.cpp: minor fix

2009-03-18 13:38  woolford

	* examples/cudaspeedtest.py: minor alterations

2009-03-18 12:38  zweig

	* libpyEM/libpyEMData2.cpp: add default option for norm_pad

2009-03-18 12:37  zweig

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h,
	  fourierfilter.cpp: add option to norm_pad to allow padding with
	  circumference

2009-03-18 12:35  zweig

	* sparx/libpy/applications.py: fix calling of
	  proj_ali_incore_local, has to pass CTF flag

2009-03-17 22:44  woolford

	* examples/cudaspeedtest.py, libEM/aligner.cpp, libEM/emdata.cpp,
	  libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/cuda/cuda_util.cu, libpyEM/libpyEMData2.cpp,
	  rt/pyem/test_emdata_cuda.py, utils/speedtest.cpp: cuda updates

2009-03-17 17:18  woolford

	* libEM/emdata.cpp, libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libpyEM/libpyEMData2.cpp, rt/pyem/test_emdata_cuda.py: cuda
	  updates

2009-03-17 16:45  zyang

	* sparx/libpy/development.py: Fix a small bug

2009-03-16 22:48  woolford

	* libEM/emdata_cuda.cpp: cuda updates

2009-03-16 22:42  woolford

	* libEM/: emdata_cuda.cpp, emdata_cuda.h, emdata_metadata.cpp: cuda
	  updates

2009-03-16 22:26  woolford

	* libEM/: aligner.cpp, emdata.cpp: cvs updates

2009-03-16 22:17  woolford

	* libEM/: aligner.cpp, emdata.cpp, emdata_cuda.cpp,
	  emdata_metadata.cpp: cuda updates

2009-03-16 21:21  woolford

	* examples/cudaspeedtest.py, libEM/aligner.cpp, libEM/emdata.cpp,
	  libEM/emdata_cuda.cpp: cuda updates

2009-03-16 21:08  woolford

	* examples/cudaspeedtest.py, libEM/emdata.cpp: cuda updates

2009-03-16 20:52  woolford

	* examples/cudaspeedtest.py, libEM/emdata.cpp,
	  libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/cuda/cuda_emfft.cu, libEM/cuda/cuda_emfft.h,
	  libEM/cuda/cuda_processor.cu, libEM/cuda/cuda_util.cu,
	  libEM/cuda/cuda_util.h: cuda updates

2009-03-16 17:26  woolford

	* examples/cudaspeedtest.py: cuda updates

2009-03-16 17:17  woolford

	* examples/cudaspeedtest.py, libEM/emdata_cuda.cpp: cuda updates

2009-03-16 17:04  woolford

	* examples/cudaspeedtest.py, libEM/emdata.cpp,
	  libEM/emdata_cuda.cpp, libEM/cuda/cuda_util.cu,
	  rt/pyem/test_emdata_cuda.py: cuda fixes

2009-03-16 16:13  zweig

	* sparx/: libpy/applications.py, bin/sxali3d_m.py: use two masks in
	  ali3d_m

2009-03-16 14:59  zyang

	* sparx/libpy/applications.py: Fix a small bug

2009-03-16 14:16  woolford

	* examples/cudaspeedtest.py, libEM/emdata.cpp,
	  libEM/emdata_core.cpp, libEM/emdata_cuda.cpp,
	  libEM/emdata_cuda.h, libEM/emdata_transform.cpp,
	  libpyEM/libpyEMData2.cpp, rt/pyem/test_emdata_cuda.py: cuda
	  testing relatated upates

2009-03-16 13:27  zweig

	* sparx/libpy/user_functions.py: fix errors in spruce_up_var_m

2009-03-16 13:27  zweig

	* sparx/libpy/applications.py: fix an error of ali3d_m_MPI

2009-03-16 13:21  jbert

	* sparx/bin/sxk_means_stability.py: change name for some params

2009-03-16 13:15  jbert

	* sparx/libpy/statistics.py: k_means_stab_update_tag remove a flag

2009-03-15 20:27  woolford

	* libEM/emdata_cuda.cpp, libEM/emdata_transform.cpp,
	  libEM/emdata_transform.h, libEM/processor.cpp,
	  libEM/cuda/cuda_processor.cu, libpyEM/libpyEMData2.cpp: cuda
	  updates

2009-03-15 19:54  woolford

	* examples/cudaspeedtest.py: cuda speed test upate

2009-03-15 19:41  woolford

	* examples/cudaspeedtest.py, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emdata_core.cpp, libEM/emdata_cuda.cpp,
	  libEM/emdata_cuda.h, libEM/processor.cpp,
	  libEM/cuda/cuda_processor.cu, libEM/cuda/cuda_processor.h,
	  libpyEM/libpyEMData2.cpp: cuda updates

2009-03-14 19:48  woolford

	* libEM/emdata.cpp, libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/cuda/cuda_processor.cu, libEM/cuda/cuda_processor.h,
	  libpyEM/libpyEMData2.cpp, rt/pyem/test_emdata_cuda.py: cuda
	  updates - gpu use becoming automatic

2009-03-14 17:52  woolford

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/libpyEMData2.cpp:
	  unwrap has radial weight flag

2009-03-14 00:23  woolford

	* examples/cudaspeedtest.py, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emdata_core.cpp, libEM/emdata_core.h,
	  libEM/emdata_cuda.cpp, libEM/emdata_cuda.h, libEM/processor.cpp,
	  libEM/cuda/cuda_processor.cu, libEM/cuda/cuda_processor.h,
	  libpyEM/libpyEMData2.cpp: cuda updates - rotational footprint
	  almost done

2009-03-13 22:38  zweig

	* sparx/libpy/user_functions.py: fix spruce_up_var_m

2009-03-13 18:28  woolford

	* examples/cudaspeedtest.py, libEM/aligner.cpp, libEM/emdata.cpp,
	  libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/emdata_metadata.cpp, libEM/cuda/cuda_processor.cu,
	  libEM/cuda/cuda_processor.h, libEM/cuda/cuda_util.cu,
	  libEM/cuda/cuda_util.h, libpyEM/libpyEMData2.cpp: cuda unwrap
	  added

2009-03-13 17:08  ppenczek

	* sparx/libpy/projection.py: sino

2009-03-13 16:51  zweig

	* sparx/libpy/applications.py: flush the progress file

2009-03-13 16:22  zweig

	* sparx/libpy/applications.py: import model_blank for ali3d_m_MPI

2009-03-13 14:59  woolford

	* programs/e2display.py: fixed display bug

2009-03-13 14:36  zyang

	* libpyEM/libpyUtils2.cpp, programs/e2display.py: Fix a bug

2009-03-13 14:33  ppenczek

	* sparx/bin/sxctf.py: sxctf

2009-03-13 14:32  zweig

	* sparx/libpy/applications.py: remove initial filter by fourier
	  var, should be done at preparation step

2009-03-13 14:24  zweig

	* sparx/libpy/applications.py: prepare ali3d_m_MPI to use
	  spruce_up_var_m

2009-03-13 14:24  zweig

	* sparx/libpy/user_functions.py: add function spruce_up_var_m

2009-03-12 22:28  woolford

	* libEM/cuda/cuda_util.cu, libpyEM/EMAN2.py,
	  libpyEM/qtgui/emform.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2boxer.py,
	  programs/e2display.py, pyemtbx/boxertools.py: interface and form
	  bug fixes

2009-03-12 15:57  zweig

	* sparx/libpy/applications.py: use fscmask for reconstruction

2009-03-12 15:52  zweig

	* sparx/libpy/applications.py: add function tomo()

2009-03-12 15:51  zweig

	* sparx/bin/sxtomo.py: initial version

2009-03-12 11:30  stevel

	* programs/e2ctf2eman1.py: Updates from ben

2009-03-11 17:07  zweig

	* sparx/libpy/: applications.py, user_functions.py: add option
	  fourvar to ali3d_m

2009-03-11 17:06  zweig

	* sparx/libpy/reconstruction.py: fix a type

2009-03-11 17:06  zweig

	* sparx/bin/sxali3d_m.py: add option fourvar

2009-03-11 16:37  woolford

	* examples/cudaspeedtest.py, libEM/emdata_cuda.cpp,
	  libEM/emdata_transform.cpp, libEM/cuda/cuda_processor.cu,
	  libEM/cuda/cuda_util.cu: cuda work

2009-03-11 15:35  zyang

	* sparx/libpy/applications.py: No seed

2009-03-11 15:18  zyang

	* sparx/libpy/applications.py: Fix a bug

2009-03-11 14:34  zyang

	* sparx/: bin/sxheader.py, libpy/applications.py: Fix an important
	  bug

2009-03-11 14:12  zyang

	* sparx/libpy/fundamentals.py: Change resample() such that it can
	  automatically adjust pixel size

2009-03-11 11:25  zyang

	* sparx/libpy/applications.py: Trival change

2009-03-10 22:44  woolford

	* rt/pyem/test_emdata_cuda.py: test updates

2009-03-10 21:59  woolford

	* libEM/emdata_cuda.cpp, libEM/cuda/cuda_processor.cu,
	  libEM/cuda/cuda_util.cu, rt/pyem/test_emdata_cuda.py: cuda fixes

2009-03-10 19:32  woolford

	* libEM/emdata_transform.cpp, libEM/cuda/cuda_processor.cu,
	  rt/pyem/test_emdata_cuda.py: cuda fft fixes

2009-03-10 14:09  zweig

	* sparx/libpy/: filter.py, user_functions.py: if fsc always > 0.5,
	  return (0.4, 0.1) for filtration

2009-03-10 13:40  zweig

	* sparx/libpy/applications.py: for ali3d_m, use linear projector
	  and use mask to calculate ccc

2009-03-09 22:13  woolford

	* examples/cudaspeedtest.py, libEM/emdata.cpp,
	  libEM/emdata_cuda.cpp, libEM/emdata_cuda.h, libEM/emdata_io.cpp,
	  libEM/emdata_transform.cpp, libEM/cuda/cuda_processor.cu,
	  rt/pyem/test_emdata_cuda.py: cuda - kernels updated, ffts work
	  for irregular sizes

2009-03-09 11:53  zweig

	* sparx/bin/sxali3d_m.py: add parameter maxit

2009-03-09 10:06  zweig

	* sparx/libpy/user_functions.py: add ref_ali3dm_ali_50S

2009-03-09 10:05  zweig

	* sparx/libpy/applications.py: add print out

2009-03-08 16:15  ppenczek

	* sparx/bin/sxctf.py: [no log message]

2009-03-06 19:53  woolford

	* examples/cudaspeedtest.py, libEM/emdata_cuda.cpp,
	  libEM/emdata_transform.cpp, libEM/cuda/cuda_emfft.cu,
	  libEM/cuda/cuda_processor.cu, libEM/cuda/cuda_util.cu,
	  rt/pyem/test_emdata_cuda.py: cuda work

2009-03-06 16:06  gtang

	* libEM/emdata.cpp: add 'datatype' attribute for EMAN2 crested
	  image

2009-03-06 16:01  gtang

	* libEM/: hdfio2.cpp, processor.cpp: not assign attribute
	  'datatype' in these places

2009-03-06 15:51  gtang

	* libEM/mrcio.cpp: fix a 16 bit MRC writing bug, SHORT vs USHORT

2009-03-06 12:32  ppenczek

	* sparx/bin/sxpdb2em.py: [no log message]

2009-03-05 22:39  woolford

	* examples/cudaerrors.py, examples/cudaspeedtest.py,
	  libEM/emdata_cuda.cpp, libEM/processor.cpp,
	  libEM/cuda/cuda_processor.cu, libEM/cuda/cuda_processor.h,
	  libEM/cuda/cuda_util.cu: cuda optimization etc

2009-03-05 17:02  gtang

	* programs/e2tomohunter.py: update for Mike Schmid

2009-03-05 16:54  woolford

	* examples/cudaspeedtest.py, libEM/emdata.cpp,
	  libEM/emdata_core.cpp, libEM/emdata_cuda.cpp,
	  libEM/emdata_cuda.h, libEM/cuda/cuda_processor.cu,
	  rt/pyem/test_emdata_cuda.py: cuda related

2009-03-05 12:07  gtang

	* libEM/hdfio2.cpp: [no log message]

2009-03-05 10:08  gtang

	* utils/CMakeLists.txt: [no log message]

2009-03-05 09:33  jbert

	* sparx/libpy/statistics.py: Fix bug k-means MPI SSE

2009-03-04 22:52  woolford

	* examples/cudaspeedtest.py, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emdata_core.h, libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/processor.cpp, libEM/cuda/cuda_processor.cu,
	  libpyEM/libpyEMData2.cpp, rt/pyem/test_emdata_cuda.py,
	  utils/CMakeLists.txt: cuda - test codes and optimizations

2009-03-04 19:55  woolford

	* libEM/processor.cpp, programs/e2modeleval.py: minor updates

2009-03-04 18:37  gtang

	* programs/e2iminfo.py: [no log message]

2009-03-04 18:32  gtang

	* programs/e2iminfo.py, utils/CMakeLists.txt: python version
	  e2iminfo

2009-03-04 18:32  gtang

	* programs/e2speedtest.py: slow option

2009-03-04 18:26  woolford

	* libEM/: emdata_metadata.cpp, processor.cpp: minor fixes

2009-03-04 18:07  gtang

	* libEM/: processor.cpp, processor.h: set "datatype" attribute for
	  test image

2009-03-04 17:19  jbert

	* sparx/bin/sxk_means_stability.py: change default parameters

2009-03-04 17:12  jbert

	* sparx/: bin/sxk_means_stability.py, libpy/applications.py: Change
	  the way the run is managed (sxk_means_stability)

2009-03-04 17:11  woolford

	* libEM/processor.cpp: minor fixes

2009-03-04 16:52  jbert

	* sparx/libpy/statistics.py: typo

2009-03-04 16:22  woolford

	* libpyEM/libpyTypeConverter2.cpp: processor work

2009-03-04 16:08  jbert

	* sparx/: bin/sxk_means_groups.py, libpy/applications.py,
	  libpy/statistics.py: add k-means group cuda

2009-03-04 16:01  woolford

	* libEM/: emdata_metadata.cpp, emdata_metadata.h: minor alteration

2009-03-04 15:53  woolford

	* libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libEM/emftgl.h, libEM/processor.cpp,
	  libEM/cuda/cuda_processor.cu, libEM/cuda/cuda_util.cu,
	  libEM/cuda/cuda_util.h, libpyEM/libpyEMData2.cpp: processor work

2009-03-04 14:39  ppenczek

	* sparx/libpy/applications.py: fix another bug

2009-03-04 14:37  zweig

	* sparx/libpy/reconstruction.py: use scratch disk to store
	  intermediate result: fftvol and weight

2009-03-04 14:33  zweig

	* sparx/libpy/user_functions.py: add function ref_ali3dm, generate
	  multiple reference volume for ali3d_m

2009-03-04 14:33  zweig

	* sparx/libpy/applications.py: move generate refvols into a
	  function ref_ali3dm

2009-03-04 14:31  zweig

	* sparx/libpy/alignment.py: fix ali_vol_func

2009-03-04 13:15  zyang

	* sparx/libpy/applications.py: Fix a bug

2009-03-04 12:31  zyang

	* sparx/libpy/applications.py: Add stability in ali2d_a_MPI()

2009-03-04 09:42  gtang

	* rt/pyem/test_processor.py: unit test update

2009-03-03 22:21  woolford

	* libEM/: emdata_core.h, marchingcubes.cpp, marchingcubes.h,
	  processor.cpp, processor.h: minor updates

2009-03-03 19:24  gtang

	* programs/e2speedtest.py: [no log message]

2009-03-03 19:11  gtang

	* programs/e2speedtest.py: e2speedtest python version

2009-03-03 12:56  ppenczek

	* sparx/bin/sxpdb2em.py: simple version for awhile

2009-03-03 12:06  zyang

	* sparx/libpy/applications.py: An overhaul of the structure of
	  ali2d_a_MPI()

2009-03-03 08:38  ppenczek

	* sparx/libpy/morphology.py: [no log message]

2009-03-03 02:03  stevel

	* .pydevproject, libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py: A little
	  parallelism work

2009-03-03 00:15  woolford

	* libEM/: emdata_cuda.h, projector.cpp: cuda header doxygen
	  documentation

2009-03-02 22:49  woolford

	* libEM/: emdata_cuda.cpp, emdata_cuda.h, projector.cpp,
	  cuda/cuda_projector.cu, cuda/cuda_projector.h: cuda caching -
	  first design completed

2009-03-02 21:49  woolford

	* examples/cudaspeedtest.py, libEM/emdata.cpp,
	  libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/emdata_metadata.cpp, libEM/emutil.h, libEM/processor.cpp,
	  libEM/projector.cpp, libEM/cuda/CMakeLists.txt,
	  libEM/cuda/cuda_processor.cu, libEM/cuda/cuda_processor.h,
	  libEM/cuda/cuda_util.cu, libEM/cuda/cuda_util.h,
	  libEM/cuda/emcudautil.cpp, libEM/cuda/emcudautil.h,
	  rt/pyem/test_emdata_cuda.py: cuda cache almost complete

2009-03-02 18:40  ppenczek

	* sparx/bin/sxpdb2em.py: box size correction

2009-03-02 18:03  woolford

	* examples/cudaspeedtest.py: adding a file

2009-03-02 18:03  woolford

	* libEM/emdata.cpp, libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/emdata_metadata.cpp, libEM/projector.cpp,
	  libEM/cuda/cuda_util.cu, libEM/cuda/cuda_util.h,
	  rt/pyem/test_emdata.py, rt/pyem/test_emdata_cuda.py: cuda cache
	  coming together

2009-03-02 16:56  ppenczek

	* sparx/bin/sxpdb2em.py: trilinear interpolation with atom shaping
	  :wq

2009-03-02 16:46  ppenczek

	* libEM/sparx/emdata_sparx.cpp: FourTruncate for complex input

2009-03-02 15:31  gtang

	* libEM/mrcio.cpp: change the machine stamp of MRC, make it
	  coincide in CCP4

2009-03-02 14:47  woolford

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/emcache.h,
	  libEM/emdata.cpp, libEM/emdata.h, libEM/emdata_core.cpp,
	  libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/emdata_metadata.cpp, libEM/emdata_transform.cpp,
	  libEM/cuda/cuda_util.cu, libEM/cuda/cuda_util.h,
	  libpyEM/qtgui/emimagemx.py, rt/pyem/test_emdata.py: Implementing
	  the cuda cache, work in progress

2009-03-02 10:59  zyang

	* sparx/libpy/applications.py: Make a change in ali2d_a_MPI() to
	  make it record the alignment parameters after each merge.

2009-03-02 10:42  stevel

	* programs/e2classifykmeans.py: Trivial

2009-03-02 02:06  stevel

	* .pydevproject, libEM/analyzer.cpp, libpyEM/EMAN2.py,
	  libpyEM/EMAN2PAR.py, libpyEM/EMAN2db.py,
	  programs/e2classifykmeans.py: Work on parallelism and k-means
	  sigma debugging

2009-02-27 16:58  jbert

	* sparx/: bin/sxk_means_stability.py, libpy/applications.py,
	  libpy/statistics.py: work on cuda k-means stability

2009-02-27 13:31  ppenczek

	* programs/e2pdb2em.py:  new version, maybe will not last

2009-02-27 13:30  woolford

	* libpyEM/qtgui/emform.py, libpyEM/qtgui/emsprworkflow.py,
	  pyemtbx/boxertools.py: form tables size automatically

2009-02-27 09:11  ppenczek

	* programs/e2pdb2em.py: obsolete part removed

2009-02-27 02:53  stevel

	* libEM/analyzer.cpp, libEM/analyzer.h, libEM/emdata_core.cpp,
	  libEM/emdata_core.h, libpyEM/EMAN2db.py,
	  libpyEM/libpyEMData2.cpp, programs/e2classifykmeans.py: Several
	  changes to kmeans analyzer and tasks in database. Hope nothing
	  broke

2009-02-26 18:57  woolford

	* libpyEM/qtgui/emform.py, programs/e2boxer.py: minor fixes

2009-02-26 18:21  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2boxer.py, pyemtbx/boxertools.py: e2boxer has an output
	  form

2009-02-26 17:50  woolford

	* libpyEM/qtgui/emimage3dslice.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2boxer.py: boxer work

2009-02-26 17:25  jbert

	* sparx/bin/sxk_means_stability.py: add option to cuda

2009-02-26 17:25  jbert

	* sparx/libpy/: applications.py, statistics.py: add cuda k-means
	  stab

2009-02-26 16:53  woolford

	* libEM/emdata_cuda.cpp, libEM/emdata_cuda.h, libEM/emutil.cpp,
	  libEM/emutil.h, libEM/cuda/cuda_emfft.cu,
	  libEM/cuda/cuda_util.cu, libEM/cuda/cuda_util.h,
	  libpyEM/qtgui/emimagemx.py, programs/e2boxer.py: minor fixes,
	  cuda and boxer related

2009-02-26 14:35  ppenczek

	* libpyEM/libpyEMData2.cpp: activated FourTruncate

2009-02-26 13:30  zyang

	* sparx/libpy/utilities.py: Fix a small bug.

2009-02-26 12:05  zyang

	* sparx/libpy/: applications.py, utilities.py: Many changes
	  regarding to the group communicators.

2009-02-25 17:19  jbert

	* libEM/sparx/cuda/: cuda_kmeans.cu, cuda_kmeans.h: work on cuda
	  k-means

2009-02-25 17:16  jbert

	* sparx/libpy/applications.py, sparx/libpy/statistics.py,
	  sparx/bin/sxk_means.py, libEM/processor.cpp, libEM/processor.h,
	  libpyEM/libpyProcessor2.cpp: work on cuda k-means

2009-02-25 16:52  woolford

	* libEM/emdata.cpp, libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/processor.cpp, libEM/cuda/cuda_processor.cu,
	  libEM/cuda/cuda_projector.cu, libEM/cuda/cuda_util.cu,
	  libpyEM/libpyEMData2.cpp, libpyEM/qtgui/emimage3dslice.py: cuda
	  ro based alterations

2009-02-25 12:50  woolford

	* libEM/: emdata.cpp, emdata_core.cpp, reconstructor.h: copy head
	  restored

2009-02-25 12:15  woolford

	* libEM/emdata.cpp, libEM/emdata.h, libEM/processor.h,
	  libEM/cuda/cuda_processor.cu, libpyEM/qtgui/emimage3dslice.py,
	  libpyEM/qtgui/emimage3dvol.py: fixed copy - nxy wasn't set

2009-02-25 11:42  zyang

	* sparx/libpy/applications.py: Fix a bug in attribute collecting.

2009-02-25 10:18  jbert

	* sparx/libpy/statistics.py: add function to cuda k-means

2009-02-25 09:42  zyang

	* sparx/libpy/applications.py: Fix a small bug

2009-02-25 00:06  woolford

	* libEM/cuda/cuda_util.cu: cuda cut slice works

2009-02-24 22:31  woolford

	* libEM/cuda/cuda_util.cu: cuda compilation fix on mac

2009-02-24 21:49  woolford

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emdata_core.cpp, libEM/emdata_cuda.cpp,
	  libEM/emdata_cuda.h, libEM/emdata_io.cpp,
	  libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libEM/emdata_transform.cpp, libEM/emutil.h, libEM/processor.cpp,
	  libEM/processor.h, libEM/cuda/CMakeLists.txt,
	  libEM/cuda/cuda_processor.cu, libEM/cuda/cuda_processor.h,
	  libEM/cuda/cuda_util.cu, libEM/cuda/cuda_util.h,
	  libEM/cuda/emcudautil.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyUtils2.cpp, libpyEM/qtgui/emimage3dslice.py: cuda
	  infrastructure, processors, cut slice, ccf etc

2009-02-24 17:37  jbert

	* libEM/: processor.cpp, processor.h: Add new class for cuda
	  k-means

2009-02-24 17:35  jbert

	* libEM/sparx/cuda/: CMakeLists.txt, cuda_kmeans.cu, cuda_kmeans.h:
	  add cuda code for k-means

2009-02-24 14:17  woolford

	* libEM/: emdata.cpp, emdata_core.cpp, emdata_metadata.cpp: get
	  data related alterations

2009-02-24 13:50  woolford

	* libEM/: emdata.cpp, emdata.h, emdata_core.cpp,
	  emdata_metadata.cpp, processor.cpp, processor.h: transform
	  processor fix, and constructor initializers

2009-02-23 22:52  woolford

	* libEM/emdata.cpp, libEM/emdata.h, libEM/emdata_core.cpp,
	  libEM/emdata_core.h, libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libEM/emdata_transform.cpp, libEM/emdata_transform.h,
	  libpyEM/libpyEMData2.cpp, rt/pyem/test_emdata.py: cuda related
	  memory management alterations

2009-02-23 20:18  woolford

	* libEM/CMakeLists.txt, libEM/emdata.cpp, libEM/emdata_core.cpp,
	  libEM/emdata_cuda.cpp, libEM/emdata_cuda.h,
	  libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libEM/emdata_transform.cpp, libEM/emdata_transform.h,
	  libEM/cuda/cuda_emfft.cu, libEM/cuda/cuda_emfft.h,
	  libEM/cuda/cuda_util.cu, libEM/cuda/cuda_util.h,
	  libpyEM/libpyEMData2.cpp: cuda work

2009-02-23 17:36  jbert

	* sparx/libpy/applications.py: add draft k-means CUDA to appli

2009-02-23 17:35  jbert

	* sparx/libpy/statistics.py: change something on k-means criterion

2009-02-23 16:34  zweig

	* sparx/libpy/applications.py: Fix a bug in ali2d_a_MPI()

2009-02-23 16:11  woolford

	* libEM/: emdata_cuda.cpp, emdata_cuda.h, cuda/cuda_util.cu: adding
	  a file

2009-02-23 13:47  woolford

	* libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2boxer.py: minor bug fixes in interfaces

2009-02-23 13:04  zweig

	* sparx/bin/sxrecons3d_n.py: init_mpi_bdb must be before
	  get_image_count

2009-02-23 12:13  ppenczek

	* sparx/libpy/alignment.py: Fix a bug in ali2d_single_iter() and
	  ali2d_random_ccf()

2009-02-22 15:39  gtang

	* libEM/processor.cpp: [no log message]

2009-02-21 00:55  stevel

	* .pydevproject, libpyEM/qtgui/emplot2d.py, programs/e2basis.py,
	  programs/e2classifykmeans.py: MSA/classification improvements

2009-02-21 00:09  woolford

	* libEM/cuda/cuda_util.cu: cuda read only memory cache works
	  properly

2009-02-21 00:05  woolford

	* libEM/cuda/cuda_util.cu: cuda read only memory cache works
	  properly

2009-02-20 20:23  woolford

	* libEM/emdata.cpp, libEM/emdata_cuda.h, libEM/projector.cpp,
	  libEM/cuda/CMakeLists.txt, libEM/cuda/cuda_projector.cu,
	  libEM/cuda/cuda_util.cu, libEM/cuda/cuda_util.h,
	  libEM/cuda/emcudautil.cpp, libEM/cuda/emcudautil.h,
	  libpyEM/qtgui/emimagemx.py: cuda work

2009-02-20 17:29  jbert

	* sparx/libpy/: applications.py, statistics.py: wrap for cuda
	  k-means

2009-02-20 17:22  gtang

	* libEM/: processor.cpp, processor.h: fix the parameter for
	  Fourierprocessor, cutoff_abc/cutoff_freq/cutoff_pixels

2009-02-20 17:16  zyang

	* sparx/libpy/utilities.py: Change some codes to make them work for
	  group communicators.

2009-02-20 17:15  zyang

	* sparx/libpy/applications.py: Add a new version of ali2d_a_MPI()
	  using group communicator.

2009-02-20 15:34  woolford

	* libpyEM/qtgui/emselector.py: selector fixes

2009-02-20 14:54  woolford

	* images/: multiple_images_3d.png,
	  macimages/multiple_images_3d.png: icon stuff

2009-02-20 14:43  woolford

	* images/: CMakeLists.txt, single_image_3d.png,
	  macimages/CMakeLists.txt, macimages/single_image_3d.png,
	  multiple_images_3d.png, macimages/multiple_images_3d.png: icon
	  stuff

2009-02-20 13:07  woolford

	* libpyEM/qtgui/emselector.py: minor fix

2009-02-20 12:40  woolford

	* libpyEM/qtgui/emselector.py: saving and previewing subsets in
	  selector

2009-02-20 09:45  zweig

	* sparx/bin/sxfactcoords.py: add calling for init_mpi_bdb

2009-02-20 00:41  woolford

	* libpyEM/qtgui/emselector.py, programs/e2classaverage.py: selector
	  automatically refreshes

2009-02-19 22:35  woolford

	* images/CMakeLists.txt, images/up_arrow.png,
	  images/macimages/CMakeLists.txt, images/macimages/up_arrow.png,
	  libEM/processor.h, libpyEM/qtgui/emselector.py,
	  programs/e2classaverage.py, programs/e2initialmodel.py:
	  maintenance

2009-02-19 21:18  ppenczek

	* sparx/libpy/utilities.py:  set range of thetat to (0,90), I do
	  not know who set it to 180, clear mistake

2009-02-19 13:44  zweig

	* sparx/libpy/reconstruction.py: add varsnr to recons_4nn

2009-02-19 10:30  ppenczek

	* sparx/libpy/: applications.py, morphology.py: simple corrections

2009-02-19 10:10  zyang

	* libEM/sparx/cuda/cuda_ccf.cu: Changes that takes consideration of
	  the size of texture.

2009-02-18 23:34  woolford

	* libEM/symmetry.h, libpyEM/EMAN2.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py: selector has save and delete

2009-02-18 10:10  zyang

	* libEM/processor.cpp: [no log message]

2009-02-18 10:03  zyang

	* libEM/: aligner.cpp, aligner.h, processor.cpp,
	  sparx/cuda/cuda_ccf.cu, sparx/cuda/cuda_ccf.h: Many changes to
	  the ccf code.

2009-02-17 22:32  woolford

	* libEM/processor.cpp, libEM/reconstructor.cpp,
	  libpyEM/qtgui/emimage.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emselector.py: browser handles particle stacks
	  correctly

2009-02-17 16:24  zweig

	* sparx/bin/: sxali2d_a.py, sxali2d_c.py, sxali2d_m.py: call for
	  init_mpi_bdb

2009-02-17 16:14  zweig

	* sparx/bin/: sxali3d_d.py, sxali3d_e.py, sxali3d_m.py: call for
	  init_mpi_bdb

2009-02-17 15:19  ppenczek

	* libEM/sparx/emdata_sparx.cpp: canceled ctf^3

2009-02-17 11:45  ppenczek

	* libEM/reconstructor.cpp: cleaning

2009-02-17 11:41  ppenczek

	* libEM/sparx/emdata_sparx.cpp: temporary change in onelinenn_ctf

2009-02-16 23:38  woolford

	* libEM/boxingtools.cpp, libEM/processor.cpp,
	  libpyEM/qtgui/emanimationutil.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emlights.py: mx has
	  sets

2009-02-16 17:47  jbert

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/libpyProcessor2.cpp: work on cuda kmeans

2009-02-16 16:51  zweig

	* sparx/libpy/applications.py: fix error of factcoords

2009-02-16 16:50  zweig

	* sparx/libpy/statistics.py: fix problem of shuffle

2009-02-16 11:14  ppenczek

	* sparx/libpy/: applications.py, statistics.py: Change the merging
	  method to ramp

2009-02-16 10:50  zyang

	* libEM/aligner.cpp, libpyEM/libpyAligner2.cpp: Add if
	  EMAN2_USING_CUDA

2009-02-16 10:39  zyang

	* libEM/: CMakeLists.txt, aligner.cpp, aligner.h,
	  cuda/CMakeLists.txt, sparx/cuda/CMakeLists.txt,
	  sparx/cuda/cuda_ccf.cu, sparx/cuda/cuda_ccf.h: Add cuda codes.

2009-02-16 10:33  zyang

	* libEM/: symmetry.h, cuda/cuda_emfft.h: Trival change

2009-02-16 10:30  zyang

	* libEM/: cuda/cuda_util.cu, cuda/cuda_util.h, emdata_cuda.h:
	  Trival change

2009-02-16 10:26  zyang

	* sparx/libpy/applications.py: Trival change

2009-02-16 10:22  zyang

	* libEM/: ctf.cpp, sparx/emdata_sparx.cpp: Fix all annoying
	  warnings.

2009-02-16 10:11  jbert

	* libpyEM/libpyUtils2.cpp: forgot to clean libpyUtils

2009-02-16 09:50  zweig

	* libpyEM/EMAN2db.py: in MPIMODE, do not attempt to make
	  directories

2009-02-16 09:46  jbert

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: clean my test on CUDA

2009-02-16 09:41  jbert

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/libpyProcessor2.cpp: add new class CUDA_kmeans()

2009-02-13 11:06  zweig

	* sparx/: libpy/applications.py, bin/sxpca.py: using newly
	  implemented parallel PCA

2009-02-13 11:05  zweig

	* sparx/libpy/statistics.py: add shuffle to pcanalyzer

2009-02-13 09:10  stevel

	* .pydevproject, programs/e2basis.py, programs/e2msa.py: Fix
	  masking in e2msa. Bugfix in e2basis.

2009-02-12 19:06  woolford

	* libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2display.py: mx work

2009-02-12 00:45  woolford

	* libpyEM/qtgui/: emimagemx.py: mx work

2009-02-12 00:33  woolford

	* libpyEM/qtgui/emimagemx.py: minor fixes to mx

2009-02-12 00:26  woolford

	* libpyEM/qtgui/emimagemx.py: minor fixes to mx

2009-02-11 22:31  woolford

	* libpyEM/qtgui/emimage.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimagemxrotor.py, programs/e2display.py: matrix
	  display work

2009-02-11 18:40  woolford

	* libpyEM/qtgui/: emimageutil.py: small alteration

2009-02-11 18:36  woolford

	* libEM/reconstructor_tools.h, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimageutil.py: viewer work

2009-02-11 14:03  zweig

	* sparx/bin/sxbootstrap_bigdisk.py: debug info

2009-02-11 14:01  zweig

	* libpyEM/libpyUtils2.cpp: add python binding for some blas/lapack
	  functions, used by pca

2009-02-11 14:00  zweig

	* sparx/: libpy/applications.py, libpy/statistics.py, bin/sxvar.py:
	  add pca to var_mpi()

2009-02-10 19:18  woolford

	* libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimagemx.py,
	  pyemtbx/boxertools.py: minor changes

2009-02-10 13:49  zweig

	* sparx/libpy/utilities.py: fix a typo

2009-02-10 13:19  woolford

	* libEM/reconstructor_tools.cpp, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2boxer.py,
	  programs/e2classaverage.py: various fixes

2009-02-10 10:26  zyang

	* libEM/aligner.cpp, libEM/aligner.h, libpyEM/libpyAligner2.cpp:
	  Fix some bugs

2009-02-10 09:55  ppenczek

	* sparx/bin/: sxssnr3d.py, sxrecons3d_f.py, sxrecons3d_n.py: patch
	  for mpi bdb

2009-02-10 09:51  ppenczek

	* sparx/bin/sxvar.py: patch for mpi bdb

2009-02-10 09:43  ppenczek

	* sparx/libpy/utilities.py: add function init_mpi_bdb

2009-02-10 00:04  woolford

	* images/macimages/ctf.png, libpyEM/EMAN2.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2classaverage.py, programs/e2ctf.py,
	  programs/e2eulerxplor.py, programs/e2workflow.py: workflow
	  updates

2009-02-09 23:07  stevel

	* libpyEM/: EMAN2.py, EMAN2db.py: Autoclosing for databases.
	  Largely untested...

2009-02-09 21:32  stevel

	* .pydevproject, libpyEM/EMAN2db.py: oops

2009-02-09 17:01  zyang

	* libEM/aligner.cpp, libEM/aligner.h, libpyEM/libpyAligner2.cpp:
	  Add a new class CUDA_Aligner()

2009-02-09 16:18  stevel

	* libpyEM/EMAN2db.py, programs/e2align3d.py,
	  programs/e2avg_ffts.py, programs/e2basis.py, programs/e2bdb.py:
	  Working on autoclose of databases

2009-02-09 15:57  jbert

	* libEM/sparx/util_sparx.cpp: change my test

2009-02-09 15:39  jbert

	* libEM/sparx/util_sparx.cpp: cuda more test

2009-02-09 11:15  ppenczek

	* sparx/test/BC.spi: [no log message]

2009-02-09 09:14  gtang

	* sparx/test/: EXAMPLES_FFT/fft-n-doc.txt, EXAMPLES_FFT/fft-n.tgz,
	  EXAMPLES_FFT/fft2.txt, EXAMPLES_FFT/fftsing-doc.txt,
	  EXAMPLES_FFT/fftsing.tgz, EXAMPLES_FFT/mixfft05.zip,
	  EXAMPLES_FFT/rsplitfft.c, FP/fint.f, FP/fint3.f, FP/four1a_fp.f:
	  remove  sparx/test/EMAMPLES_FFT and sparx/test/FP, request by
	  Pawel

2009-02-09 03:54  stevel

	* .pydevproject, libpyEM/EMAN2db.py: trivial

2009-02-09 03:42  stevel

	* .cdtproject, .pydevproject, .settings/org.eclipse.cdt.core.prefs,
	  libEM/emftgl.h, libpyEM/EMAN2.py, libpyEM/EMAN2db.py: BDB
	  overhaul. On demand opening, changed read-only behavior.

2009-02-07 22:02  zweig

	* sparx/bin/sxbootstrap_calcwgts.py: fix error for mpi version

2009-02-07 22:01  zweig

	* libEM/reconstructor.cpp: remove debug code

2009-02-06 20:43  woolford

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libEM/reconstructor_tools.cpp, libEM/reconstructor_tools.h,
	  programs/e2make3d.py: reconstructor work

2009-02-06 17:54  woolford

	* programs/e2make3d.py: minor fixes

2009-02-06 17:50  woolford

	* libEM/processor.cpp, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, programs/e2make3d.py: minor alterations

2009-02-06 16:48  zyang

	* sparx/libpy/utilities.py: Fix a strange and obscure bug.

2009-02-06 15:31  ppenczek

	* sparx/demo/5_mpi_bdb/run_through_example: [no log message]

2009-02-06 11:08  ppenczek

	* sparx/libpy/applications.py: mpi corrections

2009-02-06 11:01  ppenczek

	* sparx/libpy/applications.py: mpi corrections

2009-02-06 09:24  gtang

	* rt/pyem/test_processor.py: [no log message]

2009-02-06 08:39  ppenczek

	* sparx/libpy/applications.py: MPI fixes for bdb

2009-02-05 22:36  woolford

	* libpyEM/qtgui/emimage3dsym.py, programs/e2eulerxplor.py,
	  programs/e2initialmodel.py: minor fixes

2009-02-05 22:09  woolford

	* libpyEM/qtgui/emimage3dsym.py, programs/e2eulerxplor.py: minro
	  fixes

2009-02-05 22:01  woolford

	* images/: ctf.png, macimages/ctf.png: minor fixes

2009-02-05 21:59  woolford

	* images/CMakeLists.txt, images/eulerxplor.png, images/refine.png,
	  images/macimages/CMakeLists.txt, images/macimages/eulerxplor.png,
	  images/macimages/refine.png, libpyEM/qtgui/emimage3dsym.py,
	  programs/e2ctf.py, programs/e2eulerxplor.py,
	  programs/e2workflow.py: minor work

2009-02-05 18:00  zweig

	* sparx/libpy/applications.py: proper start of ali3d_d

2009-02-05 17:23  woolford

	* libpyEM/qtgui/emsprworkflow.py: minor

2009-02-05 14:28  zweig

	* sparx/test/bootstrap/: addnoise.py, addnoise2.py, alifilter.py,
	  apply_ctf_fix.py, apply_norm.py, average.py, bootstrap_genbuf.py,
	  bootstrap_nn.py, bootstrap_nnctf.py, bootstrap_nnctf_2.py,
	  btwl.py, ccc.py, change_norm.py, circumference.py, convert.py,
	  detail_ccc.py, extract_attr.py, filt_by_rops.py, fraccord.py,
	  fsc.py, histgram.py, incpca.py, incvar.py, incvar_only.py,
	  info.py, make_model.py, make_sigma.py, make_special_model.py,
	  mask.py, mask_by_vol.py, nn_ctf.py, pack.py, par_nn_ctf.py,
	  pca.py, pick_sphere.py, prj_eigvol.py, proj.py, proj_ctf.py,
	  renorm.py, resume_apply_norm.py, scale_by_eigval.py,
	  select_even.py, split.py, stat_even.py, subtract.py, test_mpi.py,
	  trans-applyctf.py, trans-noctf.py, trans.py, txtccc.py,
	  variance.py, varimax.py, zslice.py: remove

2009-02-05 12:47  ppenczek

	* sparx/: libpy/applications.py, bin/sxali3d_d.py: Fvariance

2009-02-05 12:43  zweig

	* sparx/test/mpi/: Numeric_macos.patch, documentation.h,
	  install_mpi.py, install_sparx.py, lib.py, mympimodule.c: remove
	  from CVS

2009-02-04 22:29  woolford

	* libEM/processor.cpp, libEM/processor.h, libEM/symmetry.cpp,
	  libEM/symmetry.h, libpyEM/libpyTransform2.cpp: general work

2009-02-04 15:27  gtang

	* libEM/reconstructor.cpp: fix for win32

2009-02-04 13:07  ppenczek

	* sparx/: bin/sxali3d_d.py, bin/sxali3d_e.py,
	  libpy/applications.py: some corrections of fourvar

2009-02-04 09:47  gtang

	* rt/pyem/test_processor.py: unit test update

2009-02-03 23:38  woolford

	* libEM/processor.cpp: minor fix

2009-02-03 23:26  woolford

	* libEM/averager.cpp, libEM/emdata_modular.cpp,
	  libEM/cuda/cuda_projector.cu, libEM/cuda/cuda_projector.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2classaverage.py,
	  programs/e2initialmodel.py: general fixes

2009-02-03 20:50  woolford

	* libEM/processor.cpp, libEM/processor.h, libpyEM/EMAN2.py: general
	  work

2009-02-03 15:09  zweig

	* libEM/reconstructor.cpp: make snr decrease with spartial
	  frequency

2009-02-03 14:23  jbert

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: cuda test

2009-02-03 14:08  jbert

	* libEM/sparx/00_README_ADDING_NEW_CODE: type mistake

2009-02-02 22:34  woolford

	* libEM/processor.h: minor fixes

2009-02-02 19:15  woolford

	* CMakeLists.txt, libEM/emdata.cpp, libEM/emdata_core.cpp,
	  libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libEM/emutil.cpp, libEM/emutil.h, libEM/processor.cpp,
	  libEM/reconstructor.cpp, libEM/cuda/cuda_emfft.cu,
	  libEM/cuda/cuda_util.cu, libEM/cuda/cuda_util.h,
	  utils/speedtest.cpp: cuda work

2009-02-02 15:10  zweig

	* sparx/libpy/applications.py: fix bug of factcoord_vol

2009-02-02 14:57  woolford

	* CMakeLists.txt, libEM/emfft.cpp, libEM/emfft.h: cuda work

2009-02-02 14:43  zweig

	* sparx/bin/sxfactcoords.py: add mpi

2009-02-02 14:42  woolford

	* libEM/: emdata_core.cpp, emdata_metadata.cpp,
	  cuda/CMakeLists.txt, cuda/cuda_emfft.cu: Cuda work

2009-02-02 14:27  woolford

	* libEM/: emdata_core.cpp, emdata_metadata.cpp,
	  cuda/CMakeLists.txt, cuda/cuda_emfft.cu, cuda/cuda_emfft.h,
	  cuda/cuda_projector.cu, cuda/cuda_util.cu, cuda/cuda_util.h,
	  sparx/cuda/CMakeLists.txt: Cuda work

2009-02-02 14:11  zweig

	* sparx/libpy/applications.py: improvement to factorial coordinates

2009-02-02 14:11  zweig

	* sparx/libpy/utilities.py: add function getvec: generate 3d vector
	  for given phi and theta

2009-02-02 11:46  ppenczek

	* sparx/bin/sxfactcoords.py: corrected sxfact

2009-02-02 11:40  ppenczek

	* sparx/bin/sxfactcoords.py: facts corrected

2009-02-02 11:02  ppenczek

	* sparx/: bin/sxfactcoords.py, libpy/applications.py: facts
	  corrected

2009-02-01 17:52  ppenczek

	* sparx/libpy/applications.py: corrected 3d facts

2009-02-01 17:46  ppenczek

	* sparx/libpy/: applications.py: corrected 3d facts

2009-02-01 15:55  ppenczek

	* sparx/libpy/applications.py: corrected 3d facts

2009-02-01 15:50  ppenczek

	* sparx/bin/sxfactcoords.py: corrected input

2009-02-01 15:46  ppenczek

	* sparx/bin/sxfactcoords.py: corrected input

2009-02-01 15:39  ppenczek

	* sparx/libpy/applications.py: corrected 3d factcoords

2009-01-30 19:58  woolford

	* CMakeLists.txt: minor fix

2009-01-30 19:55  woolford

	* CMakeLists.txt, libEM/emdata.cpp, libEM/emdata_cuda.h,
	  libEM/emdata_transform.cpp, libEM/emfft.cpp, libEM/emfft.h,
	  libEM/cuda/CMakeLists.txt, libEM/cuda/cuda_emfft.cu,
	  libEM/cuda/cuda_emfft.h, libEM/cuda/cuda_util.cu,
	  libEM/cuda/cuda_util.h: cuda work

2009-01-30 16:22  gtang

	* libEM/sparx/util_sparx.cpp: fix for win32

2009-01-30 15:04  woolford

	* libEM/processor.cpp: processor work

2009-01-29 22:19  woolford

	* libEM/: emdata.cpp, emdata.h, emdata_cuda.h, projector.cpp,
	  cuda/cuda_projector.cu, cuda/cuda_util.cu, cuda/cuda_util.h:
	  minor fixes

2009-01-29 21:02  woolford

	* libEM/cuda/: cuda_defs.h, cuda_projector.cu, cuda_util.cu: minor
	  changes

2009-01-29 20:59  woolford

	* libEM/: projector.cpp, projector.h, transform.cpp, transform.h,
	  cuda/cuda_projector.cu, cuda/cuda_projector.h, cuda/cuda_util.cu,
	  cuda/cuda_util.h: cuda work

2009-01-29 19:06  woolford

	* libEM/cuda/: cuda_projector.cu, cuda_util.cu, cuda_util.h: minor
	  fixes

2009-01-29 18:57  woolford

	* libEM/: transform.cpp, transform.h, cuda/cuda_projector.cu,
	  cuda/cuda_projector.h: minor fixes

2009-01-29 18:16  woolford

	* libEM/cuda/cuda_util.h: minor fixes

2009-01-29 18:06  woolford

	* libEM/emdata_modular.cpp, libEM/emdata_modular.h,
	  libpyEM/libpyEMData2.cpp: minor fixes

2009-01-29 18:00  woolford

	* .cproject, CMakeLists.txt, libEM/CMakeLists.txt,
	  libEM/emdata.cpp, libEM/emdata.h, libEM/emdata_cuda.h,
	  libEM/emdata_modular.cpp, libEM/emdata_modular.h,
	  libEM/cuda/CMakeLists.txt, libEM/cuda/CudaDependency.cmake,
	  libEM/cuda/FindCuda.cmake, libEM/cuda/cuda_projector.cu,
	  libEM/cuda/cuda_projector.h, libEM/cuda/cuda_util.cu,
	  libEM/cuda/cuda_util.h, libEM/cuda/empty.depend.in,
	  libEM/cuda/make2cmake.cmake, libEM/cuda/parse_cubin.cmake,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyTypeConverter2.cpp: cuda
	  stuff

2009-01-29 14:43  zstarosolski

	* sparx/libpy/statistics.py: test cvs

2009-01-29 14:26  jbert

	* sparx/libpy/statistics.py: Simple test to cvs

2009-01-29 14:02  zweig

	* libEM/reconstructor.cpp: debug bootstrap

2009-01-28 17:41  woolford

	* libEM/cuda/cuda_projector.cu: adding directory

2009-01-28 16:50  zweig

	* sparx/test/mpi/install_sparx.py: chdir to ROOT/src first

2009-01-28 12:35  zweig

	* sparx/test/mpi/install_mpi.py: fix errors

2009-01-28 12:34  zweig

	* sparx/test/mpi/: install_sparx.py, lib.py: initial version

2009-01-27 23:31  woolford

	* programs/e2proc3d.py: [no log message]

2009-01-27 19:52  ppenczek

	* sparx/test/FFT/: fmr_2.f, fmr_1.f, fftmcf.f, fmrs_1.f, fmrs_1d.f,
	  fmrs_2.f, fmrs_2dr.f, fmrs_2r.f, fmrs_3.f, fmrs_3r.f, fmrs_3dr.f:
	  [no log message]

2009-01-27 19:42  ppenczek

	* sparx/test/: 1MNF.pdb, 1MNF.pdb.gz: [no log message]

2009-01-27 19:39  ppenczek

	* sparx/demo/tteftu_with_tRNA.pdb.gz: short version of the pdb file

2009-01-27 19:38  ppenczek

	* sparx/demo/tteftu_with_tRNA.pdb: replaced by gzip

2009-01-27 17:05  woolford

	* libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emplot3d.py, programs/e2display.py: plot based
	  updates

2009-01-26 23:27  woolford

	* libpyEM/CMakeLists.txt, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emlights.py,
	  libpyEM/qtgui/emplot3d.py, programs/e2display.py: e2display takes
	  the plot3 argument

2009-01-26 22:22  woolford

	* libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emlights.py,
	  libpyEM/qtgui/emplot3d.py, programs/e2classaverage.py,
	  programs/e2ctf.py: working on plot3d

2009-01-26 17:13  woolford

	* libpyEM/qtgui/emplot3d.py: just adding a file

2009-01-26 02:16  stevel

	* programs/: e2basis.py, e2classifykmeans.py, e2refine2d.py: Fix
	  bug relating to flip vector in single file outputs of e2basis.
	  Also make e2refine2d properly ignore the mean vector.

2009-01-25 02:52  stevel

	* libEM/analyzer.cpp, libpyEM/qtgui/emplot2d.py,
	  programs/e2basis.py, programs/e2classifykmeans.py: New kmeans
	  reseeding. Plotting 1-D images as vectors.

2009-01-24 02:24  stevel

	* libEM/: analyzer.cpp, analyzer.h: Temporary fix for kmeans. More
	  work tomorrow

2009-01-23 19:35  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2ctf.py: workflow stuff

2009-01-23 19:03  woolford

	* libEM/analyzer.cpp: Anaylzer.cpp had a none in it - changed it to
	  a 0

2009-01-23 16:23  stevel

	* libEM/: analyzer.cpp, analyzer.h: kmenas work

2009-01-23 15:33  woolford

	* libpyEM/qtgui/emsprworkflow.py: workflow bugs

2009-01-23 02:06  stevel

	* libpyEM/wxgui/00_README, programs/e2basis.py, programs/e2msa.py,
	  programs/e2refine2d.py: Update to MSA so it subtracts the mean
	  first and derivative changes

2009-01-22 23:04  woolford

	* programs/e2make3d.py: minor fix

2009-01-22 21:49  woolford

	* libpyEM/qtgui/: emform.py, emsprworkflow.py: workflow fixes

2009-01-22 19:27  woolford

	* libpyEM/qtgui/emsprworkflow.py: trivial change

2009-01-22 19:24  woolford

	* libpyEM/qtgui/: emform.py, emsprworkflow.py: workflow fixes

2009-01-22 15:56  woolford

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/emdata.h,
	  libpyEM/EMAN2.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2refine2d.py: refine aligner works

2009-01-22 11:18  zweig

	* sparx/test/mpi/install_mpi.py: fix an error when generating cshrc

2009-01-22 09:40  zweig

	* sparx/test/mpi/install_mpi.py: fix a typo: e2dir should be e2lib

2009-01-22 08:18  stevel

	* programs/e2msa.py: trivial

2009-01-21 23:03  woolford

	* libEM/processor.cpp, libEM/processor.h, libpyEM/EMAN2.py,
	  libpyEM/qtgui/emdatastorage.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2classaverage.py,
	  programs/e2refine.py, programs/e2refine2d.py,
	  programs/e2workflow.py: workflow related updates

2009-01-21 11:42  zweig

	* sparx/test/mpi/install_mpi.py: fix a bug: environment PYTHONPATH
	  and LD_LIBRARY_PATH may not exist

2009-01-21 00:07  woolford

	* libEM/emutil.cpp, libEM/emutil.h, libEM/processor.cpp,
	  libEM/processor.h, libpyEM/EMAN2.py, libpyEM/libpyUtils2.cpp,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2refine.py,
	  programs/e2refine2d.py: workflow fixes

2009-01-19 18:17  ppenczek

	* sparx/libpy/applications.py: Fix two bugs.

2009-01-19 10:25  ppenczek

	* sparx/: bin/sxali3d_d.py, bin/sxali3d_e.py,
	  libpy/applications.py, libpy/reconstruction.py,
	  libpy/statistics.py, libpy/user_functions.py: changes to the
	  variance calculation, not tested

2009-01-17 09:41  gtang

	* rt/pyem/test_processor.py: unit test update

2009-01-16 21:01  woolford

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emplot2d.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2workflow.py, pyemtbx/boxertools.py: workflow based
	  work

2009-01-16 15:22  zyang

	* sparx/libpy/applications.py: [no log message]

2009-01-16 14:43  jbert

	* sparx/libpy/statistics.py: change back SA select with exp

2009-01-16 12:24  zyang

	* sparx/libpy/applications.py: Fix an important bug.

2009-01-15 22:30  woolford

	* libEM/averager.h, libpyEM/EMAN2.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2classaverage.py,
	  programs/e2eotest.py, programs/e2refine.py,
	  programs/e2workflow.py: resolution tools in workflow

2009-01-15 15:51  zyang

	* sparx/libpy/applications.py: Fix a bug

2009-01-15 13:23  zyang

	* sparx/libpy/applications.py: Trival change.

2009-01-15 10:42  zyang

	* sparx/libpy/applications.py: Trival change

2009-01-14 19:49  woolford

	* libpyEM/qtgui/emform.py, libpyEM/qtgui/emplot2d.py,
	  libpyEM/qtgui/emshape.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2eotest.py, programs/e2resolution.py,
	  programs/e2workflow.py: adding resolution tools to the workflow

2009-01-14 16:31  ppenczek

	* sparx/libpy/user_functions.py: spruce up fixed

2009-01-14 16:29  zyang

	* sparx/libpy/applications.py: Minor change

2009-01-14 15:16  zyang

	* sparx/libpy/applications.py: change

2009-01-14 13:31  zyang

	* sparx/libpy/applications.py: [no log message]

2009-01-13 22:03  woolford

	* libpyEM/qtgui/: emimage3d.py, emsprworkflow.py: workflow forms
	  remember mostly everything

2009-01-13 17:23  ppenczek

	* sparx/libpy/applications.py: added opendb in front of
	  get_all_attributes

2009-01-13 16:40  woolford

	* libpyEM/qtgui/emselector.py: solved a db problems in browser

2009-01-13 16:22  ppenczek

	* sparx/libpy/applications.py: changed order in ali3d_e_MPI

2009-01-13 16:05  ppenczek

	* sparx/libpy/applications.py: changed order in ali3d_e_MPI

2009-01-13 16:01  ppenczek

	* sparx/libpy/applications.py: changed order in ali3d_e_MPI

2009-01-13 15:54  ppenczek

	* sparx/libpy/applications.py: changed order in ali3d_e_MPI

2009-01-13 13:16  zyang

	* sparx/libpy/: alignment.py, applications.py: Some change to
	  ali2d_a_MPI()

2009-01-13 10:21  zyang

	* sparx/libpy/applications.py: Some change to ali2d_a_MPI()

2009-01-13 09:46  zyang

	* sparx/libpy/applications.py: Trival change.

2009-01-13 09:40  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2009-01-12 22:47  woolford

	* libpyEM/qtgui/: emform.py, emimage2d.py, emimage3d.py,
	  emimagemx.py, emsprworkflow.py: workflow forms remember params -
	  getting there

2009-01-12 19:50  ppenczek

	* sparx/libpy/applications.py: multi av ali2d_a corrected

2009-01-12 16:08  stevel

	* programs/e2classaverage.py: bugfix

2009-01-12 11:16  stevel

	* libEM/cmp.cpp, programs/e2refine2d.py: Fixed frc:nweight=1

2009-01-12 10:50  zyang

	* sparx/libpy/: alignment.py, applications.py: Abandon the idea of
	  multiple peaks and change code accordingly

2009-01-12 09:17  stevel

	* .cproject, .project, libEM/cmp.cpp, libEM/cmp.h,
	  programs/e2refine2d.py, programs/e2stacksort.py: Trying to fix
	  FRC comparator

2009-01-09 17:12  gtang

	* libEM/hdfio2.cpp: bug fix. Use 'E' (or 'O' for EMAN1Ctf) followed
	  by a digit to parse a string as EMAN2Ctf object. Previously use
	  only 'E' (or 'O' for EMAN1Ctf) causes crash of hdf reading.

2009-01-09 13:18  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2009-01-09 13:18  ppenczek

	* sparx/libpy/applications.py: corrected ali2d_a

2009-01-09 12:32  ppenczek

	* sparx/libpy/applications.py: corrected ali2d_a

2009-01-09 11:51  ppenczek

	* sparx/libpy/applications.py: corrected ali2d_a

2009-01-09 11:38  zyang

	* libEM/sparx/util_sparx.cpp, sparx/libpy/alignment.py: Change to
	  ali2d_ccf_list()

2009-01-09 11:25  zyang

	* libEM/sparx/util_sparx.cpp: [no log message]

2009-01-09 11:21  zyang

	* libEM/sparx/util_sparx.cpp, sparx/libpy/alignment.py: Some change
	  in ali2d_ccf_list()

2009-01-09 10:58  ppenczek

	* sparx/libpy/alignment.py: corrected ali2d_a

2009-01-09 10:49  ppenczek

	* sparx/libpy/alignment.py: corrected ali2d_a

2009-01-09 10:22  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, sparx/libpy/alignment.py: Add fucntion
	  ali2d_ccf_list()

2009-01-08 23:12  woolford

	* libpyEM/qtgui/emlights.py, programs/e2ptcltrace.py: minor fixes

2009-01-08 17:42  gtang

	* libpyEM/libpyTransform2.cpp, programs/e2ptcltrace.py: minor fix,
	  found by Yao

2009-01-08 13:36  ppenczek

	* sparx/libpy/: alignment.py, applications.py, utilities.py: timed
	  ali2d_a

2009-01-08 12:59  zyang

	* sparx/libpy/applications.py: Re-arrange the alignment order of
	  ali2d_c() and ali2d_c_MPI()

2009-01-08 12:58  zyang

	* sparx/libpy/alignment.py: Trival change

2009-01-07 19:25  woolford

	* libEM/emdata.cpp, libEM/symmetry.cpp, libEM/transform.cpp,
	  libEM/transform.h, libpyEM/libpyTransform2.cpp,
	  libpyEM/qtgui/emlights.py, libpyEM/qtgui/emsprworkflow.py:
	  general work

2009-01-07 12:22  ppenczek

	* sparx/libpy/: alignment.py, applications.py: correct ali2d_a

2009-01-07 11:49  ppenczek

	* sparx/libpy/applications.py: switch ali2d_a

2009-01-07 11:44  ppenczek

	* sparx/libpy/applications.py: switch ali2d_a

2009-01-07 10:51  ppenczek

	* sparx/libpy/: alignment.py, applications.py: corrections of
	  ali2d_a

2009-01-07 09:45  zyang

	* sparx/libpy/applications.py: Fix a trival bug

2009-01-06 17:43  gtang

	* libEM/: symmetry.cpp, transform.cpp: make the Symmetry3D name
	  case insensitive

2009-01-06 17:26  gtang

	* libEM/transform.cpp: make the Symmetry3D name case insensitive

2009-01-06 13:42  ppenczek

	* sparx/libpy/applications.py: [no log message]

2009-01-06 12:43  ppenczek

	* sparx/templates/import_SPIDER_refi.py: [no log message]

2009-01-05 10:06  zweig

	* sparx/: bin/sxbootstrap_bigdisk.py, libpy/reconstruction.py: add
	  snr to nonCTF reconstruction

2008-12-23 16:00  gtang

	* libEM/tifio.cpp: support 32 bit TIFF image I/O

2008-12-23 09:22  zweig

	* sparx/libpy/applications.py: fix a typo in pca

2008-12-23 09:21  zweig

	* sparx/bin/sxbootstrap_bigdisk.py: fix a bug

2008-12-22 14:07  ppenczek

	* sparx/libpy/applications.py: [no log message]

2008-12-22 09:55  ppenczek

	* sparx/libpy/applications.py: [no log message]

2008-12-22 09:13  ppenczek

	* sparx/libpy/applications.py: [no log message]

2008-12-22 09:07  ppenczek

	* sparx/libpy/applications.py: alia

2008-12-21 15:44  ppenczek

	* sparx/libpy/: alignment.py, applications.py: ali2d_a

2008-12-19 18:56  ppenczek

	* sparx/libpy/applications.py: [no log message]

2008-12-19 17:23  jbert

	* sparx/libpy/: applications.py, statistics.py: k-means fix some
	  bugs

2008-12-19 16:44  woolford

	* libpyEM/qtgui/: emimage3d.py, emlights.py: light work

2008-12-19 14:39  ppenczek

	* sparx/libpy/: alignment.py, applications.py: ali2d_a

2008-12-19 14:26  gtang

	* libEM/tifio.cpp: for 32 bit TIFF, not finish yet

2008-12-19 13:56  ppenczek

	* sparx/libpy/: alignment.py, applications.py, fundamentals.py,
	  projection.py, statistics.py: ali2d_a

2008-12-19 13:52  ppenczek

	* sparx/bin/sxali2d_a.py: [no log message]

2008-12-19 12:13  zweig

	* libEM/randnum.cpp: use urandom instead of random to reduce
	  initialization time

2008-12-19 00:13  woolford

	* libpyEM/qtgui/: emglobjects.py, emimage3d.py: light work

2008-12-18 22:29  woolford

	* libEM/transform.cpp, libEM/transform.h, libpyEM/CMakeLists.txt,
	  libpyEM/libpyTransform2.cpp, libpyEM/qtgui/em3Dhelloworld.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emlights.py,
	  libpyEM/qtgui/emselector.py: light work

2008-12-18 16:59  gtang

	* libEM/: emdata.h, emftgl.h, imageio.h, marchingcubes.h,
	  processor.h, reconstructor.h, symmetry.h, transform.h, vec3.h:
	  doxygen warning fix

2008-12-18 16:27  gtang

	* libEM/: util.h, vec3.h: doxygen warning fix

2008-12-18 15:06  gtang

	* doc/doxygen/Doxyfile: doxygen update

2008-12-18 15:04  gtang

	* libEM/: sparx/fundamentals.h, boxingtools.h: fix some warning
	  message

2008-12-18 14:05  ppenczek

	* sparx/libpy/utilities.py:  fixed storing of attributes in bdb

2008-12-18 12:48  jbert

	* sparx/: bin/sxk_means_stability.py, bin/sxplot_projs_distrib.py,
	  libpy/applications.py, libpy/development.py, libpy/projection.py,
	  libpy/statistics.py: Move k-means stab from dev to appli, and fix
	  bugs

2008-12-17 18:09  woolford

	* libpyEM/qtgui/: em3Dhelloworld.py, emglobjects.py,
	  emimage3diso.py, emlights.py: opengl tinkering

2008-12-17 17:00  jbert

	* sparx/: bin/sxk_means_stability.py, libpy/development.py: k-means
	  stability fix some bugs

2008-12-17 16:34  jbert

	* sparx/demo/5_mpi_bdb/run_through_example: Add k-means stability

2008-12-17 16:22  gtang

	* libEM/: sparx/emdata_sparx.h, emdata_metadata.h: fix some warning
	  message

2008-12-17 15:52  gtang

	* libEM/: cmp.cpp, processor.cpp, reconstructor.cpp, util.h: fix
	  some warning message

2008-12-17 15:27  woolford

	* libpyEM/qtgui/: em3Dhelloworld.py, emglobjects.py, emimage3d.py,
	  emimage3diso.py, emimage3dslice.py, emimage3dvol.py,
	  emsprworkflow.py: gl shading works again

2008-12-17 15:12  zweig

	* sparx/libpy/applications.py: sxvar: change output file name

2008-12-17 15:09  zweig

	* sparx/libpy/applications.py: fix pca: remove some arguments

2008-12-17 15:08  zweig

	* sparx/bin/sxpca.py: fix a typo

2008-12-17 15:08  zweig

	* sparx/bin/sxpca.py: remove some arguments

2008-12-17 15:02  gtang

	* CMakeLists.txt: fix the cmake warning for mkdoc

2008-12-17 14:09  zweig

	* sparx/bin/sxbootstrap_bigdisk.py: major revision: remove some
	  arguments

2008-12-17 08:53  woolford

	* libEM/emdata.cpp, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emsprworkflow.py:
	  fixes

2008-12-16 17:10  jbert

	* sparx/libpy/statistics.py: k-means groups minor change

2008-12-16 10:50  jbert

	* libEM/sparx/util_sparx.cpp: k-means helper clean code

2008-12-16 10:36  jbert

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: change helper for k-means

2008-12-16 10:35  jbert

	* sparx/: bin/sxk_means_stability.py, libpy/development.py,
	  libpy/statistics.py: k-means minor change

2008-12-16 00:03  stevel

	* programs/e2ctf2eman1.py: New program by Ben

2008-12-15 22:01  ppenczek

	* sparx/libpy/applications.py: ???

2008-12-15 18:17  jbert

	* sparx/libpy/statistics.py: k-means change SA

2008-12-15 16:58  gtang

	* libEM/aligner.cpp, libEM/averager.cpp, libEM/ctf.cpp,
	  libEM/ctf.h, libEM/processor.cpp, libEM/processor.h,
	  libEM/symmetry.cpp, libEM/sparx/util_sparx.cpp,
	  libpyEM/emdata_wrapitems.cpp, libpyEM/libpyAligner2.cpp,
	  libpyEM/libpyAnalyzer2.cpp, libpyEM/libpyAverager2.cpp,
	  libpyEM/libpyBoxingTools2.cpp, libpyEM/libpyCmp2.cpp,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyEMObject2.cpp,
	  libpyEM/libpyFundamentals2.cpp, libpyEM/libpyGeometry2.cpp,
	  libpyEM/libpyMarchingCubes2.cpp, libpyEM/libpyPointArray2.cpp,
	  libpyEM/libpyPolarData2.cpp, libpyEM/libpyProcessor2.cpp,
	  libpyEM/libpyProjector2.cpp, libpyEM/libpyReconstructor2.cpp,
	  libpyEM/libpyTransform2.cpp, libpyEM/libpyTypeConverter2.cpp,
	  libpyEM/libpyUtils2.cpp, libpyEM/typeconverter.cpp: fix for win32

2008-12-15 11:37  zweig

	* sparx/test/mpi/install_mpi.py: fix typo and add some notes

2008-12-14 20:07  ppenczek

	* sparx/libpy/: alignment.py, applications.py: [no log message]

2008-12-14 00:55  stevel

	* libEM/projector.cpp, libpyEM/qtgui/emselector.py,
	  programs/e2proc3d.py, programs/e2resolution.py: Various work in
	  preparation for final CTF correction.

2008-12-13 13:48  gtang

	* libEM/emdata.h, libpyEM/libpyEMData2.cpp, rt/pyem/test_emdata.py:
	  expose EMData::set_xyz_origin() to python, since e2proc3d.py has
	  an option to set image origin

2008-12-13 11:32  stevel

	* .pydevproject, libEM/processor.cpp, libEM/processor.h,
	  programs/e2ctf.py, programs/e2initialmodel.py,
	  programs/e2proc3d.py: Fixed automasking. Added to initialmodel

2008-12-13 11:14  jbert

	* sparx/libpy/: development.py, statistics.py: fix some minor bugs

2008-12-13 09:35  gtang

	* libEM/projector.cpp: "fix"  the segmentation fault for standard
	  projector.

2008-12-12 17:48  ppenczek

	* sparx/libpy/: alignment.py, applications.py, user_functions.py:
	  [no log message]

2008-12-12 16:32  zweig

	* sparx/test/mpi/install_mpi.py: remove debug code

2008-12-12 15:59  ppenczek

	* sparx/libpy/: alignment.py, applications.py, utilities.py:
	  ali2d_a broken

2008-12-12 15:48  zweig

	* libEM/sparx/util_sparx.cpp: re-implement the part which compress
	  the angle for voronoi diagram

2008-12-12 15:45  zweig

	* sparx/bin/sxbootstrap_calcwgts.py: add voronoi diagram

2008-12-12 14:40  zweig

	* sparx/test/mpi/install_mpi.py: write bashrc and cshrc

2008-12-12 14:28  ppenczek

	* sparx/test/bootstrap/Makefile: [no log message]

2008-12-12 14:16  zyang

	* sparx/libpy/user_functions.py: Add ref_ali2d_c()

2008-12-12 14:14  zyang

	* sparx/libpy/statistics.py: Fix two bugs

2008-12-12 13:33  zweig

	* sparx/test/mpi/install_mpi.py: change some notes

2008-12-12 12:38  ppenczek

	* sparx/: bin/sxali2d_a.py, bin/sxali2d_c.py, libpy/alignment.py,
	  libpy/applications.py, libpy/statistics.py,
	  libpy/user_functions.py:  corrections in ali2d

2008-12-12 11:35  woolford

	* libpyEM/: EMAN2.py, qtgui/emsprworkflow.py: mac knows memory -
	  using commands module

2008-12-12 10:52  jbert

	* sparx/libpy/statistics.py: minor change to pca

2008-12-12 10:43  jbert

	* sparx/libpy/statistics.py: minor change

2008-12-12 10:30  jbert

	* sparx/libpy/statistics.py: minor change

2008-12-12 10:08  jbert

	* sparx/libpy/statistics.py: k-means add info to logfile

2008-12-11 21:41  woolford

	* libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2boxer.py: general fixes

2008-12-11 20:55  zweig

	* sparx/test/mpi/Numeric_macos.patch: initial version

2008-12-11 20:54  zweig

	* sparx/test/mpi/install_mpi.py: fix error in python url

2008-12-11 20:39  zweig

	* sparx/test/mpi/install_mpi.py: fix a bug for not installing
	  Numeric

2008-12-11 20:35  zweig

	* sparx/test/mpi/install_mpi.py: remove debug code

2008-12-11 20:34  zweig

	* sparx/test/mpi/install_mpi.py: remove some notes

2008-12-11 20:33  zweig

	* sparx/test/mpi/install_mpi.py: major revision

2008-12-11 17:42  zweig

	* sparx/test/mpi/: documentation.h, install_mpi.py, mympimodule.c:
	  initial version

2008-12-11 15:13  zweig

	* sparx/libpy/: applications.py, statistics.py: fix memory issue
	  for inc_variance

2008-12-11 13:30  stevel

	* programs/e2initialmodel.py: added filter

2008-12-11 12:57  zweig

	* sparx/bin/sxvar.py: fix a typo

2008-12-11 12:41  zyang

	* sparx/templates/import_SPIDER_refi.py: Use new amp_contrast
	  convention

2008-12-11 12:39  zweig

	* sparx/bin/sxvar.py: initial version

2008-12-11 12:37  zweig

	* sparx/libpy/: applications.py, statistics.py: use double
	  precission for incremental variance calculation

2008-12-11 12:15  stevel

	* programs/: e2initialmodel.py, e2refine2d.py, e2workflow.py: new
	  option for initial model generation

2008-12-11 11:39  ppenczek

	* sparx/: libpy/utilities.py, templates/import_SPIDER_refi.py: new
	  template

2008-12-11 11:11  gtang

	* utils/speedtest.cpp: [no log message]

2008-12-10 15:52  ppenczek

	* sparx/bin/: sxbootstrap_bigdisk.py, sxdefvar.py: [no log message]

2008-12-10 14:03  ppenczek

	* sparx/demo/: 2_hdf_ctf/run_through_example,
	  3_bdb_ctf/run_through_example: remove exit for e2boxer

2008-12-10 08:00  ppenczek

	* libEM/sparx/util_sparx.cpp, sparx/libpy/applications.py: proj

2008-12-10 06:42  ppenczek

	* sparx/demo/: 0_hdf/run_through_example,
	  1_bdb/run_through_example, 2_hdf_ctf/run_through_example,
	  3_bdb_ctf/run_through_example, 4_mpi_hdf/run_through_example,
	  5_mpi_bdb/run_through_example, 6_mpi_hdf_ctf/run_through_example,
	  7_mpi_bdb_ctf/run_through_example:  changed proj to projection

2008-12-09 21:42  woolford

	* libpyEM/qtgui/emsprworkflow.py: small fix

2008-12-09 19:06  gtang

	* libEM/sparx/lapackblas.cpp: fix a bug for e2msa.py. 100% cpu
	  occupied but never finish.

2008-12-09 19:01  woolford

	* programs/e2workflow.py: workflow fixes

2008-12-09 18:54  woolford

	* programs/e2workflow.py: workflow fix

2008-12-09 18:48  woolford

	* programs/e2workflow.py: workflow fixes

2008-12-09 18:41  woolford

	* libpyEM/qtgui/emplot2d.py: plot fix

2008-12-09 18:32  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2desktop.py,
	  programs/e2eotest.py, programs/e2eulerxplor.py,
	  programs/e2history.py, programs/e2make3d.py,
	  programs/e2refine.py: more work

2008-12-09 17:20  stevel

	* programs/e2initialmodel.py: One more try. This seems to make good
	  initial models.

2008-12-09 17:05  zweig

	* sparx/bin/sxdefvar.py: update help message

2008-12-09 17:00  zweig

	* sparx/libpy/applications.py: remove argument nprj for defvar

2008-12-09 16:59  zweig

	* sparx/bin/sxdefvar.py: remove magic number

2008-12-09 16:45  ppenczek

	* sparx/bin/: sxbootstrap_bigdisk.py, sxbootstrap_smp.py:
	  xform.projection

2008-12-09 16:43  stevel

	* programs/e2initialmodel.py: Improved initial model generation.
	  Better similarity metric and saves more results.

2008-12-09 16:24  ppenczek

	* sparx/libpy/applications.py: [no log message]

2008-12-09 15:48  woolford

	* programs/e2eulerxplor.py: normto in eexplore

2008-12-09 15:39  stevel

	* programs/: e2proc3d.py, e2project3d.py, e2refine.py:
	  Normalization of projections

2008-12-09 15:08  stevel

	* libEM/emdata_metadata.cpp, programs/e2refine.py: oops

2008-12-09 14:42  stevel

	* programs/: e2make3d.py, e2proc2d.py, e2proc3d.py, e2refine.py:
	  Fixes to proc2d and proc3d filter->process

2008-12-09 14:39  woolford

	* libpyEM/qtgui/emimagemx.py, programs/e2eulerxplor.py: euler
	  explore fixes

2008-12-09 13:36  zyang

	* sparx/libpy/: applications.py, reconstruction.py, utilities.py:
	  Change xform.proj to xform.projection

2008-12-09 12:57  ppenczek

	* sparx/libpy/: global_def.py, projection.py, reconstruction.py:
	  [no log message]

2008-12-09 12:46  zweig

	* libEM/projector.cpp: remove setting or xform.projection from
	  PawelProjector

2008-12-09 12:15  woolford

	* libpyEM/qtgui/emsprworkflow.py: CTF workflow report update

2008-12-09 11:54  woolford

	* libEM/reconstructor.cpp, libpyEM/EMAN2.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2eotest.py: various

2008-12-09 11:31  woolford

	* libpyEM/qtgui/emform.py, programs/e2eotest.py: e2eotest

2008-12-09 11:29  zyang

	* sparx/libpy/alignment.py: Trival change

2008-12-09 11:16  woolford

	* programs/e2eotest.py: permissions

2008-12-09 11:15  woolford

	* programs/e2eotest.py: in the middle of something

2008-12-09 11:04  woolford

	* programs/: e2eotest.py, e2refine.py, e2resolution.py: fsc related
	  adaptations

2008-12-09 10:35  woolford

	* libEM/processor.cpp, libEM/processor.h, programs/e2eotest.py,
	  programs/e2workflow.py: eotest fix

2008-12-09 03:43  woolford

	* libpyEM/qtgui/emselector.py, libpyEM/qtgui/emshape.py,
	  programs/e2classaverage.py, programs/e2display.py,
	  programs/e2eotest.py, programs/e2refine.py: fsc additions

2008-12-09 00:59  woolford

	* programs/: e2eotest.py: check

2008-12-09 00:13  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2boxer.py,
	  programs/e2workflow.py, pyemtbx/boxertools.py: e2boxer related
	  fixes

2008-12-08 21:24  gtang

	* sparx/bin/: Stefan_ali3d_m.py, Stefan_sxali3d_d.py,
	  Stefan_sxali3d_m.py, bootstrap1.py, bootstrap2.py, bootstrap3.py:
	  removed these files, requested by Steve and Pawel.

2008-12-08 18:54  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2workflow.py: minor
	  fixes

2008-12-08 16:30  jbert

	* sparx/libpy/: applications.py, statistics.py: minor change, add
	  Hierarchical clustering

2008-12-08 16:29  jbert

	* sparx/bin/: sxhac_averages.py, sxhac_clustering.py: Hierarchical
	  clustering

2008-12-08 16:28  jbert

	* sparx/bin/sxplot_projs_distrib.py: plot proj dist

2008-12-08 16:22  gtang

	* programs/e2help.py: averagers for e2help.py help string

2008-12-08 16:05  gtang

	* programs/e2help.py: analyzers for e2help.py help string

2008-12-08 15:01  ppenczek

	* sparx/bin/sxbootstrap_bigdisk.py: [no log message]

2008-12-08 14:02  zweig

	* sparx/bin/sxbootstrap_bigdisk.py: minor change on calculate wgts

2008-12-08 12:50  stevel

	* libpyEM/qtgui/emplot2d.py, programs/e2ctf.py: Plot improvements

2008-12-08 12:18  woolford

	* programs/e2boxer.py: icon updates

2008-12-08 12:16  gtang

	* libEM/: reconstructor.cpp, reconstructor.h: fix for reconstructor
	  on windows

2008-12-08 12:16  gtang

	* programs/e2workflow.py: window title

2008-12-08 11:49  zyang

	* sparx/bin/: sxali2d_c.py, sxali2d_m.py: Trival change

2008-12-08 11:38  woolford

	* libEM/: reconstructor.cpp, reconstructor.h: windows fix

2008-12-08 10:49  zweig

	* sparx/bin/sxbootstrap_bigdisk.py: allow empty orientation while
	  calculation weights

2008-12-08 09:32  zweig

	* sparx/bin/sxbootstrap_calcwgts.py: initial version

2008-12-08 02:37  stevel

	* libpyEM/qtgui/emplot2d.py: plot2scr still broken

2008-12-08 01:49  stevel

	* libpyEM/qtgui/emplot2d.py: broke crosshairs...

2008-12-08 01:45  stevel

	* libpyEM/qtgui/: emplot2d.py, emshape.py: Log support for plots
	  (and labels)

2008-12-07 22:19  woolford

	* libpyEM/qtgui/emselector.py: png browsing fix for windows

2008-12-07 20:51  woolford

	* libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2ctf.py, programs/e2refine2d.py, pyemtbx/boxertools.py:
	  bug fixes

2008-12-07 17:28  ppenczek

	* sparx/bin/: sxali3d_d.py, sxali3d_e.py: updated documentation

2008-12-07 16:17  woolford

	* libpyEM/EMAN2.py: pid related issues

2008-12-05 16:50  gtang

	* libEM/emobject.cpp: fix for win32

2008-12-05 15:33  zyang

	* sparx/libpy/filter.py: Fix a bug

2008-12-05 14:44  woolford

	* libpyEM/qtgui/emsprworkflow.py: workflow updates

2008-12-05 14:41  jbert

	* sparx/libpy/statistics.py: minor change

2008-12-05 14:37  ppenczek

	* sparx/libpy/applications.py: [no log message]

2008-12-05 14:31  woolford

	* libpyEM/qtgui/emsprworkflow.py: quality added to init models
	  table

2008-12-05 14:11  ppenczek

	* sparx/libpy/applications.py: [no log message]

2008-12-05 14:09  woolford

	* programs/e2history.py: hitory fix

2008-12-05 14:07  woolford

	* programs/e2workflow.py: workflow fix

2008-12-05 13:38  woolford

	* libpyEM/qtgui/: emform.py, emsprworkflow.py: bug fix

2008-12-05 12:42  ppenczek

	* sparx/libpy/utilities.py: recv

2008-12-05 12:26  ppenczek

	* sparx/demo/: 1_bdb/run_through_example,
	  3_bdb_ctf/run_through_example, 5_mpi_bdb/run_through_example,
	  7_mpi_bdb_ctf/run_through_example:

	  moved tmp

2008-12-05 12:09  ppenczek

	* sparx/libpy/applications.py: recv

2008-12-05 12:06  woolford

	* programs/e2boxer.py: form fix

2008-12-05 11:53  woolford

	* libpyEM/qtgui/: emform.py, emsprworkflow.py: form fix

2008-12-05 11:07  woolford

	* libpyEM/qtgui/: emform.py, emsprworkflow.py: form fix

2008-12-05 10:49  ppenczek

	* sparx/libpy/: applications.py, utilities.py:	recv_attr_dict

2008-12-05 10:43  woolford

	* images/macimages/CMakeLists.txt, images/macimages/desktop.png,
	  images/macimages/single_image_3d.png,
	  images/macimages/swarm_icon.png, libpyEM/EMAN2.py,
	  programs/e2workflow.py, images/macimages/feather.png,
	  images/macimages/workflow.png: fixed icon issues

2008-12-05 10:09  ppenczek

	* sparx/libpy/: applications.py, utilities.py:	recv_attr_dict

2008-12-05 03:15  woolford

	* libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2boxer.py,
	  programs/e2history.py, pyemtbx/boxertools.py: final fixes

2008-12-05 01:59  woolford

	* programs/: e2au.py, e2eulerxplor.py, e2workflow.py: eulerxplor
	  added

2008-12-05 01:55  woolford

	* libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emsprworkflow.py, pyemtbx/boxertools.py: workflow
	  fixes

2008-12-05 01:38  stevel

	* programs/: e2classaverage.py, e2classify.py: Progress reporting
	  in more programs

2008-12-05 00:55  woolford

	* libpyEM/: EMAN2.py, qtgui/emform.py, qtgui/emsprworkflow.py:
	  workflow updates

2008-12-05 00:00  stevel

	* programs/: e2history.py, e2simmx.py: history fix and progress in
	  simmx

2008-12-04 22:54  woolford

	* libpyEM/qtgui/emsprworkflow.py: cd works in e2workflow in windows

2008-12-04 22:38  woolford

	* libpyEM/: EMAN2.py, qtgui/emselector.py: selector works on
	  windows

2008-12-04 21:40  woolford

	* images/CMakeLists.txt, images/macimages/Bag.png,
	  images/macimages/CMakeLists.txt, images/macimages/Close.png,
	  images/macimages/File.png, images/macimages/Folder.png,
	  images/macimages/FolderFiles.png, images/macimages/Key.png,
	  images/macimages/black_box.png, images/macimages/boxer_erase.png,
	  images/macimages/boxer_unerase.png,
	  images/macimages/boxhabanosclose.png,
	  images/macimages/database.png, images/macimages/desktop.png,
	  images/macimages/display_icon.png, images/macimages/eman.png,
	  images/macimages/eman_idea.png,
	  images/macimages/freeze_swirl.png,
	  images/macimages/green_boxes.png,
	  images/macimages/multiple_images.png, images/macimages/plot.png,
	  images/macimages/pp_boxer_icon.png,
	  images/macimages/single_image.png,
	  images/macimages/single_image_3d.png,
	  images/macimages/swarm_icon.png, images/macimages/white_box.png,
	  libpyEM/EMAN2.py, libpyEM/qtgui/emselector.py,
	  programs/e2boxer.py: darwin fixes

2008-12-04 20:04  woolford

	* images/CMakeLists.txt: images

2008-12-04 19:00  gtang

	* images/: Bag.png, Close.png, File.png, Folder.png,
	  FolderFiles.png, Key.png, black_box.png, boxer_erase.png,
	  boxer_unerase.png, boxhabanosclose.png, database.png,
	  desktop.png, display_icon.png, eman.png, eman_idea.png,
	  feather.png, freeze_swirl.png, green_boxes.png,
	  multiple_images.png, plot.png, pp_boxer_icon.png,
	  single_image.png, single_image_3d.png, swarm_icon.png,
	  white_box.png, workflow.png: new png file for win32

2008-12-04 18:34  gtang

	* libEM/sparx/util_sparx.cpp: fix for win32

2008-12-04 17:41  woolford

	* libpyEM/qtgui/: emform.py, emsprworkflow.py: platform dp issues

2008-12-04 15:52  ppenczek

	* sparx/libpy/: applications.py, utilities.py: desperate fix of
	  write_headers for bdb

2008-12-04 15:51  jbert

	* sparx/libpy/statistics.py: k-means minor change

2008-12-04 15:16  stevel

	* libpyEM/EMAN2.py: Minor fix

2008-12-04 14:59  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Add function get_slice()

2008-12-04 14:58  stevel

	* libpyEM/: EMAN2.py, EMAN2db.py: Fixed multiplatform bdb

2008-12-04 13:54  woolford

	* libpyEM/qtgui/: emborderdecoration.py, emselector.py: icon fixes

2008-12-04 13:44  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emborderdecoration.py,
	  libpyEM/qtgui/emform.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emplot2d.py,
	  libpyEM/qtgui/emselector.py, programs/e2boxer.py: platform dp
	  issues

2008-12-04 13:28  zweig

	* sparx/libpy/applications.py: add option to ccc

2008-12-04 12:26  woolford

	* libpyEM/qtgui/emimage2d.py, programs/e2boxer.py: tunnel error

2008-12-04 12:06  stevel

	* programs/e2initialmodel.py: oops

2008-12-04 11:57  woolford

	* libpyEM/qtgui/: emglobjects.py, emimage2d.py: tunneling list
	  error

2008-12-04 10:59  woolford

	* libpyEM/qtgui/emselector.py: .. fix

2008-12-04 03:29  woolford

	* libpyEM/qtgui/emfloatingwidgets.py, programs/e2au.py,
	  programs/e2boxer.py, programs/e2desktop.py: desktop work

2008-12-04 01:56  stevel

	* libpyEM/qtgui/emsprworkflow.py, programs/e2initialmodel.py,
	  programs/e2refine.py: Minor fixes

2008-12-04 01:07  woolford

	* libpyEM/qtgui/: emform.py, emsprworkflow.py: workflow update

2008-12-04 00:53  woolford

	* libpyEM/qtgui/emimage3dsym.py, programs/e2au.py: au updates

2008-12-04 00:25  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimage3dsym.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2au.py: sym viewer
	  updates

2008-12-03 23:48  stevel

	* programs/: e2initialmodel.py, e2proc3d.py: Cheamge initial model
	  saving.

2008-12-03 22:49  woolford

	* libpyEM/qtgui/emimage3dsym.py, programs/e2au.py,
	  programs/e2workflow.py: au work

2008-12-03 20:57  woolford

	* libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2au.py: au work

2008-12-03 18:39  woolford

	* libpyEM/qtgui/emsprworkflow.py: general fixes

2008-12-03 18:03  woolford

	* libpyEM/qtgui/emimage.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2display.py: display fixes

2008-12-03 17:24  woolford

	* libpyEM/qtgui/: emform.py, emsprworkflow.py: minitialmodel in
	  workflow

2008-12-03 16:25  woolford

	* libpyEM/qtgui/emimagemx.py, programs/e2boxer.py: general work

2008-12-03 16:14  stevel

	* programs/e2initialmodel.py: Final fixes

2008-12-03 15:06  woolford

	* libpyEM/qtgui/emimagemx.py: mx fix

2008-12-03 14:54  zweig

	* sparx/libpy/applications.py: fix error in ali3d_m

2008-12-03 14:52  woolford

	* libpyEM/qtgui/emplot2d.py, programs/e2ctf.py: glut fixes

2008-12-03 14:50  woolford

	* libpyEM/: EMAN2.py, qtgui/emimagemx.py, qtgui/emshape.py: glut
	  fix

2008-12-03 14:42  gtang

	* images/CMakeLists.txt: fix the wrong file name

2008-12-03 14:33  gtang

	* images/: CMakeLists.txt, desktop.ico, display.ico, eman.ico,
	  green_boxes.ico, workflow.ico: icon files for windows

2008-12-03 14:32  zweig

	* sparx/demo/: 0_hdf/run_through_example,
	  1_bdb/run_through_example, 2_hdf_ctf/run_through_example,
	  3_bdb_ctf/run_through_example, 4_mpi_hdf/run_through_example,
	  5_mpi_bdb/run_through_example, 6_mpi_hdf_ctf/run_through_example,
	  7_mpi_bdb_ctf/run_through_example: initial version

2008-12-03 14:31  woolford

	* libEM/reconstructor.h, libpyEM/qtgui/emimagemx.py,
	  programs/e2classaverage.py, programs/e2make3d.py: make3d updates

2008-12-03 14:23  zweig

	* sparx/demo/: SPARX_intro.pdf, generate_projections.py,
	  generate_refvols.py, tteftu_with_tRNA.pdb: initial version

2008-12-03 13:25  woolford

	* programs/e2make3d.py: temp work

2008-12-03 13:13  woolford

	* programs/e2make3d.py: temp work

2008-12-03 13:04  woolford

	* images/workflow.png, programs/e2history.py, programs/e2make3d.py:
	  temp work

2008-12-03 10:38  gtang

	* images/: desktop.ico, display.ico, eman.ico, green_boxes.ico,
	  workflow.ico: icon file for windows

2008-12-03 03:22  woolford

	* programs/: e2make3d.py, e2refine.py: one last thing

2008-12-03 03:10  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2classaverage.py,
	  programs/e2refine.py, programs/e2workflow.py: workflow updates

2008-12-03 02:16  stevel

	* programs/e2initialmodel.py: Initial model generator working
	  better.

2008-12-03 01:18  woolford

	* images/workflow.png, libpyEM/qtgui/emshape.py: ftgl fix

2008-12-03 00:51  woolford

	* images/desktop.png, images/workflow.png,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2history.py,
	  programs/e2workflow.py: selector improvements

2008-12-02 22:51  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2history.py,
	  programs/e2workflow.py: workflow has history

2008-12-02 22:35  woolford

	* programs/: e2history.py: history

2008-12-02 22:31  woolford

	* images/CMakeLists.txt, images/feather.png, libEM/emftgl.h,
	  programs/e2history.py: add history gui

2008-12-02 19:41  woolford

	* programs/e2display.py, libpyEM/qtgui/emselector.py: general fixes

2008-12-02 19:35  woolford

	* libpyEM/: EMAN2.py, qtgui/emborderdecoration.py,
	  qtgui/emfloatingwidgets.py, qtgui/emimagemx.py,
	  qtgui/emimagemxrotor.py, qtgui/emselector.py: general fixes

2008-12-02 18:24  gtang

	* libpyEM/EMAN2db.py: fix for win32

2008-12-02 18:04  zweig

	* sparx/libpy/applications.py: fix typo in ali3d_m

2008-12-02 17:56  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, sparx/libpy/alignment.py: Many change
	  relating to the new simulated annealing method

2008-12-02 17:48  zweig

	* sparx/libpy/applications.py: fix typo in ali3d_m

2008-12-02 17:42  woolford

	* libEM/util.cpp, libEM/util.h, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emshape.py: plot text works

2008-12-02 17:35  woolford

	* libpyEM/qtgui/emplot2d.py, libpyEM/qtgui/emshape.py,
	  programs/e2desktop.py: widget updates

2008-12-02 16:48  woolford

	* libEM/util.cpp, libEM/util.h, libpyEM/libpyUtils2.cpp,
	  libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3diso.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimageutil.py,
	  libpyEM/qtgui/emplot2d.py, programs/e2boxer.py,
	  programs/e2desktop.py, programs/e2workflow.py: widget updates

2008-12-02 16:17  stevel

	* programs/: e2ctf.py, e2initialmodel.py: Automatic B-factor
	  estimation

2008-12-02 16:07  woolford

	* libpyEM/qtgui/emplot2d.py: glut work

2008-12-02 15:55  woolford

	* libpyEM/: EMAN2.py, qtgui/emimagemx.py: mx fixes

2008-12-02 12:07  gtang

	* rt/pyem/test_processor.py: unit test update

2008-12-02 12:01  gtang

	* utils/speedtest.cpp: [no log message]

2008-12-02 03:10  stevel

	* programs/: e2initialmodel.py, e2make3d.py: initial model starting
	  to work

2008-12-02 02:50  woolford

	* libpyEM/qtgui/emimageutil.py, programs/e2boxer.py,
	  programs/e2desktop.py: updates

2008-12-02 00:29  woolford

	* libpyEM/qtgui/emimage2d.py, programs/e2boxer.py: erase works
	  again in boxer

2008-12-02 00:16  woolford

	* libEM/util.cpp, libEM/util.h, libpyEM/libpyUtils2.cpp,
	  libpyEM/qtgui/emform.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2history.py,
	  programs/e2refine2d.py, pyemtbx/boxertools.py: boxer efficiency
	  improvements:

2008-12-01 23:17  stevel

	* libpyEM/EMAN2db.py, programs/e2ctf.py,
	  programs/e2initialmodel.py, programs/e2simmx.py: Minor ctf fix

2008-12-01 21:48  woolford

	* libpyEM/qtgui/emsprworkflow.py: workflow work

2008-12-01 21:35  woolford

	* libpyEM/EMAN2db.py, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2boxer.py, programs/e2workflow.py,
	  pyemtbx/boxertools.py: workflow updates

2008-12-01 18:05  woolford

	* images/: single_image_3d.png, workflow.png: [no log message]

2008-12-01 18:03  zweig

	* sparx/: bin/sxdefvar.py, libpy/applications.py: non-mpi version
	  of defvar

2008-12-01 18:02  zyang

	* sparx/: bin/sxali2d_m.py, libpy/applications.py,
	  libpy/user_functions.py: Change to ali2d_m

2008-12-01 17:44  woolford

	* images/CMakeLists.txt, images/desktop.png, images/swarm_icon.png,
	  images/workflow.png, programs/e2workflow.py: icons

2008-12-01 17:42  zweig

	* libpyEM/libpyReconstructor2.cpp: add CTF option to newfile_store

2008-12-01 17:40  zweig

	* sparx/bin/sxbootstrap_bigdisk.py: non-mpi version of
	  sxbootstrap_bigdisk.py

2008-12-01 17:28  woolford

	* images/CMakeLists.txt, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emborderdecoration.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emimageutil.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2desktop.py, programs/e2workflow.py: desktop work

2008-12-01 17:23  zweig

	* libEM/: reconstructor.cpp, reconstructor.h: add CTF option to
	  newfile_store

2008-12-01 16:19  zweig

	* sparx/bin/sxbootstrap_bigdisk.py: fix error in calcwgts

2008-12-01 16:10  zweig

	* sparx/bin/sxbootstrap_bigdisk.py: new arguments

2008-12-01 11:23  zweig

	* programs/e2boxer.py: e2boxer gauss cmdline bugfix

2008-12-01 11:20  gtang

	* libEM/processor.h: fix for win32

2008-12-01 10:52  zweig

	* programs/e2boxer.py: e2boxer gauss gui & cmdline bugfixes

2008-12-01 10:04  zweig

	* programs/e2boxer.py: e2boxer gauss ctf determination

2008-12-01 06:01  zweig

	* programs/e2proc3d.py: e2proc3d bugfix

2008-12-01 03:04  stevel

	* programs/e2initialmodel.py: Initial model program. First version
	  almost done

2008-12-01 02:48  woolford

	* programs/e2workflow.py: workflow simple fix

2008-12-01 02:34  woolford

	* libpyEM/qtgui/emborderdecoration.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emimage3d.py,
	  programs/e2desktop.py, programs/e2workflow.py: desktop work

2008-12-01 02:07  stevel

	* libEM/processor.cpp, libEM/processor.h, libpyEM/EMAN2.py,
	  programs/e2initialmodel.py, programs/e2proc3d.py,
	  programs/e2refine2d.py: e2refine2d.py improvements (mostly
	  classkeep). Starting on initial model generation

2008-11-30 22:51  stevel

	* programs/: e2ctf.py, e2dumplog.py, e2history.py,
	  e2initialmodel.py, e2refine.py: Minor improvements. rename
	  e2dumplog.py e2history.py

2008-11-30 22:43  zweig

	* sparx/bin/sxali3d_m.py: fix option name

2008-11-30 22:42  zweig

	* sparx/libpy/applications.py: fix ali3d_m_MPI

2008-11-30 21:11  woolford

	* libEM/symmetry.cpp, libEM/symmetry.h, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2desktop.py: symmetry
	  fixes

2008-11-30 20:06  ppenczek

	* sparx/libpy/applications.py: [no log message]

2008-11-30 17:56  woolford

	* libpyEM/qtgui/emform.py, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2workflow.py: workflow
	  updates

2008-11-30 17:52  zweig

	* sparx/libpy/applications.py: fix errors in ali3d_m_MPI

2008-11-30 17:32  zweig

	* sparx/libpy/applications.py: remove pre-existing dirs for
	  bootstrap programs

2008-11-30 16:50  gtang

	* programs/e2help.py: minor fix to show modular class description

2008-11-30 16:34  woolford

	* libpyEM/: EMAN2.py, qtgui/emsprworkflow.py: workflow updates

2008-11-30 14:41  woolford

	* libpyEM/qtgui/emsprworkflow.py: other fixes

2008-11-30 14:34  woolford

	* libEM/reconstructor.cpp, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2classaverage.py, programs/e2make3d.py,
	  programs/e2refine.py, programs/e2refine2d.py,
	  programs/e2simmx.py, programs/e2workflow.py: workflow work :

2008-11-30 13:31  ppenczek

	* sparx/libpy/: applications.py, projection.py: [no log message]

2008-11-30 13:30  stevel

	* libpyEM/EMAN2db.py, programs/e2proc2d.py: oops

2008-11-30 13:05  jbert

	* sparx/libpy/statistics.py: k-means, minor change

2008-11-30 13:01  jbert

	* sparx/libpy/statistics.py: k-means remove print out

2008-11-30 12:58  jbert

	* sparx/: bin/sxfind_struct.py, libpy/applications.py,
	  libpy/projection.py: find_struct, change to new code again

2008-11-30 12:47  stevel

	* libpyEM/EMAN2db.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2bdb.py, programs/e2ctf.py: BDB fixes, normalization
	  added to e2ctf output

2008-11-30 10:10  zweig

	* programs/e2boxer.py, pyemtbx/boxertools.py,
	  sparx/libpy/morphology.py: e2boxer gauss cmdline

2008-11-30 09:34  ppenczek

	* sparx/: bin/sxali3d_e.py, libpy/applications.py: ali3d_e modified

2008-11-30 07:24  zweig

	* programs/e2boxer.py: e2boxer cmdline bugfix

2008-11-30 07:10  zweig

	* programs/e2boxer.py: e2boxer gauss cmdline

2008-11-30 00:29  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2classaverage.py,
	  programs/e2make3d.py, programs/e2project3d.py,
	  programs/e2refine.py: Refine is in the workflow

2008-11-29 22:13  woolford

	* libpyEM/qtgui/emsprworkflow.py: workflow work

2008-11-29 21:21  woolford

	* libpyEM/qtgui/emsprworkflow.py: workflow work

2008-11-29 19:27  woolford

	* libpyEM/qtgui/emform.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2ctf.py, programs/e2refine.py: workflow work

2008-11-29 18:28  ppenczek

	* sparx/libpy/: applications.py, user_functions.py: [no log
	  message]

2008-11-29 17:45  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2workflow.py: workflow
	  work

2008-11-29 17:13  zweig

	* sparx/: libpy/applications.py, bin/sxdefvar.py: use outdir for
	  defvar_mpi

2008-11-29 16:01  zweig

	* programs/e2boxer.py, pyemtbx/boxertools.py: e2boxer cmdline
	  bugfixes

2008-11-29 13:40  zweig

	* programs/e2boxer.py, pyemtbx/boxertools.py: e2boxer gauss cmdline

2008-11-29 12:52  zweig

	* sparx/: libpy/applications.py, libpy/reconstruction.py,
	  bin/sxbootstrap_genbuf.py, bin/sxbootstrap_run.py: add new
	  argument outdir to bootstrap_genbuf and bootstrap_run

2008-11-29 12:31  zweig

	* programs/e2boxer.py, pyemtbx/boxertools.py: e2boxer gauss cmdline

2008-11-29 00:58  woolford

	* libEM/analyzer.cpp, libpyEM/EMAN2.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2boxer.py,
	  programs/e2classifykmeans.py, programs/e2proc2d.py,
	  programs/e2refine.py, programs/e2refine2d.py,
	  programs/e2workflow.py: workflow work

2008-11-28 18:27  zyang

	* sparx/libpy/applications.py: Improvement to ali3d_d and
	  ali3d_d_MPI, fix bugs in ali2d_m and ali2d_m_MPI, add centering
	  method for ali2d_m, but not ali2d_m_MPI, which is quite
	  complicated

2008-11-28 17:10  jbert

	* sparx/libpy/development.py: fix some bugs in k-means stab MPI

2008-11-28 16:47  ppenczek

	* sparx/libpy/: filter.py, user_functions.py: minor changes

2008-11-28 12:36  zweig

	* libEM/sparx/emdata_sparx.cpp, programs/e2boxer.py: e2boxer batch
	  mode

2008-11-28 11:42  jbert

	* sparx/libpy/statistics.py: k-means minor change

2008-11-28 09:32  jbert

	* sparx/libpy/development.py: work on k-means stability MPI

2008-11-28 09:14  ppenczek

	* sparx/: bin/sxali3d_d.py, libpy/applications.py, libpy/filter.py,
	  libpy/user_functions.py: [no log message]

2008-11-28 06:49  zweig

	* programs/e2boxer.py, pyemtbx/boxertools.py,
	  sparx/libpy/morphology.py: bugfixes and ctf determination

2008-11-28 00:46  woolford

	* libpyEM/qtgui/emsprworkflow.py: workflow work

2008-11-28 00:29  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2workflow.py: workflow
	  work

2008-11-28 00:26  stevel

	* programs/: e2bdb.py, e2proc2d.py, e2refine2d.py: e2bdb
	  improvements (can take individual bdbs as parameters). apix fixes

2008-11-27 23:26  woolford

	* libpyEM/qtgui/emsprworkflow.py: workflow updates

2008-11-27 23:19  woolford

	* libpyEM/qtgui/emsprworkflow.py: workflow work

2008-11-27 22:27  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2workflow.py: workflow
	  work

2008-11-27 21:32  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2workflow.py: workflow
	  work

2008-11-27 18:02  stevel

	* libEM/ctf.h, libEM/emdata.h, libEM/emdata_metadata.cpp,
	  libEM/emdata_metadata.h, libEM/processor.cpp, programs/e2ctf.py,
	  programs/e2proc3d.py: Fixes for a/pix when shrinking. proc3d no
	  longer appends

2008-11-27 17:46  woolford

	* libpyEM/qtgui/: emform.py, emimage.py, emimage2d.py,
	  emimagemx.py, emsprworkflow.py: workflow work

2008-11-27 16:19  woolford

	* libpyEM/qtgui/emform.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2workflow.py: workflow work

2008-11-27 15:46  stevel

	* libpyEM/EMAN2db.py, programs/e2initialmodel.py: minor fixes

2008-11-27 13:57  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2boxer.py, programs/e2classaverage.py: workflow work

2008-11-27 13:16  gtang

	* libpyEM/EMAN2db.py: fix for windows

2008-11-27 12:47  stevel

	* programs/: e2basis.py, e2classifykmeans.py, e2proc3d.py,
	  e2refine2d.py: Misc debugging

2008-11-27 10:52  zweig

	* programs/e2boxer.py, pyemtbx/boxertools.py: e2boxer ctf
	  determination in gauss mode, ctf popup window

2008-11-27 01:00  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2boxer.py,
	  programs/e2classaverage.py, programs/e2ctf.py,
	  programs/e2workflow.py, pyemtbx/boxertools.py: workflow work

2008-11-26 21:31  woolford

	* programs/e2classaverage.py: class average final time

2008-11-26 21:29  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2classaverage.py,
	  pyemtbx/boxertools.py: widget work

2008-11-26 21:20  stevel

	* programs/e2classaverage.py: trivial

2008-11-26 21:09  stevel

	* .cproject, programs/e2basis.py, programs/e2classifykmeans.py:
	  debugging flip issues

2008-11-26 20:54  woolford

	* programs/e2classaverage.py: classaverage sillyness

2008-11-26 20:46  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2classaverage.py, programs/e2workflow.py: classaverage
	  fix for bootstrap

2008-11-26 19:42  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2classaverage.py, programs/e2ctf.py,
	  programs/e2workflow.py: refine updates

2008-11-26 19:35  stevel

	* libpyEM/EMAN2.py, programs/e2classaverage.py: Trying to fix class
	  averages to work with e2refine2d.py

2008-11-26 16:53  zyang

	* sparx/: bin/sxali3d_e.py, libpy/applications.py: Add average
	  centering method to ali3d_e and ali3d_e_MPI(), some other changes
	  also made.

2008-11-26 16:51  zyang

	* sparx/libpy/utilities.py: Fix a bug. (It's surpring the program
	  still runs with this bug!)

2008-11-26 15:42  zweig

	* programs/e2boxer.py, pyemtbx/boxertools.py: e2boxer ctf
	  determination in gaussian mode

2008-11-26 15:19  gtang

	* libEM/sparx/util_sparx.h: fix the link so it is clickable in
	  autogenerated html

2008-11-26 14:55  gtang

	* utils/speedtest.cpp: [no log message]

2008-11-26 14:54  zweig

	* sparx/libpy/utilities.py: fix typo

2008-11-26 14:53  zweig

	* sparx/: bin/sxbootstrap_genbuf.py, bin/sxrecons3d_f.py,
	  libpy/applications.py, libpy/reconstruction.py: add option ctf

2008-11-26 14:52  zweig

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libpyEM/libpyReconstructor2.cpp: add option ctf to file_store

2008-11-26 12:26  zweig

	* sparx/libpy/reconstruction.py, libEM/reconstructor.cpp: adopt to
	  recent CTF change

2008-11-26 12:26  zweig

	* sparx/libpy/morphology.py: fix sign of CTF

2008-11-26 01:06  stevel

	* libpyEM/EMAN2db.py: misc

2008-11-26 01:05  stevel

	* programs/e2refine2d.py: Making e2refine bdb aware

2008-11-26 00:31  woolford

	* libpyEM/qtgui/emimage3dsym.py, programs/e2au.py,
	  programs/e2classaverage.py: widget and refinement work

2008-11-25 23:16  stevel

	* programs/e2refine2d.py: Added path option

2008-11-25 23:16  stevel

	* libpyEM/EMAN2.py: New method numbered_path

2008-11-25 23:04  woolford

	* libpyEM/qtgui/emimage3dsym.py, programs/e2au.py,
	  programs/e2classaverage.py, programs/e2classify.py,
	  programs/e2simmx.py: refinement work

2008-11-25 22:06  woolford

	* libEM/util.cpp, libEM/util.h, libpyEM/EMAN2.py,
	  libpyEM/libpyUtils2.cpp, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emselector.py,
	  programs/e2au.py, programs/e2classaverage.py,
	  programs/e2classify.py, programs/e2project3d.py,
	  programs/e2simmx.py: widget work

2008-11-25 22:01  stevel

	* libpyEM/EMAN2db.py: Support EMData("bdb:dict",0,True)

2008-11-25 20:25  zyang

	* sparx/libpy/applications.py: Fix a bug

2008-11-25 20:21  zyang

	* sparx/libpy/: utilities.py, statistics.py: Fix a bug

2008-11-25 13:07  zyang

	* sparx/libpy/alignment.py: Fix some small bugs

2008-11-25 12:50  gtang

	* rt/pyem/test_processor.py: update the unit test for "math.log"
	  processor since Pawel updated this processor.

2008-11-25 12:42  gtang

	* libpyEM/qtgui/emborderdecoration.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emselector.py,
	  libEM/sparx/emdata_sparx.cpp, libpyEM/EMAN2.py,
	  libpyEM/EMAN2db.py, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimagemxrotor.py, libpyEM/qtgui/emimageutil.py,
	  libpyEM/qtgui/emplot2d.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2bdb.py, programs/e2boxer.py, programs/e2ctf.py,
	  programs/e2desktop.py, programs/e2refine2d.py,
	  programs/e2workflow.py, pyemtbx/boxertools.py,
	  sparx/libpy/__init__.py, sparx/libpy/alignment.py,
	  sparx/libpy/applications.py, sparx/libpy/sparx.py,
	  sparx/libpy/statistics.py, sparx/libpy/user_functions.py,
	  sparx/libpy/utilities.py, utils/speedtest.cpp: CVS disaster
	  recovery check in

2008-11-21 10:52  zweig

	* sparx/: bin/sxali3d_e.py, libpy/utilities.py: ??

2008-11-21 10:51  ppenczek

	* sparx/libpy/: applications.py, statistics.py: ssnr

2008-11-21 05:04  zweig

	* sparx/libpy/statistics.py: statistics.py bugfix

2008-11-21 02:30  stevel

	* libpyEM/EMAN2db.py, programs/e2bdb.py, programs/e2ctf.py: more
	  improvmemnts to preprocessing

2008-11-20 23:59  woolford

	* libpyEM/qtgui/emimagemxrotor.py: e2flick fix

2008-11-20 23:32  ppenczek

	* sparx/libpy/: applications.py, statistics.py:  ssnr

2008-11-20 22:50  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimageutil.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2boxer.py,
	  programs/e2desktop.py, programs/e2workflow.py: widget work

2008-11-20 22:32  stevel

	* libpyEM/EMAN2db.py, programs/e2proc2d.py, programs/e2proc3d.py:
	  fixes for proc2d/3d and db retry (which shouldn't be necessary)

2008-11-20 21:38  ppenczek

	* sparx/libpy/statistics.py: [no log message]

2008-11-20 21:19  ppenczek

	* sparx/libpy/reconstruction.py: restored /tmp

2008-11-20 20:13  zweig

	* sparx/libpy/statistics.py: varf3d

2008-11-20 17:56  zyang

	* sparx/libpy/alignment.py: Fix a minor bug

2008-11-20 17:54  zyang

	* sparx/libpy/: applications.py, utilities.py: Minor change

2008-11-20 17:43  zyang

	* sparx/libpy/: applications.py, utilities.py: More change on
	  centering method

2008-11-20 17:32  ppenczek

	* sparx/libpy/applications.py: [no log message]

2008-11-20 17:20  zyang

	* sparx/libpy/: applications.py, utilities.py: Change the centering
	  method to better run for MPI version

2008-11-20 17:06  zyang

	* sparx/libpy/reconstruction.py: Fix a simple bug

2008-11-20 17:04  zyang

	* sparx/libpy/alignment.py: Fix a bug in simulated annealing
	  program

2008-11-20 16:31  ppenczek

	* sparx/libpy/: applications.py, statistics.py, user_functions.py:
	  ssnr

2008-11-20 16:25  gtang

	* libpyEM/qtgui/emborderdecoration.py: minor fix

2008-11-20 15:53  gtang

	* libpyEM/qtgui/emsprworkflow.py: minor fix

2008-11-20 15:41  ppenczek

	* sparx/libpy/: applications.py, statistics.py: ssnr

2008-11-20 15:30  gtang

	* libpyEM/EMAN2db.py: getenv('USERNAME') on windows instead of
	  getenv('USER')

2008-11-20 14:22  ppenczek

	* sparx/libpy/applications.py: ssnr

2008-11-20 14:12  ppenczek

	* sparx/libpy/applications.py: ssnr

2008-11-20 12:58  zyang

	* sparx/libpy/user_functions.py: Delete printout

2008-11-20 11:54  zyang

	* sparx/libpy/: applications.py, morphology.py, utilities.py:
	  Change gen_ctf() to generate_ctf() to avoid confusion with
	  get_ctf()

2008-11-20 11:16  zyang

	* sparx/bin/sxali2d_a.py: Fix the bug correctly

2008-11-20 11:14  zyang

	* sparx/bin/sxali2d_a.py: Fix a bug

2008-11-20 11:11  zweig

	* sparx/libpy/user_functions.py: [no log message]

2008-11-20 11:08  zyang

	* sparx/bin/sxali3d_d.py: Change order of the parameters

2008-11-20 10:44  zyang

	* sparx/libpy/: applications.py, user_functions.py, utilities.py:
	  Fix some small bugs

2008-11-20 10:35  ppenczek

	* libEM/processor.h: math.log removed /max

2008-11-20 10:30  zweig

	* sparx/libpy/user_functions.py: [no log message]

2008-11-20 10:19  ppenczek

	* sparx/libpy/: sideprojectionmatch.py, sideprojectionmatchB.py,
	  stefan.py: temporarily removed

2008-11-20 09:59  zyang

	* sparx/libpy/reconstruction.py: Dump the temp file in the current
	  directory.

2008-11-20 09:26  zweig

	* sparx/libpy/user_functions.py: reworked user_functions.factory
	  allows dynamic loading of user functions

2008-11-20 05:54  zweig

	* sparx/libpy/: morphology.py, utilities.py: bugfixes in
	  morphology.py and utilities.py

2008-11-20 02:05  stevel

	* libpyEM/EMAN2db.py, programs/e2bdb.py: Work on bdb a bit, and
	  vstacks

2008-11-19 23:06  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2ctf.py, programs/e2desktop.py, programs/e2workflow.py,
	  pyemtbx/boxertools.py: workflow/desktop work

2008-11-19 22:30  stevel

	* libpyEM/EMAN2db.py: If opening bdb R/O and already open R/W, will
	  use that instead

2008-11-19 20:33  woolford

	* libpyEM/qtgui/emsprworkflow.py, pyemtbx/boxertools.py: workflow
	  work

2008-11-19 19:22  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2workflow.py,
	  pyemtbx/boxertools.py: workflow work

2008-11-19 17:47  jbert

	* sparx/: bin/sxk_means_stability.py, libpy/development.py:
	  packaging k-means stab MPI

2008-11-19 17:41  woolford

	* libpyEM/qtgui/emsprworkflow.py, pyemtbx/boxertools.py: workflow
	  work

2008-11-19 17:15  zyang

	* sparx/libpy/applications.py: Trival change

2008-11-19 16:22  ppenczek

	* sparx/libpy/fundamentals.py: [no log message]

2008-11-19 15:59  zyang

	* sparx/libpy/: applications.py, user_functions.py: Change relation
	  to new centering method, now works for MPI version too

2008-11-19 15:57  ppenczek

	* sparx/libpy/: applications.py, filter.py: ssnr

2008-11-19 15:19  woolford

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2boxer.py,
	  pyemtbx/boxertools.py: boxer fixes

2008-11-19 12:49  ppenczek

	* sparx/libpy/morphology.py: inserted gen_ctf

2008-11-19 12:35  ppenczek

	* sparx/bin/: sxrecons3d_n.py, sxssnr3d.py: [no log message]

2008-11-19 12:28  woolford

	* programs/e2boxer.py, pyemtbx/boxertools.py: valslider woops

2008-11-19 12:22  woolford

	* libpyEM/qtgui/emform.py, programs/e2boxer.py: boxer fixes

2008-11-19 11:18  irees

	* programs/e2boxer.py: minor fix to e2boxer

2008-11-19 11:04  zyang

	* sparx/libpy/applications.py: Fix a small bug

2008-11-19 10:11  zyang

	* sparx/: bin/sxali2d_a.py, bin/sxali2d_c.py, bin/sxali3d_d.py,
	  libpy/alignment.py, libpy/applications.py, libpy/development.py,
	  libpy/statistics.py, libpy/user_functions.py, libpy/utilities.py:
	  Many change relating to the new centering method

2008-11-19 09:39  gtang

	* rt/pyem/test_processor.py: unit test update

2008-11-19 02:09  stevel

	* libpyEM/EMAN2db.py, programs/e2bdb.py: Revert DB and add
	  data_path.

2008-11-18 23:21  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2boxer.py,
	  programs/e2workflow.py: workflow work

2008-11-18 20:55  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2ctf.py,
	  programs/e2workflow.py: widget work

2008-11-18 20:51  stevel

	* libEM/processor.cpp: oops

2008-11-18 18:44  stevel

	* examples/alignbystars.py, libEM/processor.h: remove non-working
	  processor

2008-11-18 17:42  jbert

	* sparx/libpy/projection.py: Cml read bdb file

2008-11-18 17:41  jbert

	* sparx/: bin/sxk_means.py, bin/sxk_means_groups.py,
	  bin/sxk_means_stability.py, libpy/applications.py,
	  libpy/development.py, libpy/statistics.py: packaging k-means
	  stability

2008-11-18 17:39  woolford

	* libpyEM/: EMAN2.py, qtgui/emform.py, qtgui/emsprworkflow.py:
	  workflow work

2008-11-18 17:26  ppenczek

	* sparx/libpy/applications.py: more ssnr

2008-11-18 17:12  gtang

	* rt/pyem/test_emdata.py: fix for the win32 platform

2008-11-18 16:59  ppenczek

	* sparx/libpy/: applications.py, projection.py: more ssnr

2008-11-18 16:16  zweig

	* sparx/libpy/applications.py: move function twoD_fine_search from
	  developement.py

2008-11-18 16:12  zweig

	* sparx/libpy/statistics.py: fix ctf related function

2008-11-18 16:12  zweig

	* sparx/libpy/applications.py: fix a typo

2008-11-18 15:32  zweig

	* sparx/libpy/utilities.py: add function get_ctf to create EMAN2Ctf
	  instance from parameters

2008-11-18 15:32  zweig

	* sparx/libpy/: statistics.py, development.py: fix multiple error
	  related to recent change on ctf

2008-11-18 15:30  zweig

	* sparx/libpy/applications.py: fix error in ali2d_c_MPI

2008-11-18 15:30  zweig

	* sparx/libpy/morphology.py: fix an error in ctf_2

2008-11-18 15:14  woolford

	* libpyEM/EMAN2.py: mac fix for num_cpus

2008-11-18 14:47  woolford

	* libpyEM/EMAN2.py: num_cpu() fixes

2008-11-18 14:36  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2desktop.py, programs/e2workflow.py:  num_cpus() added

2008-11-18 14:22  zyang

	* sparx/libpy/: alignment.py, applications.py, development.py:
	  Change ali2d_s to ali2d_single_iter

2008-11-18 13:33  zweig

	* programs/e2boxer.py: ctf estimation parameters added to gauss
	  dialog

2008-11-18 11:24  jbert

	* sparx/libpy/utilities.py: undo my previous change

2008-11-18 11:20  zyang

	* sparx/libpy/projection.py: Fix a bug

2008-11-18 11:08  ppenczek

	* sparx/libpy/: applications.py, projection.py: more ssnr

2008-11-18 11:06  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2ctf.py,
	  programs/e2workflow.py: workflow work

2008-11-18 11:02  ppenczek

	* libEM/reconstructor.cpp: ssnr

2008-11-18 11:01  ppenczek

	* sparx/libpy/: applications.py, projection.py, reconstruction.py:
	  more ssnr

2008-11-18 10:55  stevel

	* libpyEM/: EMAN2.py, EMAN2db.py: Fixed bugs in DB, interactive
	  plotting with plot()

2008-11-18 02:18  stevel

	* libpyEM/EMAN2db.py: dict_map support (incomplete)

2008-11-17 18:02  woolford

	* programs/e2simmx.py: simmx ralign updated

2008-11-17 17:54  woolford

	* libpyEM/qtgui/emimagemxrotor.py, programs/e2boxer.py,
	  programs/e2classaverage.py, programs/e2classify.py,
	  programs/e2ctf.py, programs/e2make3d.py, programs/e2refine.py,
	  programs/e2simmx.py, programs/e2workflow.py: general work

2008-11-17 17:54  gtang

	* rt/pyem/test_utils.py: fix for the win32 platform

2008-11-17 17:53  gtang

	* libEM/exception.h: suppress visual studio useless warning message

2008-11-17 16:59  ppenczek

	* sparx/libpy/global_def.py:  upgrade version

2008-11-17 16:57  ppenczek

	* libEM/reconstructor.cpp, sparx/bin/sxali3d_d.py,
	  sparx/bin/sxssnr3d.py, sparx/libpy/applications.py,
	  sparx/libpy/reconstruction.py, sparx/libpy/utilities.py: sprucing
	  up ssnr

2008-11-17 15:52  jbert

	* sparx/libpy/utilities.py: fix bug, write_header, bdb was never
	  close

2008-11-17 15:17  zweig

	* libEM/reconstructor.cpp: fix an error in calculating ctf

2008-11-17 13:38  zyang

	* sparx/: libpy/alignment.py, libpy/applications.py,
	  libpy/development.py, libpy/fundamentals.py, libpy/morphology.py,
	  libpy/projection.py, libpy/reconstruction.py,
	  libpy/statistics.py, libpy/stefan.py, libpy/utilities.py,
	  test/aaa.py, test/aab.py, test/aah.py, test/aat.py,
	  test/fourp.py, test/pdb_1.py, test/polar.py, test/sinh.py: Change
	  the python function naming convention to "word1_word2_word3".
	  Function affected are: dropImage(), getImage(), printCol(),
	  printRow(), printImage(), printSlice(), dumpRow(),
	  create_SpiderDoc(), dropSpiderDoc(), readSpiderDoc()

2008-11-17 10:51  zyang

	* sparx/libpy/alignment.py: Fix a bug

2008-11-17 09:48  zyang

	* sparx/libpy/: alignment.py, filter.py, statistics.py: Many change
	  related to simulated annealing

2008-11-17 02:30  stevel

	* libpyEM/EMAN2.py, libpyEM/EMAN2db.py, programs/e2ctf.py,
	  programs/e2proc2d.py: Work on CTF. Having BDB reliability
	  problems on arq2.

2008-11-16 23:58  stevel

	* libEM/ctf.cpp, libpyEM/libpyAligner2.cpp, programs/e2ctf.py: CTF
	  fixes

2008-11-16 21:08  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/embrowse.py,
	  libpyEM/qtgui/emform.py, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2boxer.py,
	  programs/e2ctf.py, programs/e2desktop.py, programs/e2display.py,
	  programs/e2workflow.py: workflow work

2008-11-16 17:47  zweig

	* sparx/libpy/: development.py, user_functions.py: corrections from
	  Berlin

2008-11-16 17:35  ppenczek

	* libpyEM/libpyUtils2.cpp: blocked peak_search for high dims

2008-11-16 17:31  ppenczek

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: blocked peak_search
	  for high dims

2008-11-16 17:16  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, util_sparx.cpp: blocked
	  peak_search for high dims

2008-11-16 13:54  ppenczek

	* libpyEM/libpyUtils2.cpp, libEM/sparx/emdata_sparx.cpp,
	  libEM/sparx/emdata_sparx.h, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h: vareas

2008-11-14 23:06  stevel

	* programs/e2ctf.py: Fixed minor bug

2008-11-14 22:51  stevel

	* libEM/: cmp.cpp, ctf.cpp, ctf.h: CTF work

2008-11-14 16:00  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2ctf.py: workflow work

2008-11-14 15:09  woolford

	* libpyEM/qtgui/emsprworkflow.py, programs/e2ctf.py: widget work

2008-11-14 12:07  stevel

	* libEM/: cmp.cpp, cmp.h, emobject.h: Comparitor changes for new
	  CTF scheme.

2008-11-14 11:45  zyang

	* sparx/libpy/applications.py: Change the printout to make it look
	  better

2008-11-14 09:55  zweig

	* sparx/bin/sxbootstrap_bigdisk.py: adopt to new header

2008-11-14 09:46  zweig

	* sparx/bin/sxbootstrap_bigdisk.py: initial version

2008-11-14 09:38  zweig

	* sparx/bin/sxbootstrap_smp.py: adopt to new transform header

2008-11-13 23:30  woolford

	* libEM/processor.cpp, libpyEM/EMAN2.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2ctf.py, programs/e2workflow.py: workflow and other
	  work

2008-11-13 22:19  stevel

	* programs/e2bdb.py: another minor fix

2008-11-13 22:18  stevel

	* programs/e2bdb.py: minor fix

2008-11-13 22:15  stevel

	* programs/e2bdb.py: New 'ls' like function for bdb

2008-11-13 17:41  jbert

	* sparx/libpy/development.py: work on stability packaging

2008-11-13 17:40  jbert

	* sparx/libpy/statistics.py: k-means minor change

2008-11-13 17:33  gtang

	* rt/pyem/test_processor.py: [no log message]

2008-11-13 17:24  gtang

	* rt/pyem/test_emdata.py: unit test update

2008-11-13 16:27  zyang

	* sparx/libpy/applications.py: Fix another bug

2008-11-13 16:23  zyang

	* sparx/libpy/applications.py: Fix a bug

2008-11-13 16:18  stevel

	* libpyEM/EMAN2.py, libpyEM/EMAN2db.py, programs/e2bdb.py: MANY
	  database fixes.

2008-11-13 16:17  zyang

	* sparx/libpy/applications.py: Fix a trival bug

2008-11-13 16:02  zweig

	* sparx/bin/sxali3d_em.py: add two parameters: nassign and nrefine

2008-11-13 15:59  zweig

	* sparx/libpy/applications.py: changes on ali3d_m_MPI and
	  ali3d_em_MPI

2008-11-13 15:25  zyang

	* sparx/libpy/: applications.py, development.py: Many, many changes
	  to ali3d_e() and ali3d_e_MPI() to make it updated. Also delete
	  tons of useless codes.

2008-11-13 14:42  zweig

	* libEM/reconstructor.cpp: adopt to new ctf prototype

2008-11-13 11:04  zyang

	* sparx/libpy/utilities.py: Fix a bug

2008-11-13 11:00  zyang

	* sparx/libpy/utilities.py: Change formula for ctf

2008-11-13 10:36  gtang

	* rt/pyem/test_processor.py: [no log message]

2008-11-12 22:43  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emselector.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2boxer.py, programs/e2workflow.py,
	  pyemtbx/boxertools.py: workflow based work

2008-11-12 20:36  gtang

	* utils/speedtest.cpp: [no log message]

2008-11-12 20:30  gtang

	* rt/pyem/: test_aligner.py, test_averager.py, test_cmp.py,
	  test_emdata.py, test_imageio.py, test_misc.py, test_processor.py,
	  test_reconstructor.py, test_transform.py, test_utils.py,
	  test_vec.py: unit test update

2008-11-12 18:09  jbert

	* sparx/bin/sxk_means_stability.py: parser for k-means stability

2008-11-12 18:06  jbert

	* sparx/libpy/development.py: change ctf, works on stability
	  packaging

2008-11-12 17:43  zyang

	* sparx/libpy/: applications.py, utilities.py: Make ctf a part of
	  header operation

2008-11-12 17:38  gtang

	* rt/pyem/test_typeconverter.py: unit test update

2008-11-12 17:35  gtang

	* rt/pyem/: test_emdata.py, test_imageio.py, test_processor.py,
	  test_reconstructor.py, test_transform.py: exception update

2008-11-12 16:35  zyang

	* sparx/libpy/filter.py: Fix a small bug

2008-11-12 16:21  zyang

	* sparx/libpy/applications.py: Many small changes due to new CTF

2008-11-12 16:20  zweig

	* sparx/libpy/utilities.py: add function to convert old CTF header
	  to new format

2008-11-12 15:13  zyang

	* sparx/libpy/alignment.py: Use new CTF object.

2008-11-12 15:08  zweig

	* sparx/libpy/morphology.py: using EMAN2Ctf

2008-11-12 15:05  zweig

	* sparx/libpy/applications.py: adopt to new prototype of ctf_img
	  and filt_ctf

2008-11-12 14:44  gtang

	* rt/pyem/test_reconstructor.py: [no log message]

2008-11-12 14:34  gtang

	* rt/pyem/test_emdata.py: unit test update

2008-11-12 14:29  gtang

	* rt/pyem/: test_emdata.py, test_imageio.py, test_transform.py:
	  unit test update

2008-11-12 14:16  zyang

	* sparx/libpy/applications.py: Made some change to ali3d_e() and
	  ali3d_e_MPI()

2008-11-12 11:56  zweig

	* sparx/libpy/statistics.py: adopt new prototype of ctf_img and
	  filt_ctf

2008-11-12 11:55  zweig

	* sparx/libpy/morphology.py: use EMAN2Ctf for ctf_img

2008-11-12 11:54  zweig

	* sparx/libpy/filter.py: use EMAN2Ctf

2008-11-12 11:32  zweig

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: change to use
	  EMAN2Ctf

2008-11-12 11:31  zweig

	* libEM/sparx/util_sparx.cpp: change the formula to EMAN2Ctf

2008-11-12 01:36  stevel

	* programs/e2ctf.py: Fixed problem with processing EMAN1 files with
	  CTF info already in the header

2008-11-11 22:16  woolford

	* libpyEM/CMakeLists.txt, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emform.py, libpyEM/qtgui/emselector.py,
	  libpyEM/qtgui/emsprworkflow.py, programs/e2display.py,
	  programs/e2workflow.py, pyemtbx/boxertools.py: workflow and
	  widget work

2008-11-11 17:50  jbert

	* libEM/transform.cpp, libEM/transform.h,
	  libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libEM/sparx/util_sparx.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyTransform2.cpp: change Transform3D to Transform

2008-11-11 17:43  jbert

	* sparx/: bin/sxfind_struct.py, libpy/development.py,
	  libpy/fundamentals.py, libpy/projection.py, libpy/utilities.py:
	  change Transform3D to Transform, clean code, works on k-means
	  stab

2008-11-11 17:38  gtang

	* libEM/ctf.cpp: fix EMAN2Ctf::from_vector()

2008-11-11 17:09  gtang

	* libEM/ctf.h, libpyEM/libpyAligner2.cpp: EMAN1Ctf/EMAN2Ctf
	  unpickling support.

2008-11-11 15:44  gtang

	* libpyEM/: emdata_pickle.h, libpyAligner2.cpp: EMAN1Ctf/EMAN2Ctf
	  pickling support.

2008-11-11 15:15  zyang

	* sparx/libpy/alignment.py: Change simulated annealing a little bit

2008-11-11 15:02  zyang

	* sparx/libpy/development.py: Trival change

2008-11-11 14:55  zyang

	* sparx/libpy/applications.py: Change ali3d_e() and ali3d_e_MPI()
	  from comparing images in real space to using ccf and comparing
	  image in Fourier space.

2008-11-11 14:02  stevel

	* libpyEM/EMAN2db.py, programs/e2ctf.py: Get with defaults

2008-11-11 14:01  gtang

	* libpyEM/libpyTypeConverter2.cpp: EMAN2Ctf type conversion

2008-11-11 13:32  gtang

	* utils/speedtest.cpp: score update

2008-11-11 13:27  zyang

	* sparx/libpy/applications.py: Trival change

2008-11-11 12:28  zyang

	* sparx/libpy/applications.py: Fix a minor bug in ali3d_e()

2008-11-11 10:10  ppenczek

	* sparx/libpy/applications.py: minor correction

2008-11-11 02:25  stevel

	* programs/e2ctf.py: Envelope function optimization in e2ctf.

2008-11-10 23:45  woolford

	* libpyEM/qtgui/emsprworkflow.py: workflow work

2008-11-10 23:30  woolford

	* libpyEM/qtgui/: emform.py, emsprworkflow.py: workflow work

2008-11-10 19:30  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emsprworkflow.py,
	  programs/e2boxer.py, pyemtbx/boxertools.py: form work

2008-11-10 17:13  gtang

	* libpyEM/libpyTypeConverter2.cpp: fix for the win32 platform

2008-11-10 16:07  stevel

	* libpyEM/EMAN2.py, libpyEM/EMAN2db.py, programs/e2ctf.py: Added
	  db_check_dict and db_list_dicts

2008-11-10 15:08  gtang

	* libEM/: mrcio.cpp, util.cpp, util.h: change the phase origin to
	  0,ny/2 when writing MRC file, to be compliance with TNF reader
	  and EMAN1

2008-11-10 15:06  woolford

	* libpyEM/qtgui/emform.py: form work

2008-11-10 15:02  woolford

	* libpyEM/qtgui/emform.py: form work

2008-11-10 14:46  zweig

	* libEM/: reconstructor.cpp, reconstructor.h: file store work with
	  new transform class

2008-11-10 14:38  zweig

	* sparx/bin/sxdefvar.py:  remove option nprj

2008-11-10 14:37  zweig

	* sparx/bin/sxbootstrap_run.py: add option CTF

2008-11-10 14:36  zweig

	* sparx/bin/sxali3d_em.py: add MPI to option

2008-11-10 14:32  zyang

	* sparx/libpy/applications.py: Fix a bug

2008-11-10 14:30  zyang

	* sparx/libpy/alignment.py: Many change to new Simulated Annealing
	  routines

2008-11-10 14:28  zyang

	* sparx/libpy/development.py: Trival change

2008-11-10 14:10  zweig

	* sparx/libpy/utilities.py: minor modification

2008-11-10 14:09  zweig

	* sparx/libpy/: applications.py, reconstruction.py: fix problem of
	  bootstrap_run and bootstrap_genbuf

2008-11-10 09:46  gtang

	* rt/emdata/test_emobject.cpp: [no log message]

2008-11-10 02:38  stevel

	* libEM/averager.cpp, libEM/ctf.cpp, libEM/ctf.h,
	  libEM/processor.cpp, libpyEM/libpyAligner2.cpp,
	  programs/e2ctf.py: ctf work

2008-11-09 22:23  woolford

	* libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emform.py,
	  libpyEM/qtgui/emselector.py, programs/e2boxer.py,
	  programs/e2desktop.py: desktop work

2008-11-09 15:10  gtang

	* rt/pyem/test_imageio.py: unit test update

2008-11-09 15:02  gtang

	* libEM/testutil.cpp, libEM/testutil.h, libpyEM/libpyUtils2.cpp,
	  rt/pyem/test_typeconverter.py: unit test update for Ctf,
	  Transform

2008-11-09 12:50  ppenczek

	* sparx/libpy/: alignment.py, applications.py, development.py,
	  sparx.py: comment for Yang

2008-11-09 12:10  gtang

	* utils/speedtest.cpp: [no log message]

2008-11-09 12:06  gtang

	* utils/speedtest.cpp: [no log message]

2008-11-08 22:39  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emform.py,
	  programs/e2boxer.py, programs/e2desktop.py,
	  pyemtbx/boxertools.py: form,desktop,and boxer work

2008-11-07 19:50  woolford

	* libpyEM/CMakeLists.txt, libpyEM/qtgui/emform.py,
	  programs/e2boxer.py: widget work

2008-11-07 18:53  woolford

	* libpyEM/qtgui/emform.py: forms work

2008-11-07 18:50  woolford

	* libpyEM/qtgui/emform.py: forms work

2008-11-07 18:46  woolford

	* libpyEM/qtgui/emform.py: forms work

2008-11-07 18:38  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emdatastorage.py,
	  libpyEM/qtgui/emform.py, libpyEM/qtgui/emselector.py,
	  programs/e2boxer.py: adding form stuff

2008-11-07 17:40  gtang

	* libpyEM/: typeconverter.cpp, typeconverter.h: the numpy2em and
	  em2numpy call new numpy C-API function to get rid the dprecated
	  call warning message.

2008-11-07 16:36  stevel

	* libpyEM/qtgui/emplot2d.py, programs/e2ctf.py: CTF working. GUI
	  works but incomplete.

2008-11-07 15:05  gtang

	* utils/speedtest.cpp: speed score update

2008-11-07 01:19  stevel

	* libpyEM/qtgui/valslider.py, programs/e2ctf.py: CTF GUI.

2008-11-06 19:13  woolford

	* libpyEM/qtgui/emselector.py, programs/e2display.py: browser work

2008-11-06 19:08  woolford

	* libpyEM/qtgui/: embrowse.py, emimage.py, emimage3d.py,
	  emplot2d.py, emselector.py: browser work

2008-11-06 17:53  woolford

	* images/CMakeLists.txt, images/plot.png,
	  libpyEM/qtgui/emapplication.py, libpyEM/qtgui/embrowse.py,
	  libpyEM/qtgui/emimage.py, libpyEM/qtgui/emplot2d.py,
	  libpyEM/qtgui/emselector.py: browser work

2008-11-06 17:28  zweig

	* sparx/libpy/applications.py: change on ali3d_em

2008-11-06 17:12  gtang

	* libpyEM/: libpyTypeConverter2.cpp, typeconverter.cpp,
	  typeconverter.h: Ctf type conversion for C++/Python

2008-11-06 17:09  gtang

	* libEM/imagicio.cpp: ctf I/O from imagic file(EMAN1)

2008-11-06 16:28  zyang

	* sparx/libpy/alignment.py: New simulated annealing routines.

2008-11-06 16:27  zyang

	* sparx/libpy/statistics.py: Change at add_ave_varf()

2008-11-06 16:26  zyang

	* sparx/libpy/applications.py: Some trival changes.

2008-11-06 16:13  stevel

	* programs/e2ctf.py: CTF fitting working well on many sets. Need to
	  do the GUI.

2008-11-06 15:17  woolford

	* images/CMakeLists.txt, images/display_icon.png,
	  libpyEM/qtgui/emapplication.py, libpyEM/qtgui/embrowse.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emselector.py: browser
	  updates

2008-11-06 09:10  zweig

	* sparx/libpy/: applications.py, morphology.py: printout corrected
	  in ali3d_e

2008-11-06 01:41  ppenczek

	* sparx/libpy/: fundamentals.py, morphology.py: [no log message]

2008-11-06 01:10  stevel

	* libEM/ctf.cpp, programs/e2ctf.py: Ctf working pretty well. Need
	  GUI still

2008-11-05 22:44  woolford

	* images/CMakeLists.txt, images/multiple_images.png,
	  images/single_image.png, images/single_image_3d.png,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emselector.py: widget work

2008-11-05 16:53  jbert

	* sparx/libpy/statistics.py: k-means minor bug

2008-11-05 16:33  stevel

	* libEM/ctf.cpp, libEM/ctf.h, libpyEM/libpyAligner2.cpp,
	  programs/e2ctf.py: Wiener filtration working !!!

2008-11-05 14:42  ppenczek

	* sparx/libpy/applications.py: ali3d_m_mpi

2008-11-05 14:19  woolford

	* libpyEM/qtgui/: emplot2d.py: plot fixes

2008-11-05 14:09  woolford

	* libpyEM/qtgui/emplot2d.py: plot fixes

2008-11-05 12:44  ppenczek

	* sparx/libpy/morphology.py: [no log message]

2008-11-05 11:41  woolford

	* libpyEM/qtgui/emselector.py, programs/e2display.py: widget work

2008-11-05 11:32  stevel

	* libEM/ctf.cpp, libpyEM/EMAN2db.py: Add item_type

2008-11-05 10:10  gtang

	* libEM/aligner.cpp: fix for the win32 platform

2008-11-05 06:37  zweig

	* sparx/libpy/applications.py: [no log message]

2008-11-05 02:31  stevel

	* libEM/ctf.cpp, programs/e2ctf.py: CTF working !!!  wiener still
	  broken

2008-11-05 01:33  stevel

	* libEM/imagicio.cpp, libpyEM/EMAN2.py, libpyEM/EMAN2db.py,
	  programs/e2ctf.py: Undo a couple of grant's changes and work on
	  CTF

2008-11-04 21:56  woolford

	* libpyEM/qtgui/: emfloatingwidgets.py, emimagemx.py,
	  emimagemxrotor.py: widget work

2008-11-04 20:56  woolford

	* libpyEM/qtgui/emfloatingwidgets.py,
	  rt/emdata/imagic_ctf_test.cpp: compile bug

2008-11-04 20:51  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/embrowse.py, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emplot2d.py, libpyEM/qtgui/emselector.py,
	  programs/e2display.py, pyemtbx/boxertools.py: browser work

2008-11-04 18:06  gtang

	* libpyEM/: libpyTypeConverter2.cpp, typeconverter.h: Ctf in Python

2008-11-04 18:06  gtang

	* libEM/: imagicio.cpp, imagicio.h: read ctf from image file(EMAN1)

2008-11-04 18:03  gtang

	* libEM/emdata_metadata.cpp, rt/emdata/CMakeLists.txt,
	  rt/emdata/imagic_ctf_test.cpp: [no log message]

2008-11-04 15:19  jbert

	* sparx/libpy/applications.py: fix ali_vol_rotate

2008-11-04 14:57  zyang

	* sparx/libpy/utilities.py: Fix compose_transform3

2008-11-04 12:51  stevel

	* libpyEM/EMAN2db.py: Bugfix, if bdb opened for writing then r/o

2008-11-04 10:57  jbert

	* libEM/sparx/util_sparx.cpp: change extractplane to extrac_plane
	  and Transform3D to Transform

2008-11-04 10:36  jbert

	* sparx/libpy/: projection.py, applications.py: change name func
	  extractplane to extract_plane

2008-11-04 10:35  jbert

	* libpyEM/libpyEMData2.cpp: add extract_plane with new transform

2008-11-04 10:34  zweig

	* sparx/libpy/applications.py: start ali3d_m_MPI

2008-11-04 10:03  jbert

	* sparx/libpy/: projection.py, applications.py: change Transform3D

2008-11-04 08:25  zweig

	* sparx/libpy/: alignment.py, applications.py: minor changes

2008-11-04 02:20  ppenczek

	* sparx/libpy/applications.py: ali3d_m

2008-11-04 02:14  stevel

	* libEM/ctf.cpp, programs/e2ctf.py: More ctf work

2008-11-03 22:10  woolford

	* images/Bag.png, images/CMakeLists.txt,
	  images/boxhabanosclose.png, libpyEM/EMAN2.py,
	  libpyEM/qtgui/emapplication.py, libpyEM/qtgui/embrowse.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emselector.py, programs/e2desktop.py: desktop work

2008-11-03 17:13  jbert

	* sparx/libpy/development.py: work on cml

2008-11-03 16:16  stevel

	* libEM/ctf.cpp, programs/e2ctf.py: More CTF work. Ctf computation
	  functions a bit funky...

2008-11-03 15:59  ppenczek

	* sparx/: libpy/applications.py, bin/sxali3d_m.py: ali3d_m almost
	  fine

2008-11-03 15:06  ppenczek

	* sparx/libpy/applications.py: ali3d_m almost fine

2008-11-03 14:53  ppenczek

	* sparx/: bin/sxali3d_m.py, libpy/applications.py: ali3d_m almost
	  fine

2008-11-03 13:28  stevel

	* libEM/ctf.cpp, libEM/ctf.h, libpyEM/EMAN2.py, libpyEM/EMAN2db.py,
	  programs/e2ctf.py: Ctf work, new get_file_tag

2008-11-03 13:09  ppenczek

	* sparx/: bin/sxali3d_e.py, libpy/applications.py: ali3d_e ready ??

2008-11-03 09:56  zweig

	* sparx/: bin/sxrecons3d_f.py, libpy/applications.py: ali3d_m

2008-11-03 07:47  zweig

	* sparx/: bin/sxali3d_e.py, libpy/applications.py,
	  libpy/development.py, libpy/reconstruction.py: work on ali3d_e

2008-11-03 02:27  stevel

	* libEM/ctf.cpp, libEM/ctf.h, libEM/processor.cpp,
	  libEM/processor.h, programs/e2ctf.py: Ctf measurement working.
	  Now adding Wiener filter. Still need gui work

2008-11-02 04:47  ppenczek

	* sparx/: bin/sxheader.py, libpy/applications.py,
	  libpy/utilities.py: many minor corrections to ali3d_d

2008-11-01 17:59  ppenczek

	* sparx/libpy/: alignment.py, applications.py, development.py,
	  filter.py, utilities.py: ali3d_m

2008-11-01 14:43  ppenczek

	* sparx/libpy/user_functions.py: [no log message]

2008-11-01 14:36  ppenczek

	* sparx/libpy/applications.py: [no log message]

2008-11-01 10:30  ppenczek

	* sparx/bin/sxali3d_d.py: [no log message]

2008-11-01 10:06  ppenczek

	* sparx/: bin/sxali3d_d.py, libpy/user_functions.py: [no log
	  message]

2008-11-01 06:21  ppenczek

	* sparx/bin/sxali3d_d.py: [no log message]

2008-11-01 05:49  ppenczek

	* sparx/libpy/: applications.py, reconstruction.py,
	  user_functions.py, utilities.py: ali3dd

2008-11-01 01:56  ppenczek

	* sparx/libpy/: applications.py, development.py:  nothing

2008-10-31 20:50  woolford

	* images/CMakeLists.txt, images/Key.png, images/database.png,
	  libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emborderdecoration.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emimage3dslice.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emimage3dvol.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimageutil.py,
	  libpyEM/qtgui/emplot2d.py, libpyEM/qtgui/emselector.py,
	  programs/e2boxer.py, programs/e2desktop.py: desktop work

2008-10-31 19:18  stevel

	* libpyEM/libpyAligner2.cpp: bugfix

2008-10-31 16:21  jbert

	* sparx/libpy/development.py: find_structure MPI

2008-10-31 16:20  stevel

	* libEM/ctf.h, libpyEM/libpyAligner2.cpp: More CTF work

2008-10-31 16:16  gtang

	* libEM/ctf.h, libpyEM/libpyAligner2.cpp: use property for public
	  class data member

2008-10-31 16:13  zweig

	* sparx/libpy/applications.py: nothing

2008-10-31 16:08  ppenczek

	* sparx/libpy/applications.py:	nothing

2008-10-31 16:01  ppenczek

	* sparx/libpy/applications.py:	nothing

2008-10-31 15:56  ppenczek

	* sparx/libpy/applications.py:	nothing

2008-10-31 15:44  stevel

	* libEM/ctf.cpp, libpyEM/libpyAligner2.cpp, programs/e2ctf.py:
	  Working on CTF

2008-10-31 15:42  zweig

	* sparx/libpy/user_functions.py: spruce_up

2008-10-31 15:26  ppenczek

	* sparx/libpy/applications.py:	nothing

2008-10-31 15:13  ppenczek

	* sparx/libpy/applications.py:	nothing

2008-10-31 15:05  zweig

	* sparx/: bin/sxali3d_d.py, libpy/applications.py: [no log message]

2008-10-31 14:23  gtang

	* rt/pyem/test_reconstructor.py: unit test update

2008-10-31 12:49  gtang

	* rt/pyem/: test_emdata.py, test_imageio.py: unit test update

2008-10-31 12:34  zweig

	* libEM/sparx/util_sparx.cpp: transform object in multiref local

2008-10-31 12:27  zweig

	* libEM/sparx/util_sparx.cpp: transform object in multiref local

2008-10-31 07:08  ppenczek

	* sparx/libpy/: applications.py, utilities.py:	active selection
	  working in ali3d_d

2008-10-31 05:12  ppenczek

	* libpyEM/EMAN2db.py: print removed

2008-10-31 02:08  stevel

	* libEM/ctf.h, programs/e2ctf.py: work on ctf gui

2008-10-30 22:39  woolford

	* libpyEM/qtgui/emplot2d.py: desktop work

2008-10-30 22:37  ppenczek

	* sparx/libpy/: applications.py, reconstruction.py:  work on new
	  version of ali3d_d

2008-10-30 22:09  woolford

	* libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emborderdecoration.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emimage3dslice.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emimage3dvol.py,
	  libpyEM/qtgui/emimagemx.py, programs/e2boxer.py,
	  programs/e2desktop.py: desktop work

2008-10-30 18:10  gtang

	* libpyEM/EMAN2db.py: wrap EMUtil.get_all_attributes() for bdb

2008-10-30 16:55  stevel

	* libpyEM/libpyUtils2.cpp, programs/e2ctf.py: Continuing with CTF.

2008-10-30 10:51  zweig

	* programs/e2boxer.py: e2boxer expanded to allow commandline
	  options for Gauss

2008-10-30 10:49  zweig

	* sparx/: bin/sxcpy.py, libpy/applications.py: sxcpy expanded to
	  allow multiple file names and allow concatenation of files

2008-10-30 09:41  gtang

	* libEM/: spiderio.cpp: ignore Transform object construction when
	  reading spider image if the scale<0

2008-10-30 02:33  stevel

	* programs/e2ctf.py: More work on new e2ctf

2008-10-29 22:50  woolford

	* libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emborderdecoration.py, libpyEM/qtgui/embrowse.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimage3diso.py,
	  libpyEM/qtgui/emimage3dslice.py, libpyEM/qtgui/emimage3dsym.py,
	  libpyEM/qtgui/emimage3dvol.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimageutil.py, libpyEM/qtgui/emplot2d.py,
	  programs/e2desktop.py: desktop work

2008-10-29 17:33  gtang

	* rt/: demo/test_image.py, pyem/test_imageio.py,
	  pyem/test_processor.py: test program update

2008-10-29 17:28  gtang

	* libEM/spiderio.cpp: fix for VS2005 on WinXP

2008-10-29 15:19  woolford

	* libpyEM/qtgui/emborderdecoration.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3dsym.py, programs/e2desktop.py: ortho for
	  iso in desktop works

2008-10-29 15:18  stevel

	* examples/diffractsim.py, programs/e2ctf.py: Redoing CTF fitting
	  program

2008-10-29 15:07  gtang

	* programs/e2proc2d.py: fix e2porc2d.py --split option.

2008-10-29 15:03  gtang

	* programs/e2proc2d.py: fix e2porc2d.py --split option.

2008-10-29 13:50  zweig

	* libEM/sparx/util_sparx.cpp: fix a memory leak of WTM and WTF

2008-10-29 13:27  woolford

	* libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimage3dslice.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emimage3dvol.py,
	  libpyEM/qtgui/emimageutil.py, programs/e2desktop.py: [no log
	  message]

2008-10-29 04:47  ppenczek

	* libEM/sparx/util_sparx.cpp, sparx/libpy/reconstruction.py: memory
	  leak in wtm and wts

2008-10-29 02:40  stevel

	* libEM/: ctf.cpp, ctf.h: ctf work

2008-10-29 02:02  ppenczek

	* sparx/libpy/applications.py: [no log message]

2008-10-28 22:28  woolford

	* libEM/util.cpp, libEM/util.h, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimageutil.py, programs/e2boxer.py,
	  programs/e2desktop.py: desktop work. plus boxer errors

2008-10-28 21:03  ppenczek

	* sparx/libpy/: alignment.py, applications.py, statistics.py: Add
	  center=7 option

2008-10-28 15:36  gtang

	* rt/imageio/imageio.cpp: [no log message]

2008-10-28 14:40  woolford

	* libEM/util.cpp, libEM/util.h, libpyEM/libpyUtils2.cpp,
	  libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emborderdecoration.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimageutil.py,
	  programs/e2desktop.py: desktop work

2008-10-28 14:10  gtang

	* rt/pyem/test_processor.py: unit test update

2008-10-28 12:33  gtang

	* CMakeLists.txt: fix the Dev warning for cmake 2.6

2008-10-28 11:52  gtang

	* libEM/sparx/emdata_sparx.cpp: fix for the win32 platform

2008-10-28 10:48  stevel

	* libEM/: pngio.cpp, processor.cpp, processor.h: New processor for
	  test waves

2008-10-28 02:14  stevel

	* examples/diffractsim.py: Diffraction simulator

2008-10-27 22:40  woolford

	* programs/e2desktop.py: widget work

2008-10-27 22:37  woolford

	* libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emglobjects.py,
	  programs/e2desktop.py: widget work

2008-10-27 21:57  woolford

	* libpyEM/CMakeLists.txt, libpyEM/qtgui/emanimationutil.py,
	  libpyEM/qtgui/emborderdecoration.py, libpyEM/qtgui/emdesktop2.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emimagemx.py, programs/e2desktop.py: widget work

2008-10-27 17:52  jbert

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: cml helper function
	  fix bug

2008-10-27 14:36  woolford

	* libpyEM/qtgui/valslider.py: [no log message]

2008-10-27 14:31  woolford

	* libpyEM/qtgui/emimage2d.py: [no log message]

2008-10-27 14:29  ppenczek

	* sparx/bin/sparx: [no log message]

2008-10-27 14:28  woolford

	* libpyEM/qtgui/: emimage2d.py, valslider.py: very trivial fix

2008-10-27 14:19  ppenczek

	* sparx/bin/sparx: [no log message]

2008-10-27 12:35  woolford

	* libpyEM/qtgui/: emapplication.py, emimage.py, emimage2d.py:
	  widget fixes

2008-10-27 12:23  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emimage2d.py, programs/e2.py: image 2d fixes

2008-10-27 10:08  zweig

	* libEM/reconstructor.cpp, libEM/sparx/emdata_sparx.cpp,
	  programs/e2boxer.py, pyemtbx/boxertools.py: Changes made to the
	  Charite installation to remove bugs and to update the peak_ccf
	  method.

2008-10-27 01:59  stevel

	* libpyEM/EMAN2.py: Demo function

2008-10-27 01:59  stevel

	* libEM/ctf.cpp, programs/e2ctf.py: ctf work

2008-10-24 20:41  woolford

	* libpyEM/qtgui/: emdesktop2.py, emfloatingwidgets.py: desktop work

2008-10-24 20:23  woolford

	* libpyEM/qtgui/emdesktop2.py: desktop work

2008-10-24 20:18  woolford

	* libpyEM/qtgui/: emborderdecoration.py, emdesktop2.py,
	  emfloatingwidgets.py, emglobjects.py, emimage3d.py,
	  emimage3diso.py: desktop work

2008-10-24 18:36  woolford

	* libpyEM/qtgui/: emanimationutil.py, emdesktop.py, emdesktop2.py,
	  emfloatingwidgets.py, emglobjects.py: desktop work

2008-10-24 17:42  jbert

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Helper function for cml

2008-10-24 17:40  jbert

	* sparx/libpy/development.py: work on cml

2008-10-24 17:28  gtang

	* CMakeLists.txt, libEM/CMakeLists.txt, libpyEM/CMakeLists.txt: for
	  ftgl on Windows

2008-10-24 17:04  gtang

	* libpyEM/EMAN2.py: fix the ftgl font problem on windows

2008-10-24 14:47  ppenczek

	* sparx/libpy/applications.py: [no log message]

2008-10-24 14:10  woolford

	* libpyEM/qtgui/: emanimationutil.py, emdesktop2.py: desktop work

2008-10-24 09:50  jbert

	* sparx/libpy/statistics.py: k-means MPI (cla, SSE), change the way
	  to manage empty cluster

2008-10-23 22:38  woolford

	* libpyEM/qtgui/emdesktop2.py: desktop fixes

2008-10-23 22:33  woolford

	* libpyEM/qtgui/emfloatingwidgets.py: desktop fixes

2008-10-23 22:26  stevel

	* libEM/ctf.cpp, libEM/ctf.h, programs/e2ctf.py: Ctf work

2008-10-23 22:21  woolford

	* libpyEM/: libpyUtils2.cpp, qtgui/emanimationutil.py,
	  qtgui/emborderdecoration.py, qtgui/emdesktop2.py,
	  qtgui/emfloatingwidgets.py, qtgui/emglobjects.py,
	  qtgui/emimage3d.py, qtgui/emimagemxrotor.py,
	  qtgui/emimagerotor.py: desktop work

2008-10-23 16:30  ppenczek

	* sparx/libpy/statistics.py: Fix a bug

2008-10-23 13:58  jbert

	* sparx/libpy/statistics.py: k-means SSE, change the way to manage
	  empty cluster

2008-10-23 13:33  woolford

	* libpyEM/qtgui/: emborderdecoration.py, emdesktop2.py,
	  emfloatingwidgets.py: widget fixes

2008-10-23 13:30  jbert

	* sparx/libpy/statistics.py: k-means cla, change the way to manage
	  empty cluster

2008-10-23 12:16  woolford

	* libpyEM/qtgui/: emdesktop2.py, emimage.py, emimage2d.py: widget
	  fixes

2008-10-22 22:48  woolford

	* libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2boxer.py: widget work

2008-10-22 22:30  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emborderdecoration.py,
	  libpyEM/qtgui/embrowse.py, libpyEM/qtgui/emdesktop2.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimageutil.py,
	  programs/e2display.py: desktop work

2008-10-22 17:23  jbert

	* sparx/libpy/development.py: work on cml

2008-10-22 16:35  jbert

	* sparx/libpy/statistics.py: k-means, fix bug

2008-10-22 15:58  woolford

	* libpyEM/qtgui/emimage2d.py, programs/e2boxer.py: widget fixes

2008-10-22 14:19  ppenczek

	* sparx/libpy/applications.py: [no log message]

2008-10-22 10:57  stevel

	* libpyEM/: EMAN2.py, EMAN2db.py: db_remove_dict added

2008-10-21 22:18  woolford

	* libpyEM/: CMakeLists.txt, qtgui/emborderdecoration.py,
	  qtgui/emdesktop2.py, qtgui/emfloatingwidgets.py,
	  qtgui/emglobjects.py, qtgui/emimagemx.py,
	  qtgui/emimagemxrotor.py, qtgui/emimagerotor.py: widget work

2008-10-21 16:14  woolford

	* libpyEM/qtgui/: emdesktop2.py, emglobjects.py, emimage2d.py,
	  emimage3d.py, emimagemx.py, emimagemxrotor.py, emplot2d.py:
	  widget fixes

2008-10-21 15:34  woolford

	* libpyEM/qtgui/: emapplication.py, emdesktop2.py,
	  emfloatingwidgets.py, emglobjects.py, emimage2d.py, emimagemx.py,
	  emimagemxrotor.py, emrotor.py: desktop work

2008-10-21 14:56  ppenczek

	* sparx/libpy/: fundamentals.py, statistics.py: [no log message]

2008-10-21 03:19  ppenczek

	* sparx/libpy/statistics.py: [no log message]

2008-10-20 23:56  woolford

	* libpyEM/qtgui/emfloatingwidgets.py: more widget fixes

2008-10-20 22:50  woolford

	* libpyEM/qtgui/emanimationutil.py, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emdesktop2.py, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimagemxrotor.py,
	  libpyEM/qtgui/emimageutil.py, libpyEM/qtgui/emplot2d.py,
	  programs/e2.py: desktop updates

2008-10-20 16:10  ppenczek

	* libEM/reconstructor.cpp: make sure that reconstructor returned
	  volume is internal reference

2008-10-20 15:43  ppenczek

	* sparx/libpy/statistics.py: add class def_variance: calculate
	  variance from definition

2008-10-20 13:10  woolford

	* libpyEM/qtgui/: emdesktop2.py, emfloatingwidgets.py: mac fixes

2008-10-20 13:04  ppenczek

	* programs/e2proc3d.py, sparx/bin/sxali3d_d.py,
	  sparx/libpy/alignment.py, sparx/libpy/applications.py,
	  sparx/libpy/reconstruction.py: [no log message]

2008-10-20 12:56  woolford

	* libEM/emdata_metadata.h, libpyEM/qtgui/emfloatingwidgets.py:
	  desktop fixes

2008-10-20 12:55  woolford

	* libpyEM/qtgui/: emdesktop2.py, emfloatingwidgets.py: mac fixes

2008-10-20 12:42  stevel

	* libEM/ctf.cpp: Fix mac compilation problem

2008-10-20 03:00  stevel

	* libEM/ctf.cpp, libEM/ctf.h, libpyEM/libpyAligner2.cpp: Working on
	  CTF

2008-10-18 18:39  woolford

	* libEM/emdata_metadata.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/qtgui/embrowse.py, libpyEM/qtgui/emdesktop2.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emplot2d.py, programs/e2display.py: widget work

2008-10-17 20:59  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emdesktop2.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emimage.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimagemxrotor.py,
	  libpyEM/qtgui/emimagerotor.py, programs/e2boxer.py: more widget
	  work

2008-10-17 19:15  woolford

	* libpyEM/qtgui/emanimationutil.py, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emdesktop2.py, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emimage3dslice.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emimage3dvol.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimagemxrotor.py,
	  libpyEM/qtgui/emimagerotor.py, libpyEM/qtgui/emimageutil.py,
	  libpyEM/qtgui/emplot2d.py, libpyEM/qtgui/emrotor.py,
	  programs/e2boxer.py: more widget fixes

2008-10-17 15:58  gtang

	* libEM/: ctf.cpp, imagicio.cpp, processor.cpp, util.h,
	  sparx/emdata_sparx.cpp: fix for the win32 platform

2008-10-17 14:56  gtang

	* libEM/emobject.cpp, libEM/emobject.h, libEM/hdfio2.cpp,
	  rt/emdata/test_emobject.cpp: Enable Ctf object as image
	  attribute, and can be read/write to HDF5 image file.

2008-10-17 14:22  woolford

	* libpyEM/qtgui/: emimage2d.py, emimageutil.py: widget fixes

2008-10-17 14:12  woolford

	* libpyEM/qtgui/emimagemx.py: woops

2008-10-17 14:02  woolford

	* libpyEM/qtgui/emanimationutil.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimagerotor.py,
	  libpyEM/qtgui/emimageutil.py, libpyEM/qtgui/emplot2d.py,
	  programs/e2ctf.py: widget fixes. plot2d is also a module

2008-10-17 01:17  stevel

	* libEM/averager.cpp, libEM/ctf.cpp, libEM/ctf.h,
	  libEM/emdata_metadata.cpp, libEM/imagicio.cpp, libEM/mrcio.cpp,
	  libpyEM/libpyAligner2.cpp, programs/e2ctf.py: EMAN2 Ctf object
	  added, but incomplete.

2008-10-16 22:27  stevel

	* libpyEM/EMAN2db.py: Fix read-only bug

2008-10-16 22:16  woolford

	* libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimagemxrotor.py, programs/e2flick.py: widget work

2008-10-16 21:42  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emimage3dsym.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimagemxrotor.py,
	  libpyEM/qtgui/emimagerotor.py, programs/e2boxer.py: widget fixes

2008-10-16 21:20  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emimage3dslice.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emimage3dvol.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimagemxrotor.py,
	  libpyEM/qtgui/emimagerotor.py, libpyEM/qtgui/emimageutil.py,
	  programs/e2boxer.py, programs/e2display.py,
	  pyemtbx/boxertools.py: Mac fixes

2008-10-16 17:42  jbert

	* sparx/libpy/development.py: cml change option

2008-10-16 11:29  ppenczek

	* sparx/libpy/: applications.py, projection.py, utilities.py: [no
	  log message]

2008-10-16 08:58  jbert

	* sparx/libpy/development.py: change debug mode in cml

2008-10-16 02:31  stevel

	* libEM/averager.cpp, libEM/ctf.cpp, libEM/ctf.h,
	  libEM/processor.cpp, libpyEM/libpyAligner2.cpp: Working on CTF
	  module

2008-10-15 22:49  woolford

	* libpyEM/qtgui/emfloatingwidgets.py: widget fixes

2008-10-15 22:46  woolford

	* images/CMakeLists.txt, images/Close.png, images/Close.txt,
	  libpyEM/qtgui/emanimationutil.py, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/embrowse.py, libpyEM/qtgui/emdesktop2.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimagemxrotor.py,
	  libpyEM/qtgui/emimagerotor.py, libpyEM/qtgui/emshape.py,
	  programs/e2boxer.py: desktop work

2008-10-15 16:27  ppenczek

	* sparx/bin/sparx: [no log message]

2008-10-15 16:14  ppenczek

	* sparx/bin/sparx: [no log message]

2008-10-15 16:02  ppenczek

	* sparx/libpy/applications.py: [no log message]

2008-10-15 11:54  gtang

	* libEM/sparx/util_sparx.cpp: fix for VS2005 compilation

2008-10-15 11:42  woolford

	* libpyEM/qtgui/: emapplication.py, emdesktop2.py: desktop work

2008-10-15 11:35  woolford

	* libpyEM/qtgui/: emimage2d.py, emimagemx.py: mac based widget
	  fixes

2008-10-15 11:14  woolford

	* libpyEM/qtgui/: emapplication.py, emdesktop2.py, emimage.py,
	  emimage2d.py, emimageutil.py: mac fixes

2008-10-15 02:58  stevel

	* programs/e2ctf.py: CTF work

2008-10-14 22:21  woolford

	* libpyEM/qtgui/emanimationutil.py, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emdesktop2.py, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimagemxrotor.py, libpyEM/qtgui/emimagerotor.py,
	  programs/e2boxer.py: widget updates

2008-10-14 16:42  woolford

	* libpyEM/qtgui/emanimationutil.py, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emdesktop2.py, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimagemxrotor.py,
	  programs/e2boxer.py: widget updates

2008-10-14 15:08  woolford

	* libpyEM/qtgui/emdesktop2.py, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemxrotor.py,
	  libpyEM/qtgui/emimagerotor.py, programs/e2boxer.py: widget work

2008-10-14 14:43  zyang

	* sparx/libpy/: applications.py, development.py: Trival change

2008-10-14 14:36  zyang

	* sparx/libpy/development.py: Fix a bug, delete some useless stuff

2008-10-14 13:27  jbert

	* sparx/libpy/utilities.py: fix typo mistake in print_end_msg

2008-10-14 12:01  gtang

	* libpyEM/typeconverter.h: revert my earlier changes. Let Python
	  give up the ownership once an object is wrapped as EMObject
	  created other problems. This Object still need be accessed in
	  Python.

2008-10-14 10:42  gtang

	* libpyEM/: libpyEMData2.cpp, libpyTransform2.cpp, typeconverter.h:
	  revert my earlier changes. Let Python give up the ownership once
	  an object is wrapped as EMObject created other problems. This
	  Object still need be accessed in Python.

2008-10-14 10:31  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emdesktop2.py,
	  programs/e2boxer.py, programs/e2display.py: widget fixes

2008-10-13 22:43  woolford

	* libpyEM/qtgui/: emapplication.py, embrowse.py, emdesktop2.py,
	  emfloatingwidgets.py, emglobjects.py, emimage.py, emimage2d.py,
	  emimage3d.py, emimagemx.py, emimagemxrotor.py, emimagerotor.py,
	  emrotor.py: widget work

2008-10-13 16:22  zyang

	* sparx/libpy/utilities.py: Some change to print_begin_msg and
	  begin_end_msg()

2008-10-13 16:21  zyang

	* sparx/libpy/development.py: Change the reading of 2D alignment
	  parameters.

2008-10-13 16:19  zyang

	* sparx/libpy/applications.py: Fix a minor bug.

2008-10-13 02:08  stevel

	* programs/e2ctf.py: Defocus estimation working (except Ryr)

2008-10-11 11:07  gtang

	* libEM/imagicio.cpp, libEM/mrcio.cpp, libEM/spiderio.cpp,
	  rt/pyem/test_imageio.py: construct a Transform object as image
	  attribute when reading a MRC, IMAGIC, SPIDER image.

2008-10-11 08:31  gtang

	* rt/pyem/test_processor.py: unit test update

2008-10-10 19:54  woolford

	* libpyEM/: qtgui/emanimationutil.py, CMakeLists.txt: add a new
	  file

2008-10-10 19:54  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/embrowse.py,
	  libpyEM/qtgui/emdesktop2.py, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimagemxrotor.py,
	  libpyEM/qtgui/emimagerotor.py, programs/e2boxer.py: desktop work

2008-10-10 17:35  jbert

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Helper function for cml

2008-10-10 17:34  jbert

	* sparx/libpy/development.py: work cml

2008-10-10 14:33  gtang

	* rt/pyem/test_imageio.py: unit test update

2008-10-10 13:29  woolford

	* libpyEM/qtgui/: emapplication.py, emdesktop2.py, emimage2d.py,
	  emimage3d.py, emimagemx.py: desktop work

2008-10-10 12:29  woolford

	* libpyEM/qtgui/: emapplication.py, emdesktop2.py,
	  emfloatingwidgets.py, emimage2d.py, emimage3d.py,
	  emimage3diso.py, emimage3dslice.py, emimage3dvol.py,
	  emimagemx.py: desktop work

2008-10-10 11:25  zweig

	* programs/e2boxer.py, pyemtbx/boxertools.py: fix invert problem

2008-10-10 10:20  zweig

	* pyemtbx/boxertools.py: add invert to PawelAutoBoxer

2008-10-09 22:45  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emdesktop2.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emselector.py, programs/e2boxer.py: desktop work

2008-10-09 21:08  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemxrotor.py, libpyEM/qtgui/emimagerotor.py,
	  libpyEM/qtgui/emimageutil.py, programs/e2boxer.py: darwin fixes

2008-10-09 18:17  gtang

	* libEM/spiderio.cpp, rt/pyem/test_imageio.py: support write
	  Transform object in image attribute to spider file header.

2008-10-09 18:02  gtang

	* libEM/mrcio.cpp: support write Transform object in image
	  attribute to mrc file header.

2008-10-09 15:52  woolford

	* libpyEM/qtgui/: emimage2d.py, emimagerotor.py, emshape.py: more
	  widget fixes

2008-10-09 15:52  gtang

	* rt/pyem/test_imageio.py: support write Transform object in image
	  attribute to Imagic file header as euler angles.

2008-10-09 15:23  woolford

	* libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemxrotor.py,
	  libpyEM/qtgui/emimagerotor.py, programs/e2boxer.py: boxer fixes

2008-10-09 15:20  gtang

	* libEM/imagicio.cpp: support write Transform object in image
	  attribute to Imagic file header as euler angles.

2008-10-09 14:41  woolford

	* libpyEM/: EMAN2.py, qtgui/emimage2d.py: widget updates

2008-10-09 14:28  gtang

	* utils/iminfo.cpp: print out image data type info

2008-10-09 14:06  woolford

	* libpyEM/qtgui/: emapplication.py, embrowse.py, emimage3d.py,
	  emimagemx.py, emselector.py: more widget work

2008-10-09 13:37  zweig

	* pyemtbx/boxertools.py: filt image only for old run

2008-10-09 13:34  zyang

	* sparx/libpy/applications.py: Trival change

2008-10-09 13:31  zweig

	* programs/e2boxer.py: fix invert image

2008-10-09 12:38  woolford

	* libpyEM/qtgui/: embrowse.py, emimage3dvol.py, emselector.py:
	  adding browser

2008-10-09 12:02  woolford

	* libpyEM/: typeconverter.h, qtgui/emapplication.py,
	  qtgui/emdesktop2.py, qtgui/emglobjects.py, qtgui/emimage2d.py,
	  qtgui/emimage3d.py, qtgui/emimage3diso.py,
	  qtgui/emimage3dslice.py, qtgui/emimage3dsym.py,
	  qtgui/emimage3dvol.py, qtgui/emimagemx.py,
	  qtgui/emimagemxrotor.py, qtgui/emimagerotor.py,
	  qtgui/emimageutil.py, qtgui/emrotor.py, qtgui/emselector.py:
	  darwin based fixes, 3d works again, borders,etc

2008-10-08 22:32  woolford

	* libpyEM/qtgui/emimage2d.py: more widget work

2008-10-08 22:22  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimagemxrotor.py, libpyEM/qtgui/emimagerotor.py,
	  libpyEM/qtgui/emrotor.py, programs/e2boxer.py: widget work

2008-10-08 17:26  jbert

	* sparx/libpy/development.py: work on new cml code

2008-10-08 14:46  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emimage.py,
	  programs/e2display.py: display fixes

2008-10-08 14:36  gtang

	* libpyEM/EMAN2.py: Transform3D to Transform

2008-10-08 14:35  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emimage.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimage3dvol.py,
	  libpyEM/qtgui/emrotor.py, libpyEM/CMakeLists.txt,
	  libpyEM/EMAN2.py, programs/e2.py: gui work

2008-10-08 12:27  woolford

	* libpyEM/qtgui/emselector.py: selector is beta

2008-10-08 12:03  woolford

	* libpyEM/qtgui/: emfloatingwidgets.py, emselector.py: widget fixes

2008-10-08 02:39  stevel

	* libEM/processor.cpp, libEM/processor.h, programs/e2ctf.py: Better
	  background in ctf.

2008-10-07 22:51  woolford

	* libpyEM/: CMakeLists.txt, qtgui/emapplication.py,
	  qtgui/emselector.py: widget work

2008-10-07 20:33  woolford

	* libpyEM/qtgui/: emapplication.py, emglobjects.py, emselector.py:
	  selector done'

2008-10-07 17:16  woolford

	* libpyEM/qtgui/: emapplication.py, embrowse.py, emimage2d.py,
	  emselector.py: widget updates

2008-10-07 17:02  zweig

	* programs/e2boxer.py, pyemtbx/boxertools.py: add option method for
	  e2boxer

2008-10-07 16:55  jbert

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: helper function for cml

2008-10-07 16:51  jbert

	* sparx/libpy/development.py: work on new cml

2008-10-07 15:36  zweig

	* programs/e2boxer.py, pyemtbx/boxertools.py: many changes to make
	  PawelAutoBoxer work with database

2008-10-07 14:00  woolford

	* images/CMakeLists.txt, images/eman_idea.png,
	  libpyEM/qtgui/embrowse.py, libpyEM/qtgui/emimage2d.py: display
	  fixes'

2008-10-07 12:02  woolford

	* programs/e2boxer.py: more display fixes

2008-10-07 11:59  woolford

	* libpyEM/qtgui/embrowse.py, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emimage2d.py, programs/e2display.py: display fixes

2008-10-07 09:13  jbert

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: Fix cml_euc

2008-10-06 20:42  woolford

	* libpyEM/qtgui/: emapplication.py, embrowse.py, emimage2d.py,
	  valslider.py: widget work

2008-10-06 17:32  gtang

	* libpyEM/: libpyEMData2.cpp, libpyTransform2.cpp, typeconverter.h:
	  Fix the attibute memory double deletion problem by following
	  boost FAQ solution.

2008-10-06 17:28  jbert

	* sparx/bin/sxfind_struct.py: work on cml

2008-10-06 17:28  jbert

	* sparx/libpy/development.py: work on new cml code

2008-10-06 17:22  stevel

	* programs/e2ctf.py: First version with defocus estimation

2008-10-06 17:15  zyang

	* sparx/libpy/applications.py: Make some change to ali2d_a()

2008-10-06 02:05  stevel

	* programs/e2ctf.py: CTF work

2008-10-03 20:54  woolford

	* images/CMakeLists.txt, images/File.png, images/Folder.png,
	  images/FolderFiles.png, libpyEM/qtgui/embrowse.py,
	  programs/e2boxer.py: gui work

2008-10-03 17:08  jbert

	* sparx/libpy/development.py: work on new cml code

2008-10-03 17:08  zweig

	* pyemtbx/boxertools.py, programs/e2boxer.py: fix a bug in
	  PawelAutoBoxer

2008-10-03 16:01  ppenczek

	* pyemtbx/boxertools.py: [no log message]

2008-10-03 15:50  ppenczek

	* programs/e2boxer.py, pyemtbx/boxertools.py: [no log message]

2008-10-03 15:41  zweig

	* pyemtbx/boxertools.py: add use_variance

2008-10-03 15:32  ppenczek

	* programs/e2boxer.py, pyemtbx/boxertools.py: [no log message]

2008-10-03 15:03  zweig

	* pyemtbx/boxertools.py: save PawelAutoboxer to database

2008-10-03 15:03  zweig

	* programs/e2boxer.py: restore PawelAutoboxer from database

2008-10-03 14:54  woolford

	* libpyEM/qtgui/: emglobjects.py, emimage2d.py, emimagerotor.py:
	  trivial changes

2008-10-03 12:18  woolford

	* libpyEM/: EMAN2.py, qtgui/emapplication.py: qt and app based
	  fixes

2008-10-03 09:53  woolford

	* libpyEM/CMakeLists.txt: fixed an error

2008-10-03 01:26  stevel

	* libpyEM/EMAN2db.py, programs/e2ctf.py: Work on ctf

2008-10-02 22:54  woolford

	* libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emimage.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimage2dtex.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimagemxrotor.py,
	  libpyEM/qtgui/emimagerotor.py, libpyEM/qtgui/emrotor.py,
	  programs/e2boxer.py: widget work

2008-10-02 18:23  woolford

	* libEM/marchingcubes.cpp, libpyEM/libpyMarchingCubes2.cpp,
	  libpyEM/qtgui/em3Dfonts.py, libpyEM/qtgui/em3Dhelloworld.py,
	  libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emdesktop2.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emfximage.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emglplot.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage2dtex.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimage3diso.py,
	  libpyEM/qtgui/emimage3dmorph.py, libpyEM/qtgui/emimage3dslice.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emimage3dvol.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimageutil.py,
	  programs/e2ctf.py: more widget work

2008-10-02 16:06  gtang

	* rt/pyem/test_processor.py: [no log message]

2008-10-01 22:41  woolford

	* libpyEM/qtgui/emapplication.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemx.py, programs/e2boxer.py,
	  pyemtbx/boxertools.py: widget based fixes

2008-10-01 21:51  woolford

	* examples/alignbystars.py, libpyEM/CMakeLists.txt,
	  libpyEM/EMAN2.py, libpyEM/qtgui/em3Dfonts.py,
	  libpyEM/qtgui/em3Dhelloworld.py, libpyEM/qtgui/emapplication.py,
	  libpyEM/qtgui/emdesktop.py, libpyEM/qtgui/emdesktop2.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emfximage.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emglplot.py,
	  libpyEM/qtgui/emimage.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimage2dtex.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emimage3dmorph.py,
	  libpyEM/qtgui/emimage3dslice.py, libpyEM/qtgui/emimage3dsym.py,
	  libpyEM/qtgui/emimage3dvol.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimagemxrotor.py, libpyEM/qtgui/emimagerotor.py,
	  libpyEM/qtgui/emimageutil.py, libpyEM/qtgui/emplot2d.py,
	  programs/e2boxer.py, programs/e2ctf.py, programs/e2display.py:
	  widget work, redoing design

2008-10-01 16:31  zyang

	* sparx/libpy/: applications.py, statistics.py: Trival change

2008-09-30 20:29  woolford

	* libEM/marchingcubes.cpp, libpyEM/qtgui/emdesktop2.py,
	  libpyEM/qtgui/emfloatingwidgets.py: desktop work

2008-09-30 18:20  woolford

	* libpyEM/qtgui/: emdesktop2.py, emfloatingwidgets.py: desktop work

2008-09-30 17:23  jbert

	* sparx/libpy/projection.py: work on cml

2008-09-30 16:23  ppenczek

	* sparx/: libpy/applications.py, bin/sxdefvar.py: add defvar:
	  calculate variance by definition

2008-09-30 15:50  zyang

	* sparx/libpy/statistics.py: A small bug and some trival changes.

2008-09-30 13:09  zweig

	* sparx/libpy/: alignment.py, reconstruction.py, applications.py,
	  utilities.py, development.py: use header xform.proj to replace
	  header phi,theta,psi,s2x,s2y

2008-09-30 13:07  zweig

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/libpyReconstructor2.cpp: change from Transform3D to
	  Transform

2008-09-30 11:36  woolford

	* programs/e2boxer.py: fixed e2boxer errors

2008-09-29 21:16  woolford

	* libEM/emftgl.h, libpyEM/EMAN2.py, libpyEM/qtgui/emdesktop2.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emglobjects.py:
	  desktop work

2008-09-29 18:12  woolford

	* libpyEM/qtgui/: em3Dfonts.py, em3Dhelloworld.py, emdesktop.py,
	  emdesktop2.py, emfloatingwidgets.py, emglobjects.py, emglplot.py,
	  emimage3d.py, emimage3diso.py, emimage3dmorph.py,
	  emimage3dslice.py, emimage3dsym.py, emimage3dvol.py: desktop work
	  and general fixes

2008-09-29 17:26  jbert

	* sparx/: libpy/applications.py, libpy/projection.py,
	  bin/sxfind_struct.py: work on Cml

2008-09-29 14:41  zyang

	* sparx/bin/sxali2d_a.py: Fix a bug

2008-09-29 14:27  zyang

	* sparx/bin/sxali2d_a.py: Fix a bug

2008-09-29 11:03  zyang

	* sparx/: bin/sxali2d_a.py, libpy/alignment.py,
	  libpy/applications.py: Many changes to ali2d_a()

2008-09-28 01:25  stevel

	* libpyEM/EMAN2db.py: More debugging

2008-09-28 01:22  stevel

	* libpyEM/EMAN2db.py: Minor fix

2008-09-28 01:16  stevel

	* libpyEM/EMAN2db.py: Read only support for database

2008-09-27 17:03  woolford

	* libpyEM/qtgui/: emdesktop2.py, emfloatingwidgets.py,
	  emglobjects.py: desktop work

2008-09-26 19:34  woolford

	* libpyEM/qtgui/: emdesktop.py, emdesktop2.py: desktop work

2008-09-26 19:24  woolford

	* libpyEM/qtgui/emdesktop2.py: desktop work

2008-09-26 17:39  jbert

	* sparx/: libpy/applications.py, libpy/projection.py,
	  bin/sxfind_struct.py: work on Cml

2008-09-26 14:22  woolford

	* libpyEM/qtgui/: emdesktop2.py, emglobjects.py, emimagemxrotor.py,
	  emimagerotor.py, emrotor.py: display bug fixes

2008-09-26 13:35  jbert

	* sparx/libpy/: applications.py, statistics.py: k-means, change to
	  bdb

2008-09-25 22:35  woolford

	* libpyEM/qtgui/: emdesktop.py, emdesktop2.py,
	  emfloatingwidgets.py, emglobjects.py, emimage3d.py,
	  emimage3diso.py, emimage3dmorph.py, emimage3dslice.py,
	  emimage3dsym.py, emimage3dvol.py: desktop work

2008-09-25 17:30  jbert

	* sparx/libpy/: projection.py, utilities.py: work on cml

2008-09-25 16:09  zweig

	* programs/e2boxer.py: add command line mode for Gauss auto boxer

2008-09-25 16:06  woolford

	* programs/e2boxer.py, libpyEM/qtgui/emdesktop2.py: desktop work

2008-09-25 15:07  woolford

	* libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emfximage.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emglplot.py,
	  libpyEM/qtgui/emimage.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimage2dtex.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emimage3dmorph.py,
	  libpyEM/qtgui/emimage3dslice.py, libpyEM/qtgui/emimage3dsym.py,
	  libpyEM/qtgui/emimage3dvol.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimagemxrotor.py, libpyEM/qtgui/emimagerotor.py,
	  libpyEM/qtgui/emimageutil.py, libpyEM/qtgui/emplot2d.py,
	  programs/e2boxer.py, programs/e2ctf.py, programs/e2display.py,
	  pyemtbx/boxertools.py: boxer related fixes, and naming
	  conventions fixed

2008-09-25 13:39  jbert

	* sparx/libpy/projection.py: Cml, trivial change

2008-09-25 12:03  zyang

	* sparx/libpy/statistics.py: Fix a bug in aves_wiener() (The
	  previous fix is not correct.)

2008-09-25 11:57  zweig

	* programs/e2boxer.py, pyemtbx/boxertools.py: add gauss_width

2008-09-25 11:41  zyang

	* sparx/libpy/statistics.py: Fix a bug in aves_wiener()

2008-09-25 11:32  jbert

	* sparx/libpy/projection.py: CmlLines, change the way to export

2008-09-25 10:44  ppenczek

	* sparx/libpy/applications.py: Some change relating to bdb

2008-09-25 10:28  zyang

	* sparx/libpy/applications.py: Add bdb to ali2d_c_MPI()

2008-09-25 02:19  stevel

	* libpyEM/EMAN2db.py: DB cache fixes for use on clusters. Now uses
	  one shared cache in /tmp.

2008-09-24 19:26  woolford

	* libEM/geometry.h, libpyEM/libpyGeometry2.cpp,
	  libpyEM/qtgui/emimage3dsym.py: minor changes'

2008-09-24 15:50  jbert

	* sparx/libpy/development.py: Stability, change params

2008-09-24 14:57  jbert

	* sparx/libpy/statistics.py: function aves fix bug

2008-09-24 14:10  woolford

	* libpyEM/qtgui/emdesktop.py: trivial change

2008-09-24 11:23  ppenczek

	* programs/e2boxer.py: [no log message]

2008-09-24 11:19  ppenczek

	* pyemtbx/boxertools.py: [no log message]

2008-09-24 11:16  jbert

	* sparx/libpy/: applications.py, statistics.py: k-means, simplify
	  export function for bdb

2008-09-24 10:39  zyang

	* sparx/libpy/applications.py: Fix a bug in ali2d_a_MPI()

2008-09-24 10:37  zweig

	* programs/e2boxer.py, pyemtbx/boxertools.py: add gauss ruler to
	  Gauss Auto boxer

2008-09-24 09:54  jbert

	* sparx/libpy/statistics.py: k-means, change MPI init

2008-09-23 22:18  woolford

	* pyemtbx/boxertools.py: Transform related fixes

2008-09-23 22:11  woolford

	* examples/e2alignmenttest.py, libEM/aligner.cpp, libEM/aligner.h,
	  libEM/emdata.cpp, libEM/processor.cpp, libEM/processor.h,
	  libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libEM/symmetry.cpp, libEM/symmetry.h, libEM/transform.cpp,
	  libEM/transform.h, libpyEM/libpyTransform2.cpp,
	  libpyEM/qtgui/emimage.py, programs/e2classaverage.py,
	  programs/e2flick.py, programs/e2make3d.py,
	  programs/e2ptcltrace.py, rt/pyem/test_aligner.py: Transform
	  related changes

2008-09-23 17:24  zweig

	* programs/e2boxer.py: fix CcfHistogram: enlarge the range to
	  include all

2008-09-23 17:23  zweig

	* pyemtbx/boxertools.py: fix a bug in PawelAutoBoxer: reset
	  boxable's image_name for reduced image

2008-09-23 17:18  jbert

	* sparx/libpy/statistics.py: k-means, trivial change

2008-09-23 17:15  jbert

	* sparx/libpy/: applications.py, statistics.py: k-means, bdb
	  temporary change

2008-09-23 17:00  zyang

	* sparx/libpy/applications.py: Change to ali2d_a_MPI to make it
	  work for bdb file

2008-09-23 16:44  jbert

	* sparx/libpy/: applications.py, statistics.py: k-means, simplify
	  code to open ims

2008-09-23 15:22  jbert

	* sparx/libpy/: applications.py, statistics.py: k-means MPI, change
	  the way to opens im with DBD (desync node)

2008-09-23 14:13  woolford

	* libEM/transform.h: symmetry related fixes

2008-09-23 14:09  woolford

	* libEM/transform.cpp, libpyEM/libpyTransform2.cpp: symmetry
	  related fixes

2008-09-23 13:04  woolford

	* libEM/CMakeLists.txt, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libEM/symmetry.cpp, libEM/symmetry.h,
	  libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, sparx/libpy/reconstruction.py,
	  sparx/libpy/utilities.py: symmetry related fixes

2008-09-23 12:51  zweig

	* sparx/bin/sxwelch_psp.py: remove the reference of retired flag
	  MPI

2008-09-23 12:50  jbert

	* sparx/libpy/statistics.py: k-means export, fix bug

2008-09-23 09:28  jbert

	* sparx/libpy/statistics.py: k-means SSE MPI, change inter-loop
	  update (bug)

2008-09-23 01:10  stevel

	* programs/e2ctf.py: Work on ctf

2008-09-22 22:20  woolford

	* libEM/aligner.cpp, libEM/aligner.h, libEM/cmp.h,
	  libEM/emdata.cpp, libEM/emdata.h, libEM/emdata_metadata.cpp,
	  libEM/emdata_metadata.h, libEM/emdata_transform.cpp,
	  libEM/emdata_transform.h, libEM/processor.cpp, libEM/processor.h,
	  libEM/projector.h, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libEM/transform.cpp, libEM/transform.h,
	  libEM/util.h, libpyEM/EMAN2.py, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyReconstructor2.cpp, programs/e2make3d.py,
	  programs/e2project3d.py, rt/pyem/test_aligner.py,
	  rt/pyem/test_averager.py, rt/pyem/test_emdata.py,
	  rt/pyem/test_imageio.py, rt/pyem/test_processor.py,
	  rt/pyem/test_transform.py, rt/pyem/test_typeconverter.py,
	  sparx/libpy/development.py: replacing Transform3D with Transform

2008-09-22 18:03  ppenczek

	* libEM/sparx/emdata_sparx.cpp, pyemtbx/boxertools.py: ccf_peaks
	  fixed

2008-09-22 17:28  zweig

	* sparx/bin/sparx: use multi-lines to adopt to ipython-0.9.1

2008-09-22 16:13  zyang

	* sparx/libpy/utilities.py: Fix multiple bugs in send_attr_dict()
	  and recv_attr_dict()

2008-09-22 14:30  jbert

	* sparx/libpy/projection.py: CmlLines, read and write in BDB format

2008-09-22 13:11  zyang

	* sparx/: bin/sxheader.py, libpy/applications.py: Add delete
	  function in header()

2008-09-22 13:09  ppenczek

	* libEM/sparx/emdata_sparx.cpp, programs/e2boxer.py: [no log
	  message]

2008-09-22 13:05  ppenczek

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libEM/sparx/fourierfilter.cpp, libEM/sparx/util_sparx.cpp,
	  libpyEM/libpyEMData2.cpp: [no log message]

2008-09-22 11:37  zyang

	* sparx/libpy/applications.py: Fix a big in transform2d()

2008-09-22 11:28  ppenczek

	* sparx/test/phasing.py: [no log message]

2008-09-22 10:04  jbert

	* sparx/libpy/development.py: Stability, add params to extract ave

2008-09-22 02:05  stevel

	* programs/: e2ctf.py, e2refine2d.py: Work on ctf a bit

2008-09-21 01:21  stevel

	* libpyEM/qtgui/emimage2d.py: quick fix webkit import issue

2008-09-20 04:12  ppenczek

	* libEM/reconstructor.cpp: fix bug in newfile_store

2008-09-19 19:11  woolford

	* libEM/: aligner.cpp: aligner work

2008-09-19 19:00  woolford

	* examples/e2alignmenttest.py, libEM/aligner.cpp, libEM/aligner.h,
	  libEM/emdata.cpp, libEM/emdata.h, libpyEM/qtgui/emimage2d.py:
	  aligner work

2008-09-19 17:16  zyang

	* sparx/libpy/applications.py: expand function header()

2008-09-19 16:28  zyang

	* sparx/libpy/utilities.py: Add set(get)_params_proj()

2008-09-19 16:13  jbert

	* sparx/libpy/development.py: stability, trivial change

2008-09-19 15:37  jbert

	* sparx/libpy/applications.py: K-means and BDB trivial change

2008-09-19 15:33  zyang

	* sparx/: bin/sxheader.py, libpy/applications.py: Add backup and
	  restore operation to the header function

2008-09-19 15:31  jbert

	* sparx/libpy/projection.py: Cml, change export data with new
	  params3D

2008-09-19 15:05  ppenczek

	* sparx/test/3DA/3dg.py: [no log message]

2008-09-19 14:45  jbert

	* sparx/libpy/: development.py, statistics.py: K-means and
	  stability, change process with bdb format

2008-09-19 11:59  zyang

	* sparx/libpy/applications.py: Fix a small bug in header()

2008-09-19 11:49  zyang

	* sparx/libpy/applications.py: An overhaul to the header()
	  function, now support action (zero, print, import, export,
	  randomize) on parameters xform.align2d and xform.align3d for both
	  hdf and bdb file.

2008-09-19 11:32  stevel

	* libpyEM/EMAN2db.py: Fix return 0 on image write

2008-09-19 10:25  zyang

	* sparx/libpy/utilities.py: Fix a bug in get_params3D()

2008-09-18 17:23  woolford

	* examples/e2alignmenttest.py, libEM/aligner.cpp, libEM/aligner.h,
	  libEM/emdata.cpp, libEM/emdata.h, libEM/emdata_metadata.h,
	  libEM/vec3.h: aligner work

2008-09-18 16:07  zyang

	* sparx/libpy/: alignment.py, utilities.py: Fix the bug in
	  write_header() and write_headers()

2008-09-18 15:00  stevel

	* examples/shrinkbigimage.py: Shrinks large volumes which won't fit
	  into memory

2008-09-18 14:25  jbert

	* sparx/libpy/statistics.py: k-means, code for bdb format and
	  params2D

2008-09-18 13:24  ppenczek

	* libEM/projector.cpp, sparx/test/3DA/3dg.py,
	  sparx/libpy/projection.py: [no log message]

2008-09-18 12:56  ppenczek

	* sparx/test/3DA/3dg.py, libEM/projector.cpp,
	  sparx/libpy/projection.py: [no log message]

2008-09-18 11:09  ppenczek

	* sparx/test/3DA/3dg.py: [no log message]

2008-09-17 17:21  woolford

	* examples/e2alignmenttest.py, libEM/aligner.cpp, libEM/aligner.h,
	  libEM/emdata_metadata.h, libEM/emdata_modular.cpp,
	  libEM/emdata_modular.h, libEM/projector.cpp, libEM/projector.h,
	  libEM/reconstructor_tools.cpp, libEM/transform.cpp,
	  libEM/transform.h, libpyEM/libpyEMData2.cpp: Transform porting
	  work

2008-09-17 15:13  gtang

	* libEM/emdata.h: EMData destructor does not to be virtual

2008-09-16 17:13  woolford

	* sparx/libpy/utilities.py: remove testing code

2008-09-16 17:11  woolford

	* examples/e2alignmenttest.py, libEM/aligner.cpp, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/emdata_metadata.cpp,
	  libEM/emdata_metadata.h, libEM/emobject.cpp, libEM/emobject.h,
	  libEM/hdfio2.cpp, libEM/projector.cpp, libEM/projector.h,
	  libEM/transform.cpp, libEM/transform.h,
	  libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/emdata_pickle.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyTransform2.cpp, libpyEM/libpyTypeConverter2.cpp,
	  libpyEM/typeconverter.cpp, libpyEM/typeconverter.h,
	  libpyEM/qtgui/emimage.py, rt/emdata/test_emobject.cpp,
	  sparx/libpy/utilities.py: Transform can now be an EMObject, and
	  EMData attribute, and pickled

2008-09-16 11:10  woolford

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, rt/pyem/test_transform.py: added
	  get_pre_trans_2d

2008-09-16 11:04  woolford

	* libEM/transform.h, libpyEM/libpyTransform2.cpp,
	  rt/pyem/test_transform.py: Transform supports set_pre_trans

2008-09-11 13:23  woolford

	* libEM/: transform.cpp, transform.h: Transform work -
	  orthogonalization

2008-09-11 11:47  ppenczek

	* sparx/libpy/: applications.py, development.py, fundamentals.py,
	  statistics.py: put mirror into rot_shift2D

2008-09-10 22:35  woolford

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, rt/pyem/test_transform.py: transform
	  work

2008-09-10 15:09  ppenczek

	* sparx/libpy/: alignment.py, applications.py, utilities.py: [no
	  log message]

2008-09-10 15:07  zweig

	* sparx/libpy/utilities.py: change on sen_attr_dict and
	  recv_attr_dict for handling Transform objects

2008-09-10 14:21  woolford

	* libEM/aligner.cpp, libEM/emobject.cpp, libEM/emobject.h,
	  libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, libpyEM/qtgui/emimage3dsym.py,
	  rt/pyem/test_transform.py, utils/CMakeLists.txt,
	  utils/baldwinweights.cpp: transform updates

2008-09-09 19:34  woolford

	* libEM/transform.h, rt/pyem/test_transform.py: more tests added

2008-09-09 17:42  woolford

	* libEM/: transform.cpp, transform.h: minor changes

2008-09-09 17:26  woolford

	* libEM/: transform.cpp, transform.h: minor changes

2008-09-09 17:05  woolford

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, rt/pyem/test_transform.py: minor
	  changes

2008-09-09 15:28  gtang

	* rt/pyem/test_transform.py: test Transform object as image
	  attribute

2008-09-09 15:07  gtang

	* libpyEM/: libpyTypeConverter2.cpp, typeconverter.cpp,
	  typeconverter.h: Enable Transform object to be file attribute.

2008-09-09 15:03  woolford

	* libEM/transform.cpp, rt/pyem/test_transform.py: scale error
	  limits enforced in Transform

2008-09-09 14:59  zweig

	* pyemtbx/boxertools.py: add CCF threshold to PawelAutoBoxer

2008-09-09 14:58  zweig

	* programs/e2boxer.py: add CCFHistogram

2008-09-09 14:58  zweig

	* libpyEM/qtgui/emimage2d.py: set shapechange flag for delShape

2008-09-09 14:32  woolford

	* libEM/: emdata_core.cpp, transform.cpp: minor fixes

2008-09-09 14:26  woolford

	* libEM/emdata.cpp, libEM/emdata_core.cpp, libEM/emdata_core.h,
	  libEM/emobject.cpp, libEM/emobject.h, libEM/tifio.cpp,
	  libEM/transform.cpp, libEM/transform.h, libEM/util.cpp,
	  libEM/util.h, libpyEM/libpyTransform2.cpp,
	  libpyEM/qtgui/emimage.py, programs/e2display.py: EMObject has
	  Transform, and Transform updates

2008-09-08 23:43  woolford

	* libpyEM/qtgui/emimage.py, programs/e2display.py: resolved the
	  display issue

2008-09-08 17:56  gtang

	* libEM/: aligner.cpp, byteorder.h, emdata.cpp, emdata.h,
	  polardata.cpp, reconstructor.cpp, reconstructor_tools.cpp,
	  util.h, sparx/emdata_sparx.cpp, sparx/util_sparx.cpp: fix for the
	  win32 platform

2008-09-08 17:49  woolford

	* libEM/transform.cpp, rt/pyem/test_aligner.py: case sensitivity
	  fix

2008-09-08 17:12  gtang

	* libEM/: boxingtools.cpp, processor.cpp, processor.h,
	  reconstructor.cpp, transform.cpp: fix for the win32 platform

2008-09-08 16:43  woolford

	* libEM/emobject.cpp, libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, rt/pyem/test_transform.py: Transform
	  2d adaptions and typing enforced

2008-09-08 14:10  woolford

	* libEM/transform.cpp, libEM/transform.h,
	  rt/pyem/test_transform.py: Transform uses tx not dx

2008-09-05 20:13  woolford

	* rt/pyem/test_transform.py, libEM/reconstructor.cpp,
	  libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, libpyEM/libpyTypeConverter2.cpp:
	  Symmetry3D uses Transform

2008-09-05 18:30  woolford

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, libpyEM/libpyTypeConverter2.cpp,
	  libpyEM/typeconverter.h, rt/pyem/test_transform.py: New Transform
	  stable

2008-09-05 17:56  gtang

	* sparx/doc/: Makefile, TOC.tex, rm_preamble.py, sparx.pdf,
	  sparx.ps, sparx.tex, chapters/Golem/Fundamentals.tex,
	  chapters/Golem/GOLEM_documentation.tex,
	  chapters/Golem/GOLEM_manual.tex, chapters/Golem/dev.tex,
	  chapters/intro/adding-documentation.tex,
	  chapters/intro/intro.tex: remove sparx/doc directory

2008-09-05 16:34  gtang

	* sparx/bin/CMakeLists.txt: [no log message]

2008-09-05 15:28  gtang

	* CMakeLists.txt, sparx/CMakeLists.txt, sparx/bin/CMakeLists.txt,
	  sparx/libpy/CMakeLists.txt: copy all sparx code into eman2

2008-09-05 15:19  gtang

	* sparx/: README, __init__.py, bin/Stefan_ali3d_m.py,
	  bin/Stefan_sxali3d_d.py, bin/Stefan_sxali3d_m.py,
	  bin/bootstrap1.py, bin/bootstrap2.py, bin/bootstrap3.py,
	  bin/sparx, bin/sxali2d_a.py, bin/sxali2d_b.py, bin/sxali2d_c.py,
	  bin/sxali2d_cls_mref.py, bin/sxali2d_cross_res.py,
	  bin/sxali2d_e.py, bin/sxali2d_m.py, bin/sxali2d_ra.py,
	  bin/sxali2d_rac.py, bin/sxali2d_w.py, bin/sxali2d_w_mf.py,
	  bin/sxali3d_b.py, bin/sxali3d_d.py, bin/sxali3d_e.py,
	  bin/sxali3d_em.py, bin/sxali3d_f.py, bin/sxali3d_m.py,
	  bin/sxali_SSNR.py, bin/sxali_param_2d_to_3d.py, bin/sxali_vol.py,
	  bin/sxaliunified.py, bin/sxanghist.py, bin/sxapply_ali_params.py,
	  bin/sxauto_picking.py, bin/sxave_ali.py,
	  bin/sxbootstrap_genbuf.py, bin/sxbootstrap_run.py,
	  bin/sxbootstrap_smp.py, bin/sxcmlines_optall.py,
	  bin/sxcopyfromtif.py, bin/sxcpy.py, bin/sxdefocus_calc.py,
	  bin/sxdele_alist.py, bin/sxfactcoords.py, bin/sxfind_struct.py,
	  bin/sxheader.py, bin/sxihrsr.py, bin/sximgstat.py,
	  bin/sxincpca.py, bin/sxincvar.py, bin/sxk_means.py,
	  bin/sxk_means_groups.py, bin/sxnormal_prj.py,
	  bin/sxnormal_prj_3.py, bin/sxnormal_prj_4.py,
	  bin/sxnormal_prj_5.py, bin/sxparams_2D_to_3D.py,
	  bin/sxparams_3D_to_2D.py, bin/sxpca.py,
	  bin/sxprepare_2d_forPCA.py, bin/sxproject3d.py, bin/sxpufit.py,
	  bin/sxra_cef.py, bin/sxrecons3d_f.py, bin/sxrecons3d_n.py,
	  bin/sxrefvol.py, bin/sxrot_sym.py, bin/sxselect_even.py,
	  bin/sxssnr3d.py, bin/sxstat_even.py, bin/sxtemp.py,
	  bin/sxtransform2d.py, bin/sxvarimax.py, bin/sxwelch_psp.py,
	  bin/sxwelch_psp_tilt.py, doc/Makefile, doc/TOC.tex,
	  doc/rm_preamble.py, doc/sparx.pdf, doc/sparx.ps, doc/sparx.tex,
	  doc/chapters/Golem/Fundamentals.tex,
	  doc/chapters/Golem/GOLEM_documentation.tex,
	  doc/chapters/Golem/GOLEM_manual.tex, doc/chapters/Golem/dev.tex,
	  doc/chapters/intro/adding-documentation.tex,
	  doc/chapters/intro/intro.tex, libpy/__init__.py,
	  libpy/alignment.py, libpy/applications.py, libpy/development.py,
	  libpy/filter.py, libpy/fundamentals.py, libpy/global_def.py,
	  libpy/morphology.py, libpy/projection.py,
	  libpy/reconstruction.py, libpy/sideprojectionmatch.py,
	  libpy/sideprojectionmatchB.py, libpy/sparx.py,
	  libpy/statistics.py, libpy/stefan.py, libpy/user_functions.py,
	  libpy/utilities.py, templates/3dg.py,
	  templates/import_SPIDER_refi.py, templates/randomize2d.py,
	  templates/search_ali3d.py, test/1MNF.pdb, test/3dg.py,
	  test/BC.spi, test/I0_1.75.out, test/I0_backft_1.75.out,
	  test/I0fft_1.75.out, test/I0filt_1.75.out, test/I0img_1.75.out,
	  test/Makefile, test/NOTES, test/aaa.py, test/aab.py, test/aac.py,
	  test/aad.py, test/aae.py, test/aaf.py, test/aag.py, test/aah.py,
	  test/aat.py, test/apmq.py, test/b01.mol, test/compgcc,
	  test/doapmd.cpp, test/doapmq.cpp, test/dpw2_close_b.hrs,
	  test/fourp.py, test/kbplot2.py, test/main_example.py,
	  test/model001.tcp, test/model1_var2a.pdb, test/ormq.py,
	  test/pdb_1.py, test/polar.py, test/pw2_close_b.hrs, test/sinh.py,
	  test/sinh_1.75.out, test/sinh_disc_1.75.out, test/spidfft.cpp,
	  test/spidfft.h, test/spidutil.cpp, test/spidutil.h,
	  test/test.spi, test/test30.spi, test/test_ft.py, test/test_pw.py,
	  test/testc.cpp, test/tests.cpp, test/tf2d0001.tfc,
	  test/vol001.tfc, test/2DA/2da.py, test/2DA/2db.py,
	  test/2DA/2de.py, test/3DA/3da.py, test/3DA/3db.py,
	  test/3DA/3de.py, test/3DA/3dg.py, test/3DA/rec2d_test.py,
	  test/EXAMPLES_FFT/fft-n-doc.txt, test/EXAMPLES_FFT/fft-n.tgz,
	  test/EXAMPLES_FFT/fft2.txt, test/EXAMPLES_FFT/fftsing-doc.txt,
	  test/EXAMPLES_FFT/fftsing.tgz, test/EXAMPLES_FFT/mixfft05.zip,
	  test/EXAMPLES_FFT/rsplitfft.c, test/FFT/fftmcf.f,
	  test/FFT/fmr_1.f, test/FFT/fmr_2.f, test/FFT/fmrs_1.f,
	  test/FFT/fmrs_1d.f, test/FFT/fmrs_2.f, test/FFT/fmrs_2dr.f,
	  test/FFT/fmrs_2r.f, test/FFT/fmrs_3.f, test/FFT/fmrs_3dr.f,
	  test/FFT/fmrs_3r.f, test/FP/fint.f, test/FP/fint3.f,
	  test/FP/four1a_fp.f, test/bootstrap/Makefile,
	  test/bootstrap/addnoise.py, test/bootstrap/addnoise2.py,
	  test/bootstrap/alifilter.py, test/bootstrap/apply_ctf_fix.py,
	  test/bootstrap/apply_norm.py, test/bootstrap/average.py,
	  test/bootstrap/bootstrap_genbuf.py,
	  test/bootstrap/bootstrap_nn.py,
	  test/bootstrap/bootstrap_nnctf.py,
	  test/bootstrap/bootstrap_nnctf_2.py, test/bootstrap/bs_efg0.job,
	  test/bootstrap/btwl.py, test/bootstrap/ccc.py,
	  test/bootstrap/change_norm.py, test/bootstrap/circumference.py,
	  test/bootstrap/convert.py, test/bootstrap/detail_ccc.py,
	  test/bootstrap/documentation.h, test/bootstrap/extract_attr.py,
	  test/bootstrap/filt_by_rops.py, test/bootstrap/fraccord.py,
	  test/bootstrap/fsc.py, test/bootstrap/histgram.py,
	  test/bootstrap/incpca.py, test/bootstrap/incvar.py,
	  test/bootstrap/incvar_only.py, test/bootstrap/info.py,
	  test/bootstrap/make_model.py, test/bootstrap/make_sigma.py,
	  test/bootstrap/make_special_model.py, test/bootstrap/mask.py,
	  test/bootstrap/mask_by_vol.py, test/bootstrap/mympimodule.c,
	  test/bootstrap/nn_ctf.py, test/bootstrap/pack.py,
	  test/bootstrap/par_nn_ctf.py, test/bootstrap/pca.py,
	  test/bootstrap/pick_sphere.py, test/bootstrap/prj_eigvol.py,
	  test/bootstrap/proj.py, test/bootstrap/proj_ctf.py,
	  test/bootstrap/renorm.py, test/bootstrap/resume_apply_norm.py,
	  test/bootstrap/scale_by_eigval.py, test/bootstrap/select_even.py,
	  test/bootstrap/split.py, test/bootstrap/stat_even.py,
	  test/bootstrap/subtract.py, test/bootstrap/test_mpi.py,
	  test/bootstrap/trans-applyctf.py, test/bootstrap/trans-noctf.py,
	  test/bootstrap/trans.py, test/bootstrap/txtccc.py,
	  test/bootstrap/variance.py, test/bootstrap/varimax.py,
	  test/bootstrap/zslice.py, test/test_scripts/test_rot.py: copy all
	  sparx code into eman2

2008-09-05 15:18  zweig

	* programs/e2boxer.py, pyemtbx/boxertools.py: change to Pawel's
	  method

2008-09-05 13:53  woolford

	* libEM/transform.cpp, rt/pyem/test_transform.py: in the middle of
	  changes

2008-09-05 13:31  ppenczek

	* programs/e2boxer.py: [no log message]

2008-09-05 12:11  woolford

	* libEM/emobject.h, libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, libpyEM/libpyTypeConverter2.cpp: in
	  the middle of changes

2008-09-05 11:54  zyang

	* libEM/sparx/util_sparx.cpp: Fix a bug for calculating standard
	  deviation.

2008-09-05 09:32  gtang

	* libEM/transform.cpp: small fix

2008-09-04 23:05  woolford

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, rt/pyem/test_transform.py: Transform
	  introduced

2008-09-04 09:50  zyang

	* libEM/processor.cpp: Fix a bug in puregaussian()

2008-09-04 09:23  gtang

	* rt/pyem/test_processor.py: [no log message]

2008-09-03 20:26  woolford

	* images/swarm_icon.png: image work

2008-09-03 20:12  woolford

	* images/CMakeLists.txt, images/black_box.png, images/eman.png,
	  images/freeze_swirl.png, images/green_boxes.png,
	  images/pp_boxer_icon.png, images/swarm_icon.png,
	  images/white_box.png, libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emimage2d.py, programs/e2boxer.py,
	  pyemtbx/boxertools.py: boxer work

2008-09-03 17:04  zweig

	* programs/e2boxer.py: always use self.autoboxer to write box
	  images

2008-09-03 17:03  zweig

	* pyemtbx/boxertools.py: more changes to PawelAutoBoxer

2008-09-03 16:30  gtang

	* rt/pyem/test_typeconverter.py: add unit test for numpy2em for
	  array not in 4-byte float

2008-09-03 16:29  gtang

	* libpyEM/typeconverter.cpp: fix the numpy2em() function. Python
	  float is 8 byte. Force a convertion for array not in a 4-byte
	  float.

2008-09-03 16:19  zweig

	* libpyEM/qtgui/emshape.py: fix a bug: sometime list can be
	  destroyed

2008-09-03 13:53  zweig

	* programs/e2boxer.py: function name change

2008-09-03 13:45  zweig

	* pyemtbx/boxertools.py: new normalization of the selected
	  particles

2008-09-03 11:36  gtang

	* libpyEM/: typeconverter.cpp, typeconverter.h: fix the numpy2em()
	  function. Python float is 8 byte.

2008-09-03 06:43  woolford

	* pyemtbx/boxertools.py: trivial fix

2008-09-02 22:00  woolford

	* libEM/transform.h: trivial change

2008-09-02 21:58  woolford

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, rt/pyem/test_transform.py: Transform
	  work

2008-09-02 18:30  woolford

	* pyemtbx/boxertools.py: another name change and hopefully helpful
	  comments

2008-09-02 18:05  woolford

	* pyemtbx/boxertools.py: name change conflict resolved

2008-09-02 18:03  woolford

	* libEM/transform.cpp, programs/e2boxer.py, pyemtbx/boxertools.py,
	  rt/pyem/test_transform.py: boxer fixes. cache mechanism rewritten

2008-09-02 15:40  zweig

	* pyemtbx/boxertools.py: get coordinates of the box

2008-09-02 14:11  gtang

	* rt/pyem/test_imageio.py: [no log message]

2008-09-02 12:56  zweig

	* programs/e2boxer.py, pyemtbx/boxertools.py: add options to
	  pawel's autobox method

2008-08-29 16:04  zweig

	* programs/e2boxer.py, pyemtbx/boxertools.py: add Pawel's method to
	  e2boxer

2008-08-29 12:25  woolford

	* libpyEM/: EMAN2.py, qtgui/emimagemxrotor.py: mxrotor db
	  alteration

2008-08-29 12:01  woolford

	* libEM/transform.h: trivial fix

2008-08-29 11:34  woolford

	* libEM/emobject.h, libEM/transform.cpp, libEM/transform.h,
	  libpyEM/EMAN2.py, libpyEM/libpyTransform2.cpp: non threatening
	  updates

2008-08-27 22:08  woolford

	* libpyEM/: EMAN2.py, qtgui/emimage2d.py:  display work

2008-08-27 16:48  woolford

	* programs/e2boxer.py, pyemtbx/boxertools.py: trivial changes

2008-08-27 15:45  woolford

	* libpyEM/EMAN2db.py: fixed some db thing

2008-08-27 10:20  gtang

	* libEM/transform.cpp: fix the segfault of rotate_translate() unit
	  test on CentOS5. it's because the uninitialized matrix element in
	  Transform3D object.

2008-08-26 16:13  woolford

	* libEM/transform.cpp, rt/pyem/test_transform.py: fixed flags in
	  Transform3D::get_params

2008-08-26 15:26  woolford

	* libEM/transform.cpp: removed the xform

2008-08-26 15:12  woolford

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp: add get_params and set_params to
	  Transform3D

2008-08-25 13:44  zyang

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp: Reverse the change made on Friday.
	  For unknown reason, it doesn't work properly.

2008-08-23 11:50  gtang

	* libEM/reconstructor.cpp: fix for header inclusion path

2008-08-22 17:44  woolford

	* programs/e2boxer.py: transform work

2008-08-22 17:36  woolford

	* libEM/transform.cpp, libpyEM/libpyTransform2.cpp: transform work

2008-08-22 17:29  zweig

	* libEM/sparx/emdata_sparx.cpp: fix a bug: image comes in for
	  padding might have pre-set offsets

2008-08-22 16:56  woolford

	* libEM/transform.cpp, libEM/transform.h, libpyEM/EMAN2.py,
	  libpyEM/libpyTransform2.cpp: transform work

2008-08-21 21:51  woolford

	* libEM/transform.cpp, libpyEM/qtgui/emimage2d.py: woops

2008-08-21 20:57  woolford

	* libpyEM/qtgui/emimage2d.py: transform related fixes

2008-08-21 14:56  woolford

	* libpyEM/libpyTransform2.cpp: fixes

2008-08-21 13:22  stevel

	* libpyEM/: EMAN2.py, EMAN2db.py: Change / to # in bdb: specs

2008-08-21 11:07  zweig

	* libEM/reconstructor.cpp: make changes to avoid warning messages

2008-08-20 22:32  woolford

	* pyemtbx/boxertools.py: boxer documentation and class design

2008-08-20 22:28  woolford

	* pyemtbx/boxertools.py: boxer documentation and class design

2008-08-20 22:21  woolford

	* libpyEM/qtgui/emimage2d.py, programs/e2boxer.py,
	  pyemtbx/boxertools.py: boxer documentation and class design

2008-08-20 20:04  woolford

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimagemxrotor.py, programs/e2boxer.py,
	  programs/e2display.py, pyemtbx/boxertools.py: boxer related fixes

2008-08-20 15:58  woolford

	* libEM/reconstructor.cpp, libEM/transform.cpp, libEM/transform.h,
	  libEM/vec3.h, libpyEM/libpyTransform2.cpp, programs/e2boxer.py,
	  pyemtbx/boxertools.py: transform updates

2008-08-20 14:38  woolford

	* CMakeLists.txt, images/CMakeLists.txt, images/boxer_erase.png,
	  images/boxer_unerase.png, programs/e2boxer.py,
	  pyemtbx/boxertools.py: boxer updates

2008-08-20 12:04  woolford

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp: transform work

2008-08-20 11:46  stevel

	* libpyEM/EMAN2db.py: Improved close functionality

2008-08-20 09:19  gtang

	* rt/pyem/test_processor.py: unit test update

2008-08-19 22:47  stevel

	* libpyEM/EMAN2db.py: rename db_open_env to db_open_dict

2008-08-19 22:35  woolford

	* libEM/: transform.cpp, transform.h: vector/transform work

2008-08-19 18:20  woolford

	* libEM/log.cpp, libEM/log.h, libEM/vec3.h,
	  libpyEM/libpyTransform2.cpp, rt/pyem/test_transform.py: vector
	  fixes

2008-08-19 17:31  woolford

	* libEM/: emdata.cpp, projector.cpp, vec3.h: vector work

2008-08-19 17:12  woolford

	* libEM/emdata.cpp, libEM/transform.cpp, libEM/transform.h,
	  libEM/vec3.h, libpyEM/libpyTransform2.cpp, pyemtbx/boxertools.py,
	  rt/pyem/test_transform.py: vector and transform updates

2008-08-19 16:02  stevel

	* libpyEM/EMAN2db.py: Deal with current directory dereferencing in
	  db

2008-08-19 13:57  stevel

	* libpyEM/EMAN2db.py: Fixed read_images for bdb.

2008-08-19 01:25  stevel

	* libpyEM/EMAN2db.py: Fixed problem with .eman2db in home dir.

2008-08-18 10:38  jbert

	* libEM/sparx/util_sparx.cpp: fix bug in coveig for py

2008-08-17 11:46  gtang

	* programs/e2avg_ffts.py: copy Mike Schmid's avg_ffts.py to
	  e2avg_ffts.py

2008-08-17 11:40  gtang

	* programs/e2tomohunter.py: port tomohunter from EMAN1 to EMAN2,
	  init version

2008-08-15 20:54  woolford

	* libEM/emdata_modular.cpp, libEM/emdata_modular.h,
	  libEM/processor.cpp, libEM/projector.cpp,
	  libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libEM/transform.cpp, libEM/transform.h, libpyEM/libpyEMData2.cpp,
	  programs/e2project3d.py, pyemtbx/boxertools.py: some transform
	  work, general stuff

2008-08-15 17:23  jbert

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: coveig wrap for py code

2008-08-15 15:41  woolford

	* pyemtbx/: boxertools.py: boxer updates

2008-08-15 15:37  woolford

	* pyemtbx/boxertools.py: boxer updates

2008-08-15 15:34  woolford

	* libEM/processor.cpp, libEM/processor.h, pyemtbx/boxertools.py:
	  boxer updates

2008-08-15 13:36  woolford

	* libpyEM/EMAN2.py, programs/e2boxer.py, pyemtbx/boxertools.py: in
	  the middle of boxer work

2008-08-15 09:16  ppenczek

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h, libpyEM/libpyUtils2.cpp:  downsample

2008-08-14 22:14  woolford

	* libEM/emdata.cpp, libEM/projector.cpp, libEM/reconstructor.cpp,
	  libEM/transform.cpp, libpyEM/libpyTransform2.cpp,
	  libpyEM/qtgui/emglplot.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemxrotor.py, libpyEM/qtgui/emimagerotor.py,
	  programs/e2boxer.py: general work

2008-08-14 17:52  ppenczek

	* libpyEM/: libpyEMData2.cpp, libpyUtils2.cpp: begin sB convolution

2008-08-14 17:06  ppenczek

	* libpyEM/libpyReconstructor2.cpp: change on newfile_store

2008-08-14 17:06  ppenczek

	* libEM/: reconstructor.cpp, reconstructor.h: performance
	  improvment of newfile_store

2008-08-14 16:46  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h, util_sparx.cpp,
	  util_sparx.h: begin sB convolution

2008-08-13 22:15  woolford

	* libEM/boxingtools.cpp, libEM/emdata.cpp,
	  libpyEM/libpyEMData2.cpp, libpyEM/qtgui/emglplot.py,
	  programs/e2boxer.py, pyemtbx/boxertools.py,
	  rt/pyem/test_aligner.py: rotational alignment works for odd
	  images, boxer updates

2008-08-13 20:14  woolford

	* libEM/boxingtools.cpp, libEM/boxingtools.h,
	  libpyEM/libpyBoxingTools2.cpp, libpyEM/qtgui/emimage2d.py,
	  programs/e2boxer.py, pyemtbx/boxertools.py: boxer related work

2008-08-13 15:13  woolford

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libEM/reconstructor_tools.cpp, libEM/reconstructor_tools.h,
	  libEM/transform.cpp, libpyEM/qtgui/emimagemx.py,
	  programs/e2make3d.py: reconstructor fix - weighting bug resolved

2008-08-13 10:23  gtang

	* CMakeLists.txt, fonts/CMakeLists.txt: install font file into
	  EMAN2/fonts

2008-08-13 10:18  woolford

	* libpyEM/qtgui/emimagemx.py, pyemtbx/boxertools.py: fixed display
	  bug

2008-08-12 18:52  woolford

	* CMakeLists.txt, examples/e2alignmenttest.py,
	  fonts/DejaVuSerif.ttf, fonts/readme.txt, libEM/reconstructor.cpp,
	  libpyEM/EMAN2.py, libpyEM/qtgui/em3Dfonts.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimagemxrotor.py,
	  libpyEM/qtgui/emimagerotor.py, programs/e2make3d.py: we now
	  distribute a fonts file

2008-08-12 16:00  zyang

	* libEM/sparx/emdata_sparx.cpp: Fix a bug in fsc

2008-08-12 13:35  zyang

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/libpyEMData2.cpp: Add function fouriergridrot_shift2d()

2008-08-12 10:06  zweig

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libpyEM/libpyReconstructor2.cpp: performance improvement

2008-08-12 10:02  zyang

	* libEM/sparx/emdata_sparx.cpp: Trival change

2008-08-12 09:49  stevel

	* libEM/sparx/emdata_sparx.h: fix typo from Pawel's group

2008-08-11 15:30  zyang

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h, util_sparx.cpp,
	  util_sparx.h: Change the way the function fouriergridrot() is
	  done.

2008-08-10 02:02  stevel

	* programs/e2ctf.py: Work on CTF fitting

2008-08-09 16:20  gtang

	* rt/pyem/test_emdata.py: unit test fix

2008-08-08 16:37  gtang

	* rt/pyem/test_cmp.py: fix the unit test errors

2008-08-08 15:59  gtang

	* rt/pyem/test_emdata.py: fix the unit test errors

2008-08-07 17:42  gtang

	* libEM/testutil.cpp, rt/pyem/test_imageio.py: unit test fix for
	  test_imageio

2008-08-07 17:08  jbert

	* libEM/sparx/util_sparx.cpp: change warning print out for Voronoi

2008-08-07 12:28  gtang

	* libEM/processor.h: fix the mask.ringmean processor.

2008-08-06 18:35  gtang

	* libEM/processor.cpp, libEM/util.h, rt/pyem/test_processor.py:
	  unit test fix

2008-08-06 10:36  ppenczek

	* libEM/sparx/emdata_sparx.h: cleaning

2008-08-04 13:21  zyang

	* libEM/emdata.h: [no log message]

2008-08-04 13:21  ppenczek

	* libEM/reconstructor.cpp: cleaning

2008-08-04 12:51  zweig

	* libEM/: emdata.h, processor.cpp, projector.cpp,
	  reconstructor.cpp, sparx/fundamentals.h: merge changefft patch

2008-08-04 11:41  zweig

	* libEM/CMakeLists.txt, libEM/processor.cpp,
	  libEM/reconstructor.cpp, libEM/sparx/emdata_sparx.cpp,
	  libEM/sparx/emdata_sparx.h, libEM/sparx/fourierfilter.cpp,
	  libEM/sparx/fundamentals.cpp, libEM/sparx/fundamentals.h,
	  libEM/sparx/normpadft.cpp, libEM/sparx/normpadft.h,
	  libEM/sparx/util_sparx.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyFundamentals2.cpp: merge changefft patch

2008-08-02 10:16  gtang

	* libEM/transform.cpp: fix for VS2005 compilation

2008-08-01 22:34  woolford

	* libEM/aligner.cpp: got rid of some print statements

2008-08-01 18:54  woolford

	* examples/e2alignmenttest.py: aligner test script added, general
	  tweaks

2008-08-01 18:43  woolford

	* examples/e2alignmenttest.py, libEM/aligner.cpp,
	  libEM/emdata_core.cpp, libEM/emdata_core.h,
	  libpyEM/libpyEMData2.cpp, programs/e2classaverage.py: aligner
	  test script added, general tweaks

2008-08-01 16:23  woolford

	* examples/e2alignmenttest.py, libEM/transform.cpp,
	  rt/pyem/test_aligner.py: alignment work

2008-08-01 15:57  stevel

	* libpyEM/EMAN2db.py: Backwards compatibility test

2008-08-01 15:03  gtang

	* libEM/: aligner.cpp, projector.cpp, transform.h,
	  sparx/util_sparx.cpp: fix for VS2005 compilation

2008-08-01 14:04  zweig

	* libEM/sparx/emdata_sparx.cpp: use copy_head to create new image
	  which retain the attributes from the old image

2008-08-01 14:04  zweig

	* libEM/reconstructor.cpp: use false to replace 0

2008-08-01 14:03  zweig

	* libEM/processor.cpp: delete intermediate image

2008-08-01 13:58  zyang

	* libEM/: CMakeLists.txt, emdata.h, sparx/emdata_sparx.cpp,
	  sparx/emdata_sparx.h, sparx/normpadft.cpp, sparx/normpadft.h:
	  Remove normpadft.cpp and move the contents to emdata_sparx.cpp

2008-08-01 12:27  ppenczek

	* libEM/: processor.cpp, sparx/fourierfilter.cpp,
	  sparx/fundamentals.cpp: major changes

2008-08-01 11:38  zyang

	* libEM/sparx/emdata_sparx.cpp: Fix a bug in norm_pad()

2008-08-01 11:01  ppenczek

	* libEM/projector.cpp, libEM/reconstructor.cpp,
	  libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libEM/sparx/fourierfilter.cpp, libEM/sparx/fundamentals.cpp,
	  libEM/sparx/fundamentals.h, libEM/sparx/normpadft.cpp,
	  libEM/sparx/util_sparx.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyFundamentals2.cpp: major changes

2008-07-31 22:52  woolford

	* libEM/aligner.cpp, rt/pyem/test_aligner.py: aligment related

2008-07-31 22:28  woolford

	* libEM/aligner.cpp: rotational footprint fixes

2008-07-31 22:24  woolford

	* libEM/aligner.cpp, libEM/emdata.cpp, rt/pyem/test_aligner.py:
	  rotational footprint fixes

2008-07-31 22:03  woolford

	* libEM/aligner.cpp, libEM/cmp.cpp, libEM/emdata.cpp,
	  libEM/emdata_core.cpp, libEM/emdata_core.h,
	  libpyEM/libpyEMData2.cpp: alignment related fixes

2008-07-31 18:25  woolford

	* libEM/aligner.cpp, libEM/aligner.h, libEM/emdata.cpp,
	  libEM/emdata.h, libpyEM/EMAN2.py, libpyEM/libpyEMData2.cpp:
	  alignment fixes - rfp modes temporarily introduced

2008-07-31 18:01  ppenczek

	* libEM/processor.cpp, libEM/sparx/emdata_sparx.cpp,
	  libEM/sparx/emdata_sparx.h, libEM/sparx/fourierfilter.cpp,
	  libEM/sparx/fundamentals.cpp, libpyEM/libpyEMData2.cpp: add
	  depad_corner

2008-07-31 16:56  zyang

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/libpyEMData2.cpp: Remove center_padded(), no use now,
	  image are supposed to be padded in the center.

2008-07-31 16:23  zyang

	* libEM/reconstructor.cpp, libpyEM/libpyEMData2.cpp: Delete
	  zeropad_ntimes_fft_shuffle

2008-07-31 16:11  zyang

	* libEM/sparx/: normpadft.cpp, normpadft.h: Delete
	  zeropad_ntimes_fft_shuffle()

2008-07-31 15:47  gtang

	* libpyEM/CMakeLists.txt: compile EMAN2 with static FTGL library

2008-07-31 15:40  zweig

	* libpyEM/libpyFundamentals2.cpp: replace norm_pad_ft with norm_pad

2008-07-31 15:36  zweig

	* libEM/reconstructor.cpp: replace zeropad_ntime with norm_pad

2008-07-31 15:36  ppenczek

	* libEM/sparx/: fundamentals.cpp, normpadft.cpp: [no log message]

2008-07-31 15:35  gtang

	* libpyEM/CMakeLists.txt: compile EMAN2 with static FTGL library

2008-07-31 15:33  zweig

	* libEM/sparx/: fourierfilter.cpp, normpadft.cpp, util_sparx.cpp:
	  replace pad_fft with norm_pad, replace
	  postift_depad_corner_inplace with depad

2008-07-31 15:32  zweig

	* libEM/sparx/fundamentals.cpp: replace norm_pad_ft with norm_pad +
	  do_ift_inplace, replace postift_depad_corner_inplace with depad

2008-07-31 15:24  ppenczek

	* libEM/reconstructor.cpp: [no log message]

2008-07-31 15:15  ppenczek

	* libpyEM/libpyEMData2.cpp: shrink fixed

2008-07-31 15:15  zweig

	* libEM/projector.cpp: replace pad_fft with norm_pad and
	  fft_inplace

2008-07-31 15:12  zyang

	* libEM/projector.cpp: [no log message]

2008-07-31 15:02  ppenczek

	* libEM/processor.cpp: shrink fixed

2008-07-31 15:00  gtang

	* CMakeLists.txt, libEM/CMakeLists.txt: compile EMAN2 with static
	  FTGL library

2008-07-31 14:59  zweig

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h, fundamentals.h,
	  normpadft.cpp: new function depad

2008-07-31 14:57  gtang

	* libEM/CMakeLists.txt: non-standard include path for FTGL

2008-07-31 14:55  woolford

	* libEM/aligner.cpp, libEM/aligner.h, libEM/emdata.cpp,
	  libEM/emdata_core.cpp, libEM/emdata_core.h,
	  libpyEM/libpyEMData2.cpp: fixed a memory leak problem

2008-07-31 14:43  ppenczek

	* libpyEM/libpyEMData2.cpp, libpyEM/libpyFundamentals2.cpp,
	  libEM/processor.cpp, libEM/sparx/emdata_sparx.cpp,
	  libEM/sparx/fundamentals.h, libEM/sparx/normpadft.cpp,
	  libEM/sparx/normpadft.h: [no log message]

2008-07-31 12:29  zweig

	* libEM/reconstructor.cpp: test branching

2008-07-31 12:04  ppenczek

	* libEM/emdata_transform.cpp: cleaning

2008-07-31 11:45  ppenczek

	* libEM/sparx/native_fft.cpp: cleaning

2008-07-31 11:34  ppenczek

	* libEM/sparx/fundamentals.cpp: cleaning

2008-07-31 11:02  ppenczek

	* libEM/CMakeLists.txt, libEM/SConscript, libpyEM/libpyUtils2.cpp:
	  unused code removed

2008-07-31 10:49  ppenczek

	* libEM/sparx/: SparxIO.cpp, SparxIO.h, Tokenizer.cpp, Tokenizer.h:
	  [no log message]

2008-07-30 22:18  woolford

	* libEM/emdata.cpp, libpyEM/libpyEMData2.cpp: updates

2008-07-30 19:16  woolford

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emdata_core.cpp, libEM/processor.cpp,
	  programs/e2classaverage.py: in the middle of rfp fixes. works
	  better but it's slow

2008-07-30 15:45  gtang

	* libEM/reconstructor.cpp: fix for VS2005 compilation

2008-07-29 22:55  woolford

	* programs/e2classaverage.py, rt/pyem/test_cmp.py: aligner work

2008-07-29 21:50  woolford

	* libEM/emdata_core.cpp, programs/e2classaverage.py: aligner fixes

2008-07-29 21:02  woolford

	* libEM/aligner.cpp, libEM/aligner.h, libEM/emdata.cpp,
	  libEM/emdata_core.cpp, libEM/emdata_core.h,
	  libEM/emdata_modular.h, libEM/processor.cpp, libEM/processor.h,
	  libpyEM/EMAN2.py, programs/e2classaverage.py,
	  rt/pyem/test_aligner.py, rt/pyem/test_processor.py: aligner work

2008-07-29 09:26  zweig

	* libpyEM/libpyReconstructor2.cpp: add python binding for
	  newfile_store

2008-07-29 09:25  zweig

	* libEM/: reconstructor.cpp, reconstructor.h: add newfile_store
	  used by bootstrap

2008-07-28 22:50  woolford

	* libEM/aligner.cpp, programs/e2classaverage.py: aligner work

2008-07-28 20:07  woolford

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/emftgl.cpp,
	  libEM/emftgl.h, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emimage.py, libpyEM/qtgui/emimagemxrotor.py,
	  programs/e2classaverage.py, programs/e2proc3d.py: aligner fixes

2008-07-28 02:21  stevel

	* examples/clstoclsmx.py, programs/e2refine.py: Working on
	  e2refine2d.py. Looks like a problem with e2classaverage

2008-07-25 20:34  woolford

	* programs/e2boxer.py: interface work

2008-07-25 18:01  woolford

	* libpyEM/CMakeLists.txt, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimagemxrotor.py,
	  libpyEM/qtgui/emrotor.py, programs/e2boxer.py: interface work

2008-07-25 17:49  gtang

	* rt/: pyem/rt.py, pyem/test_aligner.py, pyem/test_averager.py,
	  pyem/test_cmp.py, pyem/test_emdata.py, pyem/test_imageio.py,
	  pyem/test_misc.py, pyem/test_processor.py,
	  pyem/test_reconstructor.py, pyem/test_transform.py,
	  pyem/test_typeconverter.py, pyem/test_utils.py, pyem/test_vec.py,
	  pyem/testlib.py, timetests/test_times.py: authorship

2008-07-25 17:38  gtang

	* pyemtbx/exceptions.py: authorship

2008-07-25 17:35  gtang

	* libpyEM/: emdata_pickle.h, emdata_wrapitems.cpp,
	  emdata_wrapitems.h, libpyUtils2.cpp, util_wrapitems.h: authorship

2008-07-25 17:17  gtang

	* libEM/: emdata_io.cpp, emdata_io.h, emdata_metadata.cpp,
	  emdata_transform.cpp, portable_fileio.h, analyzer.cpp,
	  analyzer.h, boxingtools.cpp, boxingtools.h, emassert.h,
	  emdata_core.cpp, emdata_core.h, emdata_gl.cpp, emdata_gl.h,
	  emdata_metadata.h, emdata_modular.cpp, emdata_modular.h,
	  emdata_transform.h, emftgl.cpp, emftgl.h, exception.cpp,
	  exception.h, isosurface.h, marchingcubes.cpp, marchingcubes.h,
	  pointarray.cpp, pointarray.h, polardata.cpp, polardata.h,
	  randnum.cpp, randnum.h, reconstructor_tools.cpp,
	  reconstructor_tools.h, testutil.cpp, testutil.h, vecmath.h:
	  authorship

2008-07-25 16:17  gtang

	* programs/: e2ali2img.py, e2classaverage.py, e2classify.py,
	  e2msa.py, e2pdb2em.py, e2ptcltrace.py, e2refine2d.py,
	  e2refinemultinoali.py: authorship

2008-07-25 15:55  woolford

	* libpyEM/qtgui/: emimage2d.py, emimagemx.py, emimagemxrotor.py,
	  emimagerotor.py, emrotor.py: interface work

2008-07-25 15:32  woolford

	* libpyEM/qtgui/: emfloatingwidgets.py, emrotor.py: interface work

2008-07-25 14:57  woolford

	* libpyEM/qtgui/: emfloatingwidgets.py, emimage2d.py,
	  emimagemxrotor.py, emimagerotor.py, emrotor.py: interface work

2008-07-25 12:19  woolford

	* libpyEM/CMakeLists.txt, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emimagemxrotary.py,
	  libpyEM/qtgui/emimagemxrotor.py, libpyEM/qtgui/emimagerotary.py,
	  libpyEM/qtgui/emimagerotor.py, programs/e2boxer.py: renamed
	  rotary to rotor

2008-07-25 11:44  zyang

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: Change
	  multiref_peaks_ali2d() to fix the memory leak problem CS:
	  ----------------------------------------------------------------------

2008-07-24 23:12  woolford

	* libpyEM/qtgui/emimagemxrotary.py, pyemtbx/boxertools.py:
	  adaptations to new DB interface

2008-07-24 22:34  stevel

	* libpyEM/EMAN2db.py: Bugfix

2008-07-24 22:16  woolford

	* libEM/aligner.cpp, libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimagemxrotary.py,
	  programs/e2boxer.py, rt/pyem/test_processor.py: mx rotor
	  officially used by boxer

2008-07-24 21:29  stevel

	* libpyEM/EMAN2.py, libpyEM/EMAN2db.py,
	  libpyEM/emdata_wrapitems.cpp, programs/e2dumplog.py: Database
	  updates. DB gone. DBHOME central database for history. im[key]
	  accesses attributes

2008-07-24 15:44  gtang

	* rt/pyem/test_utils.py: fix for the win32 platform

2008-07-24 15:44  gtang

	* libEM/util.cpp: fix for VS2005 compilation

2008-07-24 14:33  gtang

	* libEM/emdata_gl.cpp: fix for Visual Studio 2005 compilation

2008-07-24 10:53  zyang

	* libEM/sparx/util_sparx.cpp: Trival change

2008-07-24 00:34  woolford

	* libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemxrotary.py,
	  programs/e2boxer.py, pyemtbx/boxertools.py: interface fixes

2008-07-23 22:55  woolford

	* libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimagemxrotary.py, libpyEM/qtgui/emimagerotary.py,
	  programs/e2boxer.py: interface fixes

2008-07-23 16:18  gtang

	* libEM/geometry.h: Region::get_ndim() still use origin instead of
	  size, to fix the broken get_clip() operations.

2008-07-22 21:12  woolford

	* programs/e2boxer.py: boxer fix

2008-07-22 18:47  woolford

	* libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimagemxrotary.py, libpyEM/qtgui/emimagerotary.py,
	  programs/e2boxer.py, pyemtbx/boxertools.py: mxrotary being ported
	  to boxer

2008-07-22 15:43  gtang

	* libEM/mrcio.cpp: fix the mrc header to make it consisten with
	  CCP4 software, i.e. IMOD, chimera, etc.

2008-07-22 15:11  gtang

	* libEM/mrcio.cpp: fix the mrc header to make it consisten with
	  CCP4 software, i.e. IMOD, chimera, etc.

2008-07-22 14:49  zyang

	* libEM/sparx/util_sparx.cpp: Trival change

2008-07-22 14:04  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, util_sparx.cpp: crosrng vector

2008-07-22 13:19  woolford

	* libpyEM/qtgui/: emfloatingwidgets.py, emimagemx.py,
	  emimagemxrotary.py: emimagemxrotary stable and fully functional

2008-07-22 10:24  woolford

	* libpyEM/qtgui/: emimagemx.py, emimagemxrotary.py: interface work
	  from mac

2008-07-21 22:39  woolford

	* libEM/emftgl.h, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimagemxrotary.py:
	  interface work

2008-07-21 18:15  ppenczek

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: corrections in crosrng

2008-07-21 14:16  woolford

	* libpyEM/qtgui/emimagemx.py: interface fixes

2008-07-21 14:14  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: [no log message]

2008-07-21 13:15  gtang

	* CMakeLists.txt: add /usr/include/freetype2 to include path, for
	  FTGL

2008-07-21 11:48  gtang

	* libEM/mrcio.cpp: fix the mrc header to make it consisten with
	  CCP4 software, i.e. IMOD, chimera, etc.

2008-07-21 11:25  ppenczek

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: [no log message]

2008-07-20 12:00  ppenczek

	* libEM/sparx/util_sparx.cpp: clearing format

2008-07-19 16:22  gtang

	* libEM/mrcio.cpp, libEM/mrcio.h, programs/e2proc2d.py,
	  programs/e2proc3d.py: fix the mrc 16 bit IO, use short instead
	  unsigned short, which is used by IMOD.

2008-07-18 20:08  woolford

	* libpyEM/qtgui/: emfloatingwidgets.py, emglobjects.py,
	  emimagemx.py, emimagemxrotary.py: interface work, efficiency in
	  emimagemxrotary improved

2008-07-18 12:44  jbert

	* libEM/sparx/util_sparx.cpp: change the helper function for
	  k-means

2008-07-18 12:16  woolford

	* libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimagemxrotary.py, programs/e2boxer.py,
	  pyemtbx/boxertools.py: boxer bugs

2008-07-18 10:58  woolford

	* programs/e2boxer.py: boxer bug fix

2008-07-18 10:37  woolford

	* libpyEM/qtgui/emimagemx.py, programs/e2boxer.py: fixed display
	  error in emimagemx.py

2008-07-18 10:28  woolford

	* libpyEM/qtgui/emimagemx.py: fixed display bug in emimagemx

2008-07-17 22:33  woolford

	* libpyEM/qtgui/: emfloatingwidgets.py, emimage2d.py,
	  emimage2dtex.py, emimage3d.py, emimage3dmorph.py, emimagemx.py,
	  emimagemxrotary.py, emimagerotary.py: emimagemxrotary maturing,
	  nearly done

2008-07-17 17:11  woolford

	* libpyEM/qtgui/emimagemx.py: boxer bug fixes

2008-07-17 17:04  woolford

	* libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimagemxrotary.py, programs/e2boxer.py: boxer bug
	  fixes

2008-07-17 14:52  woolford

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimagemxrotary.py:
	  changed 2D fourier reconstructor name, other interface work

2008-07-17 14:07  woolford

	* libpyEM/qtgui/: emimage3diso.py, emimagemx.py,
	  emimagemxrotary.py: mx rotary related work

2008-07-17 10:43  woolford

	* libpyEM/libpyUtils2.cpp: fixed a compilation problem

2008-07-17 00:13  woolford

	* libEM/emftgl.h: added comments to emftgl.h

2008-07-16 22:36  woolford

	* libEM/emftgl.h, libpyEM/qtgui/emimagemxrotary.py: ftgl and
	  interface work

2008-07-16 22:19  woolford

	* libEM/emftgl.cpp, libEM/emftgl.h, libpyEM/libpyUtils2.cpp,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimagemxrotary.py: ftgl and interface work

2008-07-16 19:16  woolford

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/emdata_gl.cpp,
	  libEM/emftgl.cpp, libEM/emftgl.h, libpyEM/libpyUtils2.cpp,
	  libpyEM/qtgui/em3Dfonts.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimagerotary.py: ftgl is optional (compiler flag,
	  default is OFF) and interface work

2008-07-16 19:02  stevel

	* libpyEM/EMAN2db.py: Permit nodata on read_image.

2008-07-15 22:57  woolford

	* libEM/emdata_gl.cpp, libpyEM/CMakeLists.txt,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/emimagemxrotary.py,
	  libpyEM/qtgui/emimagerotary.py, libpyEM/qtgui/emshape.py,
	  programs/e2boxer.py, pyemtbx/boxertools.py: interface work

2008-07-15 18:08  stevel

	* libpyEM/EMAN2db.py: Can now access DB[string]. set_header,
	  get_header added

2008-07-14 21:41  woolford

	* libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemxrotary.py, programs/e2boxer.py,
	  pyemtbx/boxertools.py: rotary widget and boxer work

2008-07-14 00:18  stevel

	* libpyEM/: EMAN2.py, EMAN2db.py: db->DB, added support for
	  bdb:test?key,key,key specifications

2008-07-11 21:43  woolford

	* libEM/projector.cpp, libpyEM/CMakeLists.txt,
	  libpyEM/qtgui/emdesktop.py, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemxrotary.py,
	  programs/e2boxer.py: boxer uses rotary for thumbs

2008-07-11 17:01  woolford

	* libpyEM/qtgui/emimagemxrotary.py, programs/e2boxer.py: boxer work

2008-07-11 16:19  woolford

	* libEM/emdata.cpp, libEM/emdata_core.cpp, libEM/util.h,
	  pyemtbx/boxertools.py: interface to Util::bilinear_interpolate
	  has changed. EMData::rotate bug fix relating to treatment of
	  boundaries

2008-07-11 10:44  woolford

	* libpyEM/qtgui/emimagemxrotary.py: working on a new widget

2008-07-11 01:29  stevel

	* libpyEM/: EMAN2.py, EMAN2db.py: New database access via
	  read_image, etc

2008-07-10 22:20  woolford

	* libpyEM/qtgui/emfloatingwidgets.py: desktop updates

2008-07-10 21:14  woolford

	* programs/e2boxer.py, pyemtbx/boxertools.py: boxer bug fix

2008-07-10 18:52  woolford

	* libpyEM/qtgui/emfloatingwidgets.py: desktop work

2008-07-10 18:44  woolford

	* libpyEM/qtgui/emfloatingwidgets.py: desktop work

2008-07-10 17:10  gtang

	* programs/e2proc3d.py: mrc8bit and mrc16bit option for MRC for
	  e2proc3d.py

2008-07-10 15:44  zyang

	* libEM/sparx/fourierfilter.cpp: Fix an important bug in filt_ctf()

2008-07-09 22:37  woolford

	* libpyEM/qtgui/emfloatingwidgets.py: desktop work

2008-07-09 13:47  woolford

	* libEM/projector.cpp, libpyEM/qtgui/emfloatingwidgets.py: 2D
	  projector testing code

2008-07-09 13:26  woolford

	* rt/pyem/test_emdata.py: test script fix

2008-07-09 13:22  woolford

	* rt/pyem/test_processor.py: test script fix

2008-07-08 22:11  woolford

	* libEM/processor.h, rt/pyem/test_processor.py: desktop work

2008-07-08 18:55  woolford

	* libpyEM/qtgui/emfloatingwidgets.py: desktop work

2008-07-08 18:30  woolford

	* libpyEM/qtgui/emfloatingwidgets.py: desktop updates

2008-07-08 18:20  woolford

	* libpyEM/qtgui/: emfloatingwidgets.py, emglobjects.py: desktop
	  updates

2008-07-08 15:51  woolford

	* libEM/processor.cpp, rt/pyem/test_processor.py:
	  math.radialaverage processor works in 3D, some test cases made
	  more thorough

2008-07-08 15:02  woolford

	* libEM/processor.cpp, libpyEM/qtgui/emfloatingwidgets.py,
	  pyemtbx/boxertools.py: radial average processor works correctly
	  for odd dimensions

2008-07-08 10:50  jbert

	* libEM/sparx/util_sparx.cpp: fix Voronoi

2008-07-08 01:24  stevel

	* libpyEM/EMAN2db.py: Still working on db: open ops.

2008-07-08 00:09  woolford

	* libpyEM/qtgui/emfloatingwidgets.py: trivial fixes

2008-07-07 22:36  woolford

	* libpyEM/qtgui/emfloatingwidgets.py: desktop work

2008-07-07 19:22  woolford

	* libpyEM/qtgui/: emfloatingwidgets.py, emglobjects.py: desktop
	  work

2008-07-07 15:39  stevel

	* libpyEM/EMAN2db.py: Working on read_image/write_image with db

2008-07-07 01:46  stevel

	* libpyEM/EMAN2db.py: Working on task system

2008-07-06 09:52  gtang

	* rt/pyem/test_processor.py: improve the unit test for 'normalize'
	  processor

2008-07-04 11:14  gtang

	* libEM/: pngio.cpp, tifio.cpp: trivial improvement for
	  readability.

2008-07-04 11:09  gtang

	* programs/e2proc2d.py: add --mrc8bit and --mrc--16bit option.

2008-07-04 10:36  gtang

	* libEM/: imageio.cpp, imageio.h: add 3D image support for
	  ImageIO::getRenderMinMax().

2008-07-04 10:34  gtang

	* libEM/mrcio.cpp: Implement 16 bit MRC file writing support.

2008-07-04 00:24  stevel

	* libpyEM/EMAN2db.py: Minor change. Breaks compatibility in old
	  databases.

2008-07-03 22:02  woolford

	* programs/e2boxer.py, pyemtbx/boxertools.py: e2boxer uses berkeley
	  db

2008-07-03 11:02  woolford

	* pyemtbx/: boxertools.py: boxer bug

2008-07-03 01:54  stevel

	* libpyEM/EMAN2db.py: Replaced EMData i/o functions with new
	  wrapper for intercepting db: names

2008-07-02 22:41  woolford

	* programs/e2boxer.py, pyemtbx/boxertools.py: boxer updates

2008-07-02 16:09  gtang

	* libEM/mrcio.cpp: Fixed MRC/CCP4 compatibility issue.

2008-07-02 15:53  gtang

	* programs/: e2proc2d.py, e2proc3d.py: get the --apix option work
	  for e2proc2d.py and e2proc3d.py

2008-07-02 14:05  woolford

	* programs/e2boxer.py: fixed boxer bug

2008-07-02 12:44  woolford

	* libpyEM/qtgui/: emimage2d.py, emimagemx.py: fixed closed hand
	  cursor issue

2008-07-02 10:34  gtang

	* rt/pyem/test_processor.py: unit test update

2008-07-02 02:06  stevel

	* libpyEM/EMAN2.py, libpyEM/EMAN2db.py, programs/e2dumplog.py:
	  Further additions to database, including its use instead of
	  'shelve' for history when bsddb is available.

2008-07-01 22:31  woolford

	* libpyEM/qtgui/emshape.py, programs/e2boxer.py: boxer updates

2008-07-01 21:42  woolford

	* libEM/projector.cpp: projector stuff

2008-07-01 20:49  woolford

	* libEM/projector.cpp: projector fixes and boxer stuff

2008-07-01 18:34  woolford

	* libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emshape.py, programs/e2boxer.py,
	  pyemtbx/boxertools.py: boxer - boxsize change works, lots of
	  other fixes

2008-07-01 01:09  woolford

	* programs/e2boxer.py, pyemtbx/boxertools.py: boxer updates

2008-07-01 00:47  stevel

	* libpyEM/EMAN2db.py: Further fixes to make database object fully
	  functional

2008-06-30 22:40  woolford

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/util.h, libpyEM/EMAN2.py, programs/e2boxer.py,
	  pyemtbx/boxertools.py: boxer fixes

2008-06-30 18:02  woolford

	* libEM/projector.cpp: projection fixes - boundaries are dealt with

2008-06-30 16:48  woolford

	* libEM/processor.cpp, libEM/processor.h, libEM/projector.cpp,
	  libEM/util.h, libpyEM/qtgui/emimagemx.py, programs/e2boxer.py,
	  pyemtbx/boxertools.py: boxer bugs

2008-06-30 01:59  stevel

	* libpyEM/EMAN2db.py: Database fully functional now, may need more
	  testing. Image deletion mb imperfect...

2008-06-29 21:49  stevel

	* libpyEM/EMAN2db.py: Working on database.

2008-06-27 22:19  woolford

	* libpyEM/: EMAN2.py, qtgui/emdesktop.py,
	  qtgui/emfloatingwidgets.py, qtgui/emimage2d.py,
	  qtgui/emimagemx.py: desktop work

2008-06-27 17:11  gtang

	* libEM/emdata_metadata.cpp: remove is_complex from "read only"
	  attribute

2008-06-27 17:06  gtang

	* libEM/emdata_metadata.h, rt/pyem/test_emdata.py: fix the problems
	  caused by set_attr() change.

2008-06-27 14:31  woolford

	* libpyEM/qtgui/emdesktop.py: desktop work

2008-06-26 14:42  woolford

	* libEM/marchingcubes.cpp, libpyEM/qtgui/emimage3diso.py,
	  pyemtbx/boxertools.py: boxer fixes

2008-06-26 09:41  gtang

	* libEM/emdata_metadata.cpp: ignore set_attr() for read only
	  attribute, warning message logged.

2008-06-25 21:58  woolford

	* programs/e2boxer.py, pyemtbx/boxertools.py: more boxer fixes

2008-06-25 21:12  woolford

	* programs/e2boxer.py: boxer updates

2008-06-25 13:20  woolford

	* libpyEM/EMAN2.py, pyemtbx/boxertools.py: boxer fixes

2008-06-25 09:30  gtang

	* libEM/imagicio.cpp: IMAGIC image write attribute "IMAGIC.label"
	  as "" if it does not exist.

2008-06-25 01:43  stevel

	* libEM/emdata_metadata.cpp, libpyEM/EMAN2db.py: Database working
	  except for deleting images

2008-06-24 22:33  woolford

	* programs/e2boxer.py, pyemtbx/boxertools.py: more boxer fixes

2008-06-24 21:43  woolford

	* programs/e2boxer.py, pyemtbx/boxertools.py: more boxer fixes

2008-06-24 21:05  woolford

	* libpyEM/qtgui/emimage2d.py, programs/e2boxer.py,
	  pyemtbx/boxertools.py: boxer updates

2008-06-24 16:55  gtang

	* libEM/emdata_metadata.cpp: reset attribute nx, ny, nz will resize
	  the image. set_attr_dict() can resize x,y,z dimension at the same
	  time.

2008-06-24 11:38  gtang

	* rt/pyem/test_reconstructor.py: [no log message]

2008-06-24 11:28  gtang

	* rt/pyem/test_cmp.py: [no log message]

2008-06-24 11:09  woolford

	* programs/e2boxer.py: e2boxer updates

2008-06-24 09:00  gtang

	* libEM/geometry.h: fix get_ndim() from image size

2008-06-24 02:20  stevel

	* libpyEM/EMAN2db.py: More database work. Writes binary data now.
	  Still need to implement reading.

2008-06-24 00:58  stevel

	* libEM/emdata_metadata.cpp, libpyEM/libpyEMData2.cpp: Bugfix

2008-06-24 00:43  stevel

	* libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libpyEM/EMAN2db.py, programs/e2display.py: Work on database

2008-06-23 22:37  woolford

	* programs/e2boxer.py, pyemtbx/boxertools.py: more boxer stuff

2008-06-23 21:57  woolford

	* libpyEM/qtgui/emimagemx.py, programs/e2boxer.py,
	  pyemtbx/boxertools.py: e2boxer improvements

2008-06-23 17:44  gtang

	* libEM/emdata_metadata.cpp: reset attribute nx, ny, nz will resize
	  the image

2008-06-23 16:40  gtang

	* rt/pyem/test_emdata.py: unit test update

2008-06-23 15:44  gtang

	* libEM/: emdata_metadata.cpp, emdata_metadata.h: set image
	  attribute of nx, ny, nz will resize the image.

2008-06-23 15:43  gtang

	* libEM/geometry.h: get image dimension from image size is better
	  than from image origin.

2008-06-23 02:34  stevel

	* libpyEM/EMAN2db.py: Partially functional database.

2008-06-21 02:42  stevel

	* libpyEM/EMAN2db.py: DB work

2008-06-20 14:47  woolford

	* programs/e2boxer.py, pyemtbx/boxertools.py: e2boxer fix the
	  --auto=db option

2008-06-20 11:02  woolford

	* libEM/emdata_gl.cpp: fixed glTexImage3D compiler problem

2008-06-20 09:02  gtang

	* CMakeLists.txt: [no log message]

2008-06-20 08:53  gtang

	* libEM/emdata_gl.cpp: small fix

2008-06-20 08:53  gtang

	* CMakeLists.txt: [no log message]

2008-06-20 02:09  stevel

	* libpyEM/EMAN2db.py: More database work

2008-06-19 22:07  woolford

	* libEM/emdata_gl.cpp, libpyEM/qtgui/emimagemx.py: fixed a MAC
	  compile problem

2008-06-19 22:05  woolford

	* libEM/boxingtools.cpp, libEM/emdata_gl.cpp, programs/e2boxer.py,
	  pyemtbx/boxertools.py: boxer updates - fixes

2008-06-19 17:17  woolford

	* libpyEM/EMAN2.py, programs/e2boxer.py, pyemtbx/boxertools.py:
	  boxer - support of multiple autoboxers finally

2008-06-19 13:54  woolford

	* programs/e2boxer.py, programs/e2ptcltrace.py,
	  pyemtbx/boxertools.py: ptcltrace writes more stuff, e2boxer
	  supports multiple autoboxers, still fixing

2008-06-19 12:41  gtang

	* CMakeLists.txt: [no log message]

2008-06-19 01:57  stevel

	* libpyEM/EMAN2db.py: Work on local database

2008-06-18 22:19  woolford

	* libpyEM/EMAN2.py, programs/e2boxer.py, pyemtbx/boxertools.py:
	  boxer updates - adding multiple autoboxer support

2008-06-18 13:18  woolford

	* programs/e2boxer.py, pyemtbx/boxertools.py: boxer fixes - manual
	  box related

2008-06-18 02:29  stevel

	* libpyEM/EMAN2db.py: Working on db

2008-06-17 19:01  woolford

	* libpyEM/qtgui/emimagemx.py: image matrix fixes

2008-06-17 18:57  woolford

	* libpyEM/qtgui/emimagemx.py, programs/e2boxer.py: image matrix
	  fixes

2008-06-17 18:20  woolford

	* libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2ptcltrace.py: fixing ptcltrace related stuff

2008-06-17 15:45  woolford

	* libpyEM/qtgui/emimagemx.py: image matrix display fixes

2008-06-17 14:48  woolford

	* libpyEM/qtgui/emimagemx.py, programs/e2boxer.py,
	  pyemtbx/boxertools.py: boxer updates

2008-06-17 12:57  gtang

	* libEM/: transform.cpp, sparx/util_sparx.cpp: fix for VS2005
	  compilation

2008-06-17 01:37  stevel

	* libpyEM/EMAN2db.py: Bring bsddb usage bak.

2008-06-16 22:20  woolford

	* libpyEM/qtgui/emimagemx.py: image matrix runs much faster - still
	  work to be done

2008-06-16 18:07  gtang

	* programs/e2boxer.py: use win32 version of kill() function on
	  windows instead of os.kill()

2008-06-16 17:32  gtang

	* libEM/: cmp.cpp, vec3.h: fix for VS2005 compilation

2008-06-16 02:20  stevel

	* libpyEM/: EMAN2.py, EMAN2db.py: Working on beginnings of database
	  and parallelism

2008-06-13 18:34  woolford

	* libpyEM/qtgui/emimagemx.py, programs/e2display.py: image matrix
	  writes lst files

2008-06-13 17:49  woolford

	* libEM/boxingtools.cpp, libEM/emdata_gl.cpp, libEM/emdata_gl.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/qtgui/emimage2d.py,
	  programs/e2boxer.py, pyemtbx/boxertools.py: more boxer fixes

2008-06-13 17:24  gtang

	* programs/e2proc3d.py: fix the --clip option,wrong indent level
	  hide the get_clip() call.

2008-06-13 16:30  woolford

	* libEM/boxingtools.cpp, libEM/boxingtools.h,
	  libpyEM/libpyBoxingTools2.cpp, libpyEM/qtgui/emimagemx.py,
	  programs/e2boxer.py, pyemtbx/boxertools.py: boxer updates

2008-06-12 19:06  woolford

	* libpyEM/qtgui/emimage2d.py, programs/e2boxer.py,
	  pyemtbx/boxertools.py: boxer fixes

2008-06-12 18:21  jbert

	* libEM/sparx/util_sparx.cpp: [no log message]

2008-06-12 14:50  zyang

	* libEM/sparx/emdata_sparx.cpp: Trival change just to make program
	  more clear.

2008-06-12 13:48  ppenczek

	* libEM/sparx/util_sparx.cpp: changed equalsize

2008-06-12 13:03  ppenczek

	* libEM/sparx/util_sparx.cpp: changed equalsize

2008-06-12 12:03  ppenczek

	* libEM/sparx/util_sparx.cpp: changed equalsize

2008-06-12 11:18  ppenczek

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: changed equalsize

2008-06-11 21:17  woolford

	* pyemtbx/boxertools.py: fixed a bad boxer bug

2008-06-11 16:29  woolford

	* libpyEM/qtgui/: emdesktop.py, emfloatingwidgets.py: minor fixes

2008-06-11 15:31  ppenczek

	* libEM/sparx/util_sparx.cpp: cluster_equalsize

2008-06-11 14:57  woolford

	* libpyEM/qtgui/emdesktop.py, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emglobjects.py, programs/e2boxer.py: gui fixes

2008-06-11 13:48  ppenczek

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: cluster_equalsize

2008-06-11 12:27  jbert

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: add SA for
	  pairwise_cluster

2008-06-10 18:41  woolford

	* libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2boxer.py, pyemtbx/boxertools.py: boxer bug fixes

2008-06-09 20:37  woolford

	* libpyEM/qtgui/emimagemx.py, programs/e2boxer.py: more boxer
	  updates

2008-06-09 20:17  woolford

	* pyemtbx/boxertools.py: e2boxer ready for testing

2008-06-09 19:20  woolford

	* programs/e2boxer.py, pyemtbx/boxertools.py: e2boxer ready for
	  testing

2008-06-09 17:18  woolford

	* programs/e2boxer.py, pyemtbx/boxertools.py: boxer updates - new
	  centering

2008-06-09 14:17  woolford

	* libEM/aligner.cpp, libEM/boxingtools.cpp, libEM/boxingtools.h,
	  libEM/emdata.cpp, libEM/processor.cpp,
	  libpyEM/libpyBoxingTools2.cpp, programs/e2boxer.py,
	  pyemtbx/boxertools.py: remove DIFFERENCE from BoxingTools enum
	  because its reserved on Windows

2008-06-09 13:07  zyang

	* libpyEM/libpyUtils2.cpp: Fix a bug

2008-06-09 12:42  gtang

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: fix for VS2005
	  compilation

2008-06-09 09:44  gtang

	* libEM/: marchingcubes.cpp, reconstructor.cpp: fix for VS2005
	  compilation

2008-06-08 18:35  ppenczek

	* libEM/sparx/util_sparx.cpp: working version of cluster

2008-06-08 17:22  ppenczek

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: working on cluster

2008-06-07 08:48  ppenczek

	* libEM/sparx/util_sparx.cpp:  beginning of cluster

2008-06-06 20:11  woolford

	* libEM/aligner.cpp, libEM/processor.cpp, pyemtbx/boxertools.py:
	  centering and boxer updates

2008-06-06 19:20  woolford

	* libEM/emdata.cpp, programs/e2boxer.py, programs/e2fileinfo.py,
	  pyemtbx/boxertools.py: boxer updates - warning calc_ccf has
	  changed

2008-06-06 16:40  zyang

	* libEM/sparx/fundamentals.cpp: Slightly change the program to make
	  it more clear.

2008-06-06 16:05  woolford

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/emdata_metadata.cpp,
	  libEM/emdata_metadata.h, libEM/processor.cpp,
	  libEM/sparx/fundamentals.cpp, libpyEM/libpyEMData2.cpp,
	  programs/e2boxer.py, pyemtbx/boxertools.py: boxer updates -
	  fundamentals is unchanged

2008-06-06 11:08  zyang

	* libEM/cmp.cpp: Change long int to float to avoid overflow.

2008-06-05 23:11  woolford

	* programs/e2boxer.py, pyemtbx/boxertools.py: boxer work

2008-06-05 18:54  gtang

	* libEM/spiderio.cpp: minor change

2008-06-05 18:42  woolford

	* libpyEM/EMAN2.py, programs/e2boxer.py, pyemtbx/box.py,
	  pyemtbx/boxertools.py: e2boxer is almost there

2008-06-04 20:36  woolford

	* libpyEM/qtgui/emglplot.py, programs/e2boxer.py,
	  pyemtbx/boxertools.py: boxer updates - parallelism support

2008-06-04 09:53  gtang

	* libEM/imagicio.cpp: support swap byte order writing for IMAGIC
	  image

2008-06-04 09:53  gtang

	* libEM/mrcio.cpp: support swap byte order writing for MRC image

2008-06-03 21:42  woolford

	* programs/e2boxer.py: fixed scope based error in e2boxer

2008-06-03 20:25  woolford

	* libEM/boxingtools.cpp, libEM/boxingtools.h, libpyEM/EMAN2.py,
	  libpyEM/libpyBoxingTools2.cpp, libpyEM/qtgui/emglplot.py,
	  libpyEM/qtgui/emimage3d.py, programs/e2boxer.py,
	  pyemtbx/boxertools.py: boxer related updates

2008-06-03 13:58  jbert

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: add function Util.min_dist for k-means

2008-06-03 01:58  stevel

	* programs/e2basis.py: Fixed bug in new basis projection mech.

2008-06-02 20:55  woolford

	* libpyEM/qtgui/emglplot.py, programs/e2boxer.py: profile viewing
	  improvements - boxer

2008-06-02 20:20  woolford

	* libpyEM/qtgui/emglplot.py, pyemtbx/boxertools.py: boxer updates,
	  glplot works on mac

2008-06-02 19:29  woolford

	* programs/e2boxer.py, pyemtbx/boxertools.py: boxer updates -
	  correlation profile viewer works again

2008-06-02 18:00  woolford

	* pyemtbx/boxertools.py: adding boxertools.py

2008-06-02 17:52  woolford

	* libEM/emdata_transform.cpp, programs/e2boxer.py: boxer updates

2008-06-02 16:26  woolford

	* libEM/emdata.cpp, libEM/transform.cpp, libEM/transform.h,
	  programs/e2boxer.py: fixed the transform compilation error on
	  .net

2008-06-02 16:25  woolford

	* libpyEM/libpyTypeConverter2.cpp, rt/pyem/test_processor.py,
	  rt/pyem/test_transform.py: test script fixes and other updates

2008-06-02 15:32  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: cleaning

2008-06-02 10:33  zyang

	* libEM/sparx/emdata_sparx.cpp: Fix a bug in extractpoint()

2008-06-02 02:46  stevel

	* libEM/processor.cpp, programs/e2basis.py,
	  programs/e2classifykmeans.py: Still trying to figure out
	  alignment program in class-averaging first round (non-bootstrap)

2008-06-01 02:36  stevel

	* programs/: e2refine2d.py, e2stacksort.py: Working on refine2d
	  again

2008-05-31 22:47  zyang

	* libEM/sparx/emdata_sparx.cpp: Change the angle in
	  fouriergridrot2d from radian to degree.

2008-05-30 00:16  stevel

	* libEM/cmp.h, programs/e2stacksort.py: More stacksort work

2008-05-30 00:15  woolford

	* programs/e2boxer.py: boxer updates

2008-05-29 16:02  woolford

	* programs/: e2boxer.py, e2display.py: boxer updates

2008-05-29 15:27  ppenczek

	* libEM/sparx/emdata_sparx.cpp: helicise added

2008-05-29 14:22  woolford

	* programs/: e2boxer.py, e2ptcltrace.py: changing computers

2008-05-29 13:37  ppenczek

	* libEM/sparx/emdata_sparx.h: added interpolation to helicise

2008-05-29 13:32  ppenczek

	* libEM/sparx/emdata_sparx.cpp: added interpolation to helicise

2008-05-29 13:20  ppenczek

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/libpyEMData2.cpp: helicise added

2008-05-28 22:09  woolford

	* libpyEM/qtgui/emimage2d.py, programs/e2boxer.py: boxer related
	  updates

2008-05-28 16:18  woolford

	* programs/e2ptcltrace.py: tracer updates

2008-05-28 02:46  stevel

	* programs/e2refine2d.py: More work on refine2d

2008-05-28 02:25  stevel

	* programs/e2refine2d.py: contd

2008-05-28 02:24  stevel

	* programs/: e2basis.py, e2classifykmeans.py: Working on reducing
	  file size for basis projections

2008-05-27 22:25  woolford

	* libEM/marchingcubes.cpp, libEM/marchingcubes.h,
	  libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, libpyEM/qtgui/emimage3dsym.py,
	  programs/e2ptcltrace.py: reduction and tracing related updates

2008-05-27 19:15  gtang

	* libEM/spiderio.cpp, libEM/spiderio.h, libEM/sspiderio.cpp,
	  programs/e2proc2d.py, programs/e2proc3d.py: SPIDER file support
	  swap byte order. Add option --swap in e2proc2d.py and
	  e2proc3d.py.

2008-05-27 02:07  stevel

	* libpyEM/EMAN2.py, programs/e2proc2d.py, programs/e2refine2d.py:
	  Beginning to work on parallelism

2008-05-25 00:00  stevel

	* install-dependencies.py, programs/e2refine2d.py: Update versions,
	  and make sure iterclassav>0 for bootstrap

2008-05-23 12:35  woolford

	* libpyEM/libpyTypeConverter2.cpp: removing unecessary	text

2008-05-23 12:28  woolford

	* libEM/hdfio.cpp, libpyEM/libpyTypeConverter2.cpp: hdfio should
	  work now

2008-05-23 12:00  woolford

	* libEM/: emobject.cpp, hdfio2.cpp: hdf io writes unsigned int

2008-05-23 09:02  stevel

	* programs/e2refine2d.py: Still working on it, but much better

2008-05-22 21:39  woolford

	* libEM/transform.h: documentation alteration

2008-05-22 21:04  woolford

	* libEM/emobject.cpp, libEM/emobject.h, libEM/marchingcubes.cpp,
	  libEM/marchingcubes.h, libEM/transform.h,
	  libpyEM/libpyTypeConverter2.cpp: trying to integrate a u3d writer

2008-05-22 16:10  stevel

	* programs/: e2classaverage.py, e2refine2d.py: Fixed a problem in
	  e2classaverage with inital angle being negative.

2008-05-22 01:40  stevel

	* programs/: e2refine2d.py, e2stacksort.py: Working on 2d
	  refinement

2008-05-22 01:00  stevel

	* programs/e2display.py: Working on e2 display in class average
	  particle mode

2008-05-21 21:12  woolford

	* libpyEM/qtgui/emimage3diso.py, programs/e2boxer.py: boxer -
	  introducing databasing

2008-05-21 20:24  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, fourierfilter.cpp: corrected
	  annoying undefined nline

2008-05-21 12:38  woolford

	* programs/e2boxer.py: boxer updates - in the middle of changes

2008-05-20 21:01  woolford

	* programs/e2boxer.py: boxer related updates - design alterations

2008-05-20 12:43  woolford

	* programs/: e2boxer.py, e2classaverage.py: switching computer,
	  boxer updates

2008-05-19 20:47  woolford

	* libEM/boxingtools.cpp, libEM/boxingtools.h, libEM/transform.h,
	  libpyEM/qtgui/emimagemx.py, programs/e2boxer.py,
	  programs/e2classaverage.py: e2boxer -  pickling parameters works

2008-05-19 17:58  gtang

	* libEM/analyzer.cpp, libEM/boxingtools.cpp, libEM/processor.cpp,
	  libEM/randnum.cpp, libEM/reconstructor.cpp, libEM/transform.cpp,
	  libEM/sparx/util_sparx.cpp, rt/emdata/test_emobject.cpp: fix for
	  VS2005 on WinXP

2008-05-19 00:56  stevel

	* libEM/aligner.cpp, libEM/exception.h, programs/e2basis.py,
	  programs/e2classifykmeans.py, programs/e2refine2d.py: Continuing
	  to improve refine2d

2008-05-18 02:30  stevel

	* libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libpyEM/emdata_pickle.h, programs/e2basis.py,
	  programs/e2classifykmeans.py, programs/e2refine2d.py: Another
	  try. Eliminated flip from alignment. Store alignment parameters
	  from similarity matrix, and use them in the bootstrap

2008-05-17 01:44  stevel

	* programs/e2refine2d.py: oops

2008-05-17 01:43  stevel

	* programs/: e2classaverage.py, e2refine2d.py: Yea ! seems to be
	  working better now.

2008-05-17 00:50  stevel

	* programs/e2classaverage.py: More tweaks to e2classaverage

2008-05-16 23:47  stevel

	* programs/e2classaverage.py: Another try

2008-05-16 23:21  stevel

	* programs/e2classaverage.py: Trying to see why some class averages
	  come out bad

2008-05-16 20:19  woolford

	* programs/: e2boxer.py, e2refine2d.py: boxer related updates

2008-05-16 19:02  woolford

	* programs/e2classaverage.py: woops

2008-05-16 19:01  woolford

	* libEM/aligner.cpp, libEM/emdata.cpp, programs/e2boxer.py,
	  programs/e2classaverage.py, programs/e2refine2d.py:
	  make_rotational_footprint caching fixed - it is regenerated now
	  if the update flag is set

2008-05-16 16:19  gtang

	* libEM/averager.cpp, libEM/dm3io.cpp, libEM/emcache.h,
	  libEM/emdata_core.cpp, libEM/emdata_metadata.cpp,
	  libEM/emdata_transform.cpp, libEM/emimio.cpp, libEM/emio.cpp,
	  libEM/fitsio.cpp, libEM/gatan2io.cpp, libEM/hdfio.cpp,
	  libEM/hdfio2.cpp, libEM/icosio.cpp, libEM/imagicio.cpp,
	  libEM/log.cpp, libEM/lstfastio.cpp, libEM/lstio.cpp,
	  libEM/mrcio.cpp, libEM/pifio.cpp, libEM/pngio.cpp,
	  libEM/pointarray.cpp, libEM/processor.h, libEM/reconstructor.cpp,
	  libEM/reconstructor_tools.cpp, libEM/salio.cpp, libEM/tifio.cpp,
	  libEM/util.cpp, libEM/vecmath.h, libEM/vtkio.cpp,
	  libEM/xplorio.cpp, libEM/sparx/emdata_sparx.cpp,
	  libEM/sparx/normpadft.cpp, libEM/sparx/util_sparx.cpp,
	  utils/iminfo.cpp: fix the compilation for GCC 4.3 on Fedora 9,
	  more strict header declaration.

2008-05-16 15:26  gtang

	* libEM/: hdfio.h, hdfio2.h: add flag to compile with HDF5 1.8

2008-05-16 09:43  ppenczek

	* libpyEM/libpyUtils2.cpp, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h: [no log message]

2008-05-16 09:18  woolford

	* libpyEM/libpyEMData2.cpp: fixed the m-shrink compilation error in
	  libpyEMData2

2008-05-15 21:57  stevel

	* libEM/mrcio.cpp, libEM/mrcio.h, programs/e2proc3d.py,
	  pyemtbx/imagetypes.py: Fix some compliance issues for submitting
	  specs to Jose-Maria's server.

2008-05-15 21:54  stevel

	* programs/: e2refine2d.py, e2stacksort.py: More improvements to
	  refine2d

2008-05-15 21:41  woolford

	* libEM/transform.cpp, libEM/transform.h, libEM/util.cpp,
	  libEM/util.h, libpyEM/libpyTransform2.cpp,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2boxer.py: boxer updates and symmetry stuff

2008-05-15 14:43  ppenczek

	* libEM/reconstructor.cpp, libEM/sparx/emdata_sparx.cpp,
	  libEM/sparx/emdata_sparx.h, libEM/sparx/util_sparx.h,
	  libpyEM/libpyEMData2.cpp: converted 3D SSNR code to variance

2008-05-15 09:09  ppenczek

	* libEM/reconstructor.cpp:  moved division by the averaging factor
	  in 3D SSNR to a logical place

2008-05-15 02:07  stevel

	* programs/: e2refine2d.py, e2stacksort.py: Working on alignment
	  options in e2refine2d

2008-05-14 22:18  woolford

	* libEM/emdata.cpp, libEM/emdata.h, libEM/reconstructor.cpp,
	  libEM/transform.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/qtgui/emimage3dsym.py, programs/e2make3d.py,
	  utils/speedtest.cpp: general updates - symmetry (icos is still
	  the same), and remove EMData::mean_shrink and median_shrink

2008-05-14 10:42  gtang

	* libpyEM/libpyTypeConverter2.cpp: quick fix for compilation
	  failure

2008-05-14 08:52  ppenczek

	* libEM/sparx/: emdata_sparx.h, util_sparx.cpp, util_sparx.h: [no
	  log message]

2008-05-14 00:55  stevel

	* programs/e2stacksort.py: Working on alignment in stacksort

2008-05-14 00:27  stevel

	* programs/e2stacksort.py: Bugfix in align mode

2008-05-13 20:46  woolford

	* libEM/boxingtools.cpp, libEM/boxingtools.h, libEM/emdata_gl.cpp,
	  libEM/emdata_gl.h, libEM/marchingcubes.cpp,
	  libpyEM/libpyBoxingTools2.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyTypeConverter2.cpp, libpyEM/qtgui/emimage2d.py,
	  programs/e2boxer.py: boxer related

2008-05-13 18:01  zyang

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h, util_sparx.cpp,
	  util_sparx.h: Introduce inline function to simplify the repeated
	  part.  Also delete some outdate comments.

2008-05-13 16:50  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: FINALLY CORRECT!

2008-05-13 14:56  ppenczek

	* libEM/sparx/emdata_sparx.cpp: [no log message]

2008-05-13 14:33  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, util_sparx.cpp: simplified pixel
	  count

2008-05-13 11:14  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, util_sparx.cpp: major changes in
	  modulo calculation of coordinates in rot_scale_conv and in
	  get_pixel_conv also in polar2dmi

2008-05-12 22:19  woolford

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/emfft.cpp,
	  libEM/emfft.h, libpyEM/qtgui/emimage2d.py, programs/e2boxer.py:
	  boxer related updates

2008-05-12 18:21  stevel

	* programs/: e2basis.py, e2refine2d.py, e2simmx.py: More e2refine2d
	  work

2008-05-12 13:49  stevel

	* programs/: e2basis.py, e2classifykmeans.py, e2refine2d.py,
	  e2simmx.py, e2stacksort.py: e2refine2d is working now, still
	  needs some improvement, but it works

2008-05-09 20:33  woolford

	* rt/pyem/test_processor.py: fixed test script error

2008-05-09 19:31  woolford

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libEM/processor.cpp, libEM/processor.h, libEM/transform.cpp,
	  libEM/transform.h, libpyEM/qtgui/emglobjects.py,
	  libpyEM/qtgui/emimage2d.py, programs/e2align3d.py,
	  programs/e2boxer.py, programs/e2foldfitter.py,
	  programs/e2proc2d.py, programs/e2proc3d.py,
	  programs/e2stacksort.py, programs/e2tilefile.py,
	  rt/pyem/test_emdata.py, rt/pyem/test_processor.py: boxer work -
	  and replacing all reference to EMData::mean_shrink and
	  EMData::median_shrink

2008-05-09 15:24  stevel

	* programs/: e2basis.py, e2proc2d.py, e2refine2d.py,
	  e2stacksort.py: More work on e2refine2d.py

2008-05-09 02:15  stevel

	* programs/: e2basis.py, e2refine2d.py, e2simmx.py: simmx now
	  writes stack of 4 images instead of one nz=4 image.

2008-05-08 20:15  woolford

	* libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emshape.py, programs/e2boxer.py: boxer updates

2008-05-08 16:44  stevel

	* programs/e2refine2d.py: trivial

2008-05-08 16:39  stevel

	* programs/e2simmx.py: take verbose option as integer

2008-05-08 16:35  stevel

	* libEM/lstfastio.cpp, libpyEM/qtgui/emglplot.py,
	  programs/e2refine2d.py: refine2d complete, but still debugging

2008-05-08 10:18  ppenczek

	* libEM/processor.h: [no log message]

2008-05-08 02:08  stevel

	* programs/: e2basis.py, e2refine2d.py: Working on e2refine2d again

2008-05-07 22:22  woolford

	* libEM/boxingtools.cpp, libEM/boxingtools.h, libEM/processor.h,
	  libpyEM/libpyBoxingTools2.cpp, libpyEM/qtgui/emglobjects.py,
	  programs/e2boxer.py, programs/e2refine2d.py: boxer related upates

2008-05-07 17:31  gtang

	* libpyEM/CMakeLists.txt: fix the boost.python 1.35.0 compilation
	  problem

2008-05-07 14:27  gtang

	* libEM/CMakeLists.txt: GL library should not be linked into libEM2
	  when no ENABLE_OPENGL

2008-05-07 13:34  ppenczek

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: [no log message]

2008-05-06 22:34  stevel

	* install-dependencies.py: More minor fixes to install-dependencies

2008-05-06 22:13  woolford

	* libEM/boxingtools.cpp, libEM/boxingtools.h, libEM/transform.cpp,
	  libpyEM/libpyBoxingTools2.cpp, libpyEM/libpyTypeConverter2.cpp,
	  libpyEM/typeconverter.h, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3dsym.py, programs/e2boxer.py: boxer and
	  symmetry related stuff

2008-05-06 16:02  stevel

	* CMakeLists.txt, install-dependencies.py: Fixed HDF 1.8 problem

2008-05-06 15:18  stevel

	* CMakeLists.txt, install-dependencies.py: Script for setting up
	  dependencies on OSX

2008-05-06 11:15  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2008-05-06 01:56  stevel

	* programs/e2refine2d.py: Working on refine2d still

2008-05-05 17:45  ppenczek

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyUtils2.cpp: [no log
	  message]

2008-05-05 01:37  stevel

	* programs/: e2ctf.py, e2refine2d.py, e2stacksort.py: Working on
	  improvements to 2D analysis.

2008-05-01 21:57  woolford

	* libEM/transform.cpp: general fixes

2008-05-01 16:57  woolford

	* libpyEM/qtgui/emimage3dsym.py: emimage3dsym updates

2008-05-01 14:18  woolford

	* libEM/boxingtools.cpp, libEM/boxingtools.h, programs/e2boxer.py:
	  boxer updates

2008-05-01 12:29  woolford

	* libpyEM/qtgui/: emimage3d.py, emimage3diso.py, emimage3dmorph.py,
	  emimage3dslice.py, emimage3dsym.py, emimage3dvol.py: added
	  emimage3dmorph

2008-04-30 21:21  woolford

	* libEM/emobject.cpp, libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, utils/CMakeLists.txt: symmetry
	  related updates

2008-04-30 13:20  woolford

	* rt/pyem/test_transform.py: Symmetry::reduce is fully tested in
	  test_transform.py

2008-04-30 13:00  woolford

	* libEM/transform.cpp, programs/e2make3d.py: symmetry fixes

2008-04-30 11:40  woolford

	* libEM/transform.cpp, rt/pyem/test_transform.py: still symmetry
	  stuff

2008-04-30 10:25  woolford

	* libEM/transform.cpp: symmetry work - reduce almost done

2008-04-30 02:06  stevel

	* libpyEM/qtgui/emplot2d.py, programs/e2ctf.py: Working on new CTF
	  model.

2008-04-29 23:57  woolford

	* libEM/transform.cpp: minor symmetry revisions

2008-04-29 22:22  woolford

	* libEM/transform.cpp, libpyEM/qtgui/emimage3dsym.py,
	  programs/e2make3d.py: in the middle of symmetry work

2008-04-29 22:20  woolford

	* rt/pyem/test_transform.py: test script changes

2008-04-29 18:57  woolford

	* libEM/transform.cpp: symmetry stuff

2008-04-29 18:54  woolford

	* libEM/transform.cpp: symmetry stuff

2008-04-29 18:50  woolford

	* rt/pyem/test_transform.py: fixed test script

2008-04-29 18:48  woolford

	* libEM/transform.cpp: symmetry stuff

2008-04-29 18:21  woolford

	* libEM/transform.cpp, rt/pyem/test_transform.py: working on
	  Symmetry3D::reduce

2008-04-29 17:21  woolford

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, libpyEM/libpyTypeConverter2.cpp,
	  libpyEM/qtgui/emimage3dsym.py, rt/pyem/test_transform.py: working
	  on Symmetry3D::reduce

2008-04-28 22:23  woolford

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp: in the middle of symmetry work

2008-04-28 15:46  woolford

	* libEM/transform.cpp, libpyEM/qtgui/emimage3d.py: bug fixes for
	  emimage3d

2008-04-28 14:13  woolford

	* libpyEM/qtgui/emimage3dsym.py: display symmetry stuff better

2008-04-25 17:32  woolford

	* libEM/boxingtools.cpp: uncommente something

2008-04-25 17:32  woolford

	* libEM/boxingtools.cpp, libEM/marchingcubes.cpp,
	  libpyEM/qtgui/emglplot.py, libpyEM/qtgui/emimage3dslice.py,
	  libpyEM/qtgui/emimage3dvol.py, programs/e2boxer.py: general fixes

2008-04-25 14:36  gtang

	* programs/e2proc2d.py: bug fix, int(line) -> int(line.split()[0])

2008-04-25 01:02  stevel

	* programs/: e2ctf.py, e2proc2d.py: Bugfix in proc2d

2008-04-24 19:18  woolford

	* libpyEM/CMakeLists.txt, libpyEM/qtgui/em3Dhelloworld.py,
	  libpyEM/qtgui/emglplot.py, libpyEM/qtgui/emimage3diso.py,
	  programs/e2boxer.py, programs/e2make3d.py: boxer related updates

2008-04-24 02:19  stevel

	* programs/e2ctf.py: e2ctf background estimation beginning to work

2008-04-23 18:57  woolford

	* libpyEM/qtgui/emimage2d.py, programs/e2boxer.py,
	  programs/e2classaverage.py: boxer related updates

2008-04-23 02:50  stevel

	* programs/e2ctf.py: e2ctf broken in this commit, but as it wasn't
	  really working before...

2008-04-22 19:13  woolford

	* libEM/boxingtools.cpp, programs/e2boxer.py: boxer updates

2008-04-22 12:31  woolford

	* libpyEM/qtgui/emimagemx.py, programs/e2boxer.py: boxer changes

2008-04-22 10:16  woolford

	* programs/e2boxer.py: boxer debug change

2008-04-22 02:09  stevel

	* programs/e2ctf.py: Working on background determination using
	  edges of particle boxes.

2008-04-21 22:25  woolford

	* libEM/boxingtools.cpp, libEM/boxingtools.h,
	  libpyEM/libpyBoxingTools2.cpp, libpyEM/qtgui/emimage2d.py,
	  programs/e2boxer.py, programs/e2make3d.py, programs/e2refine.py:
	  boxer related updates

2008-04-21 17:20  gtang

	* libEM/: tifio.cpp, imageio.cpp: Fix the TIFF writing support in
	  EMAN2.

2008-04-21 13:51  zweig

	* libEM/sparx/normpadft.cpp: fix an error for 2D case,

2008-04-21 13:35  woolford

	* programs/e2make3d.py: minor e2make3d.py bug

2008-04-21 12:44  zyang

	* libEM/sparx/normpadft.cpp: Reverse the previous change

2008-04-21 12:37  zyang

	* libEM/sparx/normpadft.cpp: Change the way of padding

2008-04-18 18:11  woolford

	* libEM/boxingtools.cpp, programs/e2boxer.py, programs/e2make3d.py:
	  boxer related upates

2008-04-18 15:16  woolford

	* rt/pyem/: test_processor.py, test_reconstructor.py: minor fixes
	  to reconstructor tests

2008-04-18 14:46  woolford

	* programs/e2make3d.py: make3d fixes

2008-04-18 10:05  zweig

	* libEM/reconstructor.cpp: add 2d reconstruction

2008-04-17 17:55  gtang

	* libEM/: tifio.cpp, tifio.h: support color Image reading for TIFF.
	  Convert to greyscale.

2008-04-17 17:13  woolford

	* libEM/emdata.cpp, libEM/emdata.h, programs/e2boxer.py: boxer
	  related updates

2008-04-17 15:15  woolford

	* libEM/exception.h: fixed name() irregularities in exceptions

2008-04-17 14:43  woolford

	* libEM/emdata.cpp, libEM/emdata.h, libEM/processor.cpp,
	  libEM/processor.h, libEM/transform.h, rt/pyem/test_processor.py:
	  added FlattenBackgroundFilter, other boxer related upates

2008-04-17 11:10  gtang

	* rt/pyem/test_emdata.py: update unit test since
	  EMAN::calc_flcf()'s interface changed.

2008-04-16 19:06  woolford

	* libEM/boxingtools.cpp, libEM/boxingtools.h, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyBoxingTools2.cpp, libpyEM/libpyTypeConverter2.cpp,
	  programs/e2boxer.py: boxer related updates

2008-04-16 15:44  zweig

	* libpyEM/libpyUtils2.cpp: add an entry for merge_peaks

2008-04-15 19:22  woolford

	* libEM/CMakeLists.txt, libEM/boxingtools.cpp, libEM/boxingtools.h,
	  libpyEM/CMakeLists.txt, libpyEM/EMAN2.py,
	  libpyEM/EMAN2_cppwrap.py, libpyEM/libpyBoxingTools2.cpp,
	  programs/e2boxer.py: boxer related updates

2008-04-15 18:07  ppenczek

	* libEM/sparx/util_sparx.cpp: cleaning up

2008-04-14 22:49  woolford

	* libEM/emdata.cpp, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemx.py, programs/e2boxer.py: boxer related
	  updates

2008-04-14 16:21  gtang

	* libEM/tifio.cpp: add ckeck for TIFFTAG_PHOTOMETRIC to warn user
	  only greyscale image is supported

2008-04-14 01:55  stevel

	* libEM/sparx/emdata_sparx.cpp: Someone committed a bug...

2008-04-11 18:54  woolford

	* libEM/emdata.cpp, libEM/emdata.h, libEM/processor.cpp,
	  libpyEM/libpyEMData2.cpp, programs/e2boxer.py: correlation and
	  boxer related updates

2008-04-11 10:59  gtang

	* libEM/: averager.h, ctf.cpp, processor.cpp, reconstructor.cpp,
	  reconstructor.h, reconstructor_tools.h, transform.cpp,
	  sparx/emdata_sparx.cpp, sparx/normpadft.cpp: remove warnings

2008-04-10 14:56  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2008-04-10 13:54  zweig

	* libEM/sparx/util_sparx.cpp: remove debug code

2008-04-09 12:38  zweig

	* libEM/: reconstructor.cpp, reconstructor.h: add 2d recontruction
	  to nn4Reconstructor

2008-04-09 10:01  zweig

	* libEM/sparx/emdata_sparx.cpp: fix a bug: m could be zero here
	  (for 1D case)

2008-04-09 02:28  stevel

	* programs/e2refinemultinoali.py: New program for refining sets of
	  monomer images without alignment, with multile output targets.

2008-04-08 18:25  gtang

	* libEM/mrcio.cpp: CTF parameter r/w.

2008-04-08 17:22  gtang

	* libEM/imagicio.cpp: CTF parameter r/w.

2008-04-03 15:31  gtang

	* rt/pyem/test_utils.py: test Util.get_randnum_seed()

2008-04-03 14:14  zweig

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: add function get_biggest_cluster()

2008-04-02 18:49  gtang

	* libEM/transform.h: get rid of the "unused variable" warnings

2008-04-02 17:32  stevel

	* programs/e2stacksort.py: Fixed incompletely modified stacksort

2008-04-02 17:07  gtang

	* libEM/: randnum.cpp, randnum.h, util.cpp, util.h: for
	  Util::get_randnum_seed()

2008-04-02 14:34  zyang

	* libEM/randnum.cpp, libEM/randnum.h, libEM/util.cpp, libEM/util.h,
	  libpyEM/libpyUtils2.cpp: Some change to random number generator
	  (probably need more improvement)

2008-04-01 20:22  gtang

	* libEM/: hdfio.h, hdfio2.h: add comment for h5check.

2008-03-31 18:55  gtang

	* programs/e2proc3d.py: add a out layer loop to process 3d image
	  stack

2008-03-28 16:51  gtang

	* libEM/util.cpp, libEM/util.h, libpyEM/libpyUtils2.cpp,
	  rt/pyem/test_utils.py: add Util::set_randnum_seed() function for
	  changing seed in Python.

2008-03-28 15:49  woolford

	* libEM/reconstructor.cpp, libpyEM/qtgui/emdesktop.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emimage3dslice.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emimage3dvol.py,
	  libpyEM/qtgui/emimagemx.py, programs/e2ali2img.py,
	  programs/e2boxer.py: general fixes

2008-03-28 14:46  ppenczek

	* libEM/cmp.cpp:  add normalize to dot

2008-03-28 13:35  ppenczek

	* libEM/sparx/util_sparx.cpp: pad and window inherit the input file
	  header

2008-03-28 12:28  gtang

	* libEM/randnum.h: [no log message]

2008-03-28 12:24  gtang

	* libEM/: randnum.cpp, randnum.h, util.cpp, util.h:
	  Util::get_irand() etc will get random number from Randnum class.

2008-03-28 12:23  gtang

	* libpyEM/libpyUtils2.cpp: no need to wrap Randnum to Python

2008-03-28 12:22  gtang

	* rt/emdata/randnum_test.cpp: [no log message]

2008-03-28 01:58  stevel

	* programs/e2stacksort.py: Working on stacksort

2008-03-27 20:41  gtang

	* libEM/processor.cpp, libEM/randnum.cpp, libEM/randnum.h,
	  libpyEM/libpyUtils2.cpp: modify Randnum to a singleton class nad
	  use /dev/random as seed.

2008-03-27 16:16  stevel

	* programs/e2skelpath.py: Matt's modified version

2008-03-26 19:42  woolford

	* libpyEM/qtgui/: emdesktop.py, emfloatingwidgets.py,
	  emglobjects.py, emimage3d.py, emimage3diso.py: desktop work

2008-03-26 17:19  zyang

	* libEM/randnum.cpp: Change the way the seed is generated

2008-03-26 14:11  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Add function ener_tot

2008-03-25 18:29  woolford

	* libpyEM/qtgui/: emdesktop.py, emfloatingwidgets.py, emimage3d.py:
	  desktop work

2008-03-25 12:52  ppenczek

	* libEM/: cmp.cpp, cmp.h: ccc changed default to negative value

2008-03-25 08:10  stevel

	* programs/: e2refine2d.py, e2stacksort.py: Work on refine2d

2008-03-24 21:16  woolford

	* libpyEM/qtgui/: emdesktop.py, emfloatingwidgets.py, emimage3d.py:
	  interface related changes

2008-03-24 17:25  zyang

	* libEM/sparx/util_sparx.cpp: Fix an important bug in function
	  ener()

2008-03-23 20:22  gtang

	* libEM/: dm3io.h, emcache.h, emdata.h, emimio.h, emio.h,
	  exception.h, fitsio.h, gatan2io.h, geometry.h, hdfio.h, hdfio2.h,
	  icosio.h, imagicio.h, jpegio.h, lstfastio.h, lstio.h,
	  marchingcubes.h, mrcio.h, pgmio.h, pifio.h, pngio.h,
	  pointarray.h, quaternion.h, randnum.h, salio.h, spiderio.h,
	  sspiderio.h, tifio.h, v4l2io.h, vtkio.h, xplorio.h,
	  sparx/emarray.h: add explicit to single argument constructor to
	  avoid implicit type conversion.

2008-03-22 20:49  gtang

	* libEM/: lstfastio.cpp, lstfastio.h, lstio.cpp: release imagio in
	  lstio's destructor.

2008-03-20 21:08  woolford

	* libpyEM/qtgui/emimage3d.py: translate added to properties in
	  emimage3d.py

2008-03-20 20:54  woolford

	* libpyEM/qtgui/: emimage3d.py: forgot zoom in properties tab

2008-03-20 20:38  woolford

	* libpyEM/qtgui/emdesktop.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emimage3dslice.py,
	  libpyEM/qtgui/emimage3dsym.py, libpyEM/qtgui/emimage3dvol.py,
	  programs/e2fileinfo.py: ortho supported in emimage3d

2008-03-20 17:10  stevel

	* programs/e2refine2d.py: More tweaks

2008-03-20 16:50  stevel

	* programs/e2refine2d.py: Work on refine2d.py

2008-03-20 16:24  zyang

	* libEM/sparx/util_sparx.cpp: Just fix the identation

2008-03-20 16:01  stevel

	* programs/e2display.py: oops

2008-03-20 15:31  stevel

	* libEM/CMakeLists.txt, libEM/all_imageio.h, libEM/emdata_io.cpp,
	  libEM/emutil.cpp, libEM/emutil.h, libEM/lstfastio.cpp,
	  libEM/lstfastio.h, libpyEM/qtgui/emimage3dsym.py,
	  programs/e2display.py, programs/e2proc2d.py,
	  programs/e2refine2d.py: Added new class for reading 'fast' LST
	  files.

2008-03-20 12:07  woolford

	* libpyEM/qtgui/: EMAN2.0.big.jpg, emdesktop.py: small desktop
	  updates

2008-03-20 10:53  stevel

	* programs/e2refine2d.py: oops

2008-03-20 10:50  woolford

	* libpyEM/qtgui/: emimage2d.py, emimageutil.py: fixed close event
	  issue

2008-03-20 01:16  stevel

	* programs/e2display.py: Extract particles from classes in
	  e2display.py

2008-03-19 18:02  woolford

	* libpyEM/EMAN2.py, libpyEM/qtgui/emdesktop.py,
	  libpyEM/qtgui/emfloatingwidgets.py, programs/e2fileinfo.py:
	  fileinfo options added

2008-03-19 15:46  zyang

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: Make change to
	  function ener

2008-03-19 14:14  zyang

	* libEM/sparx/util_sparx.h: Just add a comment

2008-03-19 13:17  woolford

	* libpyEM/qtgui/: emfloatingwidgets.py, emglobjects.py,
	  emimage3d.py, emimage3dslice.py, emimagemx.py: minor fixes

2008-03-18 16:29  woolford

	* programs/e2display.py: e2display.py shows image name in header

2008-03-18 16:22  woolford

	* libpyEM/qtgui/emimage3diso.py: more basic fixes

2008-03-18 16:20  woolford

	* libpyEM/qtgui/emimage2d.py: fixed basic error

2008-03-18 16:15  woolford

	* libpyEM/qtgui/emimagemx.py: fixed small issue

2008-03-18 14:21  woolford

	* libpyEM/qtgui/: emfloatingwidgets.py, emglobjects.py,
	  emimagemx.py: minor changes

2008-03-18 13:19  woolford

	* libpyEM/qtgui/emfloatingwidgets.py: interface changes

2008-03-18 03:00  stevel

	* libpyEM/qtgui/emimagemx.py, programs/e2display.py: Fixed
	  emimagemx bug with events. classes feature in e2display

2008-03-17 21:30  woolford

	* libEM/transform.h, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimage2dtex.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimage3diso.py,
	  libpyEM/qtgui/emimage3dslice.py, libpyEM/qtgui/emimage3dsym.py,
	  libpyEM/qtgui/emimage3dvol.py: interface work - 3D widgets float

2008-03-17 14:30  woolford

	* programs/e2classaverage.py: e2classaverage supports
	  bootstrapping, and will write the result matrix

2008-03-17 11:50  woolford

	* libpyEM/qtgui/emimagemx.py: imagemx fix

2008-03-17 11:32  woolford

	* programs/e2display.py: fixed display problem

2008-03-17 01:30  stevel

	* libpyEM/qtgui/emimage2d.py, programs/e2display.py: Working on
	  e2display

2008-03-14 18:35  woolford

	* libpyEM/CMakeLists.txt, libpyEM/qtgui/em3Dfonts.py,
	  libpyEM/qtgui/em3Dhelloworld.py,
	  libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emfximage.py,
	  libpyEM/qtgui/emglobjects.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emimage3dobject.py,
	  libpyEM/qtgui/emimage3dslice.py, libpyEM/qtgui/emimage3dvol.py,
	  libpyEM/qtgui/emimagemx.py, programs/e2classaverage.py,
	  programs/e2project3d.py: e2classaverage rewritten, general
	  interface work

2008-03-14 01:53  stevel

	* programs/: e2classaverage.py, e2display.py: New 'display' options

2008-03-13 14:29  woolford

	* libEM/projector.cpp: fixed Pawel projector issue, other bugs

2008-03-13 14:12  woolford

	* libEM/projector.cpp, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emimage3d.py: fixed Pawel projector issue

2008-03-13 10:46  woolford

	* libpyEM/qtgui/: emfloatingwidgets.py, emimagemx.py: image matrix
	  fixes for eman2 ui

2008-03-12 18:55  woolford

	* libpyEM/qtgui/: emfloatingwidgets.py, emimage2d.py,
	  emimage3dobject.py, emimage3dslice.py, emimage3dvol.py,
	  emimagemx.py: emimagemx uses textures, works in the desktop

2008-03-12 13:56  woolford

	* libpyEM/qtgui/emfloatingwidgets.py, libpyEM/qtgui/emimage2d.py,
	  programs/e2display.py: interface work

2008-03-11 16:48  gtang

	* rt/pyem/test_emdata.py: fix the unit test error

2008-03-11 14:51  gtang

	* rt/pyem/test_imageio.py: [no log message]

2008-03-11 10:26  woolford

	* libpyEM/qtgui/: emfloatingwidgets.py, emimage2d.py: display stuff
	  again

2008-03-11 10:08  woolford

	* libpyEM/qtgui/: emfloatingwidgets.py, emimage2d.py: removed
	  brackets

2008-03-11 09:48  woolford

	* libEM/transform.h, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emimage2d.py: e2display works in 2D

2008-03-10 18:38  gtang

	* rt/emdata/: CMakeLists.txt, randnum_test.cpp: test code for
	  Randnum class.

2008-03-10 18:38  gtang

	* libEM/CMakeLists.txt, libEM/processor.cpp, libEM/processor.h,
	  libEM/randnum.cpp, libEM/randnum.h, libEM/util.h,
	  libpyEM/libpyUtils2.cpp: Randnum is a wrapper class for gsl's
	  random number generator.

2008-03-10 18:21  woolford

	* libpyEM/qtgui/: emfloatingwidgets.py, emimage2d.py: work on the
	  3D desktop

2008-03-10 16:23  woolford

	* libEM/transform.cpp, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3dobject.py: in
	  the middle of updates

2008-03-10 14:13  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h:  rationalized
	  peak search

2008-03-07 23:45  gtang

	* rt/pyem/test_processor.py: unit test update for processor
	  "xform.fourierorigin"

2008-03-07 15:10  woolford

	* libEM/emdata.cpp, libEM/transform.cpp,
	  programs/e2classaverage.py, programs/e2classify.py: calc_ccf was
	  generating correlation maps with peaks in the center, not the
	  corner! Fixed some classify problems

2008-03-07 10:29  ppenczek

	* libpyEM/libpyReconstructor2.cpp: add file_store for bootstrap

2008-03-07 10:18  woolford

	* libEM/transform.cpp, libpyEM/qtgui/emimage3dsym.py,
	  programs/e2classaverage.py: minor changes

2008-03-07 01:02  stevel

	* libpyEM/EMAN2.py, programs/e2classaverage.py,
	  programs/e2classifykmeans.py: classifykmeans now writes a
	  standard classification matrix

2008-03-06 11:16  woolford

	* libEM/transform.cpp, libpyEM/EMAN2.py,
	  libpyEM/qtgui/emimage3dsym.py: change a regular expression in
	  EMAN2.py

2008-03-05 18:25  woolford

	* libEM/transform.cpp: icos change, nothing major

2008-03-05 18:21  woolford

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/qtgui/emimage3dsym.py: symmetry related modifications

2008-03-05 13:26  woolford

	* libEM/transform.cpp: minor fixes

2008-03-05 12:52  woolford

	* libEM/analyzer.h, libEM/emobject.h, libEM/transform.cpp,
	  libEM/transform.h, libpyEM/libpyTransform2.cpp,
	  libpyEM/qtgui/emimage3dsym.py: added OptimumOrientationGenerator,
	  and code cleaning

2008-03-05 02:31  stevel

	* libEM/analyzer.cpp: Further optimization

2008-03-05 02:11  stevel

	* libEM/analyzer.cpp: Optimizing kmeans a bit.

2008-03-04 23:32  stevel

	* examples/comparepairs.py, libEM/aligner.h, libEM/analyzer.cpp,
	  libEM/analyzer.h, libEM/cmp.h, libEM/emobject.h, libEM/util.h,
	  libEM/sparx/util_sparx.cpp, libpyEM/qtgui/emimageutil.py,
	  programs/e2basis.py, programs/e2classifykmeans.py,
	  programs/e2refine2d.py, rt/emdata/rotate_translate.cpp,
	  rt/pyem/test_cmp.py, utils/speedtest.cpp: Made modular functions
	  mostly case-insensitive. New k-means analyzer.

2008-03-04 19:16  woolford

	* libEM/reconstructor.h, libEM/reconstructor_tools.h,
	  libEM/transform.cpp, libEM/transform.h, libEM/vec3.h,
	  libpyEM/qtgui/emimage3dsym.py: various minor improvements

2008-03-04 13:46  woolford

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/qtgui/emimage3dsym.py: saff, even angles added to
	  orientation generators

2008-03-03 19:18  woolford

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, libpyEM/qtgui/emimage3dsym.py:
	  adding orientation generators - random works, debugging Saff and
	  others

2008-03-03 10:05  gtang

	* rt/pyem/test_processor.py: unit test update

2008-02-29 17:42  woolford

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, libpyEM/qtgui/emimage3dsym.py:
	  symmetry related updates

2008-02-29 14:06  woolford

	* libEM/emobject.h, libEM/transform.cpp, libEM/transform.h,
	  libpyEM/qtgui/emimage3dsym.py: added tools for demarcating
	  asymmetric units

2008-02-29 12:06  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2008-02-28 19:15  woolford

	* libEM/emobject.h, libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, libpyEM/libpyTypeConverter2.cpp,
	  libpyEM/qtgui/emimage3dsym.py: added exhaustive comments and
	  get_asymm_unit_points to Symmetry3D classes, moved FactoryBase,
	  various other small changes

2008-02-27 18:58  woolford

	* libEM/emdata_gl.cpp, libEM/transform.cpp, libEM/transform.h,
	  libpyEM/qtgui/emimage3dobject.py: in the middle of adding
	  symmetry comments

2008-02-27 17:54  woolford

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emimage3dobject.py,
	  libpyEM/qtgui/emimage3dslice.py, libpyEM/qtgui/emimage3dsym.py,
	  libpyEM/qtgui/emimage3dvol.py: minor fixes

2008-02-27 16:28  woolford

	* libpyEM/qtgui/: emimage3dobject.py, emimage3dslice.py,
	  emimage3dvol.py: detection of support for glBlendEquation added

2008-02-27 16:26  gtang

	* libEM/: emdata_gl.cpp, marchingcubes.cpp: fix for Visual Studio
	  2005 compilation

2008-02-27 15:20  gtang

	* libEM/: emdata.cpp, log.cpp: fix for Visual Studio 2005
	  compilation

2008-02-27 15:15  gtang

	* libEM/: CMakeLists.txt, reconstructor_tools.cpp: fix for Visual
	  Studio 2005 compilation

2008-02-27 15:11  woolford

	* libpyEM/qtgui/emimage3dobject.py: wrapped
	  GL_FUNC_REVERSE_SUBTRACT in try except block

2008-02-27 13:21  woolford

	* libpyEM/qtgui/: emimage3dobject.py, emimage3dslice.py,
	  emimage3dvol.py: view tracking in slices added. volume viewer
	  works with 2D textures

2008-02-26 19:21  gtang

	* libEM/projector.cpp: fix for Visual Studio 2005 compilation

2008-02-26 19:18  gtang

	* libEM/: aligner.cpp, cmp.cpp, ctf.cpp, emdata_metadata.cpp,
	  emdata_transform.cpp, transform.cpp, util.cpp, processor.cpp: fix
	  for Visual Studio 2005 compilation

2008-02-26 18:51  woolford

	* libpyEM/qtgui/: emimage3dobject.py, emimage3dvol.py: minor
	  adaptions

2008-02-26 17:57  woolford

	* libEM/emdata.cpp, libpyEM/qtgui/emimage3dobject.py,
	  libpyEM/qtgui/emimage3dslice.py, libpyEM/qtgui/emimage3dvol.py,
	  plugins/processor_template.cpp, plugins/processor_template.h:
	  fixes to improve slice and volume viewing - volume viewing works
	  for 2D textures

2008-02-26 16:21  gtang

	* libEM/: reconstructor.cpp, averager.cpp: fix for Visual Studio
	  2005 compilation

2008-02-26 16:13  gtang

	* libEM/reconstructor.cpp: fix for Visual Studio 2005 compilation

2008-02-26 15:26  gtang

	* rt/CMakeLists.txt, libEM/emdata_gl.cpp, libEM/emdata_io.cpp,
	  libEM/transform.cpp: fix for Visual Studio 2005 compilation

2008-02-25 18:47  woolford

	* libpyEM/qtgui/: emimage3dobject.py, emimage3dslice.py,
	  emimage3dvol.py: 2D texturing in volume rendering is almost
	  working

2008-02-25 01:37  stevel

	* programs/e2boxer.py: Fixes for emimage

2008-02-22 17:43  woolford

	* libEM/emdata.cpp, libEM/emdata.h, libEM/processor.cpp,
	  libEM/processor.h, libEM/reconstructor.cpp,
	  libEM/sparx/emdata_sparx.cpp, libpyEM/EMAN2.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3dslice.py,
	  libpyEM/qtgui/emimage3dvol.py, rt/pyem/test_emdata.py,
	  rt/pyem/test_processor.py: slice viewer works with 2D and 3D
	  textures, non power of 2 hardware support detected

2008-02-22 11:19  woolford

	* libpyEM/qtgui/emimage2d.py: more minor changes

2008-02-22 10:45  woolford

	* libpyEM/qtgui/emimage2d.py: more trivial changes

2008-02-22 10:07  woolford

	* libpyEM/qtgui/emimage2d.py, programs/e2help.py: trivial
	  alterations

2008-02-22 08:19  prb

	* libEM/transform.cpp:
	  changed SPIDER part of get_rotation so that azimuthal angles are
	  always positive

2008-02-21 17:13  woolford

	* libEM/emdata_metadata.h, libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyTransform2.cpp,
	  libpyEM/libpyTypeConverter2.cpp, libpyEM/qtgui/emimage3dsym.py,
	  programs/e2help.py, programs/e2project3d.py: libEM symmetries and
	  orientation generators working - Pawel's display problem resolved

2008-02-20 18:30  woolford

	* libEM/emobject.cpp, libEM/emobject.h, libEM/transform.cpp,
	  libEM/transform.h, libpyEM/EMAN2.py, libpyEM/libpyTransform2.cpp,
	  libpyEM/qtgui/emimage3dsym.py, programs/e2project3d.py: in the
	  middle of symmetry related updates

2008-02-20 14:17  ppenczek

	* libpyEM/libpyUtils2.cpp: added multiref_polar_ali_2d_nom

2008-02-20 14:06  ppenczek

	* libpyEM/libpyUtils2.cpp: added multiref_polar_ali_2d_nom

2008-02-19 19:07  woolford

	* libEM/emdata_transform.cpp, libEM/projector.cpp,
	  libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emimage2d.py, programs/e2help.py,
	  utils/CMakeLists.txt: symmetry classes added and work with eman2
	  factories. see e2help.py sym

2008-02-18 17:23  ppenczek

	* libEM/sparx/: util_sparx.cpp, util_sparx.h:  added apnq

2008-02-18 00:19  stevel

	* libpyEM/qtgui/emplot2d.py, programs/e2display.py: Make e2display
	  also do plotting.

2008-02-15 11:57  woolford

	* libEM/reconstructor.cpp, programs/e2make3d.py: 2D recon related
	  fixes

2008-02-15 11:21  woolford

	* libEM/reconstructor_tools.cpp, programs/e2make3d.py: padding in
	  2D reconstruction works

2008-02-15 11:04  woolford

	* libEM/: reconstructor.cpp, reconstructor_tools.cpp: fixed a bug
	  in 2D reconstruction

2008-02-14 16:38  woolford

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  programs/e2make3d.py: 2D fourier reconstructor added

2008-02-14 15:32  woolford

	* libEM/projector.cpp, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emimage3dsym.py: general improvements

2008-02-14 11:53  woolford

	* libEM/projector.cpp: standard projector works in 2D

2008-02-13 18:30  woolford

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libpyEM/CMakeLists.txt, libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimage3dobject.py,
	  libpyEM/qtgui/emimage3dsym.py, programs/e2make3d.py:
	  reconstruction related mods and polishing, new asymm unit viewer

2008-02-12 18:46  woolford

	* libEM/processor.cpp, libEM/processor.h, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libEM/reconstructor_tools.cpp,
	  libEM/reconstructor_tools.h, libEM/transform.cpp,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimage3diso.py,
	  programs/e2make3d.py: reconstructor related improvements

2008-02-11 17:40  woolford

	* libEM/processor.h, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libEM/reconstructor_tools.cpp,
	  programs/e2make3d.py, programs/e2proc2d.py,
	  programs/e2project3d.py: reconstructor related updates

2008-02-08 11:06  jbert

	* libEM/sparx/util_sparx.h: flip angles phi and theta on the
	  function util.vrdg (voronoi)

2008-02-08 11:03  jbert

	* libEM/sparx/util_sparx.cpp: voronoi: manage if the first three
	  angles are close

2008-02-06 17:34  gtang

	* libEM/mrcio.cpp: update the MRC.mx, MRC.my, MRC.mz in the
	  EMData::get_clip() function.Because IMOD uses these value to
	  calculate the A/Pixel.

2008-02-06 17:33  woolford

	* libEM/processor.h, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libpyEM/qtgui/emfloatingwidgets.py,
	  programs/e2make3d.py: main fourier reconstructor works for odd
	  dimensions (bug fix), other minor changes

2008-02-05 16:34  woolford

	* libEM/reconstructor.cpp, libpyEM/qtgui/emimage3dobject.py,
	  programs/e2project3d.py: minor changes

2008-02-05 11:41  woolford

	* libEM/reconstructor_tools.cpp, libpyEM/qtgui/em3Dhelloworld.py,
	  libpyEM/qtgui/emfloatingwidgets.py,
	  libpyEM/qtgui/emimage2dtex.py, libpyEM/qtgui/emimage3dobject.py,
	  utils/baldwinweights.cpp: fixed some compilation warnings, other
	  basic fixes

2008-02-04 14:27  stevel

	* libpyEM/EMAN2.py: get,set aliases

2008-02-01 18:34  woolford

	* libpyEM/qtgui/: emfloatingwidgets.py, emimage2dtex.py,
	  emimage3dobject.py: gui updates

2008-01-31 18:49  woolford

	* utils/baldwinweights.cpp: added a test script

2008-01-31 18:49  woolford

	* libEM/reconstructor_tools.cpp, libEM/reconstructor_tools.h,
	  libEM/util.cpp, libEM/util.h, libpyEM/qtgui/emfloatingwidgets.py,
	  programs/e2display.py, programs/e2make3d.py,
	  utils/CMakeLists.txt: python ui updates and reconstructor updates

2008-01-31 01:59  stevel

	* programs/: e2basis.py, e2classifykmeans.py: Minor changes

2008-01-30 17:46  woolford

	* libpyEM/qtgui/emfximage.py: conflict resolved

2008-01-30 17:44  woolford

	* libpyEM/qtgui/: emfloatingwidgets.py, emfximage.py, emimage2d.py,
	  emimage2dtex.py, emimage3dobject.py, emimage3dslice.py,
	  emimage3dvol.py: UI related updates - emimage2Dtex is new

2008-01-30 14:26  zyang

	* libEM/sparx/fundamentals.cpp: Fix two critical bugs in
	  auto-correlation and self-correlation

2008-01-30 10:20  stevel

	* libpyEM/qtgui/emimageutil.py: Mac gui fix

2008-01-30 00:59  stevel

	* libEM/emdata_transform.cpp, programs/e2basis.py,
	  programs/e2msa.py: Work on msa

2008-01-29 18:55  woolford

	* libpyEM/qtgui/: emfloatingwidgets.py, emfximage.py, emimage.py:
	  minor alterations

2008-01-29 17:55  woolford

	* libpyEM/qtgui/: emfloatingwidgets.py, emfximage.py,
	  emimage3diso.py: python updates - use PyOpenGL 3.0.01b if
	  possible

2008-01-29 16:28  zyang

	* libEM/: emdata.cpp, sparx/fundamentals.cpp, sparx/fundamentals.h:
	  Change correlation, convolution, autocorrelation,
	  self_correlation such that they will all take a parameter
	  "center" and pass this paramter to fourierproduct. If center is
	  true, the origin is at the center; if it is false, the origin is
	  at (0,0). The latter approach is faster, but it is probably
	  inconvenient to use.

2008-01-29 15:15  woolford

	* libpyEM/qtgui/emfximage.py: emfximage - filedialog support closer
	  to robust

2008-01-29 09:42  woolford

	* libpyEM/qtgui/: emfximage.py, emimage3dobject.py: python script
	  updates

2008-01-25 17:32  woolford

	* libpyEM/qtgui/emfximage.py: emfximage in development

2008-01-25 17:22  woolford

	* libpyEM/qtgui/emfximage.py: emfx - trying to get combos working

2008-01-25 16:45  woolford

	* libpyEM/qtgui/: emfximage.py, emimage3dobject.py: emfx - trying
	  to get combos working

2008-01-24 17:58  woolford

	* libpyEM/qtgui/emfximage.py: events are sent correctly in
	  emfximage.py

2008-01-24 17:32  woolford

	* libpyEM/qtgui/emfximage.py: events are sent correctly in
	  emfximage.py

2008-01-24 17:23  woolford

	* libpyEM/qtgui/emfximage.py: events are sent correctly in
	  emfximage.py

2008-01-24 10:21  woolford

	* libpyEM/qtgui/emfximage.py: bug fix

2008-01-23 19:44  woolford

	* libpyEM/qtgui/emfximage.py: trivial changes

2008-01-23 18:49  woolford

	* libpyEM/qtgui/emfximage.py: emfximage has a file dialog

2008-01-23 16:25  stevel

	* libEM/analyzer.cpp, libEM/analyzer.h, programs/e2msa.py: GSL SVD
	  is working

2008-01-23 16:06  woolford

	* libpyEM/qtgui/: emfximage.py, emimage3dobject.py: emfximage -
	  widget panels can be positioned interactively

2008-01-23 02:44  stevel

	* libEM/: analyzer.cpp, analyzer.h: Adding GSL SVD analyzer for
	  comparison with Chao's code. Not quite done.

2008-01-22 22:35  woolford

	* libpyEM/qtgui/: emfximage.py, emimage3dobject.py: emfximage.py -
	  updates

2008-01-22 20:21  woolford

	* libpyEM/qtgui/emfximage.py: trivial changes

2008-01-22 15:58  gtang

	* libEM/: analyzer.h, analyzer.cpp, sparx/analyzer_sparx.h:
	  Analyzer::insert_image_list() call insert_image() for all images
	  in the list.

2008-01-22 15:22  woolford

	* libpyEM/qtgui/emfximage.py: mouse events fixed in emfximage.py

2008-01-22 11:12  woolford

	* libpyEM/qtgui/emfximage.py: emfximage - replaced Numeric with
	  numpy

2008-01-22 11:08  woolford

	* libpyEM/qtgui/emfximage.py: emfximage - replaced Numeric with
	  numpy

2008-01-22 01:58  stevel

	* programs/: e2basis.py, e2msa.py: New program (e2basis),
	  incomplete

2008-01-21 22:53  stevel

	* CMakeLists.txt, libEM/analyzer.cpp, libEM/analyzer.h,
	  libEM/emdata.cpp, programs/e2msa.py, programs/e2proc2d.py:
	  Standardization changes to PCA Analyzers. Rewrote e2msa.py

2008-01-21 17:04  ppenczek

	* libEM/sparx/util_sparx.cpp: introduced temporary array for local
	  apmq, major acceleration

2008-01-20 18:31  woolford

	* libpyEM/qtgui/emfximage.py: emfximage.py - mouse tracking fixed

2008-01-18 18:49  zweig

	* libEM/emfft.cpp: fix a bug of fftw plan caching: ip not stored

2008-01-18 18:35  woolford

	* libpyEM/qtgui/: em3Dfonts.py, emfximage.py: trivial changes

2008-01-18 10:56  woolford

	* libpyEM/qtgui/em3Dhelloworld.py: 3D gui updates - added
	  em3Dhelloworld.py

2008-01-18 02:00  stevel

	* programs/e2refine2d.py: Template for refine2d.py

2008-01-17 18:17  woolford

	* libpyEM/qtgui/em3Dfonts.py: minor changes

2008-01-17 18:09  woolford

	* libpyEM/qtgui/: em3Dfonts.py, emfximage.py, emimage3diso.py,
	  emimage3dobject.py, emimage3dslice.py: python updates

2008-01-17 13:08  zweig

	* libEM/sparx/normpadft.cpp: set fftodd to false after inverse
	  fourier transform, it causes multiple problems

2008-01-17 11:11  woolford

	* libEM/reconstructor.h, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emimage3dobject.py,
	  libpyEM/qtgui/emimage3dslice.py, libpyEM/qtgui/emimage3dvol.py:
	  cool 3d widgit updates

2008-01-14 17:22  woolford

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libpyEM/qtgui/emimage3dobject.py: Reconstructor uses new
	  processor

2008-01-11 17:05  woolford

	* libEM/: processor.cpp, processor.h: commenting and cleaning
	  processors

2008-01-11 12:53  ppenczek

	* libEM/sparx/fourierfilter.cpp: Increase the length of table to
	  make filt_table() safer to use

2008-01-10 18:59  woolford

	* libEM/: processor.cpp, processor.h, reconstructor.cpp: fix
	  trivial (new) processor bugs

2008-01-10 18:46  woolford

	* libEM/emobject.h, libEM/exception.h, libEM/processor.cpp,
	  libEM/processor.h, rt/pyem/test_processor.py: added tomo edge
	  masking processor, another test image, and templated a function
	  in Dict

2008-01-03 22:35  zyang

	* libEM/sparx/normpadft.cpp, libEM/sparx/normpadft.h,
	  libpyEM/libpyEMData2.cpp: [no log message]

2008-01-03 18:12  woolford

	* libEM/: reconstructor.cpp, reconstructor.h, transform.cpp: [no
	  log message]

2008-01-03 13:57  woolford

	* rt/pyem/: test_averager.py, test_emdata.py,
	  test_reconstructor.py: fixed test scripts concerning projectors

2008-01-03 09:35  zyang

	* libEM/sparx/emdata_sparx.cpp: Change the order of boundary
	  checking

2008-01-02 17:35  woolford

	* libEM/: reconstructor.cpp, transform.cpp, transform.h:
	  reconstructor work

2008-01-02 16:54  gtang

	* libEM/: pifio.cpp, pifio.h: implement float data PIF image
	  reading

2007-12-29 18:10  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, util_sparx.cpp:  corrected
	  interpolation in 2D and switched to trilinear in 3D

2007-12-18 16:54  woolford

	* libEM/emobject.h, libEM/projector.cpp, libEM/projector.h,
	  libEM/reconstructor.cpp, libEM/reconstructor.h, libEM/util.h,
	  libEM/sparx/emdata_sparx.cpp, libEM/sparx/util_sparx.h,
	  programs/e2project3d.py: Fixed projectors so they work using
	  Transform3D objects, in the middle of reconstructor fixes

2007-12-18 14:52  zweig

	* libEM/reconstructor.cpp: fix an error in the weighting function
	  of nearest neighbouring reconstructor, the weight should be 1.0
	  if no neighbour is empty

2007-12-18 10:09  ppenczek

	* libEM/sparx/util_sparx.cpp: Fix a critical bug.

2007-12-14 17:41  woolford

	* libEM/reconstructor.cpp: in between modifications reconstructors

2007-12-13 17:35  woolford

	* libEM/emdata.cpp, libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libpyEM/libpyReconstructor2.cpp, programs/e2foldfitter.py: in the
	  middle of reconstructor work

2007-12-11 17:25  gtang

	* libEM/: mrcio.cpp, mrcio.h: fix the wrong label for MRC image. It
	  should be "MAP " not "MAP". which cause problem on chimera
	  display.  Also fix the wrong machine stamp.

2007-12-10 12:42  gtang

	* rt/pyem/test_aligner.py: fix name testimage.x to testimage.axes

2007-12-10 12:13  gtang

	* rt/pyem/test_aligner.py: minor fix

2007-12-10 12:07  gtang

	* rt/pyem/test_aligner.py: [no log message]

2007-12-10 11:53  gtang

	* rt/pyem/test_processor.py: [no log message]

2007-12-10 02:06  stevel

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emplot2d.py, programs/e2classifykmeans.py,
	  programs/e2ctf.py: Working on CTF stuff a bit more

2007-12-07 16:11  gtang

	* libEM/analyzer.cpp: Throw a NullPointerException when not set
	  mask image before calling insert_image() for Analyzer.

2007-12-07 11:41  zweig

	* libEM/sparx/util_sparx.cpp: fix an error in cyclic_shift

2007-12-07 11:02  zweig

	* libEM/sparx/util_sparx.cpp: just cleaning

2007-12-06 16:09  gtang

	* libEM/sparx/analyzer_sparx.h: parameter documentation

2007-12-06 14:01  woolford

	* libEM/emdata_metadata.cpp, rt/pyem/test_emdata.py: minor fixes

2007-12-06 10:28  zweig

	* libEM/processor.h: thresholdtominval fixed

2007-12-06 02:39  stevel

	* programs/e2ctf.py: Work on CTF

2007-12-05 14:35  woolford

	* libEM/reconstructor.cpp: in between computers

2007-12-04 23:47  stevel

	* libEM/processor.cpp: Fix typo

2007-12-04 18:10  woolford

	* libEM/emdata_metadata.cpp, libEM/processor.cpp,
	  libEM/processor.h, rt/pyem/test_processor.py: added
	  edge.xgradient edge.ygradient and edge.zgradient (and
	  convolution) processors

2007-12-04 14:01  woolford

	* libEM/emdata_metadata.cpp: got rid of some extraneous print
	  statements

2007-12-04 14:00  woolford

	* libEM/emdata_metadata.cpp, libEM/processor.cpp,
	  libEM/processor.h, libpyEM/qtgui/emimage3dvol.py,
	  plugins/processor_template.cpp: get_attr does deep copy median,
	  plus tomo test image

2007-12-03 03:00  stevel

	* programs/e2ctf.py: Working on ctf autofilter still

2007-11-29 10:27  woolford

	* libEM/: processor.cpp, reconstructor.cpp: fixed Pawel's warnings

2007-11-29 03:01  stevel

	* libpyEM/qtgui/emplot2d.py, programs/e2ctf.py: More fixes for
	  changes required by OSX

2007-11-29 02:30  stevel

	* libpyEM/qtgui/: emimage2d.py, emplot2d.py: Trivial bugs

2007-11-28 17:59  woolford

	* libEM/geometry.cpp, libEM/processor.cpp, libEM/processor.h,
	  plugins/processor_template.cpp, plugins/processor_template.h,
	  programs/e2proc3d.py, rt/pyem/test_processor.py: tomography
	  related changes

2007-11-28 10:38  woolford

	* libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimage3diso.py,
	  libpyEM/qtgui/emimage3dslice.py, libpyEM/qtgui/emimage3dvol.py,
	  programs/e2proc3d.py: e2proc3d.py writes outfiles

2007-11-27 16:15  woolford

	* libEM/reconstructor.cpp, programs/e2proc2d.py: trivial changes

2007-11-27 15:37  stevel

	* libpyEM/qtgui/emshape.py: Fixed plot label scaling problem

2007-11-26 17:00  woolford

	* libEM/reconstructor.cpp, programs/e2make3d.py: in the middle of
	  reconstruction adaptations

2007-11-26 14:38  woolford

	* libEM/emdata.cpp, libEM/reconstructor.cpp, programs/e2proc2d.py,
	  programs/e2proc3d.py: trivial reconstructor adaptations

2007-11-26 11:29  woolford

	* programs/e2proc2d.py: fixes for e2proc2d.py

2007-11-26 11:17  woolford

	* libpyEM/EMAN2.py, programs/e2proc2d.py, programs/e2proc3d.py:
	  e2proc2d does mrc slices in any plane

2007-11-22 11:22  zweig

	* libEM/analyzer.cpp: initialize Av to 0.0

2007-11-21 23:39  stevel

	* programs/e2boxer.py: Resizing boxes

2007-11-20 15:35  woolford

	* libEM/reconstructor.cpp, programs/e2ali2img.py: updates to
	  Fourier reconstructor preprocess_slice

2007-11-20 15:08  woolford

	* libEM/: reconstructor.cpp, reconstructor.h: option added to
	  Fourier reconstructor

2007-11-20 14:01  woolford

	* libEM/processor.cpp, libEM/processor.h,
	  rt/pyem/test_processor.py: added theshold.clampminmax and
	  threshold.clampminmax.nsigma processors, and accompanying test
	  code

2007-11-19 15:44  woolford

	* libEM/emdata_gl.cpp, libEM/marchingcubes.cpp,
	  libpyEM/qtgui/emfximage.py, libpyEM/qtgui/emimage3diso.py,
	  libpyEM/qtgui/emimage3dslice.py, libpyEM/qtgui/emimage3dvol.py:
	  in the middle of adapting emfximage.py

2007-11-19 10:33  woolford

	* programs/e2ali2img.py: added e2ali2img.py - script still needs
	  work

2007-11-15 19:33  stevel

	* programs/e2display.py: Make it display properly...

2007-11-15 16:49  woolford

	* libEM/isosurface.h, libEM/marchingcubes.cpp,
	  libEM/marchingcubes.h, libpyEM/libpyMarchingCubes2.cpp,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimage3diso.py,
	  libpyEM/qtgui/emimage3dvol.py: can texture 3d isosurfaces

2007-11-15 15:53  stevel

	* libpyEM/qtgui/: emimage.py, emplot2d.py, emshape.py: Some
	  additional mac and non-mac GUI improvements

2007-11-15 00:20  stevel

	* libpyEM/qtgui/emfximage.py, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3diso.py, libpyEM/qtgui/emimage3dslice.py,
	  libpyEM/qtgui/emimage3dvol.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimageutil.py, libpyEM/qtgui/emplot2d.py,
	  programs/e2display.py: Fixed gui objects for leopard

2007-11-14 10:36  gtang

	* libEM/emdata_transform.cpp: extra tokens at end of #endif
	  directive

2007-11-13 20:23  stevel

	* libEM/emdata_transform.cpp, libpyEM/qtgui/emdesktop.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3diso.py,
	  libpyEM/qtgui/emimage3dvol.py: Trying for Leopard support. not
	  much luck

2007-11-13 13:14  zweig

	* libEM/reconstructor.cpp: get rid of warning message from
	  recontruction by using get_attr_default()

2007-11-13 12:35  zweig

	* libEM/reconstructor.cpp: get rid of warning message from
	  recontruction by using get_attr_default()

2007-11-13 10:23  woolford

	* libpyEM/qtgui/emimage3d.py: fix near and far clipping plane
	  problem

2007-11-13 01:30  stevel

	* libpyEM/qtgui/: emimage2d.py, emimage3d.py, emshape.py: Some
	  bugfixes OSX detected...

2007-11-12 18:49  woolford

	* libpyEM/qtgui/emimage3d.py: more fixes

2007-11-12 18:35  stevel

	* libpyEM/CMakeLists.txt: installer update

2007-11-12 18:27  woolford

	* libpyEM/qtgui/emimage3d.py: more fixes

2007-11-12 18:18  woolford

	* libpyEM/qtgui/: emimage3d.py, emimage3dslice.py: more fixes

2007-11-12 18:08  woolford

	* libpyEM/qtgui/: emimage3d.py, emimage3diso.py,
	  emimage3dobject.py, emimage3dslice.py, emimage3dvol.py: more
	  fixes

2007-11-12 18:00  woolford

	* libpyEM/qtgui/: emimage3diso.py, emimage3dobject.py,
	  emimage3dslice.py, emimage3dvol.py: trivial changes

2007-11-12 17:39  woolford

	* libpyEM/qtgui/: emimage3d.py, emimage3diso.py,
	  emimage3dobject.py, emimage3dslice.py, emimage3dvol.py: 3d slice
	  viewer works, emimage3d display three things

2007-11-12 15:17  gtang

	* rt/emdata/CMakeLists.txt: remove EMAN1 library dependency

2007-11-12 15:12  woolford

	* libpyEM/qtgui/emimage3dvol.py: in the middle of changes

2007-11-12 15:04  woolford

	* libpyEM/qtgui/: emimage3d.py, emimage3diso.py, emimage3dvol.py,
	  emimage3dvr.py: in the middle of changes

2007-11-11 01:32  stevel

	* libpyEM/CMakeLists.txt: install fix

2007-11-11 01:28  stevel

	* CMakeLists.txt, libEM/emdata.cpp: Fix memory corruption

2007-11-09 18:18  gtang

	* CMakeLists.txt: minor change to indicate user where is the numpy
	  header file

2007-11-09 17:47  woolford

	* libEM/emdata_gl.cpp, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimage3diso.py: 3D widget updates

2007-11-09 12:33  woolford

	* libpyEM/qtgui/emimage2d.py: removed debug code

2007-11-09 12:32  woolford

	* libpyEM/qtgui/: emimage2d.py, emimage3diso.py, emimage3dvr.py:
	  adding emimage3diso.py

2007-11-08 18:03  woolford

	* libEM/emdata_gl.cpp: silly error

2007-11-08 18:02  woolford

	* libEM/emdata.h, libEM/emdata_gl.cpp, libEM/emdata_gl.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/qtgui/emimage3dvr.py: more
	  emimage3dvr.py related adaptations

2007-11-08 16:51  woolford

	* libEM/processor.cpp, libpyEM/qtgui/emfximage.py,
	  libpyEM/qtgui/emimage3dvr.py: fixed a bug in testimage.x, updates
	  to volume rendering and fximage

2007-11-08 16:23  gtang

	* libEM/sparx/emdata_sparx.cpp, libpyEM/libpyMarchingCubes2.cpp,
	  libpyEM/emdata_wrapitems.h: fix Visual Studio .NET 2003
	  compilation warnings

2007-11-08 15:07  gtang

	* libEM/sparx/lapackblas.cpp: fix for the warning message from
	  Visual Studio "warning C4723: potential divide by 0"

2007-11-08 09:51  woolford

	* libpyEM/qtgui/emimage3dvr.py: emimage3dvr.py tweaks

2007-11-08 09:21  gtang

	* libpyEM/libpyEMData2.cpp: fix for compilation on VC++

2007-11-07 18:32  woolford

	* libEM/: emdata_gl.cpp, emdata_gl.h: forgot to add emdata_gl.cpp/h

2007-11-07 18:03  woolford

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/emdata.h,
	  libEM/isosurface.h, libEM/marchingcubes.cpp,
	  libEM/marchingcubes.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyMarchingCubes2.cpp, libpyEM/qtgui/emfximage.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimage3dvr.py: add
	  OpenGL compiler flag, volume rendering works (emimage3dvr.py)

2007-11-07 16:09  gtang

	* libEM/reconstructor.cpp: fix Visual Studio .NET 2003 compilation
	  warnings

2007-11-07 15:40  gtang

	* libEM/sparx/: steepest.cpp, util_sparx.cpp, varimax.cpp: fix
	  Visual Studio .NET 2003 compilation warnings

2007-11-07 12:53  gtang

	* libEM/sparx/fourierfilter.cpp: fix Visual Studio .NET 2003
	  compilation warnings

2007-11-07 12:30  gtang

	* libEM/processor.cpp: fix for compilation on VC++

2007-11-07 12:25  gtang

	* libEM/: aligner.cpp, emdata.cpp, emdata_io.cpp,
	  emdata_transform.cpp, fitsio.cpp, imageio.cpp, imagicio.cpp,
	  pointarray.cpp, util.cpp: fix for compilation on VC++

2007-11-07 01:44  stevel

	* libEM/processor.cpp: More work on Wiener.

2007-11-06 22:05  stevel

	* libEM/: processor.cpp, processor.h: oops

2007-11-06 21:10  stevel

	* libEM/processor.h: Working on wiener filters

2007-11-06 12:57  gtang

	* libEM/projector.cpp: fix for compilation warnings on VC++

2007-11-06 12:43  gtang

	* libEM/reconstructor_tools.cpp: fix for compilation warnings on
	  VC++

2007-11-06 12:31  gtang

	* libEM/: analyzer.cpp, spiderio.cpp: fix for compilation warnings
	  on VC++

2007-11-06 11:54  gtang

	* libEM/marchingcubes.cpp: fix for compilation warnings on VC++

2007-11-06 11:40  gtang

	* libEM/marchingcubes.cpp: fix for compilation on VC++

2007-11-06 01:41  stevel

	* libEM/processor.cpp, libEM/processor.h, programs/e2ctf.py:
	  Working towards new wiener filters

2007-11-05 19:10  gtang

	* libEM/reconstructor.cpp: fix Visual Studio compilation error

2007-11-05 19:05  gtang

	* libEM/sparx/: emdata_sparx.cpp: fix Visual Studio compilation
	  error

2007-11-05 19:00  gtang

	* libEM/reconstructor.cpp: fix Visual Studio compilation error

2007-11-05 18:51  gtang

	* libEM/: reconstructor.cpp, sparx/steepest.cpp,
	  sparx/util_sparx.cpp: fix Visual Studio compilation error

2007-11-05 18:23  gtang

	* libEM/: averager.cpp, processor.h, emdata_transform.cpp,
	  processor.cpp, reconstructor_tools.cpp: fix Visual Studio
	  compilation error

2007-11-05 15:50  stevel

	* libEM/averager.cpp, libpyEM/qtgui/emplot2d.py, programs/e2ctf.py:
	  Working on ctf some more

2007-11-05 12:52  woolford

	* libEM/isosurface.h, libEM/marchingcubes.cpp,
	  libEM/marchingcubes.h, libEM/processor.cpp,
	  libEM/reconstructor_tools.cpp, libEM/reconstructor_tools.h,
	  libpyEM/libpyMarchingCubes2.cpp, libpyEM/qtgui/emimage3d.py:
	  emimage3d meets initial specs, marching cubes code cleaned and
	  commented

2007-11-05 02:38  stevel

	* libEM/averager.cpp, libEM/averager.h, programs/e2ctf.py: Adding
	  new CTF features.

2007-11-04 16:13  stevel

	* libpyEM/qtgui/emplot2d.py: Zooming in plot2d

2007-11-03 13:04  gtang

	* rt/pyem/test_processor.py: [no log message]

2007-11-02 17:22  woolford

	* libEM/transform.h, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/valslider.py, pyemtbx/imagetypes.py: emimage3d
	  updates

2007-11-02 02:06  stevel

	* libpyEM/qtgui/: emimage2d.py, emshape.py: Finished improvements
	  to emimage2d shapes, etc.

2007-11-02 01:09  stevel

	* libpyEM/CMakeLists.txt, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emshape.py, programs/e2boxer.py: Finished update in
	  how shapes are generated.

2007-11-01 18:39  woolford

	* libEM/emobject.cpp, libEM/emobject.h, libEM/hdfio2.cpp,
	  libEM/marchingcubes.cpp, libpyEM/typeconverter.cpp,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3d.py: emimage3d
	  navigation works (control modifier or mouse wheel for zoom)

2007-11-01 16:32  stevel

	* libpyEM/qtgui/: emimage2d.py, emplot2d.py, emshape.py: Working on
	  plots, shapes, etc.

2007-11-01 14:56  gtang

	* libEM/marchingcubes.h: fix the compilation failure on water (gcc
	  3.2)

2007-11-01 10:58  stevel

	* libEM/emdata_transform.cpp, libpyEM/qtgui/emimage3d.py: Fix bug
	  in emimage3d

2007-11-01 02:28  stevel

	* libpyEM/qtgui/emplot2d.py: Workign on plot widget.

2007-10-31 17:33  woolford

	* libEM/marchingcubes.cpp: more emimage3d related optimizations

2007-10-31 12:35  woolford

	* libEM/marchingcubes.cpp, libEM/marchingcubes.h,
	  libpyEM/qtgui/emimage3d.py: more emimage3d related modifications

2007-10-31 12:23  zyang

	* libEM/sparx/fourierfilter.cpp: Undo the recent change of shift
	  filter. It saves very little time, but causes some unexpected
	  problems.

2007-10-30 17:40  woolford

	* libEM/marchingcubes.cpp, libpyEM/qtgui/emimage3d.py: fixed
	  inefficiency in emimage3d.py

2007-10-30 17:12  woolford

	* libEM/emdata_core.h, libEM/isosurface.h, libEM/marchingcubes.cpp,
	  libEM/marchingcubes.h, libEM/processor.cpp, libEM/processor.h,
	  libpyEM/libpyMarchingCubes2.cpp, libpyEM/qtgui/emimage3d.py:
	  emimage3d related updates - performance is fairly good

2007-10-30 01:50  stevel

	* libEM/emdata_transform.cpp, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemx.py: New FFT buttons in 2-D image view

2007-10-29 15:10  gtang

	* rt/pyem/test_processor.py: unit test update

2007-10-29 11:01  gtang

	* libEM/: reconstructor.h, reconstructor_tools.h, cmp.h,
	  marchingcubes.h, processor.h, sparx/emdata_sparx.h: "fix" the
	  Doxygen warnings for function comment

2007-10-29 02:36  stevel

	* libEM/emdata_transform.cpp, libEM/emdata_transform.h,
	  libEM/processor.cpp, libEM/processor.h, libEM/util.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/valslider.py: Drawing works in 2d image view.
	  Adding color to complex image display... not done.

2007-10-28 02:45  stevel

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emimage2d.py: Things compile, though emimage2d
	  still in process of update

2007-10-28 00:38  stevel

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/processor.h,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emplot2d.py: Fixed
	  problem with GL libs and compilation.

2007-10-26 17:49  woolford

	* libEM/isosurface.h, libEM/marchingcubes.cpp,
	  libEM/marchingcubes.h, libpyEM/libpyMarchingCubes2.cpp,
	  libpyEM/qtgui/emimage3d.py: emimage3d related updates

2007-10-26 16:31  stevel

	* libpyEM/qtgui/emimage2d.py: New additions to 2D image inspector

2007-10-25 14:26  gtang

	* rt/pyem/rt.py: minor change for binary EMAN2

2007-10-25 12:03  woolford

	* libEM/marchingcubes.cpp, libEM/marchingcubes.h,
	  libpyEM/qtgui/emimage3d.py: emimage3d related updates

2007-10-25 09:57  zyang

	* libEM/sparx/fourierfilter.cpp, libEM/sparx/normpadft.cpp,
	  libEM/sparx/normpadft.h, libpyEM/libpyEMData2.cpp: Add some code
	  to improve the speed of projection

2007-10-24 02:22  stevel

	* libpyEM/qtgui/: emplot2d.py, valslider.py: Work on plot

2007-10-23 21:32  ppenczek

	* libEM/sparx/: normpadft.cpp, util_sparx.cpp, util_sparx.h: [no
	  log message]

2007-10-23 20:14  stevel

	* libpyEM/qtgui/emplot2d.py: Working on 2d plotting

2007-10-23 17:39  woolford

	* libpyEM/qtgui/emimage3d.py, programs/e2classaverage.py,
	  programs/e2classify.py, programs/e2make3d.py,
	  programs/e2project3d.py, programs/e2refine.py,
	  programs/e2simmx.py: emimage3d.py updates

2007-10-23 17:35  gtang

	* libtbx_refresh.py, examples/sortsimilar.py,
	  examples/transalignavg.py, libpyEM/EMAN2.py,
	  libpyEM/EMAN2_cppwrap.py, libpyEM/qtgui/emdesktop.py,
	  libpyEM/qtgui/emfximage.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimageutil.py, libpyEM/qtgui/emplot2d.py,
	  libpyEM/qtgui/valslider.py, libpyEM/wxgui/wxValSlider.py,
	  libpyEM/wxgui/wxemimageframe.py, libpyEM/wxgui/wximagecontrol.py,
	  programs/e2classaverage.py, programs/e2classifykmeans.py,
	  programs/e2make3d.py, programs/e2proc2d.py, programs/e2proc3d.py,
	  programs/e2refine.py, programs/e2startcsym.py,
	  programs/e2tilefile.py, pyemtbx/exceptions.py, pyemtbx/files.py,
	  pyemtbx/imagetypes.py, rt/demo/align.py, rt/demo/cmp.py,
	  rt/demo/reconstruction.py, rt/pyem/rt.py,
	  rt/pyem/test_aligner.py, rt/pyem/test_averager.py,
	  rt/pyem/test_cmp.py, rt/pyem/test_emdata.py,
	  rt/pyem/test_imageio.py, rt/pyem/test_misc.py,
	  rt/pyem/test_processor.py, rt/pyem/test_reconstructor.py,
	  rt/pyem/test_transform.py, rt/pyem/test_typeconverter.py,
	  rt/pyem/test_utils.py, rt/pyem/test_vec.py, rt/pyem/testlib.py,
	  rt/timetests/test_times.py: all python wcript end with a return
	  for Binary EMAN2 installer script

2007-10-23 14:30  woolford

	* libpyEM/qtgui/emimage3d.py, programs/e2classaverage.py,
	  programs/e2classify.py, programs/e2make3d.py,
	  programs/e2project3d.py, programs/e2refine.py,
	  programs/e2simmx.py: e2refine.py related fixes, plus adding
	  updated emimage3d.py

2007-10-23 11:44  stevel

	* libpyEM/qtgui/emplot2d.py: Working on 2-D plots

2007-10-23 11:38  gtang

	* libtbx_refresh.py, test-imports.py, examples/alignbystars.py,
	  examples/telescope.py, libpyEM/EMAN2.py,
	  libpyEM/EMAN2_cppwrap.py, libpyEM/qtgui/emimageutil.py,
	  libpyEM/qtgui/valslider.py, libpyEM/wxgui/wxemimage.py,
	  libpyEM/wxgui/wxemimagecanvas.py,
	  libpyEM/wxgui/wxemimageframe.py, programs/e2make3d.py,
	  programs/e2tilefile.py, pyemtbx/box.py, pyemtbx/exceptions.py,
	  pyemtbx/files.py, pyemtbx/imagetypes.py, pyemtbx/options.py,
	  rt/demo/align.py, rt/demo/averager.py, rt/demo/processor1.py,
	  rt/demo/processor2.py, rt/demo/processor3.py, rt/demo/project.py,
	  rt/demo/tomrc.py, rt/pyem/test_aligner.py,
	  rt/pyem/test_averager.py, rt/pyem/test_cmp.py: correct the path
	  to Python interpreter

2007-10-22 18:25  woolford

	* libEM/aligner.cpp, libpyEM/EMAN2.py, programs/e2classaverage.py,
	  programs/e2classify.py, programs/e2make3d.py,
	  programs/e2project3d.py, programs/e2refine.py,
	  programs/e2simmx.py: e2refine.py and related python scripts -
	  almost finished updating the error testing framework

2007-10-22 02:30  stevel

	* libEM/emdata_transform.cpp, libpyEM/CMakeLists.txt,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emplot2d.py,
	  programs/e2ctf.py: Work on ctf. e2ctf will now display data.

2007-10-19 16:41  woolford

	* programs/: e2classaverage.py, e2make3d.py, e2project3d.py,
	  e2refine.py: updating python scripts

2007-10-19 14:14  cyang

	* libEM/sparx/temp/rununified.cpp: enable user to pass in the
	  'maxit' parameter

2007-10-19 14:00  zyang

	* libEM/sparx/fundamentals.cpp: Fix a small bug

2007-10-19 13:52  zyang

	* libEM/sparx/fourierfilter.cpp: Change the structure of the
	  program to save time slightly.

2007-10-19 13:07  zyang

	* libEM/sparx/fundamentals.cpp: Improve the speed of ccf using
	  multipling -1

2007-10-18 17:34  woolford

	* programs/e2refine.py: e2refine.py changes

2007-10-18 17:07  woolford

	* libpyEM/EMAN2.py, programs/e2classaverage.py,
	  programs/e2classify.py, programs/e2make3d.py,
	  programs/e2project3d.py, programs/e2refine.py,
	  programs/e2simmx.py: e2refine.py is working

2007-10-18 15:15  zyang

	* libEM/sparx/fundamentals.cpp: Just doing some tests, already
	  commented out.

2007-10-18 12:01  zyang

	* libpyEM/libpyFundamentals2.cpp: Trival change

2007-10-17 21:52  stevel

	* programs/e2ctf.py: more work on CTF program

2007-10-17 17:44  woolford

	* libEM/cmp.cpp, libEM/emdata.cpp, libEM/emdata_transform.cpp,
	  libEM/pointarray.cpp, libEM/processor.cpp, libEM/processor.h,
	  libEM/projector.cpp, libEM/reconstructor.cpp,
	  programs/e2project3d.py, rt/pyem/test_cmp.py,
	  rt/pyem/test_processor.py: Updated the names of processors, so
	  lots of files had trivial changes

2007-10-17 14:50  woolford

	* libEM/processor.cpp, libEM/processor.h,
	  rt/pyem/test_processor.py: xform.fourierorigin replaced by
	  xform.fourierorigin.forward and xform.fourierorigin.backward...
	  works in 2D and 3D, and for all combinations of evenness and
	  oddness

2007-10-17 10:13  woolford

	* libEM/: processor.cpp, processor.h: added comments

2007-10-17 01:46  stevel

	* programs/e2ctf.py: Beginning new program e2ctf.py

2007-10-16 19:14  woolford

	* libEM/processor.cpp, libEM/processor.h, rt/pyem/test_aligner.py,
	  rt/pyem/test_cmp.py, rt/pyem/test_emdata.py,
	  rt/pyem/test_processor.py: xform.phaseorigin processor divided
	  into xform.phaseorigin.forward and xform.phaseoriging.backward
	  processors - this processor now supports 1D,2D and 3D images and
	  works for all combinations of even and oddness

2007-10-15 18:43  woolford

	* libEM/emdata.cpp, libEM/emdata.h, rt/pyem/test_emdata.py:
	  EMData::calc_flcf now works - return image origin is at bottom
	  left

2007-10-15 16:40  stevel

	* CMakeLists.txt, libEM/emdata.cpp, libEM/emdata_transform.cpp,
	  libEM/emdata_transform.h, libpyEM/libpyEMData2.cpp: Working on
	  power spectrum functions.

2007-10-15 14:11  woolford

	* libEM/: aligner.cpp, processor.cpp: Removed reference to
	  Translational3DAligner in processor.cpp

2007-10-15 13:42  gtang

	* rt/pyem/test_emdata.py: unit test update

2007-10-15 13:24  gtang

	* rt/pyem/test_cmp.py: unit test update

2007-10-15 12:43  gtang

	* rt/pyem/: test_misc.py, test_imageio.py: unit test update

2007-10-15 12:35  woolford

	* libEM/aligner.cpp, libEM/aligner.h, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/emdata_core.cpp, libEM/emdata_core.h,
	  libEM/polardata.h, libEM/processor.cpp, libpyEM/libpyEMData2.cpp,
	  rt/pyem/test_aligner.py, rt/pyem/test_emdata.py:
	  Translational3DAligner subsumed by TranslationAligner, added
	  EMData()::zero_corner_circulant

2007-10-15 12:32  gtang

	* rt/pyem/test_processor.py: unit test update

2007-10-15 08:21  woolford

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emdata_core.cpp, libEM/emdata_core.h,
	  libEM/emdata_metadata.cpp, rt/pyem/test_aligner.py,
	  rt/pyem/test_emdata.py: optimizations - in between changes (and
	  computers)

2007-10-15 02:28  stevel

	* libEM/processor.cpp, libEM/processor.h,
	  libpyEM/qtgui/emplot2d.py, programs/e2boxer.py: Working on new
	  processor (wiener2d). Fixed e2boxer to handle new aligners,
	  though accuracy not checked.

2007-10-12 10:41  woolford

	* rt/pyem/test_emdata.py: trivial change to test_emdata.py

2007-10-12 10:40  woolford

	* libEM/emdata.cpp, libEM/emdata.h, libEM/emdata_transform.cpp,
	  libEM/exception.h, libEM/processor.cpp, libEM/processor.h,
	  libEM/sparx/fundamentals.cpp, libEM/sparx/fundamentals.h,
	  rt/pyem/test_emdata.py: in the middle of changes, working on
	  optimizations, changing computers

2007-10-08 17:17  woolford

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emdata_core.cpp, libEM/emdata_core.h,
	  libEM/emdata_metadata.cpp, libEM/emdata_transform.cpp,
	  libEM/emdata_transform.h, libEM/processor.cpp,
	  libEM/reconstructor.cpp, libpyEM/libpyEMData2.cpp,
	  programs/e2classaverage.py, programs/e2project3d.py,
	  programs/e2refine.py, programs/e2simmx.py: various optimizations,
	  also added skeleton for e2refine.py

2007-10-08 02:39  stevel

	* libpyEM/qtgui/: emplot2d.py, valslider.py: Plotting improvements,
	  int only mode for valslider

2007-10-07 10:58  ppenczek

	* libEM/sparx/normpadft.cpp:
	  ----------------------------------------------------------------------

2007-10-06 14:36  gtang

	* libEM/CMakeLists.txt, libEM/emdata.h, libEM/projector.cpp,
	  libEM/util.h, libEM/sparx/emdata_sparx.cpp,
	  libEM/sparx/emdata_sparx.h, libEM/sparx/fourierfilter.cpp,
	  libEM/sparx/rsconvolution.cpp, libEM/sparx/steepest.cpp,
	  libEM/sparx/steepest.h, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h, libpyEM/kaiserbessel_pickle.h,
	  libpyEM/libpyUtils2.cpp, rt/pyem/test_utils.py: KaiserBessel
	  class pickle implementation

2007-10-06 14:31  gtang

	* libEM/sparx/: kaiserbessel.cpp, kaiserbessel.h: KaiserBessel
	  class pickle implementation

2007-10-06 14:25  gtang

	* programs/e2foldhunter.py: [no log message]

2007-10-05 11:53  zyang

	* libEM/sparx/normpadft.cpp: A change to my test program

2007-10-04 12:41  woolford

	* libEM/cmp.cpp, libEM/emdata.cpp, libEM/emdata.h,
	  programs/e2project3d.py: e2project3d supporst the --numproj
	  argument, as opposed to just the --prop argument

2007-10-03 11:03  zyang

	* libEM/sparx/util_sparx.cpp: Trival change

2007-10-03 10:43  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, normpadft.cpp, util_sparx.cpp:
	  corrected normalization of pad fft

2007-10-03 01:19  stevel

	* libpyEM/qtgui/: emplot2d.py, valslider.py: Error in valslider

2007-10-02 14:47  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, util_sparx.cpp: normalization
	  factor of 4 added to gridding convolution

2007-10-02 14:18  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, normpadft.cpp, normpadft.h,
	  util_sparx.cpp: inserted normalization factor 0.25 into all
	  gridding convolutions

2007-10-02 14:17  woolford

	* libEM/: emdata.cpp, emfft.cpp, emfft.h: Fixed FFTW2
	  FFTW_PLAN_CACHING error, added comments

2007-10-02 11:24  zyang

	* libEM/sparx/emdata_sparx.cpp: Just add some comments.

2007-10-02 10:12  woolford

	* CMakeLists.txt: CMakeLists.txt has ENABLE_FFTW_PLAN_CACHE option,
	  default is ON

2007-10-02 10:09  woolford

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/emdata_core.cpp,
	  libEM/emdata_transform.cpp, libEM/emfft.cpp, libEM/emfft.h,
	  rt/pyem/test_emdata.py, rt/pyem/test_processor.py: Added FFTW2&3
	  plan caching - toggled with a compiler flag - gives a significant
	  performance boost

2007-10-01 16:10  stevel

	* libpyEM/qtgui/: emplot2d.py, valslider.py: New emplot2d widget.
	  Still in progress.

2007-09-28 17:14  zweig

	* libEM/sparx/fourierfilter.cpp: fix an error in tophat band filter

2007-09-27 08:54  zweig

	* libEM/reconstructor.cpp: revert the recent change on weighting
	  method

2007-09-25 19:33  cyang

	* libEM/sparx/temp/sirt_Cart.cpp: move the symmetry loop out as the
	  outmost loop and reinitialize the projection data to zero in each
	  outer loop iteration.

2007-09-25 16:33  gtang

	* libEM/emutil.cpp: fix the bug 3D mrc file has 2G file size limit

2007-09-24 16:36  zyang

	* libEM/sparx/normpadft.cpp, libEM/sparx/normpadft.h,
	  libpyEM/libpyEMData2.cpp: Some experimental code

2007-09-24 12:15  zweig

	* libEM/reconstructor.cpp: adjust the weighting method used in nn
	  reconstruction

2007-09-24 11:23  gtang

	* rt/pyem/test_processor.py: minor fix

2007-09-21 17:17  woolford

	* libEM/: cmp.cpp, cmp.h: [no log message]

2007-09-21 16:38  gtang

	* libEM/: processor.cpp, processor.h: implement the radial filter
	  for real image, "filter.radialtable"

2007-09-21 15:06  gtang

	* libEM/mrcio.cpp: Fix the MRC I/O to handle the extra bytes for
	  symmetry information

2007-09-21 13:02  woolford

	* libEM/cmp.cpp, libEM/emdata_transform.cpp, libEM/exception.h,
	  rt/pyem/test_cmp.py: added some test scenarios in test_cmp.py

2007-09-21 11:41  woolford

	* rt/pyem/: test_cmp.py: added some test scenarios in test_cmp.py

2007-09-20 18:45  woolford

	* libEM/aligner.cpp, libEM/aligner.h, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/emdata_metadata.cpp,
	  libEM/emdata_metadata.h, libEM/emdata_transform.cpp,
	  libEM/emdata_transform.h, libEM/exception.h,
	  libpyEM/libpyEMData2.cpp, programs/e2classaverage.py,
	  programs/e2classify.py, programs/e2project3d.py,
	  programs/e2simmx.py, rt/pyem/test_aligner.py,
	  rt/pyem/test_averager.py, rt/pyem/test_emdata.py,
	  rt/timetests/test_times.py: python scripts for EMAN2 pipeline
	  updates

2007-09-19 13:35  zyang

	* libEM/sparx/util_sparx.cpp: Fix a bug in twoD_to_3D_ali() that
	  causes memory leak

2007-09-18 17:43  gtang

	* rt/pyem/test_emdata.py: unit test update, add EMData arithmetic
	  operation test for EMdata at teh right hand of operator

2007-09-17 09:33  zyang

	* libEM/sparx/util_sparx.cpp: Trival change.

2007-09-14 19:14  prb

	* programs/e2classify.py:
	    tidied up, shortened and commented

2007-09-14 16:59  ppenczek

	* libEM/: emdata_transform.cpp, sparx/normpadft.cpp: added
	  fft_odd=false in two places

2007-09-14 13:31  ppenczek

	* libEM/sparx/fourierfilter.cpp: [no log message]

2007-09-14 12:33  ppenczek

	* libEM/sparx/fourierfilter.cpp: [no log message]

2007-09-14 10:36  gtang

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/libpyEMData2.cpp: fix
	  the EMData __rsub__ and __rdiv__ bugs.

2007-09-13 18:32  woolford

	* libEM/aligner.cpp, libEM/emobject.cpp, libEM/emobject.h,
	  libEM/hdfio2.cpp, libEM/reconstructor_tools.cpp, libEM/util.cpp,
	  programs/e2classaverage.py, rt/pyem/test_aligner.py:
	  e2classaverage.py up and running, some aligner debug

2007-09-13 12:07  sternberg

	* libEM/sparx/temp/ali3d_d_mpi.cpp: Add code to set psi = -phi, as
	  in python.

2007-09-13 11:53  zyang

	* libEM/sparx/util_sparx.cpp: Change ccc to SqEuclidean in some of
	  my tests

2007-09-12 16:00  woolford

	* libEM/util.cpp, libEM/util.h, libpyEM/libpyUtils2.cpp,
	  programs/e2classaverage.py, rt/timetests/test_times.py: get_stats
	  added to Util, timing code

2007-09-12 12:42  ppenczek

	* libEM/sparx/normpadft.cpp: filter_by_image added, ready

2007-09-12 11:42  prb

	* programs/e2classify.py:
	    made output "number of peaks" by "number of particles"

2007-09-12 11:02  ppenczek

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/fourierfilter.cpp,
	  libEM/sparx/normpadft.cpp, libEM/sparx/normpadft.h,
	  libpyEM/libpyEMData2.cpp: filter_by_image added, but not ready
	  yet

2007-09-12 10:57  gtang

	* libEM/: reconstructor_tools.cpp, sparx/normpadft.cpp: fix the
	  compilation warning message

2007-09-12 10:45  woolford

	* libEM/util.cpp, libEM/util.h, libpyEM/libpyUtils2.cpp,
	  programs/e2classaverage.py, programs/e2classify.py: added
	  e2classify.py (real author PRB)

2007-09-11 16:28  woolford

	* libEM/averager.cpp, libEM/averager.h, libEM/exception.h,
	  libEM/util.cpp, libEM/util.h, libpyEM/libpyAverager2.cpp,
	  libpyEM/libpyUtils2.cpp, programs/e2classaverage.py,
	  programs/e2simmx.py: eman2 classification programs updates and
	  supplementary changes

2007-09-11 14:55  ppenczek

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/libpyEMData2.cpp: added real space n-D mult by a 1D image

2007-09-10 17:31  ppenczek

	* libEM/sparx/fourierfilter.cpp: tanh filter fixed

2007-09-07 17:29  woolford

	* libpyEM/EMAN2.py, libpyEM/libpyEMData2.cpp,
	  programs/e2classaverage.py, programs/e2make3d.py,
	  programs/e2project3d.py, programs/e2simmx.py: added
	  e2classaverage.py (work in progress), plus some changes to
	  e2simmx.py

2007-09-07 11:37  zyang

	* libEM/cmp.cpp: Fix a bug in DotCmp (Similar to the one in
	  SqEuclidean)

2007-09-06 17:32  woolford

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libEM/reconstructor_tools.cpp, libEM/reconstructor_tools.h,
	  libpyEM/libpyReconstructor2.cpp, programs/e2make3d.py,
	  rt/pyem/test_emdata.py, rt/pyem/test_reconstructor.py: Back
	  projection reconstructor works properly, python testing code for
	  reconstructors started

2007-09-06 13:40  cyang

	* libEM/sparx/temp/sirt_Cart.cpp: changed some of the print formats

2007-09-06 13:39  cyang

	* libEM/sparx/temp/: runsirt.cpp, runsirt_Cart.cpp: allow symmetry,
	  lam and tol options to be passed from the command line

2007-09-06 13:38  ppenczek

	* libEM/sparx/fourierfilter.cpp: irrelevant editing

2007-09-06 13:20  woolford

	* libEM/emobject.h, libEM/exception.h, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libEM/reconstructor_tools.cpp,
	  libpyEM/EMAN2.py, programs/e2make3d.py, programs/e2simmx.py:
	  Fourier reconstructor updates, x_pad and y_pad work, code
	  cleaning

2007-09-05 15:28  zyang

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/libpyEMData2.cpp: Add function get_pixel_conv7(), which
	  uses get_pixel_conv_new() but has the format as get_pixel_conv().
	  My test has shown the maximum relative error between these two
	  functions is about 8.e-7, so the new version should be no
	  problem.

2007-09-05 14:00  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, normpadft.cpp: formatting cleaned

2007-09-05 09:18  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, normpadft.cpp: [no log message]

2007-09-05 07:18  ppenczek

	* libEM/sparx/normpadft.cpp: [no log message]

2007-08-31 18:44  zyang

	* libEM/cmp.cpp: Fix two bugs in comparator

2007-08-31 18:05  woolford

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libEM/reconstructor_tools.cpp, programs/e2make3d.py: Fourier
	  recon works on non-square images and slice preprocessing enhanced

2007-08-31 15:30  stevel

	* programs/e2display.py: Double glutinit

2007-08-31 10:27  zyang

	* libEM/cmp.cpp: Fix a bug in SqEuclidean distance

2007-08-30 12:19  stevel

	* libEM/emdata_transform.cpp: e2display now does averaging when
	  scaling down. Scaled down images look much better.

2007-08-29 21:08  woolford

	* libEM/processor.cpp, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libEM/reconstructor_tools.cpp,
	  libEM/reconstructor_tools.h, libpyEM/libpyReconstructor2.cpp,
	  programs/e2make3d.py, programs/e2project3d.py,
	  rt/pyem/test_emdata.py: various reconstructor_tools and reconstor
	  adaptations, also added some testing code to test odd sized
	  images

2007-08-27 11:44  woolford

	* libEM/processor.h, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libEM/reconstructor_tools.cpp,
	  libEM/reconstructor_tools.h, programs/e2make3d.py: Adaptations
	  for tomographic reconstruction

2007-08-26 14:17  gtang

	* rt/pyem/test_processor.py: unit test unpdate to change

2007-08-24 13:22  ppenczek

	* libEM/sparx/emdata_sparx.cpp: nothing

2007-08-24 12:34  ppenczek

	* libEM/: processor.cpp, processor.h, sparx/emdata_sparx.cpp:
	  threshold_to_minval added

2007-08-23 20:06  ppenczek

	* libEM/sparx/emdata_sparx.cpp: emdata formatted

2007-08-23 16:27  stevel

	* libpyEM/qtgui/emimage.py: Fix glutinit

2007-08-22 17:37  ppenczek

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/fundamentals.cpp,
	  libEM/sparx/fundamentals.h, libpyEM/libpyFundamentals2.cpp: error
	  in cc functions corrected

2007-08-22 13:06  ppenczek

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/libpyEMData2.cpp: added function conjg

2007-08-22 12:01  ppenczek

	* libEM/sparx/fundamentals.cpp, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h, libpyEM/libpyUtils2.cpp: added
	  pack_complex_to_real, which does just that

2007-08-21 14:43  gtang

	* rt/: emdata/projector_test.cpp, imageio/basic.cpp: use emassert.h
	  instead of <assert.h> or <cassert> directly

2007-08-21 14:43  gtang

	* libEM/: Assert.h, ctf.cpp, emassert.h, emdata.cpp, emutil.cpp,
	  emutil.h, hdfio.cpp, hdfio2.cpp, imagicio.cpp, marchingcubes.cpp,
	  processor.cpp, reconstructor.cpp, spiderio.cpp, testutil.cpp,
	  util.cpp, vecmath.h, xplorio.cpp, sparx/emdata_sparx.cpp,
	  sparx/temp/ali3d_d_mpi.cpp, sparx/temp/ali3d_unified_mpi.cpp,
	  sparx/temp/runali3d_d.cpp, sparx/temp/runhybrid.cpp,
	  sparx/temp/rununified.cpp: us emassert.h instead of <assert.h> or
	  <cassert> directly

2007-08-21 12:51  gtang

	* rt/pyem/test_imageio.py: [no log message]

2007-08-21 09:48  prb

	* libEM/transform.cpp:
	  expanded a few things in Taylor series

2007-08-20 17:14  woolford

	* libEM/emdata.cpp, libEM/emobject.h, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libEM/reconstructor_tools.cpp,
	  libEM/reconstructor_tools.h, programs/e2fileinfo.py,
	  programs/e2make3d.py: added extensive comments and a compiler
	  optimization flag in reconstructor_tools.h

2007-08-20 11:40  gtang

	* rt/pyem/test_imageio.py: unit test for Transform3D as HDF5 image
	  attribute

2007-08-19 10:08  ppenczek

	* libpyEM/qtgui/emimage.py: remove glutinit, it was in wrong place.

2007-08-18 11:57  gtang

	* libEM/hdfio2.cpp: Implement HDF5 I/O support for Transform3D
	  object as image attribute

2007-08-18 11:53  gtang

	* libEM/transform.h: remove unnecessary virtual for Transform3D's
	  destructor

2007-08-17 18:57  prb

	* libEM/transform.cpp:
	  changed the get_rotation for EULER_SPIN so that it works better
	  for small rotations

2007-08-17 13:54  ppenczek

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: [no log message]

2007-08-15 17:57  woolford

	* libEM/imagicio.cpp, libpyEM/EMAN2.py, programs/e2fileinfo.py:
	  more changes to e2fileinfo.py - also made it so that imagic
	  write_header writes the label, which stores CTF values

2007-08-15 15:47  ppenczek

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Frngs_inv added - inverse FT to Frngs,
	  just for testing

2007-08-15 13:11  cyang

	* libEM/sparx/temp/utilnum.cpp: remove hybr.h

2007-08-15 12:59  jchung

	* libEM/sparx/temp/Makefile: I included HyBR_Cart.o as a dependency
	  for compiling runsirt_cart

2007-08-15 12:57  jchung

	* libEM/sparx/temp/hybr.h: This header file is needed for the HyBR
	  implementation.

2007-08-15 12:57  jchung

	* libEM/sparx/temp/HyBR_Cart.h: This header file is needed for
	  running the HyBR algorithm using MPI Cartesian virtual topology.

2007-08-15 11:02  gtang

	* libEM/sparx/emdata_sparx.cpp: fix warnings

2007-08-15 11:02  gtang

	* libEM/sparx/: lapackblas.cpp, lapackblas.h: in function
	  declaration, use const char * for string as parameter

2007-08-14 22:50  stevel

	* libpyEM/qtgui/emimage.py: Modified GLUT import.

2007-08-14 20:05  cyang

	* libEM/sparx/temp/runsirt_Cart.cpp: added the option to use HyBR
	  for reconstruction

2007-08-14 20:00  cyang

	* libEM/sparx/temp/: utilnum.cpp, utilnum.h: added numerical
	  utilities required by HyBR

2007-08-14 19:59  cyang

	* libEM/sparx/temp/HyBR_Cart.cpp: add Hybrid Bidiagonalization
	  Regularization method for 3-D image reconstruction in real space

2007-08-14 19:56  cyang

	* libEM/sparx/: lapackblas.cpp, lapackblas.h: add functions
	  required for SVD

2007-08-14 13:01  woolford

	* programs/e2fileinfo.py: fixing a bug in e2fileinfo.py

2007-08-14 12:45  cyang

	* libEM/sparx/temp/: runsirt.cpp, sirt.cpp: minor cleanup

2007-08-14 12:34  cyang

	* libEM/sparx/temp/: runsirt_Cart.cpp, sirt_Cart.cpp: minor cleanup

2007-08-14 12:25  woolford

	* libEM/emdata.h, libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libpyEM/libpyEMData2.cpp, programs/e2fileinfo.py,
	  programs/e2make3d.py: added some functionality to e2fileinfo.py

2007-08-14 12:19  ppenczek

	* libEM/sparx/util_sparx.cpp: code shifted

2007-08-13 00:17  cyang

	* libEM/sparx/temp/runsirt_Cart.cpp: define ROW and COL using
	  macros

2007-08-12 15:23  gtang

	* libEM/tifio.cpp: add the tiled tiff image reading suport

2007-08-10 17:10  cyang

	* libEM/sparx/temp/: runsirt.cpp, runsirt_Cart.cpp: add more error
	  checking for input parameters

2007-08-10 17:09  cyang

	* libEM/sparx/temp/: sirt.cpp, sirt_Cart.cpp: added documentation
	  on the sign convention used for shifts in SIRT

2007-08-10 16:09  cyang

	* libEM/sparx/temp/sirt_Cart.cpp: do not change the sign of shift
	  in SIRT

2007-08-10 16:09  cyang

	* libEM/sparx/temp/: runsirt_Cart.cpp, utilcomm_Cart.cpp,
	  utilcomm_Cart.h: move the code for reading angles and shifts into
	  utilcomm_Cart.cpp

2007-08-10 15:48  cyang

	* libEM/sparx/temp/sirt.cpp: do not change the sign of shift inside
	  SIRT.

2007-08-10 15:48  cyang

	* libEM/sparx/temp/runsirt.cpp: remove old codes for reading angles
	  and shifts

2007-08-10 13:45  cyang

	* libEM/sparx/temp/: utilcomm.cpp, utilcomm.h, runsirt.cpp,
	  rununified.cpp: added ReadAngTrandDist()

2007-08-09 16:47  cyang

	* libEM/sparx/temp/ali3d_d_mpi.cpp: changed the files included in
	  this code

2007-08-09 16:12  gtang

	* programs/e2proc2d.py: fix the bug when working with a stack
	  images

2007-08-09 13:06  ppenczek

	* libpyEM/libpyEMData2.cpp, libEM/reconstructor.cpp,
	  libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libEM/sparx/util_sparx.cpp: delete_disconnected regions added

2007-08-08 18:46  cyang

	* libEM/sparx/temp/Makefile: modify the Makefile to accomodate the
	  addition new codes and the reorganization of previous codes

2007-08-08 18:45  cyang

	* libEM/sparx/temp/utilcomm.h: removed unnecessary declarations.

2007-08-08 18:44  cyang

	* libEM/sparx/temp/utilcomm.cpp: removed option parsing and
	  background average calculation

2007-08-08 18:39  cyang

	* libEM/sparx/temp/sirt.cpp: removed ali3d_unified_mpi.h

2007-08-08 18:36  cyang

	* libEM/sparx/temp/runhybrid.cpp: added include "utilparse.h"

2007-08-08 18:35  cyang

	* libEM/sparx/temp/: ali3d_unified_mpi.cpp, ali3d_unified_mpi.h:
	  removed projection and backprojection, function and gradient
	  calculation from ali3d_unified_mpi and placed them somewhere else
	  (project3d.cpp and fgcalc.cpp)

2007-08-08 18:31  cyang

	* libEM/sparx/temp/: project3d_Cart.cpp, project3d_Cart.h,
	  runsirt_Cart.cpp, sirt_Cart.cpp, sirt_Cart.h, utilcomm_Cart.cpp,
	  utilcomm_Cart.h: added a special version of SIRT that allows the
	  images and volume data to be distributed on a 2-D processor grid.

2007-08-08 18:28  cyang

	* libEM/sparx/temp/: fgcalc.cpp, fgcalc.h: separate function and
	  gradient calculation from the unified code.

2007-08-08 18:27  cyang

	* libEM/sparx/temp/: project3d.cpp, project3d.h, runsirt.cpp,
	  utilnum.cpp, utilnum.h, utilparse.cpp, utilparse.h: added a new
	  SIRT driver runsirt.cpp reorganized the codes:    added
	  utilparse.cpp, utilparse.h	   to separate parameter parsing
	  from communication utilities	  added utilnum.cpp, utilnum.h
	  to separate numerical utilities from projection    added
	  project3d.cpp project3d.h	  to separate projection codes from
	  the unified codes

2007-08-08 16:59  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Add function twoD_to_3D_ali() using
	  LBFGSB algorithm, works great

2007-08-08 14:30  zyang

	* libEM/projector.cpp: Trival change

2007-08-07 11:42  ppenczek

	* libEM/sparx/: emdata_sparx.h, util_sparx.h:  nothing

2007-08-06 11:39  gtang

	* rt/pyem/test_emdata.py: unit test fix.

2007-08-06 10:11  zyang

	* libEM/sparx/util_sparx.cpp: Trival change

2007-08-03 17:59  woolford

	* libEM/emdata.cpp, libEM/emdata.h, libEM/emdata_modular.cpp,
	  libEM/emdata_modular.h, libEM/emobject.h, libEM/processor.cpp,
	  libEM/processor.h, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libEM/reconstructor_tools.cpp,
	  libEM/reconstructor_tools.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyProcessor2.cpp, libpyEM/libpyReconstructor2.cpp,
	  programs/e2make3d.py: Fourier reconstructor mutual slice
	  normalization works for all seven pixel interpolation modes,
	  added comments, cleaned redundancies in reconstructor.cpp/h.
	  Reverted Reconstructor::set_params, created
	  Reconstructor::insert_params

2007-08-03 16:29  zyang

	* libEM/sparx/steepest.cpp, libEM/sparx/steepest.h,
	  libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Use steepest descent method for 2D
	  alignment. Just for experimental purpose, no pratical value.

2007-08-03 11:43  zyang

	* libEM/sparx/steepest.cpp, libEM/sparx/steepest.h,
	  libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Add steepest descent algorithm for 2-D
	  alignment, just for experimental purposes.

2007-08-02 11:50  zyang

	* libEM/: CMakeLists.txt, sparx/steepest.cpp, sparx/steepest.h: Add
	  steepest descent algorithm

2007-07-31 15:39  zyang

	* libEM/: reconstructor.cpp, reconstructor.h: Just remove some
	  outdated comments.

2007-07-31 13:53  ppenczek

	* libEM/: reconstructor.cpp, sparx/emdata_sparx.cpp: [no log
	  message]

2007-07-31 11:51  zyang

	* libEM/reconstructor.cpp: Fix a bug in nn_SSNR_ctf()

2007-07-30 18:20  ppenczek

	* libEM/reconstructor.cpp: [no log message]

2007-07-30 18:18  zyang

	* libEM/reconstructor.cpp: [no log message]

2007-07-30 18:04  zyang

	* libEM/reconstructor.cpp: Fix a bug in nn_SSNR_ctf()

2007-07-30 17:47  ppenczek

	* libEM/: reconstructor.cpp, sparx/emdata_sparx.cpp: [no log
	  message]

2007-07-30 16:17  zyang

	* libEM/: reconstructor.cpp, reconstructor.h,
	  sparx/emdata_sparx.cpp, sparx/emdata_sparx.h,
	  sparx/util_sparx.cpp: Made some change to nn_SSNR_ctf()

2007-07-30 13:13  zweig

	* programs/e2display.py: add call to glutInit, it is necessary for
	  freeglut

2007-07-29 20:31  zyang

	* libEM/sparx/util_sparx.cpp: Just add some comments

2007-07-29 17:30  gtang

	* libEM/: emdata.cpp, emdata.h, emdata_core.cpp, emdata_core.h: fix
	  the performance slowdown, the BOUNDS_CHECKING was defined in
	  emdata_core.h

2007-07-29 10:11  gtang

	* libEM/sparx/CMakeLists.txt: bug fix, sparx header should go to
	  EMAN2/include/sparx directory.

2007-07-28 21:07  gtang

	* libEM/: emdata.cpp, emdata.h, emdata_core.cpp, emdata_core.h:
	  revert Dave's code change at 6/25/2007 to solve the performance
	  issue

2007-07-28 12:17  stevel

	* libpyEM/EMAN2.py: Removed GUI import from E2init.

2007-07-26 12:11  gtang

	* libEM/sparx/: lbfgsb.cpp, lbfgsb.h: fix the compilation warnings

2007-07-26 11:09  gtang

	* libEM/: averager.cpp, emdata_io.cpp: fix compilation warning,
	  compare string with const char *

2007-07-25 18:52  ppenczek

	* libEM/reconstructor.cpp: removed comments in ssnr

2007-07-25 16:56  woolford

	* libEM/: reconstructor.cpp, reconstructor.h,
	  reconstructor_tools.cpp, reconstructor_tools.h: normalization and
	  interpolation works for all 7 modes in InterpolatedFRC

2007-07-25 15:47  ppenczek

	* libEM/reconstructor.cpp: still on ssnr

2007-07-25 11:14  woolford

	* libEM/CMakeLists.txt, libEM/emdata.h, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libEM/util.h, programs/e2make3d.py,
	  libEM/reconstructor_tools.cpp, libEM/reconstructor_tools.h: moved
	  fourier reconstructor tools into a new file called
	  reconstructor_tools.h/cpp

2007-07-24 16:09  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Add function twoD_fine_ali_G()

2007-07-24 16:06  zyang

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/libpyEMData2.cpp: Add function rot_scale_conv7() (For
	  testing purpose)

2007-07-23 18:34  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Add function twoD_fine_ali()

2007-07-23 18:31  zyang

	* libEM/CMakeLists.txt: Add lbfgsb to CMakelist

2007-07-23 18:30  zyang

	* libEM/sparx/: lbfgsb.cpp, lbfgsb.h: Add optimization algorithm
	  LBFGSB which is independent of cctbx and free of FORTRAN
	  subroutines.

2007-07-20 12:55  gtang

	* utils/CMakeLists.txt: [no log message]

2007-07-20 12:05  zweig

	* libEM/reconstructor.h: add new parm weighting to indicate whether
	  use weighting or not

2007-07-20 02:10  stevel

	* libpyEM/qtgui/emimage3d.py, programs/e2fileinfo.py: Doesn't crash
	  now at least...

2007-07-19 16:38  gtang

	* utils/MarchingCubes/: Isosurface.h, MCubes.cpp,
	  MarchingCubes.cpp, MarchingCubes.h, Mesh.h, VoxelData.h, dbh.cpp,
	  dbh.h, gorgon.pyw, reader.h, stdafx.cpp, stdafx.h, vecmath.h,
	  volume.h: [no log message]

2007-07-19 15:13  gtang

	* libEM/reconstructor.cpp: fix compilation error on gcc 3.2

2007-07-19 14:37  gtang

	* libEM/reconstructor.h: fix doxygen warnings

2007-07-18 15:14  gtang

	* libEM/vecmath.h: Bug fix

2007-07-17 23:00  stevel

	* libpyEM/qtgui/emimage3d.py: Trying to recover working version

2007-07-17 22:59  stevel

	* programs/e2fileinfo.py: New program

2007-07-17 13:23  zyang

	* libEM/reconstructor.cpp: Trival change

2007-07-16 15:01  gtang

	* libEM/sparx/util_sparx.cpp: fix a warning

2007-07-16 14:56  gtang

	* libEM/hdfio2.cpp: fix a warning

2007-07-16 14:33  woolford

	* libEM/reconstructor.h: Fixed the Fourier reconstructor
	  free_memory problem

2007-07-16 14:24  woolford

	* libEM/: emobject.cpp, reconstructor.h, spiderio.cpp:
	  Reconstructor.cpp added comments, reconstructors code modified,
	  still not finished

2007-07-16 12:01  woolford

	* libEM/emobject.cpp, libEM/emobject.h, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, rt/emdata/test_emobject.cpp: Fourier pixel
	  inserter factory replaced by Liwei's factory

2007-07-15 14:35  gtang

	* libEM/reconstructor.h: fix Dave's mistake.

2007-07-15 14:09  zyang

	* libEM/sparx/fundamentals.h, libEM/sparx/rsconvolution.cpp,
	  libpyEM/libpyFundamentals2.cpp: Change function name of
	  filt_median, filt_dilation and filt_erosion

2007-07-15 13:59  ppenczek

	* libEM/reconstructor.cpp: ssnr, I think I am done

2007-07-15 12:33  ppenczek

	* libEM/reconstructor.cpp: working on ssnr, not done yet

2007-07-15 11:10  ppenczek

	* libpyEM/libpyUtils2.cpp: histogram added

2007-07-15 11:09  ppenczek

	* libEM/: emdata.cpp, emdata.h, reconstructor.cpp,
	  sparx/util_sparx.cpp, sparx/util_sparx.h: calc_hist corrected and
	  histogram added

2007-07-15 07:08  gtang

	* libEM/reconstructor.h: Ooops, David's code break the whole EMAN2,
	  temporary fix!

2007-07-14 14:28  ppenczek

	* libEM/cmp.cpp: deleted some extra spaces

2007-07-13 19:01  woolford

	* libEM/reconstructor.cpp, libEM/reconstructor.h,
	  programs/e2make3d.py: reconstructor updates, in between jobs

2007-07-13 18:25  ppenczek

	* programs/e2pdb2em.py: corrected processor

2007-07-13 16:19  ppenczek

	* libpyEM/libpyUtils2.cpp:  forgot to add local in one place

2007-07-13 16:09  gtang

	* libpyEM/libpyEMData2.cpp: fix the memory leak for arithmetic
	  operators

2007-07-13 10:43  gtang

	* libEM/reconstructor.h: parameter comment place holder to fix
	  doxygen warnings

2007-07-13 10:32  gtang

	* libEM/: pointarray.h, reconstructor.h: parameter comment place
	  holder to fix doxygen warnings

2007-07-13 10:18  gtang

	* libEM/sparx/: emdata_sparx.h, fundamentals.h: parameter comment
	  place holder to fix doxygen warnings

2007-07-13 09:41  zweig

	* libEM/sparx/emdata_sparx.cpp: add the remove function to nn and
	  nn_ctf

2007-07-13 09:40  zweig

	* libEM/: reconstructor.cpp, reconstructor.h: add new parameter
	  weighting

2007-07-12 18:52  woolford

	* libEM/analyzer.cpp, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libpyEM/libpyReconstructor2.cpp, programs/e2make3d.py,
	  rt/emdata/test_inplace_clip.cpp: reconstructor updates - in
	  between changes

2007-07-12 18:14  ppenczek

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: added local
	  refinement for ali3d_d

2007-07-12 18:13  ppenczek

	* libpyEM/libpyUtils2.cpp: added multiref_local

2007-07-12 17:36  zweig

	* libEM/emdata_transform.cpp: fix a small bug, set fftodd to false
	  when offset is 0

2007-07-12 15:29  zweig

	* libEM/sparx/normpadft.cpp: set npad to 1 after depad

2007-07-12 14:42  ppenczek

	* libEM/sparx/fourierfilter.cpp: [no log message]

2007-07-10 18:10  gtang

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/emobject.cpp,
	  libEM/fitsio.cpp, libEM/hdfio.cpp, libEM/hdfio2.cpp,
	  libEM/jpegio.cpp, libEM/pngio.cpp, libEM/pointarray.cpp,
	  libEM/polardata.cpp, libEM/processor.h, libEM/projector.cpp,
	  libEM/sspiderio.cpp, libEM/testutil.cpp,
	  libEM/sparx/emdata_sparx.cpp, libEM/sparx/lapackblas.cpp,
	  libEM/sparx/lapackblas.h, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/varimax.cpp, libEM/sparx/varimax.h,
	  plugins/aligner_template.cpp, plugins/reconstructor_template.cpp,
	  rt/emdata/test_emobject.cpp, rt/pyem/test_typeconverter.py: fix
	  the compilation warnings

2007-07-10 15:42  zyang

	* libEM/emdata_core.cpp, libEM/emdata_core.h,
	  libpyEM/libpyEMData2.cpp: Add function absi()

2007-07-10 13:17  gtang

	* libpyEM/typeconverter.h: fix the compilation warnings

2007-07-10 13:17  gtang

	* rt/pyem/test_typeconverter.py: unit test for None as EMObject

2007-07-10 13:03  gtang

	* rt/pyem/test_typeconverter.py: [no log message]

2007-07-10 12:40  gtang

	* rt/CMakeLists.txt, utils/speedtest.cpp: fix the compilation
	  warnings

2007-07-10 12:18  gtang

	* libEM/: aligner.cpp, pointarray.cpp, pointarray.h,
	  sparx/emdata_sparx.cpp, sparx/pca.cpp: fix the compilation
	  warnings

2007-07-09 22:17  zyang

	* libEM/sparx/util_sparx.h: Trival change.

2007-07-06 19:08  sternberg

	* libEM/sparx/temp/sirt.cpp: sign flip for shifts

	  Already had it for first iteration, but not for subsequent
	  iterations

2007-07-06 19:06  sternberg

	* libEM/sparx/temp/utilcomm.cpp: set s2x and s2y to 0.0, regardless
	  of header

	  eventually will have an option to use header or not, but for
	  current testing purposes, always use 0.0

2007-07-06 19:05  sternberg

	* libEM/sparx/temp/sirt.h: fix #define PI

	  Add a digit for consistency, and protect from redefining `

2007-07-06 19:04  sternberg

	* libEM/sparx/temp/ali3d_d_mpi.cpp: Added workaround to prevent
	  segfault

	  before fourier filters are used, call volume->set_attr("npad",1);

2007-07-06 11:41  zhuang

	* libEM/reconstructor.cpp: add returned vol_ssnr to non_ctf 3D SSNR

2007-07-06 11:11  zhuang

	* libEM/reconstructor.cpp: add returned vol_ssnr to 3D SSNR
	  function

2007-07-05 16:44  woolford

	* libEM/emdata.cpp, rt/pyem/test_emdata.py: added some exceptions
	  to EMData clipping operations, and added corresponding tests in
	  test_emdata.py

2007-07-05 16:10  woolford

	* libEM/emdata.cpp, libEM/reconstructor.cpp,
	  rt/pyem/test_emdata.py: added testing functionality for
	  clip_inplace

2007-07-05 15:44  gtang

	* libEM/aligner.cpp: comment out the debug printing

2007-07-05 15:44  gtang

	* rt/pyem/test_aligner.py: hide the failure aligner, will be fixed
	  in the future

2007-07-05 15:31  gtang

	* libEM/emdata.cpp: minor fix

2007-07-03 20:07  woolford

	* libEM/: emdata.cpp: added EMData::clip_inplace

2007-07-03 19:52  woolford

	* libEM/emdata.cpp, libEM/emdata.h, libEM/emdata_core.cpp,
	  libEM/emdata_io.cpp, libEM/emdata_metadata.cpp,
	  libEM/emdata_transform.cpp, libEM/mrcio.cpp, libEM/processor.cpp,
	  libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libEM/sparx/normpadft.cpp, libpyEM/libpyEMData2.cpp,
	  programs/e2make3d.py, programs/e2project3d.py: clip_inplace added
	  for EMData

2007-07-03 14:26  wjiang

	* libEM/: emutil.h, vecmath.h: more small fixes to compile on Linux
	  and Mac

2007-07-03 13:32  wjiang

	* libEM/analyzer.cpp, libEM/emutil.h, libEM/imageio.cpp,
	  libEM/pgmio.cpp, libEM/reconstructor.cpp, libEM/vecmath.h,
	  libEM/sparx/emdata_sparx.cpp, libEM/sparx/util_sparx.cpp,
	  libpyEM/CMakeLists.txt, rt/imageio/basic.cpp: fix compile errors
	  on Mac OS X. Both Makefile and Xcode targets are fine now.

2007-07-02 11:31  stevel

	* libpyEM/EMAN2.py, programs/e2resolution.py: Work on e2resolution

2007-06-30 18:36  cyang

	* libEM/sparx/temp/utilcomm.cpp: cosmetic changes

2007-06-30 18:22  cyang

	* libEM/sparx/temp/ali3d_d_mpi.cpp: cosmetic changes

2007-06-30 13:21  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h, util_sparx.cpp,
	  util_sparx.h: [no log message]

2007-06-29 18:54  cyang

	* libEM/sparx/temp/runali3d_d.cpp: check file existence

2007-06-29 18:50  sternberg

	* libEM/sparx/temp/runali3d_d.cpp: Use new form of ReadStackandDist

	  takes &nloc as fourth argument

2007-06-29 18:44  sternberg

	* libEM/sparx/temp/utilcomm.cpp: broadcast use_sirt

2007-06-29 18:29  cyang

	* libEM/sparx/temp/utilcomm.cpp: check for 'use_sirt' option, and
	  print out list of options when the option file contains an
	  invalid option string

2007-06-29 16:30  cyang

	* libEM/sparx/temp/: runhybrid.cpp, rununified.cpp, utilcomm.cpp,
	  utilcomm.h: add some sanity check for input filenames

2007-06-29 12:17  sternberg

	* libEM/sparx/temp/runhybrid.cpp: fix refinement cycle

	  Use cleanimages rather than expimages as input to unified

	  Use options.maxit for total number of refinement cycles, set
	  number of projection matching cycles within each refinement cycle
	  to 1

2007-06-27 18:54  sternberg

	* libEM/sparx/temp/ali3d_d_mpi.cpp: replace radius with last_ring
	  in maskdict

	  The "radius" attribute of the maskdict Dict is now last_ring,
	  rather than ri.  Also, re-indent Numrinit

2007-06-27 17:50  sternberg

	* libEM/sparx/temp/ali3d_d_mpi.cpp: fix numrinit

	  exponent is now largest int such that 2**exponent <= jp, not the
	  smallest int such that 2**exponent > jp

2007-06-27 15:33  stevel

	* programs/e2resolution.py: New program to measure resolution

2007-06-26 18:12  cyang

	* libEM/sparx/temp/alignoptions.cpp: changed the default sirt_tol
	  to 0.1

2007-06-26 17:19  sternberg

	* libEM/sparx/temp/ali3d_d_mpi.cpp: Remove eman1 prefix from
	  processor name

2007-06-26 10:33  gtang

	* rt/pyem/test_averager.py: unit test fix

2007-06-25 15:55  woolford

	* libEM/emdata.cpp, libEM/emdata.h, libEM/emdata_core.cpp,
	  libEM/emdata_core.h, libEM/sparx/emdata_sparx.cpp,
	  libpyEM/libpyEMData2.cpp, rt/pyem/test_emdata.py: Added copy
	  constructor and assignment for EMData, added some tests to
	  test_emdata.py

2007-06-25 11:19  gtang

	* libEM/emdata_core.cpp: minor fix

2007-06-22 17:13  gtang

	* libEM/hdfio2.cpp: fix bug

2007-06-22 16:54  woolford

	* libEM/reconstructor.cpp: reconstructor.cpp formatting issues
	  (trivial)

2007-06-22 16:13  gtang

	* libEM/testutil.cpp: [no log message]

2007-06-22 16:03  gtang

	* libEM/aligner.cpp, libEM/averager.cpp, libEM/ctf.cpp,
	  libEM/emdata.cpp, libEM/emdata_core.cpp,
	  libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libEM/emdata_transform.cpp, libEM/emutil.cpp,
	  libEM/pointarray.cpp, libEM/processor.cpp, libEM/projector.cpp,
	  libEM/reconstructor.cpp, libEM/testutil.cpp,
	  libpyEM/libpyEMData2.cpp, libEM/sparx/emdata_sparx.cpp,
	  libEM/sparx/fourierfilter.cpp, libEM/sparx/fundamentals.cpp,
	  libEM/sparx/normpadft.cpp, libEM/sparx/rsconvolution.cpp,
	  libEM/sparx/util_sparx.cpp, libpyEM/typeconverter.cpp,
	  rt/emdata/blankimg.cpp, rt/emdata/fft.cpp,
	  rt/pyem/test_imageio.py, utils/speedtest.cpp: remove
	  EMData::done_data(), substitute with update() if necessary.

2007-06-22 14:21  stevel

	* libEM/emdata.cpp, libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libpyEM/qtgui/emimage3d.py: Fix merging bugs

2007-06-22 13:58  stevel

	* doc/developer-guide.html, doc/latex/misc-developers-guide.tex,
	  examples/alignbystars.py, examples/comparepairs.py,
	  examples/makebigfromseq.py, examples/sortsimilar.py,
	  examples/transalignavg.py, libEM/aligner.cpp, libEM/aligner.h,
	  libEM/emdata.cpp, libEM/emdata.h, libEM/emdata_io.cpp,
	  libEM/emdata_io.h, libEM/emdata_metadata.cpp,
	  libEM/emdata_transform.cpp, libEM/emobject.cpp, libEM/emobject.h,
	  libEM/hdfio.cpp, libEM/hdfio2.cpp, libEM/imagicio.cpp,
	  libEM/pointarray.cpp, libEM/pointarray.h, libEM/processor.cpp,
	  libEM/processor.h, libEM/projector.cpp, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libEM/transform.cpp, libEM/transform.h,
	  libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libEM/sparx/native_fft.h, libpyEM/EMAN2.py,
	  libpyEM/libpyPointArray2.cpp, libpyEM/libpyReconstructor2.cpp,
	  libpyEM/libpyTransform2.cpp, libpyEM/typeconverter.cpp,
	  libpyEM/qtgui/emdesktop.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/wxgui/wxemimage.py, libpyEM/wxgui/wxemimageframe.py,
	  plugins/reconstructor_template.cpp,
	  plugins/reconstructor_template.h, programs/e2align3d.py,
	  programs/e2boxer.py, programs/e2classifykmeans.py,
	  programs/e2display.py, programs/e2findsubunit.py,
	  programs/e2foldfitter.py, programs/e2make3d.py,
	  programs/e2msa.py, programs/e2pdb2mrc.py, programs/e2proc2d.py,
	  programs/e2project3d.py, programs/e2scannereval.py,
	  programs/e2skelpath.py, programs/e2tilefile.py,
	  programs/e2tomogram.py, rt/CMakeLists.txt, rt/demo/processor1.py,
	  rt/demo/processor2.py, rt/emdata/CMakeLists.txt,
	  rt/emdata/rotate_translate.cpp, rt/emdata/test_emobject.cpp,
	  rt/emdata/testprocessor.cpp, rt/pyem/test_misc.py,
	  rt/pyem/test_processor.py, utils/proc2d.cpp, utils/speedtest.cpp:
	  Merging in fix_transform branch

2007-06-22 12:24  woolford

	* CMakeLists.txt: removed spectral from cmakelists.txt

2007-06-22 12:19  prb

	* CMakeLists.txt, libEM/aligner.cpp,
	  plugins/reconstructor_template.cpp,
	  plugins/reconstructor_template.h:
	     DSAW and PRB are working through final changes before
	  recommitting the fix_transform branch to the main branch

2007-06-22 11:51  woolford

	* libEM/emdata.cpp, libEM/emdata.h, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libEM/sparx/emdata_sparx.cpp,
	  libEM/sparx/emdata_sparx.h, libpyEM/libpyReconstructor2.cpp:
	  reconstructor infrastructure updates

2007-06-21 18:43  woolford

	* libEM/emdata.cpp, libEM/emdata_transform.cpp,
	  libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libEM/sparx/native_fft.h, libpyEM/libpyReconstructor2.cpp,
	  programs/e2make3d.py: updates to the reconstructors

2007-06-21 16:49  ppenczek

	* libpyEM/libpyUtils2.cpp, libEM/pointarray.h, libEM/util.cpp,
	  libEM/util.h, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h: [no log message]

2007-06-21 16:27  sternberg

	* libEM/sparx/temp/: sirt.h, ali3d_d_mpi.h, ali3d_unified_mpi.h:
	  prevent multiple includes

2007-06-21 15:29  sternberg

	* libEM/sparx/temp/sirt.cpp: Patch two memory leaks

	  psize and nbase were not deallocated

2007-06-20 18:25  sternberg

	* libEM/sparx/temp/utilcomm.cpp: Added output reporting number of
	  images total and on each processor

2007-06-20 18:24  sternberg

	* libEM/sparx/temp/runhybrid.cpp: Take out several things no longer
	  being used

	  paramfname and have_options removed optionsfname defaults to
	  empty string use ParseAlignOptions rather than big parse block in
	  code

2007-06-20 18:19  sternberg

	* libEM/sparx/temp/runali3d_d.cpp: Default optionsfname to empty
	  string

2007-06-20 13:10  sternberg

	* libEM/sparx/temp/: alignoptions.cpp, alignoptions.h: Pass volsize
	  to AlignOptions constructor by reference rather than by value

2007-06-19 19:56  sternberg

	* libEM/sparx/temp/: ali3d_d_mpi.cpp, ali3d_d_mpi.h,
	  alignoptions.cpp, alignoptions.h, runhybrid.cpp: Move max_iter to
	  AlignOptions class

	  Instead of passing the maximum number of projection matching
	  major iterations to ali3d_d, it gets included as a member of the
	  AlignOptions class

2007-06-19 19:55  sternberg

	* libEM/sparx/temp/: runali3d_d.cpp, utilcomm.cpp, utilcomm.h: Add
	  function ParseAlignOptions to utilcomm.cpp; remove option parsing
	  from runali3d

	  New function that handles parsing the input file with options for
	  projection matching.	Reads options in on the master node and
	  then broadcasts them.

2007-06-19 19:49  sternberg

	* libEM/sparx/temp/Makefile: Correct dependencies

	  target rununified referred to literal object filenames, not
	  $(OBJ)

2007-06-19 15:57  gtang

	* libEM/sparx/native_fft.h: the extra qualifier failed to compile
	  on some compiler

2007-06-19 15:45  sternberg

	* libEM/sparx/temp/: runali3d_d.cpp, runhybrid.cpp, rununified.cpp,
	  sirt.cpp, utilcomm.cpp: .cpp files now include utilcomm.h, rather
	  than separate function prototypes

2007-06-19 15:42  sternberg

	* libEM/sparx/temp/utilcomm.h: initial commit

2007-06-19 14:47  sternberg

	* libEM/sparx/temp/: ali3d_d_mpi.cpp, alignoptions.cpp,
	  alignoptions.h: Add sirt options to AlignOptions class

	  sirt_maxit is an integer giving maximum number of sirt iterations
	  sirt_lam is a float giving default lambda for sirt sirt_tol is a
	  float giving tolerance for sirt

2007-06-15 15:23  sternberg

	* libEM/sparx/temp/: ali3d_d_mpi.cpp, ali3d_d_mpi.h,
	  runali3d_d.cpp, runhybrid.cpp, sirt.cpp: ali3d_d now gets passed
	  two image stacks, projdata and cleandata.  projdata consists of
	  the original experimental images, cleandata has the images with
	  the average background subtracted.  The reconstruction is carried
	  out using cleandata.

2007-06-13 18:09  sternberg

	* libEM/sparx/temp/runali3d_d.cpp: Echo options passed in via
	  options file to std::cout as they're read in

2007-06-13 11:47  woolford

	* libEM/emobject.h, rt/emdata/CMakeLists.txt,
	  rt/emdata/test_emobject.cpp: updates to emobject.h and testing
	  code

2007-06-12 18:57  woolford

	* libEM/emdata.cpp, libEM/emdata_io.cpp, libEM/emdata_io.h,
	  libEM/emobject.cpp, libEM/emobject.h, libEM/hdfio.cpp,
	  libEM/hdfio2.cpp, libEM/processor.h, libEM/reconstructor.cpp,
	  rt/CMakeLists.txt, rt/emdata/CMakeLists.txt,
	  rt/emdata/test_emobject.cpp: reconstructor and emobject updates

2007-06-12 17:18  sternberg

	* libEM/sparx/temp/runhybrid.cpp: Allow options to be passed in by
	  file specified on command line

2007-06-12 17:17  sternberg

	* libEM/sparx/temp/runali3d_d.cpp: Add options file to usage
	  message; output filename base string defaults to empty string

2007-06-11 16:10  gtang

	* doc/developer-guide.html, doc/latex/misc-developers-guide.tex,
	  examples/alignbystars.py, examples/comparepairs.py,
	  examples/makebigfromseq.py, examples/sortsimilar.py,
	  examples/transalignavg.py, libEM/aligner.cpp, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/emdata_metadata.cpp, libEM/emobject.cpp,
	  libEM/emobject.h, libEM/pointarray.cpp, libEM/processor.cpp,
	  libEM/processor.h, libEM/projector.cpp, libEM/reconstructor.cpp,
	  libEM/sparx/emdata_sparx.cpp, libpyEM/qtgui/emimage2d.py,
	  libpyEM/wxgui/wxemimage.py, libpyEM/wxgui/wxemimageframe.py,
	  programs/e2align3d.py, programs/e2boxer.py,
	  programs/e2classifykmeans.py, programs/e2findsubunit.py,
	  programs/e2foldfitter.py, programs/e2make3d.py,
	  programs/e2msa.py, programs/e2pdb2mrc.py, programs/e2proc2d.py,
	  programs/e2project3d.py, programs/e2scannereval.py,
	  programs/e2skelpath.py, programs/e2tilefile.py,
	  programs/e2tomogram.py, rt/demo/processor1.py,
	  rt/demo/processor2.py, rt/emdata/rotate_translate.cpp,
	  rt/emdata/testprocessor.cpp, rt/pyem/test_misc.py,
	  rt/pyem/test_processor.py, utils/proc2d.cpp, utils/speedtest.cpp:
	  remove eman1 for processors except "eman1.filter"

2007-06-11 15:05  jchung

	* libEM/sparx/temp/voldist/utilcomm2d.cpp: The new utilcomm2d.cpp
	  code contains:

	  - all previous functions to perform data partition and
	  distribution - fwdpj3_Cart and bckpj3_Cart to perform forward and
	  backward projection on the Cartesian topology - fwdpj3 and bckpj3
	  to perform forward and backward projection in serial

2007-06-11 15:01  jchung

	* libEM/sparx/temp/voldist/runcartrec.cpp: The new codes 1. Perform
	  back projection in parallel 2. Perform back projection in serial
	  and compute the total error in Euclidean norm 3. Perform forward
	  projection in parallel 4. Perform forward projection in serial
	  and computes the total error in Euclidean norm

	  Note: Small errors occur in the forward projection case, so I
	  also print the pixel with largest absolute error and
	  corresponding values.

2007-06-11 11:55  sternberg

	* libEM/sparx/temp/sirt.cpp: Set old_rnorm to 1.0001 on first
	  iteration. Allow reduction in lam on all iterations, not just
	  first.

2007-06-11 00:45  stevel

	* libpyEM/qtgui/emimagemx.py: Write image support in imagemx

2007-06-08 18:35  sternberg

	* libEM/sparx/temp/ali3d_d_mpi.cpp: Print number of reference
	  projections created to cout

2007-06-08 15:56  zhuang

	* libEM/reconstructor.cpp: [no log message]

2007-06-08 13:25  sternberg

	* libEM/sparx/temp/runali3d_d.cpp: Uses new AlignOptions(volsize)

2007-06-08 13:24  sternberg

	* libEM/sparx/temp/: alignoptions.cpp, alignoptions.h: Added
	  constructor AlignOptions(Vec3i volsize) that sets radius and
	  last_ring to min(nx,ny,nz) / 2 - 2

2007-06-08 12:57  sternberg

	* libEM/sparx/temp/ali3d_d_mpi.cpp: Added code to reduce dtheta if
	  number of reference angles is less that max(nx,ny,nz)

2007-06-07 18:21  woolford

	* libEM/: emobject.cpp, emobject.h, reconstructor.cpp,
	  reconstructor.h: reconstructor and emdata updates

2007-06-07 18:19  woolford

	* libEM/: reconstructor.cpp, reconstructor.h: changes from
	  d.woolford

2007-06-07 17:20  zhuang

	* libEM/reconstructor.cpp: [no log message]

2007-06-07 14:11  cyang

	* libEM/sparx/temp/voldist/: Makefile, runcartrec.cpp,
	  utilcomm2d.cpp: first set of codes for projection and
	  back-projection calculations using distributed volume

2007-05-31 16:32  zhuang

	* libEM/reconstructor.cpp: [no log message]

2007-05-31 15:39  zhuang

	* libEM/reconstructor.h: [no log message]

2007-05-31 09:14  gtang

	* libpyEM/typeconverter.h: [no log message]

2007-05-30 17:57  ppenczek

	* libEM/reconstructor.cpp: [no log message]

2007-05-30 12:05  zhuang

	* libEM/reconstructor.cpp: [no log message]

2007-05-28 14:05  prb

	* libEM/: aligner.cpp, emdata.cpp, emobject.h:
	  got rotational aligner working properly

2007-05-24 16:17  sternberg

	* libEM/sparx/temp/Makefile: Add sirt.o to OBJ, add -O3 compiler
	  flag

2007-05-22 11:51  sternberg

	* libEM/sparx/temp/runhybrid.cpp: Set xrng and yrng to 1.0, same as
	  runali3d_d include -out= command line option in output filenames

2007-05-22 01:13  stevel

	* libpyEM/qtgui/emimage3d.py: Basic functionality in emimage3d
	  widget

2007-05-21 16:42  stevel

	* libpyEM/qtgui/emimage3d.py: Working on 3-D rendering

2007-05-21 15:28  sternberg

	* libEM/sparx/temp/ali3d_d_mpi.cpp: Can now use sirt for
	  reconstruction

2007-05-21 15:18  sternberg

	* libEM/sparx/temp/sirt.cpp: typo fix

2007-05-21 14:57  sternberg

	* libEM/sparx/temp/: sirt.cpp, sirt.h: Change interface to use
	  angleshift array for angles and shifts, rather than image header.
	  This is more consistent with the unified/hybrid codes.  The
	  parameters for image i are stored as phi   = angleshift[5*i + 0]
	  theta = angleshift[5*i + 1] psi   = angleshift[5*i + 2] in SPIDER
	  format, and -sx   = angleshift[5*i + 3] -sy	= angleshift[5*i +
	  4] note the sign change!  This is due to the convention taken in
	  the projection matching code in ali3d_d.

2007-05-21 12:20  woolford

	* libEM/emobject.h, libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libEM/transform.cpp, libEM/transform.h, libpyEM/EMAN2.py,
	  libpyEM/libpyTransform2.cpp, programs/e2make3d.py,
	  programs/e2project3d.py: updates associated with getgin 3D
	  reconstruction working from the command line

2007-05-21 11:28  sternberg

	* libEM/sparx/temp/: alignoptions.cpp, alignoptions.h: added
	  options for using sirt as reconstruction algorithm

2007-05-21 11:26  zweig

	* libEM/sparx/fourierfilter.cpp: add undo ctf

2007-05-21 11:26  sternberg

	* libEM/sparx/temp/: sirt.cpp, sirt.h, ali3d_unified_mpi.h: added
	  #include "mpi.h" directive

2007-05-21 01:09  stevel

	* libEM/marchingcubes.cpp, libpyEM/qtgui/emfximage.py,
	  libpyEM/qtgui/emimage3d.py: Work on isosurface rendering

2007-05-18 17:50  woolford

	* libEM/emobject.cpp, libEM/emobject.h, libpyEM/EMAN2.py,
	  libpyEM/libpyReconstructor2.cpp, libpyEM/typeconverter.cpp,
	  programs/e2make3d.py: modifications to get e2make3d.py working --
	  e2make3d.py is not finished but will give some output

2007-05-18 14:28  stevel

	* libpyEM/qtgui/emimage3d.py: oops

2007-05-18 13:02  stevel

	* libpyEM/qtgui/emimage3d.py: Working on isosurface display.

2007-05-17 17:44  woolford

	* libEM/emdata.cpp, libEM/emobject.cpp, libEM/emobject.h,
	  libEM/reconstructor.cpp, libEM/reconstructor.h, libpyEM/EMAN2.py,
	  libpyEM/libpyReconstructor2.cpp, programs/e2make3d.py,
	  programs/e2project3d.py: reconstructor updates

2007-05-17 14:07  gtang

	* libEM/vecmath.h: fix a compilation error on Chao's computer.

2007-05-17 09:05  gtang

	* libEM/: marchingcubes.cpp, marchingcubes.h: reverse the change.

2007-05-16 18:52  cyang

	* libEM/: marchingcubes.cpp, marchingcubes.h: commented out the
	  buggy marchingcubes code

2007-05-16 16:33  sternberg

	* libEM/sparx/temp/: sirt.cpp, sirt.h: functions to reconstruct 3d
	  volume using real-space iterative method.  Parallelized in terms
	  of image data.  Requires angles and shifts to be stored in
	  headers of image objects.

2007-05-16 16:21  gtang

	* libEM/marchingcubes.h, libpyEM/libpyMarchingCubes2.cpp:
	  MarchingCubes default constructor set to private.

2007-05-16 15:27  sternberg

	* libEM/sparx/temp/ali3d_unified_mpi.cpp: Add shift parameters and
	  index checking to bckpj3(); Changed make_proj_mat() to use sincos

2007-05-16 09:58  gtang

	* libEM/isosurface.h, libEM/marchingcubes.cpp,
	  libEM/marchingcubes.h, libEM/util.cpp, libpyEM/EMAN2.py,
	  libpyEM/libpyMarchingCubes2.cpp: change IsoSurface function name
	  to EMAN2's convention: lowe case + under score

2007-05-16 09:31  gtang

	* libEM/CMakeLists.txt, libEM/Isosurface.h,
	  libEM/MarchingCubes.cpp, libEM/MarchingCubes.h,
	  libEM/isosurface.h, libEM/marchingcubes.cpp,
	  libEM/marchingcubes.h, libEM/util.cpp,
	  libpyEM/libpyMarchingCubes2.cpp: change the capital file name to
	  lower case

2007-05-15 16:33  woolford

	* libEM/reconstructor.cpp: Added a comment in reconstructor.cpp

2007-05-15 16:18  woolford

	* libEM/emdata.h, libEM/reconstructor.cpp, libEM/transform.cpp,
	  libEM/transform.h, programs/e2make3d.py, programs/e2project3d.py:
	  reconstruction routines updates

2007-05-14 17:11  zyang

	* libEM/sparx/emdata_sparx.cpp: Fix a dangerous bug in
	  peak_search()

2007-05-13 13:23  stevel

	* libpyEM/libpyTransform2.cpp: oops

2007-05-13 12:15  gtang

	* CMakeLists.txt: add python2.5 search path

2007-05-13 02:36  stevel

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp: Fix python bindings for transform.

2007-05-11 11:04  woolford

	* programs/e2project3d.py: e2project3d.py improvements

2007-05-11 10:53  woolford

	* programs/e2project3d.py: e2project3d.py improvements

2007-05-10 16:34  prb

	* libEM/: aligner.cpp, emdata.cpp, transform.cpp, transform.h:
	  fixed the rotational aligner	PRB

2007-05-10 15:14  zhuang

	* libEM/: reconstructor.cpp, reconstructor.h,
	  sparx/emdata_sparx.cpp, sparx/emdata_sparx.h: [no log message]

2007-05-10 12:25  zyang

	* libEM/sparx/util_sparx.cpp: Trival change

2007-05-10 12:01  gtang

	* libpyEM/EMAN2.py: isosurface() function in EMAN2.py

2007-05-09 12:41  gtang

	* libEM/: MarchingCubes.h, emdata.h, emdata_transform.h,
	  pointarray.h, util.h, sparx/emdata_sparx.h, sparx/fundamentals.h:
	  fix parameter in comment for Doxygen

2007-05-08 15:14  gtang

	* libEM/Isosurface.h, libEM/MarchingCubes.cpp,
	  libEM/MarchingCubes.h, libEM/hdfio2.cpp, libEM/util.cpp,
	  libEM/util.h, libpyEM/CMakeLists.txt, libpyEM/EMAN2_cppwrap.py,
	  libpyEM/SConscript, libpyEM/libpyMarchingCubes2.cpp,
	  libpyEM/libpyUtils2.cpp: wrap MarchingCubes class to Python
	  directly

2007-05-07 15:34  gtang

	* libEM/MarchingCubes.cpp, libEM/MarchingCubes.h, libEM/util.cpp,
	  libEM/util.h, libpyEM/EMAN2.py, libpyEM/libpyUtils2.cpp: wrap the
	  isosurface call to Python

2007-05-04 17:12  gtang

	* libEM/: MarchingCubes.cpp, Isosurface.h, MarchingCubes.h:
	  Isosurface, some progress.

2007-05-04 15:38  gtang

	* CMakeLists.txt, libEM/MarchingCubes.cpp: remove OpenGL dependency
	  from EMAN2.

2007-05-04 15:09  gtang

	* libEM/: Isosurface.h, MarchingCubes.cpp, MarchingCubes.h, Mesh.h:
	  Isosurface, some progress, remove Mesh.h.

2007-05-03 17:33  sternberg

	* libEM/sparx/temp/runali3d_d.cpp: Add functionality to allow
	  alignment options (as in python function ali3d_d()) to be set
	  from a text file specified on the command line by
	  -options=<option filename>

2007-05-03 17:30  sternberg

	* libEM/sparx/temp/: alignoptions.cpp, alignoptions.h: Add member
	  ref_angle_type, along with getter and setter methods, to specify
	  which quasi-uniform angle generator should be used.

2007-05-01 00:38  stevel

	* examples/alignbystars.py, libEM/aligner.cpp, libEM/aligner.h,
	  libEM/imagicio.cpp, libpyEM/libpyPointArray2.cpp,
	  libpyEM/libpyTransform2.cpp, libpyEM/qtgui/emimage2d.py: Working
	  on transform classes

2007-04-30 10:00  woolford

	* programs/e2project3d.py: e2project3d.py updated

2007-04-29 14:30  zyang

	* libEM/sparx/util_sparx.cpp: Trival change

2007-04-27 18:29  cyang

	* libEM/sparx/temp/runhybrid.cpp: removed hardcoded radius

2007-04-27 17:40  sternberg

	* libEM/sparx/temp/ali3d_d_mpi.cpp: Fixed for loops after allreduce
	  in even/odd volume reconstruction

2007-04-27 15:10  cyang

	* libEM/sparx/temp/README: fixed a few typos

2007-04-27 15:05  cyang

	* libEM/sparx/temp/README: Instructions for compiling and running
	  refinement codes

2007-04-27 14:50  sternberg

	* libEM/sparx/temp/ali3d_d_mpi.cpp: use ri rather than last_ring as
	  volparam["radius"] in the dictionary passed to volume->project()

2007-04-27 14:47  cyang

	* libEM/sparx/temp/Makefile: fixed a few minor things

2007-04-27 14:44  cyang

	* libEM/sparx/temp/runali3d_d.cpp: changed some options in the
	  driver

2007-04-27 14:42  cyang

	* libEM/sparx/temp/Makefile: added runali3d_d

2007-04-27 13:17  sternberg

	* libEM/sparx/temp/rununified.cpp: Added "> " to "-param..." error
	  output string

2007-04-27 12:53  cyang

	* libEM/sparx/temp/runali3d_d.cpp: add a driver to run projection
	  matching alone in parallel

2007-04-27 12:50  sternberg

	* libEM/sparx/temp/ali3d_d_mpi.cpp: Set new_angles and old_angles
	  to 0 inside outer for loop, so they will be coherent for multiple
	  projection matching iterations

2007-04-27 12:27  cyang

	* libEM/sparx/temp/rununified.cpp: Add a driver for running unified
	  refinement by itself.

2007-04-27 12:25  cyang

	* libEM/sparx/temp/Makefile: Update to include two additional
	  targets rununified and runali3d_d

2007-04-27 12:21  cyang

	* libEM/sparx/temp/runhybrid.cpp: renamed from runrefine.cpp

2007-04-27 12:20  cyang

	* libEM/sparx/temp/runrefine.cpp: remove runrefine and rename it as
	  runhybrid

2007-04-27 12:19  sternberg

	* libEM/sparx/temp/ali3d_unified_mpi.cpp: set ri to nx/2 - 1

2007-04-27 10:06  zyang

	* libEM/sparx/: util_sparx.h, util_sparx.cpp: Trival change

2007-04-26 19:44  sternberg

	* libEM/sparx/temp/: ali3d_unified_mpi.cpp, runrefine.cpp,
	  utilcomm.cpp: Move background subtraction to function
	  CleanStack() in utilcomm.cpp, so both ali3d_d and unified are
	  working with the same data

2007-04-26 19:39  sternberg

	* libEM/sparx/temp/ali3d_d_mpi.cpp: Report number of images for how
	  many new angles and shifts are used (from projection matching) vs
	  how many are reused from previous unified run

2007-04-25 13:37  gtang

	* libEM/sparx/rsconvolution.cpp: minor fix

2007-04-25 13:25  gtang

	* libEM/MarchingCubes.cpp: minor fix for warning msg.

2007-04-25 13:20  gtang

	* libEM/pointarray.cpp: minor fix

2007-04-25 13:15  gtang

	* libpyEM/typeconverter.h: minor fix, g++ 4.1.2 on Ubuntu 7.04 has
	  stricter sytax check.

2007-04-25 13:03  gtang

	* libEM/util.cpp: minor fix

2007-04-25 12:21  sternberg

	* libEM/sparx/temp/utilcomm.cpp: get s2x and s2y from image stack,
	  if available

2007-04-25 10:55  zyang

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/libpyEMData2.cpp: Add function rot_scale_conv_new()

2007-04-25 10:54  zyang

	* libEM/sparx/util_sparx.cpp: Fix a minor bug

2007-04-25 10:52  zyang

	* libEM/cmp.cpp: Trival change

2007-04-24 19:13  sternberg

	* libEM/sparx/temp/ali3d_d_mpi.cpp: removed std::cout

2007-04-24 18:09  sternberg

	* libEM/sparx/temp/runrefine.cpp: set radius to be consistent
	  between projection matching and unified

2007-04-24 13:38  sternberg

	* libEM/sparx/temp/ali3d_d_mpi.cpp: added MPI call to get psize and
	  nbase for writing out correlation peaks; use options.have_angles
	  to determine of angleshift contains data from a unified run, and
	  if so, test to see if projection matching has improved the
	  residual; fixed loop index error, was using j in two levels of
	  for loop

2007-04-24 13:21  sternberg

	* libEM/sparx/temp/: ali3d_unified_mpi.cpp, ali3d_unified_mpi.h:
	  fixed indexing bug in converting angleshift back to degrees;
	  serialized fcalc()

2007-04-24 10:48  woolford

	* programs/e2project3d.py: e2project3d.py is being renovated

2007-04-23 17:03  zyang

	* libEM/projector.cpp: Correct a minor bug.

2007-04-23 16:33  sternberg

	* libEM/sparx/temp/: alignoptions.cpp, alignoptions.h,
	  runrefine.cpp: AlignOptions class given 'have_angles' member to
	  indicate if angleshift contains data or not

2007-04-23 13:59  zyang

	* libEM/sparx/util_sparx.cpp: Trival change

2007-04-20 19:30  sternberg

	* libEM/sparx/temp/ali3d_d_mpi.cpp: after projection matching,
	  compare residual for each image between old and new angles; use
	  the best of these for reconstruction and the next refinement by
	  unified

2007-04-20 19:27  sternberg

	* libEM/sparx/temp/: ali3d_unified_mpi.cpp, ali3d_unified_mpi.h:
	  took aba (average background) out of interface to fcalc()

2007-04-20 18:47  sternberg

	* libEM/sparx/temp/ali3d_unified_mpi.cpp: removed writing residual
	  info to disk in fcalc()

2007-04-20 18:00  sternberg

	* libEM/sparx/temp/ali3d_unified_mpi.cpp: convert angles back to
	  degrees, and swap the sign of the shifts

2007-04-20 17:35  sternberg

	* libEM/sparx/temp/: ali3d_d_mpi.cpp, ali3d_d_mpi.h: pass options
	  to ali3d_d() by reference

2007-04-20 17:34  sternberg

	* libEM/sparx/temp/ali3d_unified_mpi.cpp: recopy new angles to
	  angleshift from x

2007-04-20 17:32  sternberg

	* libEM/sparx/temp/Makefile: change CC to mpic++ from mpicxx

2007-04-20 17:21  cyang

	* libEM/sparx/temp/Makefile: added more include paths

2007-04-20 16:26  sternberg

	* libEM/sparx/temp/ali3d_unified_mpi.cpp: removed call to bckpj3()
	  in fcalc()

2007-04-20 16:24  sternberg

	* libEM/sparx/temp/: ali3d_unified_mpi.cpp, ali3d_unified_mpi.h:
	  Added fcalc() to calculate residual only (no grad)

2007-04-20 16:00  zyang

	* libEM/sparx/util_sparx.cpp: Some major changes to
	  get_pixel_conv_new() to make it much faster

2007-04-20 15:38  sternberg

	* libEM/sparx/temp/ali3d_unified_mpi.cpp: subtract background only
	  inside 2D mask

2007-04-20 14:26  sternberg

	* libEM/sparx/temp/ali3d_d_mpi.cpp: Added CTF functionality; Custom
	  mask3D may be specified; Subtract mean from X-validation volumes
	  before fsc calculation; shift by phase center of gravity

2007-04-20 14:26  cyang

	* libEM/sparx/temp/alignoptions.h: added the missing include
	  "mpi.h"

2007-04-20 13:47  sternberg

	* libEM/sparx/temp/Makefile: added Makefile with relative paths

2007-04-20 13:46  sternberg

	* libEM/sparx/temp/ali3d_unified_mpi.cpp: Terminate test uses >=,
	  so max_iter is reached, not exceeded

2007-04-20 13:23  sternberg

	* libEM/sparx/temp/ali3d_unified_mpi.cpp: Any node can print error
	  if nloc != nangloc, not just node 0

2007-04-20 13:16  sternberg

	* libEM/sparx/temp/ali3d_unified_mpi.cpp: Deleted psize and nbase
	  in unified()

2007-04-20 13:08  sternberg

	* libEM/sparx/temp/ali3d_unified_mpi.cpp: changed radius to depend
	  on model size in pixels

2007-04-20 13:01  sternberg

	* libEM/sparx/temp/runrefine.cpp: set CTF-related options

2007-04-20 12:52  sternberg

	* libEM/sparx/temp/: alignoptions.cpp, alignoptions.h: added
	  CTF-related options

2007-04-20 12:40  sternberg

	* libEM/sparx/temp/utilcomm.cpp: Repository :
	  sternberg@blake.3dem.bioch.bcm.tmc.edu:/usr/local/CVS/CVS Module
	     : eman2/libEM/sparx/temp Working dir:
	  ~/spx/eman2/eman2/libEM/sparx/temp/

	  In directory .:		Unknown 		Makefile
		     Up-To-Date  1.1	     ali3d_d_mpi.cpp
	  Up-To-Date  1.1	  ali3d_d_mpi.h 	      Up-To-Date
	  1.2	      ali3d_unified_mpi.cpp		  Up-To-Date  1.1
		ali3d_unified_mpi.h		  Up-To-Date  1.1
	  alignoptions.cpp		 Up-To-Date  1.1
	  alignoptions.h	       Unknown
	  corr_major0_pm0.dat		    Unknown
	  corr_major1_pm0.dat		    Unknown
	  fsc_major0_pm0.dat		   Unknown
	  fsc_major1_pm0.dat		   Unknown
	  res_major0_fg0.dat		   Unknown
	  res_major0_fg1.dat		   Unknown
	  res_major0_fg2.dat		   Unknown
	  res_major0_fg3.dat		   Unknown
	  res_major0_fg4.dat		   Unknown
	  res_major0_fg5.dat		   Unknown
	  res_major1_fg0.dat		   Unknown
	  res_major1_fg1.dat		   Unknown
	  res_major1_fg2.dat		   Unknown
	  res_major1_fg3.dat		   Unknown
	  res_major1_fg4.dat		   Unknown
	  res_major1_fg5.dat		   Unknown
	  runrefine		  Up-To-Date  1.1	  runrefine.cpp
		    Unknown		    shrt_stck.hdf
	  Unknown		  tf2dstack.hdf 	      Modified
		    utilcomm.cpp	       Unknown
	  vol001.tfc		   Unknown
	  vol_f_major0_pm0.spi		     Unknown
	  vol_f_major1_pm0.spi		     Unknown
	  vol_major0_pm0.spi		   Unknown
	  vol_major1_pm0.spi		   Unknown
	  vol_r_major0.spi		 Unknown
	  vol_r_major1.spi

	  --------------------- End --------------------- -- last cmd: cvs
	  -f status -v --

2007-04-20 12:06  sternberg

	* libEM/sparx/temp/utilcomm.cpp: removed parenths from
	  (EMData*)[size_of_array]

2007-04-20 11:00  zyang

	* libEM/sparx/util_sparx.cpp: Minor correction

2007-04-20 10:41  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Add function get_pixel_conv_new(),
	  supposed to be a better version of get_pixel_conv(), still in
	  stage of improvement.

2007-04-19 18:05  cyang

	* libEM/sparx/temp/ali3d_unified_mpi.cpp: fix a bug in the
	  MPI_Allgatherv call (scale psize and nbase by 5)

2007-04-19 17:25  cyang

	* libEM/sparx/temp/: alignoptions.cpp, alignoptions.h,
	  runrefine.cpp, utilcomm.cpp: add some utilities and a driver for
	  refinement functions.

2007-04-19 17:20  cyang

	* libEM/sparx/temp/: ali3d_d_mpi.cpp, ali3d_d_mpi.h,
	  ali3d_unified_mpi.cpp, ali3d_unified_mpi.h: check in preliminary
	  version of unified and other refinement code

2007-04-19 15:18  stevel

	* libpyEM/qtgui/emimage2d.py: Default size increased

2007-04-19 08:24  woolford

	* libpyEM/qtgui/: emdesktop.py, emimage2d.py: mouse wheel causes
	  zoom in e2display

2007-04-17 17:20  gtang

	* libEM/: Isosurface.h, MarchingCubes.cpp, MarchingCubes.h,
	  VoxelData.h, emdata.h, reader.h, volume.h: keep working on
	  MarchingCubes

2007-04-17 15:42  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Split Crosrng_msg() into two functions
	  Crosrng_msg_s() and Crosrng_msg_m() so that if necessary, only
	  half of it can be invoked, but I retain Crosrng_msg() just in
	  case.

2007-04-16 16:28  zhuang

	* libEM/reconstructor.cpp: [no log message]

2007-04-16 15:27  zhuang

	* libEM/reconstructor.cpp: trivial change in nn_SSNR output file

2007-04-13 16:03  zyang

	* libEM/reconstructor.cpp: Trival change

2007-04-13 16:00  zyang

	* libEM/reconstructor.cpp: Add variance

2007-04-13 14:48  zyang

	* libEM/reconstructor.cpp: Trival change

2007-04-13 14:46  zyang

	* libEM/sparx/emdata_sparx.cpp: Wei Zhang fixed a serious bug which
	  affects all CTF-related reconstruction.

2007-04-13 08:58  prb

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp:
	   fixed set_posttrans get_posttrans, set_pretrans, get_pretrans

2007-04-12 15:57  zyang

	* libEM/: reconstructor.cpp, reconstructor.h: Add
	  nnSSNR_ctfReconstructor

2007-04-12 15:55  zyang

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: Add function
	  symplane2() and nn_SSNR_ctf()

2007-04-12 15:53  zyang

	* libpyEM/libpyEMData2.cpp: [no log message]

2007-04-12 09:33  prb

	* libEM/: transform.cpp, transform.h:
	  added flags so that one can say set_pretrans while keeping the
	  overall translation the same or the posttrans the same.

	  Thus there are calls for set_pretrans, get_pretrans,
	  set_posttrans, get_posttrans

	  flag=0 is the old way flag=1 means while keeping the overall
	  rotation the same for set calls	 means interpreting the
	  entire rotation as pre or post   for get calls

2007-04-11 02:12  stevel

	* libpyEM/qtgui/emdesktop.py: more desktop work

2007-04-10 01:52  stevel

	* libpyEM/qtgui/emdesktop.py: Work on desktop.

2007-04-09 21:48  zhuang

	* programs/e2pdb2em.py: [no log message]

2007-04-09 01:42  stevel

	* libpyEM/qtgui/emdesktop.py: Work on EMDesktop

2007-04-06 02:07  prb

	* libEM/: emdata.cpp, transform.cpp, transform.h:

	  fixed      inverse method in transform.cpp now takes directly the
	  inverse		  without converting first to angles. Still
	  need to check on				    post,  pre
	  settings.

		rotate_translate
			   i) now uses the correct matrix inverse. Avoids
	  extracting angles first.
			   ii) now does 3d correctly

2007-04-05 15:51  stevel

	* libpyEM/EMAN2.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemx.py, programs/e2boxer.py: Boxer
	  improvements and related changes

2007-04-05 02:17  stevel

	* examples/alignbystars.py, libEM/pointarray.cpp,
	  libEM/pointarray.h, libpyEM/EMAN2.py,
	  libpyEM/libpyPointArray2.cpp, libpyEM/qtgui/emdesktop.py,
	  libpyEM/qtgui/emfximage.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemx.py, programs/e2boxer.py: e2boxer
	  remembers window locations. Worked a little on point alingment.
	  Added new emdesktop.py (which does nothing atm)

2007-04-04 21:07  stevel

	* libEM/emdata_transform.cpp: minor fix

2007-04-04 18:25  ppenczek

	* programs/e2pdb2em.py: [no log message]

2007-04-04 17:48  ppenczek

	* libEM/emdata_transform.cpp: [no log message]

2007-04-04 16:33  stevel

	* libpyEM/: EMAN2.py, qtgui/emimage2d.py: Added app default
	  mechanism.

2007-04-04 13:01  ppenczek

	* programs/e2pdb2em.py: [no log message]

2007-04-04 10:56  gtang

	* libEM/MarchingCubes.cpp, CMakeLists.txt: [no log message]

2007-04-04 10:31  eman

	* libEM/: Isosurface.h, MarchingCubes.h, Mesh.h, reader.h,
	  vecmath.h: [no log message]

2007-04-04 02:16  stevel

	* examples/alignbystars.py, libEM/pointarray.cpp,
	  libEM/pointarray.h, libEM/processor.cpp, libEM/processor.h,
	  libpyEM/libpyPointArray2.cpp, programs/e2display.py,
	  programs/e2proc2d.py, programs/e2scannereval.py: More point
	  alignment issues.

2007-04-03 20:56  prb

	* libEM/emdata.cpp:

	  twiddled a few things.

2007-04-03 16:06  gtang

	* libEM/: CMakeLists.txt, Isosurface.h, MarchingCubes.cpp,
	  MarchingCubes.h, Mesh.h, VoxelData.h, reader.h, vecmath.h,
	  volume.h: merge Isosurface code into libEM, first step make it
	  compilable

2007-04-03 14:10  zweig

	* libEM/sparx/util_sparx.cpp: fix a bug in reconstitute_image_mask

2007-04-02 21:18  stevel

	* libEM/emdata.cpp: Revert rotate_translate

2007-04-02 17:27  zyang

	* libEM/sparx/util_sparx.cpp: Trival change

2007-04-02 08:12  stevel

	* examples/alignbystars.py: alignbystars working

2007-04-02 00:17  stevel

	* examples/alignbystars.py, libpyEM/libpyUtils2.cpp: More point
	  alignment

2007-04-01 13:40  ppenczek

	* libEM/reconstructor.cpp: fix a bug in file_store

2007-03-31 13:22  stevel

	* libEM/: emdata.cpp, pointarray.cpp, transform.cpp, transform.h,
	  util.cpp, util.h: 2D transform class modified to use matrix. more
	  work on point alignment.

2007-03-30 16:30  stevel

	* libEM/pointarray.cpp, libEM/pointarray.h, libEM/util.cpp,
	  libEM/util.h, libpyEM/libpyPointArray2.cpp: bilinear least
	  squares code in util (untested). More pointarray work.

2007-03-30 11:50  gtang

	* rt/pyem/test_imageio.py: unit test for integer array attribute

2007-03-30 11:41  gtang

	* libEM/hdfio2.cpp: support Integer array as EMObject, int array
	  can be set as image attribute now

2007-03-30 10:29  zyang

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: Trival change

2007-03-30 08:53  stevel

	* examples/alignbystars.py, libEM/pointarray.cpp,
	  libEM/pointarray.h: More work on point alignment.

2007-03-29 18:05  zyang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: Made some change to Crosrng_msg(),
	  hopefully nothing is broken this time.

2007-03-29 17:44  gtang

	* libpyEM/typeconverter.h: support Integer array as EMObject, int
	  array can be set as image attribute now

2007-03-29 17:34  gtang

	* rt/pyem/test_utils.py: support Integer array as EMObject, int
	  array can be set as image attribute now

2007-03-29 17:23  gtang

	* libpyEM/: typeconverter.cpp, typeconverter.h: support Integer
	  array as EMObject, int array can be set as image attribute now

2007-03-29 17:19  gtang

	* libEM/: emobject.cpp, emobject.h, reconstructor.cpp,
	  sparx/emdata_sparx.cpp: support Integer array as EMObject, int
	  array can be set as image attribute now

2007-03-29 15:50  stevel

	* libEM/pointarray.cpp, libEM/pointarray.h,
	  libpyEM/libpyPointArray2.cpp: More work on point alignment.

2007-03-29 09:53  gtang

	* libEM/sparx/00_README_ADDING_NEW_CODE: [no log message]

2007-03-29 02:34  stevel

	* examples/alignbystars.py, libEM/pointarray.cpp,
	  libEM/pointarray.h, libEM/transform.cpp,
	  libpyEM/libpyPointArray2.cpp, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemx.py: Working on some alignment routnes in
	  pointarray

2007-03-28 11:21  gtang

	* libEM/hdfio2.cpp: fix the 2G hdf5 file size limit on 32 bit linux
	  system

2007-03-28 11:12  zweig

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: change vrdg prototype

2007-03-28 11:11  zweig

	* libEM/sparx/emdata_sparx.cpp: eluciden distance function for
	  common line

2007-03-27 15:13  zweig

	* libpyEM/EMAN2.py: add call to glutInit to enable e2display

2007-03-27 14:29  zyang

	* libpyEM/qtgui/: emimage2d.py, emimagemx.py: [no log message]

2007-03-26 16:02  zhuang

	* libEM/sparx/util_sparx.cpp: [no log message]

2007-03-26 10:30  zhuang

	* libEM/sparx/util_sparx.cpp: fix a bug in reconstitue_mask, add
	  background option

2007-03-25 20:33  gtang

	* rt/pyem/test_imageio.py: test case fot ignoring image_index for
	  single image format

2007-03-25 20:32  gtang

	* libEM/: dm3io.cpp, emimio.cpp, emio.cpp, fitsio.cpp,
	  gatan2io.cpp, mrcio.cpp, pgmio.cpp, pngio.cpp, icosio.cpp,
	  salio.cpp, tifio.cpp, vtkio.cpp, xplorio.cpp: ignore image_index
	  for single image format

2007-03-25 15:05  gtang

	* INSTALL, doc/INSTALL, doc/develop_system_setup.html,
	  doc/developer-guide.html: eliminate pyste

2007-03-24 23:10  stevel

	* libpyEM/: Makefile.pyste, aligner.pyste, analyzer.pyste,
	  averager.pyste, cmp.pyste, create_boost_python, emdata.pyste,
	  emobject.pyste, fundamentals.pyste, geometry.pyste,
	  pointarray.pyste, polardata.pyste, processor.pyste,
	  projector.pyste, reconstructor.pyste, transform.pyste,
	  typeconverter.pyste, utils.pyste: Remove Pyste.

2007-03-24 12:04  gtang

	* libEM/emdata_metadata.h: correct comment

2007-03-24 01:27  zhuang

	* libEM/sparx/util_sparx.cpp: [no log message]

2007-03-24 00:01  zhuang

	* libEM/sparx/util_sparx.cpp: [no log message]

2007-03-23 18:13  zhuang

	* libEM/sparx/emdata_sparx.cpp: add padded corner to rotavg_i

2007-03-23 16:03  gtang

	* utils/CMakeLists.txt: Dr. Tao Ju's Isosurface code. first step
	  just put code in CVS.

2007-03-23 15:58  gtang

	* utils/MarchingCubes/: Isosurface.h, MCubes.cpp,
	  MarchingCubes.cpp, MarchingCubes.h, Mesh.h, VoxelData.h, dbh.cpp,
	  dbh.h, gorgon.pyw, reader.h, stdafx.cpp, stdafx.h, vecmath.h,
	  volume.h: Dr. Tao Ju's Isosurface code. first step just put code
	  in CVS.

2007-03-23 15:29  gtang

	* libpyEM/libpyTransform2.cpp: fix the broken pickling for Vec3f

2007-03-23 15:10  gtang

	* rt/emdata/: CMakeLists.txt, storage_order_test.cpp,
	  storage_order_test.py: testing code

2007-03-23 13:58  zyang

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/emdata.pyste, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyFundamentals2.cpp, libpyEM/libpyPointArray2.cpp,
	  libpyEM/libpyTransform2.cpp, libpyEM/libpyUtils2.cpp: Add C++
	  function rotave_i()

2007-03-23 11:01  gtang

	* libpyEM/: libpyEMData2.cpp, libpyPointArray2.cpp: Fix the broken
	  file because of unpatched Pyste run.

2007-03-23 02:14  stevel

	* libpyEM/libpyPointArray2.cpp, programs/e2boxer.py: Work on point
	  alignment. Trivial on e2boxer.

2007-03-22 23:17  stevel

	* libpyEM/pointarray.pyste: Trivial

2007-03-22 22:52  stevel

	* libEM/: pointarray.cpp, pointarray.h: New alignment routines in
	  pointarray

2007-03-22 17:06  zyang

	* libEM/sparx/normpadft.cpp: Change PI to M_PI

2007-03-22 15:31  zhuang

	* libEM/sparx/emdata_sparx.cpp: [no log message]

2007-03-22 15:09  zhuang

	* libEM/sparx/emdata_sparx.cpp: [no log message]

2007-03-22 15:03  zhuang

	* libEM/sparx/emdata_sparx.cpp: [no log message]

2007-03-22 13:04  gtang

	* libEM/reconstructor.cpp: fix the broken EMAN2

2007-03-22 12:12  zyang

	* libpyEM/libpyEMData2.cpp: [no log message]

2007-03-21 20:34  zyang

	* libEM/: reconstructor.cpp, sparx/emdata_sparx.cpp,
	  sparx/normpadft.cpp: Yang revised center_origin_fft() in
	  normpadft.cpp and nnSSNR_Reconstructor::finish() in
	  reconstructor.cpp so that the reconstruction works for odd-sized
	  volume now.

2007-03-21 17:08  gtang

	* libEM/hdfio2.cpp: fix the dataspace definition for HDF5 image in
	  EMAN2. The dimension definition is different in EMAN2 and HDF5.
	  refer to the link:
	  http://hdf.ncsa.uiuc.edu/HDF5/doc/UG/12_Dataspaces.html the
	  (nx=3, ny=5) array in this page is a (nx=5, ny=3) image to EMAN2.

2007-03-21 12:04  gtang

	* rt/emdata/storage_order_test.py: test script to show the storage
	  order in EMData array and numpy.

2007-03-21 11:55  gtang

	* libpyEM/typeconverter.cpp: revert the change

2007-03-21 11:52  gtang

	* libpyEM/typeconverter.h: Revert the change for EM2NumPy's shape.
	  EMData store in row major order, fortran_storage_order.

2007-03-20 16:40  zyang

	* libEM/: reconstructor.cpp, reconstructor.h,
	  sparx/emdata_sparx.cpp, sparx/emdata_sparx.h: Yang add
	  nnSSNR_Reconstructor

2007-03-20 10:35  stevel

	* examples/alignbystars.py: New discrete alignment program. May
	  eventually turn into tomography tool...

2007-03-17 13:17  gtang

	* libpyEM/typeconverter.h: fix the transposed array dims

2007-03-17 10:58  gtang

	* libpyEM/typeconverter.h: fix the transposed array dims

2007-03-17 10:55  gtang

	* libpyEM/typeconverter.cpp: fix the transposed array dims in
	  em2numpy

2007-03-17 10:25  gtang

	* libpyEM/typeconverter.cpp: fix the transposed array dims in
	  em2numpy

2007-03-16 18:51  zhuang

	* libEM/sparx/util_sparx.cpp: fix bug in im_diff

2007-03-15 16:36  zyang

	* libEM/reconstructor.cpp: Yang fix a bug in
	  nn4Reconstructor::buildFFTVolume()

2007-03-14 19:36  zyang

	* libEM/: reconstructor.cpp, sparx/emdata_sparx.cpp,
	  sparx/normpadft.cpp: Yang fix a bug in zeropad_ntimes() at
	  normpadft.cpp

2007-03-14 17:40  zhuang

	* libEM/sparx/util_sparx.cpp: swap subtraction of image1 and image2
	  in im_diff

2007-03-13 22:43  stevel

	* libpyEM/qtgui/emimage2d.py: Compatibility with pyopengl3

2007-03-13 11:11  gtang

	* INSTALL: new dependency IPython

2007-03-12 14:46  stevel

	* libpyEM/EMAN2.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2boxer.py: New GUI features. Better boxer GUI.

2007-03-12 03:03  stevel

	* libpyEM/EMAN2.py, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2.py: Improvements to GUI handling. Drag into
	  EMImage2D.

2007-03-12 01:42  stevel

	* libpyEM/EMAN2.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimageutil.py, libpyEM/qtgui/pyshed.py,
	  programs/e2.py, programs/e2boxer.py: e2.py now uses ipython 0.7.3
	  or above for its interactive prompt. Finally !

2007-03-09 07:52  gtang

	* libEM/hdfio2.cpp: correct comment

2007-03-08 15:34  zyang

	* libEM/sparx/rsconvolution.cpp: Yang tested filt_erosion and fixed
	  a bug

2007-03-08 12:13  zyang

	* libEM/sparx/fundamentals.h, libEM/sparx/rsconvolution.cpp,
	  libpyEM/fundamentals.pyste, libpyEM/libpyFundamentals2.cpp: Yang
	  add function filt_erosion

2007-03-08 11:49  zyang

	* libEM/sparx/rsconvolution.cpp: Yang tested and fixed the bug in
	  filt_dilation

2007-03-07 19:04  zyang

	* libEM/sparx/rsconvolution.cpp: Yang finished filt_dilation

2007-03-07 16:42  gtang

	* INSTALL: [no log message]

2007-03-07 15:56  zyang

	* libEM/sparx/rsconvolution.cpp: Yang fix a bug in filt_median

2007-03-07 12:46  zyang

	* libEM/sparx/rsconvolution.cpp: Yang made some changes on
	  filt_median

2007-03-07 10:40  zyang

	* libEM/sparx/: fundamentals.h, rsconvolution.cpp: Yang working on
	  filt_dilation

2007-03-07 10:39  zyang

	* libpyEM/libpyFundamentals2.cpp: Yang fix a bug

2007-03-07 10:31  gtang

	* CMakeLists.txt: search numpy in PYTHON_ROOT first

2007-03-06 19:07  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h, util_sparx.h:
	  rot_shift3D  slightly corrected, that is rot_scale_trans or
	  something

2007-03-06 16:11  zyang

	* libpyEM/: fundamentals.pyste, libpyFundamentals2.cpp: Yang add
	  dilation

2007-03-06 14:26  zyang

	* libEM/sparx/: fundamentals.h, rsconvolution.cpp: Yang finished
	  filt_median

2007-03-05 21:17  zyang

	* libpyEM/: fundamentals.pyste, libpyFundamentals2.cpp: Yang add
	  filt_median function

2007-03-05 19:21  zyang

	* libEM/processor.h: Yang Minor Change

2007-03-05 19:20  zyang

	* libEM/sparx/: fundamentals.h, rsconvolution.cpp: Yang add
	  filt_median

2007-03-05 18:25  gtang

	* programs/e2proc2d.py: --process take argument in format
	  processor_name(param1=value1,param2=value2, ...)

2007-03-05 18:05  gtang

	* libpyEM/Makefile.pyste: modify the header search path for Pyste

2007-03-05 18:02  gtang

	* libpyEM/Makefile.pyste: modify the header search path for Pyste

2007-03-05 17:57  gtang

	* libpyEM/: Makefile.pyste: modify the header search path for Pyste

2007-03-05 17:26  gtang

	* libEM/sparx/processor_sparx.h: add "cutoff_abs" parameter to
	  NewFourierProcessor

2007-03-04 21:16  eman

	* CMakeLists.txt: search numpy header

2007-03-04 01:13  stevel

	* CMakeLists.txt: Now finds numpy include files without extra
	  installation.

2007-03-03 21:57  stevel

	* programs/: e2boxer.py, e2classesbysim.py, e2simmx.py,
	  e2stackanim.py: Working on several programs

2007-03-03 16:22  gtang

	* rt/pyem/test_processor.py: add unit test for CutToZeroProcessor

2007-03-02 16:50  gtang

	* rt/pyem/test_processor.py: unit test update

2007-03-02 14:45  gtang

	* doc/: CMakeLists.txt,
	  WindowsVisualStudioDotNet2003CompilationNotes.txt: doc change,
	  move this content to EMAN2's wiki page

2007-03-01 18:02  zyang

	* libEM/: processor.cpp, processor.h: Yang add threshold_to_zero

2007-02-28 17:18  gtang

	* INSTALL: Numeric -> numpy transition

2007-02-28 17:12  gtang

	* libpyEM/typeconverter.cpp: Numeric -> numpy transition

2007-02-28 15:42  gtang

	* doc/latex/: help-opt-prog-inst.tex, misc-developers-guide.tex,
	  development-policy-faq.tex: Numeric -> numpy transition

2007-02-28 15:33  gtang

	* doc/: develop_system_setup.html: Numeric -> numpy transition

2007-02-28 15:19  gtang

	* libpyEM/qtgui/emimage2d.py: Numeric -> numpy transition

2007-02-28 11:53  gtang

	* libpyEM/typeconverter.cpp: Numeric -> numpy transition.

2007-02-28 11:24  gtang

	* doc/development_policy_faq.html, INSTALL, doc/INSTALL,
	  doc/developer-guide.html, libpyEM/EMAN2.py,
	  libpyEM/libpyTypeConverter2.cpp, libpyEM/typeconverter.cpp,
	  libpyEM/typeconverter.h, libpyEM/typeconverter.pyste,
	  libpyEM/qtgui/emimage.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimageutil.py, programs/e2display.py,
	  programs/e2msa.py, rt/pyem/test_emdata.py,
	  rt/pyem/test_processor.py, rt/pyem/test_typeconverter.py: Numeric
	  -> numpy transition.

2007-02-27 20:59  gtang

	* libEM/: emdata.cpp, emdata.h: minor change

2007-02-27 16:15  stevel

	* libEM/emdata_transform.cpp, libpyEM/qtgui/emimagemx.py: Minor gui
	  fixes.

2007-02-27 02:52  stevel

	* libpyEM/qtgui/emimagemx.py, programs/e2boxer.py: Scrolling in
	  emimagemx. Improvements to particle picker

2007-02-26 11:59  gtang

	* libEM/emobject.cpp, libEM/emobject.h,
	  libpyEM/libpyTypeConverter2.cpp, libpyEM/typeconverter.cpp,
	  libpyEM/typeconverter.h, libpyEM/typeconverter.pyste: Transform3D
	  object now can be image attribute

2007-02-26 02:16  stevel

	* programs/: e2boxer.py, e2help.py, e2scannereval.py: Working on
	  new boxer method.

2007-02-23 16:36  gtang

	* rt/pyem/test_emdata.py: add unit test for new EMData
	  constructors.

2007-02-23 16:26  gtang

	* libEM/emdata.cpp: new EMData(nx, ny, nz, r_c) construct a blank
	  image with flag set

2007-02-23 15:03  gtang

	* rt/pyem/test_emdata.py: add unit test for new EMData
	  constructors.

2007-02-23 14:31  gtang

	* libEM/emdata.cpp, libEM/emdata.h, libEM/emdata_core.cpp,
	  libpyEM/libpyEMData2.cpp: add two new constructor for EMData():
	  EMData(nx,ny,nz,r_c)        # makes an image of the
	  specified size, either real or
	                    # complex. I would say that
	  if complex is selected,                    #
	  the user would specify the real-space dimensions
	                     # of the object, so the
	  constructor can properly set
	                     # the is_fftodd flag, etc.

	   EMData(filespec,n)  # Create an EMData object, and read image
	  n from filespec

2007-02-21 12:07  gtang

	* libEM/sparx/varimax.cpp: remove warning

2007-02-21 11:58  gtang

	* libEM/sparx/: lapackblas.cpp, lapackblas.h: fix warnings

2007-02-21 11:31  gtang

	* libEM/sparx/SparxIO.cpp: fix the warnings

2007-02-21 11:11  gtang

	* libEM/sparx/: Tokenizer.cpp, Tokenizer.h: remove warnings

2007-02-21 10:18  gtang

	* libEM/sparx/util_sparx.cpp: remove the warning message

2007-02-21 10:02  gtang

	* libEM/sparx/util_sparx.cpp: fix a warning for "control reach the
	  end of non-void function"

2007-02-21 09:56  gtang

	* libEM/emdata_transform.cpp: fix the data type conversion warning.

2007-02-21 02:18  stevel

	* libpyEM/EMAN2.py, programs/e2boxer.py, programs/e2simmx.py:
	  Worked on plot and simmx a bit.

2007-02-16 16:35  gtang

	* rt/pyem/test_emdata.py: unit test update for
	  EMData::render_amp8() interface change

2007-02-15 02:06  stevel

	* libEM/emdata_transform.cpp, libEM/emdata_transform.h,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2boxer.py, programs/e2simmx.py: Added gamma to image
	  display widgets. Slow, though...

2007-02-14 16:35  zweig

	* libEM/reconstructor.cpp: do the similar thing for
	  nn4Reconstructor

2007-02-14 16:22  zweig

	* libEM/reconstructor.cpp: for nn4_ctfReconstructor, do not init
	  vol if it has been initialized

2007-02-14 15:45  gtang

	* doc/INSTALL: doc update

2007-02-14 15:05  gtang

	* doc/: cvshowto.html, developer-guide.html: doc update

2007-02-14 14:20  gtang

	* doc/CMakeLists.txt: doc update

2007-02-14 13:00  gtang

	* doc/: adding_processor.html, adding_processor.txt, eman2doc.h:
	  doc update

2007-02-14 12:38  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2007-02-14 12:14  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2007-02-14 10:59  gtang

	* doc/eman2doc.h: doc update

2007-02-13 17:03  gtang

	* doc/eman2doc.h: doc update

2007-02-13 16:24  gtang

	* doc/index.html: fix the broken link

2007-02-13 16:23  gtang

	* doc/CMakeLists.txt: "make install" copy EMAN2's logo image

2007-02-13 15:56  stevel

	* libEM/emdata_core.cpp: Minor fixes

2007-02-13 15:50  gtang

	* libEM/reconstructor.h: fix error message for DOxygen

2007-02-13 15:36  gtang

	* libEM/sparx/emdata_sparx.h: fix error message for DOxygen

2007-02-13 14:19  gtang

	* libEM/: CMakeLists.txt, analyzer.cpp: fix the broken compilation

2007-02-12 11:22  zweig

	* libEM/: varimax.cpp, varimax.h: moved to sparx/

2007-02-12 11:21  zweig

	* libEM/sparx/: varimax.cpp, varimax.h: varimax implementation

2007-02-09 11:50  gtang

	* libpyEM/: libpyEMData2.cpp, libpyTransform2.cpp, libpyUtils2.cpp:
	  update Python wrapping file due to unpatched pyste run.

2007-02-09 11:48  gtang

	* libpyEM/emdata.pyste: update due to removal of rot_trans2D()
	  function

2007-02-09 11:48  gtang

	* rt/pyem/test_emdata.py: unit test update due to removal of
	  rot_trans2D() function

2007-02-08 18:20  zhuang

	* libEM/sparx/emdata_sparx.cpp: [no log message]

2007-02-08 13:41  ppenczek

	* libpyEM/libpyEMData2.cpp: [no log message]

2007-02-08 13:41  ppenczek

	* libpyEM/sparx_apmq.cpp: NOT NEEDED

2007-02-08 12:26  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: Corrected 2D rot
	  shift

2007-02-08 09:35  ppenczek

	* libEM/sparx/util_sparx.cpp: memory leak in apmq removed

2007-02-07 14:13  zhuang

	* libEM/sparx/util_sparx.h: [no log message]

2007-02-07 14:13  zhuang

	* libEM/sparx/util_sparx.cpp: add flip options to infomask

2007-02-06 17:15  zhuang

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: [no log message]

2007-02-06 14:26  zhuang

	* libEM/processor.h: [no log message]

2007-02-06 13:12  zhuang

	* libpyEM/: libpyEMData2.cpp, libpyReconstructor2.cpp,
	  libpyTransform2.cpp, libpyUtils2.cpp: [no log message]

2007-02-06 12:46  zhuang

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: [no log message]

2007-02-06 09:29  gtang

	* rt/demo/project.py: unit test update for MRC->IMAGE_MRC,
	  IMAGIC->IMAGE_IMAGIC.

2007-02-06 09:26  gtang

	* rt/pyem/test_cmp.py: unit test update for MRC->IMAGE_MRC,
	  IMAGIC->IMAGE_IMAGIC.

2007-02-05 17:39  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2007-02-05 15:12  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2007-02-05 15:11  zweig

	* libEM/: reconstructor.cpp, reconstructor.h,
	  sparx/emdata_sparx.cpp, sparx/emdata_sparx.h: changes to make
	  nn4Reconstructor also parallel

2007-02-05 02:47  stevel

	* rt/pyem/: test_emdata.py, test_misc.py, test_processor.py,
	  test_typeconverter.py, test_utils.py: More unit test fixes.

2007-02-05 02:41  stevel

	* rt/pyem/test_imageio.py: Fix unit test for name change in image
	  types

2007-02-05 02:32  stevel

	* libpyEM/EMAN2.py, programs/e2help.py, programs/e2proc2d.py,
	  programs/e2simmx.py, pyemtbx/imagetypes.py: Working on a few
	  'real' programs for EMAN2. Also changed MRC,IMAGIC,etc ->
	  IMAGE_MRC,etc

2007-02-03 00:52  stevel

	* libEM/fitsio.cpp, programs/e2boxer.py, programs/e2display.py,
	  programs/e2scannereval.py: various changes

2007-02-02 16:25  zweig

	* libpyEM/libpyReconstructor2.cpp: add file_store

2007-02-02 14:16  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2007-02-02 12:00  gtang

	* libEM/hdfio2.cpp: [no log message]

2007-02-02 11:44  gtang

	* rt/pyem/test_processor.py: [no log message]

2007-02-02 02:32  stevel

	* libpyEM/qtgui/: emimage2d.py, emimage3d.py, emimagemx.py: Drag
	  and drop in imagemx mostly working

2007-02-01 16:39  gtang

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/CMakeLists.txt, libpyEM/libpyUtils2.cpp: move apmq() to
	  libEM/sparx as a member function of Util class

2007-02-01 13:37  ppenczek

	* libEM/: processor.cpp, reconstructor.h:
	  Corrected nomr.mask, PLEASE DO NTO CHANGE IT!

2007-02-01 12:05  gtang

	* libEM/: processor.cpp, processor.h: fix the bug in
	  NormalizeMaskProcessor, which the flag no_sigma was not
	  implemeted.

2007-01-31 12:12  mhhohn

	* libpyEM/sparx_apmq.cpp: Changed from boost::python::len to
	  PyObject_Length for backward compatibility.

2007-01-31 10:34  gtang

	* libpyEM/sparx_apmq.cpp: fix the warning message

2007-01-31 10:29  gtang

	* libpyEM/sparx_apmq.cpp: fix the compilation error, include
	  necessary header for boost:python::len() function

2007-01-30 17:29  mhhohn

	* libpyEM/sparx_apmq.cpp: renamed C++ apmq to sparx_apmq to avoid
	  name clashes

2007-01-30 17:11  gtang

	* utils/speedtest.cpp: enable speedtest

2007-01-30 16:53  mhhohn

	* libpyEM/: CMakeLists.txt, libpyUtils2.cpp, sparx_apmq.cpp: added
	  sparx_apmq.cpp

2007-01-30 11:53  zweig

	* libEM/reconstructor.cpp: fix a bug in reconstructor, remove the
	  usage of temporary copy of fftvol

2007-01-29 16:47  gtang

	* libEM/hdfio2.cpp: When overwriting an image in hdf stack: If the
	  image is the same size as the one being replaced: 1) unlink the
	  'header' information 2) overwrite the existing data in-place

	  If the image is a different size: 1) unlink both the header and
	  data 2) write a completely new header/data

2007-01-27 14:19  ppenczek

	* libEM/sparx/emdata_sparx.cpp: reversed myself!

2007-01-27 13:58  ppenczek

	* libEM/sparx/emdata_sparx.cpp: undone change by Wei

2007-01-27 08:52  ppenczek

	* libEM/reconstructor.cpp: CHANGED SHIFT to S2X in the
	  reconstructor

2007-01-26 15:30  zweig

	* libEM/: reconstructor.cpp, reconstructor.h: use 64 bits integer
	  to hold file offset

2007-01-26 11:25  zweig

	* libEM/reconstructor.cpp: use a tmp volume to hold fft result

2007-01-26 10:42  ppenczek

	* libEM/sparx/fourierfilter.cpp: memory leak in fourierfilter
	  removed

2007-01-25 16:18  zweig

	* libEM/reconstructor.cpp: something strange happened during the
	  last checkin, have to redo it

2007-01-25 15:35  zweig

	* libEM/: reconstructor.cpp, reconstructor.h: fix a memory leak of
	  nn4_ctfReconstructor

2007-01-25 12:55  zweig

	* libEM/reconstructor.cpp: use absoulte offset for file seeking

2007-01-24 18:45  ppenczek

	* libEM/sparx/normpadft.cpp: [no log message]

2007-01-24 11:08  gtang

	* libEM/hdfio2.cpp: support HDF5 overwrite existing single image in
	  an image stack

2007-01-24 11:02  gtang

	* libEM/analyzer.cpp: remove a warning meesage.

2007-01-23 16:39  zweig

	* libEM/sparx/: normpadft.cpp, emdata_sparx.cpp: use copy() to
	  replace new EMData() to reserve all the header info

2007-01-23 12:25  gtang

	* libEM/hdfio2.cpp: support HDF5 overwrite existing single image in
	  an image stack

2007-01-22 17:23  zweig

	* libEM/analyzer.cpp: return eigen volumes in descending order

2007-01-22 10:16  gtang

	* libpyEM/: libpyEMData2.cpp, libpyTransform2.cpp, libpyUtils2.cpp:
	  fix the broken default argument handling due to upatched pyste
	  running

2007-01-20 16:14  gtang

	* libEM/jpegio.cpp: change the "#ifdef EM_PNG" to "#ifdef EM_JPEG"

2007-01-20 13:31  ppenczek

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyTransform2.cpp,
	  libpyEM/libpyUtils2.cpp: scale added to 2D gridding

2007-01-19 17:46  zweig

	* libpyEM/typeconverter.h: undo the recent change, which cause
	  python::list convert to vector<int>

2007-01-19 11:32  ppenczek

	* libEM/sparx/: fundamentals.cpp, util_sparx.cpp: voronoi code
	  cleaned

2007-01-19 10:59  zweig

	* libEM/sparx/emdata_sparx.cpp: fix some problem in extractline

2007-01-18 16:17  zweig

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/typeconverter.h: Simplified calculation of weights in
	  vrdg

2007-01-18 14:02  zweig

	* libpyEM/libpyEMData2.cpp: add function cm_euc

2007-01-18 14:02  zweig

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: add function
	  cm_euc to calculate elucidian distance

2007-01-18 12:46  ppenczek

	* libEM/sparx/: util_sparx.cpp, util_sparx.h:
	  simplified voronoi diag for one band

2007-01-17 18:03  zhuang

	* libEM/sparx/util_sparx.cpp: remove warning in call_c1

2007-01-17 18:01  zhuang

	* libEM/sparx/fourierfilter.cpp: remove warnings

2007-01-17 12:19  gtang

	* libpyEM/: libpyEMData2.cpp, libpyTransform2.cpp, libpyUtils2.cpp:
	  fix the broken default argument handling due to upatched pyste
	  running

2007-01-16 23:39  prb

	* libEM/sparx/emdata_sparx.cpp: fixed a minor compilation problem.
	  There exists still some other issue that has arisen, which was
	  not present when I originally wrote and tested the Fourier
	  Harmonic calls:    FH2Real, FH2F.   PRB

2007-01-15 17:54  ppenczek

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyReconstructor2.cpp,
	  libpyEM/libpyTransform2.cpp, libpyEM/libpyUtils2.cpp: [no log
	  message]

2007-01-14 16:24  ppenczek

	* libEM/processor.cpp: [no log message]

2007-01-14 15:22  ppenczek

	* libEM/sparx/util_sparx.cpp: some cleaning, warnings removed in
	  crosrng

2007-01-12 12:43  zweig

	* libEM/: reconstructor.cpp, reconstructor.h: add a data member to
	  hold the result

2007-01-12 11:11  gtang

	* libpyEM/: libpyEMData2.cpp, libpyTransform2.cpp, libpyUtils2.cpp:
	  fix the broken default argument handling due to upatched pyste
	  running

2007-01-12 10:54  zweig

	* libpyEM/libpyReconstructor2.cpp: add file_store for bootstrap

2007-01-12 02:25  stevel

	* programs/e2display.py: title display

2007-01-11 15:31  ppenczek

	* libpyEM/: libpyEMData2.cpp, libpyTransform2.cpp, libpyUtils2.cpp:
	  [no log message]

2007-01-11 14:55  zweig

	* libEM/: reconstructor.cpp, reconstructor.h,
	  sparx/emdata_sparx.cpp, sparx/emdata_sparx.h: make some changes
	  to implement parallel reconstruction

2007-01-11 10:54  zhuang

	* libpyEM/: emdata.pyste, utils.pyste: [no log message]

2007-01-11 10:50  zhuang

	* libEM/sparx/: emdata_sparx.h, emdata_sparx.cpp: add ctf_img

2007-01-11 10:49  zhuang

	* libEM/sparx/: util_sparx.h, util_sparx.cpp: move ctf_img to
	  emdata_sparx

2007-01-10 12:52  ppenczek

	* libEM/: emdata_core.cpp, sparx/util_sparx.cpp: [no log message]

2007-01-10 10:33  zhuang

	* libEM/sparx/util_sparx.cpp: [no log message]

2007-01-10 10:24  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, util_sparx.cpp: [no log message]

2007-01-09 17:43  ppenczek

	* libEM/cmp.cpp: [no log message]

2007-01-09 16:46  ppenczek

	* libEM/cmp.cpp: [no log message]

2007-01-09 14:25  zweig

	* libEM/: reconstructor.cpp, sparx/emarray.h,
	  sparx/emdata_sparx.cpp: change attribute name from pixel to
	  Pixel_size

2007-01-09 13:44  stevel

	* programs/e2stackanim.py: New pingpong option for animations

2007-01-09 02:13  stevel

	* libEM/emdata_transform.cpp, libEM/emdata_transform.h,
	  libpyEM/qtgui/emimagemx.py: Beginning of drag/drop in EMImagemx

2007-01-08 16:50  stevel

	* doc/index.html: Minor fixes

2007-01-08 11:46  ppenczek

	* libEM/sparx/fourierfilter.cpp: [no log message]

2007-01-08 11:38  gtang

	* libpyEM/: libpyEMData2.cpp, libpyTransform2.cpp: fix the unit
	  test errors due to unpatched pyste running

2007-01-08 10:50  ppenczek

	* libEM/sparx/emdata_sparx.cpp: [no log message]

2007-01-08 09:43  ppenczek

	* libEM/sparx/util_sparx.h: [no log message]

2007-01-08 09:33  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2007-01-08 09:18  ppenczek

	* libEM/sparx/fourierfilter.cpp, libEM/sparx/util_sparx.cpp,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyTransform2.cpp,
	  libpyEM/libpyUtils2.cpp: [no log message]

2007-01-07 22:46  zhuang

	* libEM/sparx/fourierfilter.cpp: [no log message]

2007-01-07 16:07  ppenczek

	* libEM/sparx/fourierfilter.cpp, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h, libpyEM/libpyUtils2.cpp,
	  libpyEM/utils.pyste: CTF attributes corrected

2007-01-07 12:41  gtang

	* libpyEM/: emdata.pyste, libpyEMData2.cpp, libpyTransform2.cpp,
	  transform.pyste: fix the EMData class pickling support.

2007-01-04 15:10  ppenczek

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, libpyEM/utils.pyste: [no log message]

2007-01-04 11:33  zweig

	* libEM/varimax.cpp: add license comment

2007-01-04 11:12  zweig

	* libEM/: varimax.cpp, varimax.h: varimax implementation from
	  maconava

2007-01-04 11:12  zweig

	* libEM/: analyzer.cpp, sparx/analyzer_sparx.h: add varimax
	  analyzer

2007-01-04 11:11  zweig

	* libEM/CMakeLists.txt: add varimax.cpp to source list

2007-01-04 02:04  stevel

	* programs/: e2stackanim.py, e2stacksort.py: Added a couple of
	  simple new utilities.

2007-01-03 20:50  ppenczek

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: [no log message]

2007-01-03 20:23  zhuang

	* libEM/sparx/util_sparx.cpp: change Util.tf

2007-01-02 10:56  ppenczek

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: [no log message]

2006-12-31 19:22  zhuang

	* libEM/sparx/util_sparx.cpp: update extract_pw

2006-12-31 18:41  ppenczek

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h, libpyEM/libpyUtils2.cpp: more changes
	  in util_sparx

2006-12-30 21:48  ppenczek

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: added stuff in util_sparx

2006-12-29 15:32  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2006-12-28 18:28  ppenczek

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyTransform2.cpp: [no log
	  message]

2006-12-28 14:16  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2006-12-28 13:54  ppenczek

	* libpyEM/: libpyGeometry2.cpp, libpyPointArray2.cpp,
	  libpyReconstructor2.cpp, libpyTransform2.cpp: [no log message]

2006-12-27 23:03  ppenczek

	* libpyEM/: libpyUtils2.cpp, utils.pyste: [no log message]

2006-12-27 22:52  ppenczek

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/Makefile.pyste, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyTypeConverter2.cpp: [no log message]

2006-12-27 22:14  ppenczek

	* libpyEM/: libpyUtils2.cpp, util_wrapitems.h: [no log message]

2006-12-27 22:05  ppenczek

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: [no log message]

2006-12-22 19:25  gtang

	* libEM/spiderio.cpp: EMAN2's spider stack image can not be read
	  correctly in SPIDER, due to an "unused" flag "irec" is actually
	  used by SPIDER.

2006-12-22 15:18  gtang

	* examples/comparepairs.py, examples/makebigfromseq.py,
	  examples/sortsimilar.py, examples/transalignavg.py,
	  libpyEM/qtgui/emfximage.py, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimage3d.py,
	  libpyEM/qtgui/emimagemx.py, libpyEM/qtgui/pyshed.py,
	  programs/e2display.py, rt/demo/cmp.py, rt/demo/reconstructor.py,
	  rt/emdata/exception1.py: change /bin/env to /usr/bin/env

2006-12-15 14:08  zweig

	* libEM/sparx/fourierfilter.cpp: add comments on function
	  EMFourierFunc which doInPlace

2006-12-15 12:08  zweig

	* libpyEM/libpyReconstructor2.cpp: add file_store

2006-12-15 12:06  zweig

	* libEM/: reconstructor.h, reconstructor.cpp: fix bugs in
	  file_store

2006-12-14 17:12  zweig

	* libEM/: reconstructor.h, reconstructor.cpp: add class file_store

2006-12-14 16:02  ppenczek

	* libEM/sparx/fourierfilter.cpp: [no log message]

2006-12-13 13:28  zweig

	* libEM/sparx/emdata_sparx.cpp: do not use pre-store ctf to save
	  ctf computation efford, since some data has different defocus
	  value for each particle

2006-12-12 16:07  zweig

	* libEM/reconstructor.cpp: fix a memory leak in
	  nn4_ctfReconstructor

2006-12-12 15:23  barry

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, libpyEM/utils.pyste: [no log message]

2006-12-11 15:07  zweig

	* libEM/reconstructor.cpp: remove debug information

2006-12-11 14:34  zweig

	* libEM/reconstructor.cpp: using parameter mult to get multipler
	  for each projection for nnctf reconstructor

2006-12-07 12:54  zweig

	* libEM/analyzer.cpp: fix memory leak and save eigen values in
	  header

2006-12-06 15:31  gtang

	* libpyEM/libpyEMData2.cpp: fix the broken Python wrapping file.

2006-12-06 14:51  gtang

	* libEM/sparx/emdata_sparx.cpp: make the screen output to DEBUG
	  mode

2006-12-06 14:40  gtang

	* libpyEM/libpyGeometry2.cpp: fix the broken Python wrapping file.

2006-12-06 14:36  gtang

	* libpyEM/: libpyUtils2.cpp, libpyTypeConverter2.cpp,
	  libpyTransform2.cpp, libpyPointArray2.cpp: fix the broken Python
	  wrapping file.

2006-12-06 13:41  barry

	* libEM/sparx/util_sparx.cpp: [no log message]

2006-12-06 13:32  barry

	* libEM/sparx/util_sparx.cpp: [no log message]

2006-12-06 11:42  barry

	* libEM/sparx/util_sparx.h: [no log message]

2006-12-05 00:07  stevel

	* libpyEM/qtgui/emimagemx.py: New attribute display option in image
	  matrix display.

2006-12-04 15:35  zweig

	* libEM/analyzer.cpp: fix a bug in PCA which cause segfault in 3D
	  vol analyze

2006-12-01 19:29  zhuang

	* libpyEM/utils.pyste: [no log message]

2006-12-01 19:28  zhuang

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: update pw_extract

2006-12-01 14:54  zweig

	* libEM/sparx/util_sparx.cpp: fix a typo in the code

2006-12-01 11:14  zhuang

	* libpyEM/libpyUtils2.cpp: add new function

2006-12-01 10:45  zhuang

	* libpyEM/utils.pyste: exclude double precision related functions
	  from util_sparx

2006-12-01 10:38  zhuang

	* libEM/sparx/util_sparx.h: add pw_extract

2006-12-01 10:38  zhuang

	* libEM/sparx/util_sparx.cpp: add pw_extract functions

2006-11-27 01:57  stevel

	* libpyEM/qtgui/emimagemx.py: matrix inspector bugfix

2006-11-27 00:25  stevel

	* examples/transalignavg.py, libEM/aligner.cpp,
	  libpyEM/qtgui/emimagemx.py: Fixed memory leak in rotational
	  alignment

2006-11-19 17:59  gtang

	* libEM/CMakeLists.txt, libEM/SConscript,
	  libEM/sparx/fundamentals.h, libEM/sparx/tflm.cpp,
	  libpyEM/fundamentals.pyste, libpyEM/libpyFundamentals2.cpp:
	  remove tflm.cpp, which is not necessary as Zhong said, and this
	  file can not get compiled on Fedora Core 6(ld version 2.17).

2006-11-17 14:13  prb

	* libEM/emdata.cpp, libEM/transform.cpp,
	  libEM/sparx/emdata_sparx.cpp, libEM/sparx/util_sparx.cpp,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyGeometry2.cpp,
	  libpyEM/libpyPointArray2.cpp, libpyEM/libpyTransform2.cpp,
	  libpyEM/libpyTypeConverter2.cpp, libpyEM/qtgui/emimage2d.py:
	  small changes to some rotations call

2006-11-16 13:15  stevel

	* libpyEM/EMAN2.py: Image display fixes.

2006-11-16 10:42  zweig

	* libEM/: reconstructor.cpp, reconstructor.h: add
	  bootstrap_nnctfReconstructor, fix bootstrap_nnReconstructor

2006-11-15 13:39  zweig

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: accelarte
	  onelinenn_ctf by tabulating ctf

2006-11-15 13:38  zweig

	* libEM/sparx/util_sparx.cpp: fix a minor bug on Cs conversion

2006-11-15 13:38  zweig

	* libEM/: reconstructor.cpp, reconstructor.h: clear and add
	  weighting method to nn4_ctfReconsctructor

2006-11-15 00:10  stevel

	* libpyEM/qtgui/emimagemx.py, programs/e2display.py: Revamped image
	  matrix display.

2006-11-13 15:30  barry

	* libpyEM/libpyUtils2.cpp: [no log message]

2006-11-13 15:27  barry

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: [no log message]

2006-11-13 14:37  barry

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/emdata.pyste: [no log message]

2006-11-10 15:58  barry

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: [no log message]

2006-11-10 15:32  barry

	* libEM/sparx/: util_sparx.h, util_sparx.cpp: [no log message]

2006-11-10 12:28  stevel

	* examples/transalignavg.py, libEM/sparx/fourierfilter.cpp,
	  libpyEM/EMAN2.py, libpyEM/qtgui/emimagemx.py,
	  programs/e2display.py: Fixed memory leak in filter.

2006-11-08 17:27  gtang

	* doc/latex/CMakeLists.txt: fix broken latex make file

2006-11-08 16:33  gtang

	* CMakeLists.txt: make AUTODOC as advanced option.

2006-11-06 09:39  stevel

	* libEM/emdata_transform.cpp: vertical flip option in render_amp8

2006-11-05 02:58  stevel

	* libpyEM/qtgui/emimagemx.py, programs/e2skelpath.py: Skelpath now
	  produces list of points associated with each pair.

2006-11-03 15:08  stevel

	* programs/e2ssematch.py: now outputs helix ends as well

2006-11-01 16:26  stevel

	* libpyEM/qtgui/emimagemx.py, programs/e2boxer.py,
	  programs/e2foldfitter.py, programs/e2ssematch.py: Working on
	  e2boxer

2006-10-31 15:55  gtang

	* rt/imageio/basic.cpp, rt/imageio/imageio.cpp, utils/iminfo.cpp,
	  utils/proc2d.cpp, utils/speedtest.cpp: clean the unknown
	  charaters in copyright notice

2006-10-31 15:50  gtang

	* rt/emdata/: blankimg.cpp, ccf1.cpp, ccf2.cpp, emdata_api.cpp,
	  fft.cpp, fft_test.cpp, mem_test.cpp, projector_test.cpp,
	  rotate.cpp, rotate1.cpp, rotate_phi.cpp, rotate_translate.cpp,
	  testalign.cpp, testpolardata.cpp, testprocessor.cpp: clean the
	  unknown charaters in copyright notice

2006-10-31 15:43  gtang

	* plugins/: aligner_template.cpp, aligner_template.h,
	  averager_template.cpp, averager_template.h, cmp_template.cpp,
	  cmp_template.h, io_template.cpp, io_template.h,
	  processor_template.cpp, processor_template.h,
	  projector_template.cpp, projector_template.h,
	  reconstructor_template.cpp, reconstructor_template.h: clean the
	  unknown charaters in copyright notice

2006-10-31 15:39  gtang

	* libpyEM/: emdata_pickle.h, emdata_wrapitems.cpp,
	  emdata_wrapitems.h, pyexception.cpp, pyexception.h,
	  typeconverter.cpp, typeconverter.h, util_wrapitems.h: clean the
	  unknown charaters in copyright notice

2006-10-31 15:36  gtang

	* libpyEM/: sparx.cpp, sparx.h: clean the unknown charaters in
	  copyright notice

2006-10-31 15:29  gtang

	* libEM/sparx/: SparxIO.h, Tokenizer.cpp, Tokenizer.h,
	  analyzer_sparx.h, emarray.h, emconstants.h, emdata_sparx.cpp,
	  emdata_sparx.h, fourierfilter.cpp, fundamentals.cpp,
	  fundamentals.h, lapackblas.cpp, lapackblas.h, native_fft.cpp,
	  native_fft.h, normpadft.cpp, normpadft.h, pca.cpp, pca.h,
	  processor_sparx.h, rsconvolution.cpp, tflm.cpp, util_sparx.cpp,
	  util_sparx.h: clean the unknown charaters in copyright notice

2006-10-31 15:20  gtang

	* libEM/: aligner.cpp, aligner.h, all_imageio.h, amiraio.cpp,
	  amiraio.h, analyzer.cpp, analyzer.h, averager.cpp, averager.h,
	  byteorder.cpp, byteorder.h, cmp.cpp, cmp.h, ctf.cpp, ctf.h,
	  dm3io.cpp, dm3io.h, emcache.cpp, emcache.h, emdata.cpp, emdata.h,
	  emdata_core.cpp, emdata_core.h, emdata_io.cpp, emdata_io.h,
	  emdata_metadata.cpp, emdata_metadata.h, emdata_modular.cpp,
	  emdata_modular.h, emdata_transform.cpp, emdata_transform.h,
	  emfft.cpp, emfft.h, emimio.cpp, emimio.h, emio.cpp, emio.h,
	  emobject.cpp, emobject.h, emutil.cpp, emutil.h, exception.cpp,
	  exception.h, fitsio.cpp, fitsio.h, gatan2io.cpp, gatan2io.h,
	  geometry.cpp, geometry.h, hdfio.cpp, hdfio.h, hdfio2.cpp,
	  hdfio2.h, icosio.cpp, icosio.h, imageio.cpp, imageio.h,
	  imagicio.cpp, imagicio.h, interp.cpp, interp.h, jpegio.cpp,
	  jpegio.h, log.cpp, log.h, lstio.cpp, lstio.h, mrcio.cpp, mrcio.h,
	  pgmio.cpp, pgmio.h, pifio.cpp, pifio.h, pngio.cpp, pngio.h,
	  pointarray.cpp, pointarray.h, polardata.cpp, polardata.h,
	  portable_fileio.h, processor.cpp, processor.h, projector.cpp,
	  projector.h, quaternion.cpp, quaternion.h, reconstructor.cpp,
	  reconstructor.h, salio.cpp, salio.h, spiderio.cpp, spiderio.h,
	  sspiderio.cpp, sspiderio.h, testutil.cpp, testutil.h, tifio.cpp,
	  tifio.h, transform.cpp, transform.h, util.cpp, util.h,
	  v4l2io.cpp, v4l2io.h, vec3.h, vtkio.cpp, vtkio.h, xplorio.cpp,
	  xplorio.h, xydata.cpp, xydata.h, sparx/SparxIO.cpp: clean the
	  unknown charaters in copyright notice

2006-10-31 11:51  gtang

	* libEM/Assert.h: clean the unknown charaters in copyright notice

2006-10-31 11:43  gtang

	* libpyEM/: EMAN2.py, EMAN2_cppwrap.py, qtgui/emfximage.py,
	  qtgui/emimage.py, qtgui/emimage2d.py, qtgui/emimage3d.py,
	  qtgui/emimageutil.py, qtgui/pyshed.py, qtgui/valslider.py,
	  wxgui/wxemimage.py, wxgui/wxemimagecanvas.py,
	  wxgui/wxemimageframe.py: clean the unknown charaters in copyright
	  notice

2006-10-31 11:35  gtang

	* libpyEM/qtgui/emimagemx.py: clean the unknown charaters in
	  copyright notice

2006-10-30 02:32  stevel

	* programs/e2boxer.py: Boxer reads existing db.

2006-10-25 11:40  zweig

	* libEM/sparx/emdata_sparx.cpp: set b_factor to 0.0 for all cases
	  for now

2006-10-25 11:35  zweig

	* libEM/: reconstructor.cpp, reconstructor.h: add ctf function to
	  nn4Reconstructor and some minor modification to
	  nn4_ctfReconstructor

2006-10-25 11:35  zweig

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: change on
	  function onelinenn_ctf and onelinenn_ctf_applied: defocus now
	  read from the emdata not from argument, and an argument mult for
	  multiplicy

2006-10-24 11:11  gtang

	* doc/: CMakeLists.txt, modular_class_html/CMakeLists.txt,
	  modular_class_html/docgen.py, processor_html/CMakeLists.txt,
	  processor_html/docgen.py: auto doc generation for all modular
	  class

2006-10-23 16:21  zweig

	* libEM/: reconstructor.cpp, reconstructor.h: add new parameter
	  weight to bootstrap reconstrator, a new argument weighting to
	  nn4Reconstrator::setup()

2006-10-23 15:50  gtang

	* libEM/reconstructor.cpp: fix the warning, comparison between
	  signed and unsigned integer.

2006-10-23 14:29  gtang

	* libEM/: processor.h, processor.cpp: add processor 'basis.fft'

2006-10-23 14:28  gtang

	* rt/pyem/test_processor.py: add unit test for 'basis.fft',
	  'basis.wavelet' processor

2006-10-23 10:56  stevel

	* libEM/: fitsio.cpp, fitsio.h: oops forgot to add

2006-10-23 02:40  stevel

	* examples/transalignavg.py, libEM/CMakeLists.txt,
	  libEM/aligner.cpp, libEM/aligner.h, libEM/all_imageio.h,
	  libEM/emutil.cpp, libEM/emutil.h, programs/e2proc2d.py: Working
	  on problems with aligners.

2006-10-21 13:11  gtang

	* INSTALL: gsl version change to 1.6+ because of the wavelet
	  support.

2006-10-21 09:44  gtang

	* doc/doxygen/makedoc.sh: minor fix

2006-10-19 09:59  zweig

	* libEM/reconstructor.cpp: add weight estimation for
	  nn4Reconstructor

2006-10-19 09:58  zweig

	* libEM/reconstructor.h: remove member variable m_wghts

2006-10-19 09:52  zweig

	* libEM/reconstructor.h: add new parameter weighting to
	  nn4Reconstructor

2006-10-19 02:42  stevel

	* libpyEM/EMAN2.py: Better 'plot' functionality

2006-10-18 02:06  stevel

	* libEM/processor.cpp, libEM/processor.h, libpyEM/EMAN2.py: plot
	  command in EMAN2.py

2006-10-04 15:08  mhhohn

	* libpyEM/CMakeLists.txt:     On linux, do not use
	  ${PYTHON_LIBRARY} in LINK_LIBRARIES(...).
	      Fixes linking error.

2006-10-04 10:55  zweig

	* libEM/: processor.cpp, processor.h: update on gauss model
	  generator

2006-10-04 10:39  gtang

	* INSTALL, README: doc update

2006-10-04 10:00  gtang

	* utils/docgen.py: docgen.py moved to doc/processor_html. directory

2006-10-04 09:54  gtang

	* TODO: update

2006-10-03 18:17  gtang

	* doc/latex/CMakeLists.txt: [no log message]

2006-10-03 17:56  gtang

	* doc/CMakeLists.txt, doc/Doxyfile, doc/EMAN2.dvi, doc/EMAN2.pdf,
	  doc/EMAN2.ps, doc/processor_groups.html, doc/processors.html,
	  doc/doxygen/CMakeLists.txt, doc/doxygen/Doxyfile,
	  doc/doxygen/makedoc.sh, doc/latex/CMakeLists.txt,
	  doc/processor_html/CMakeLists.txt, doc/processor_html/docgen.py,
	  CMakeLists.txt, INSTALL, makedoc.sh: involve autogenerated
	  doxygen, latex etc. into CMake system, set an option to control
	  document generation.

2006-10-02 16:00  gtang

	* rt/pyem/test_emdata.py: unit test update

2006-10-02 15:55  gtang

	* rt/pyem/test_typeconverter.py: unit test update

2006-10-02 14:26  gtang

	* rt/demo/test_image.py: script to create test images for Michael
	  Hohn

2006-10-02 06:04  prb

	* rt/pyem/test_transform.py: fixed!

2006-09-30 18:16  gtang

	* doc/developer-guide.html: doc update

2006-09-30 18:11  gtang

	* doc/develop_system_setup.html: doc update

2006-09-30 17:59  gtang

	* doc/cvshowto.html: doc update

2006-09-30 17:27  gtang

	* doc/coding_style.html: doc update

2006-09-29 11:26  gtang

	* doc/latex/Makefile: copy Deepy's original Makefile back, will
	  create a CMakeList.txt file to include this into cmake system in
	  the future.

2006-09-29 10:38  gtang

	* libEM/sparx/emdata_sparx.h: parameter fix

2006-09-29 02:42  prb

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp: added transform and rotate methods
	  to operate on Vec3f's

2006-09-28 15:25  gtang

	* libEM/: hdfio2.cpp, reconstructor.cpp: fix unnecessary warning
	  message

2006-09-27 15:45  zweig

	* libEM/: reconstructor.cpp, reconstructor.h: add new bootstrap_nn
	  reconstructor, update nn4_reconstructor

2006-09-27 15:44  zweig

	* libEM/sparx/emdata_sparx.cpp: remove debug code

2006-09-27 15:10  zweig

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: add new memory
	  function onelinenn_mult and remove the default argument mult of
	  onelinenn for efficiency reason

2006-09-27 14:03  ppenczek

	* libEM/sparx/emdata_sparx.cpp: bug in average_c corrected

2006-09-27 02:44  prb

	* libEM/emdata.cpp, libEM/transform.cpp, libEM/transform.h,
	  libEM/vec3.h, libEM/sparx/util_sparx.h,
	  libpyEM/libpyTransform2.cpp: made some changes to the transform
	  class. The Transform3D matrix is still stored as a 4 by 4, but
	  you can recover the post translation, rotation and pretranslation
	  independently (The first three elements of the last row store the
	  post trans:

	  Also Trans_final = Trans_post + R* Trans_Pre	is a key relation
	  that is used)

2006-09-25 17:14  gtang

	* libEM/Assert.h, libEM/aligner.cpp, libEM/aligner.h,
	  libEM/all_imageio.h, libEM/amiraio.cpp, libEM/amiraio.h,
	  libEM/analyzer.cpp, libEM/analyzer.h, libEM/averager.cpp,
	  libEM/averager.h, libEM/byteorder.cpp, libEM/byteorder.h,
	  libEM/cmp.cpp, libEM/cmp.h, libEM/ctf.cpp, libEM/ctf.h,
	  libEM/dm3io.cpp, libEM/dm3io.h, libEM/emcache.cpp,
	  libEM/emcache.h, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emdata_core.cpp, libEM/emdata_core.h, libEM/emdata_io.cpp,
	  libEM/emdata_io.h, libEM/emdata_metadata.cpp,
	  libEM/emdata_metadata.h, libEM/emdata_modular.cpp,
	  libEM/emdata_modular.h, libEM/emdata_transform.cpp,
	  libEM/emdata_transform.h, libEM/emfft.cpp, libEM/emfft.h,
	  libEM/emimio.cpp, libEM/emimio.h, libEM/emio.cpp, libEM/emio.h,
	  libEM/emobject.cpp, libEM/emobject.h, libEM/emutil.cpp,
	  libEM/emutil.h, libEM/exception.cpp, libEM/exception.h,
	  libEM/gatan2io.cpp, libEM/gatan2io.h, libEM/geometry.cpp,
	  libEM/geometry.h, libEM/hdfio.cpp, libEM/hdfio.h,
	  libEM/hdfio2.cpp, libEM/hdfio2.h, libEM/icosio.cpp,
	  libEM/icosio.h, libEM/imageio.cpp, libEM/imageio.h,
	  libEM/imagicio.cpp, libEM/imagicio.h, libEM/interp.cpp,
	  libEM/interp.h, libEM/jpegio.cpp, libEM/jpegio.h, libEM/log.cpp,
	  libEM/log.h, libEM/lstio.cpp, libEM/lstio.h, libEM/mrcio.cpp,
	  libEM/mrcio.h, libEM/pgmio.cpp, libEM/pgmio.h, libEM/pifio.cpp,
	  libEM/pifio.h, libEM/pngio.cpp, libEM/pngio.h,
	  libEM/pointarray.cpp, libEM/pointarray.h, libEM/polardata.cpp,
	  libEM/polardata.h, libEM/portable_fileio.h, libEM/processor.cpp,
	  libEM/processor.h, libEM/projector.cpp, libEM/projector.h,
	  libEM/quaternion.cpp, libEM/quaternion.h,
	  libEM/reconstructor.cpp, libEM/reconstructor.h, libEM/salio.cpp,
	  libEM/salio.h, libEM/spiderio.cpp, libEM/spiderio.h,
	  libEM/sspiderio.cpp, libEM/sspiderio.h, libEM/testutil.cpp,
	  libEM/testutil.h, libEM/tifio.cpp, libEM/tifio.h,
	  libEM/transform.cpp, libEM/transform.h, libEM/util.cpp,
	  libEM/util.h, libEM/v4l2io.cpp, libEM/v4l2io.h, libEM/vec3.h,
	  libEM/vtkio.cpp, libEM/vtkio.h, libEM/xplorio.cpp,
	  libEM/xplorio.h, libEM/xydata.cpp, libEM/xydata.h,
	  libEM/sparx/SparxIO.cpp, libEM/sparx/analyzer_sparx.h,
	  libEM/sparx/fundamentals.cpp, libEM/sparx/normpadft.cpp,
	  libEM/sparx/SparxIO.h, libEM/sparx/Tokenizer.cpp,
	  libEM/sparx/Tokenizer.h, libEM/sparx/emarray.h,
	  libEM/sparx/emconstants.h, libEM/sparx/emdata_sparx.cpp,
	  libEM/sparx/emdata_sparx.h, libEM/sparx/fourierfilter.cpp,
	  libEM/sparx/fundamentals.h, libEM/sparx/lapackblas.cpp,
	  libEM/sparx/lapackblas.h, libEM/sparx/native_fft.cpp,
	  libEM/sparx/native_fft.h, libEM/sparx/normpadft.h,
	  libEM/sparx/pca.cpp, libEM/sparx/pca.h,
	  libEM/sparx/processor_sparx.h, libEM/sparx/rsconvolution.cpp,
	  libEM/sparx/tflm.cpp, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h, libpyEM/emdata_wrapitems.cpp,
	  libpyEM/emdata_wrapitems.h, libpyEM/pyexception.cpp,
	  libpyEM/pyexception.h, libpyEM/sparx.cpp, libpyEM/sparx.h,
	  libpyEM/typeconverter.cpp, libpyEM/typeconverter.h,
	  libpyEM/util_wrapitems.h, plugins/aligner_template.cpp,
	  plugins/aligner_template.h, plugins/averager_template.cpp,
	  plugins/averager_template.h, plugins/cmp_template.cpp,
	  plugins/cmp_template.h, plugins/io_template.cpp,
	  plugins/io_template.h, plugins/processor_template.cpp,
	  plugins/processor_template.h, plugins/projector_template.cpp,
	  plugins/projector_template.h, plugins/reconstructor_template.cpp,
	  plugins/reconstructor_template.h, rt/emdata/blankimg.cpp,
	  rt/emdata/ccf1.cpp, rt/emdata/ccf2.cpp, rt/emdata/emdata_api.cpp,
	  rt/emdata/fft.cpp, rt/emdata/fft_test.cpp,
	  rt/emdata/mem_test.cpp, rt/emdata/projector_test.cpp,
	  rt/emdata/rotate.cpp, rt/emdata/rotate1.cpp,
	  rt/emdata/rotate_phi.cpp, rt/emdata/rotate_translate.cpp,
	  rt/emdata/testalign.cpp, rt/emdata/testpolardata.cpp,
	  rt/emdata/testprocessor.cpp, rt/imageio/basic.cpp,
	  rt/imageio/imageio.cpp, utils/iminfo.cpp, utils/proc2d.cpp,
	  utils/speedtest.cpp: remove >127 ascii characters in release note

2006-09-25 16:14  ppenczek

	* libEM/reconstructor.cpp: [no log message]

2006-09-25 13:18  stevel

	* doc/latex/Makefile, programs/e2foldfitter.py: Work on foldfitter

2006-09-21 00:42  barry

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: [no log message]

2006-09-20 15:42  prb

	* libEM/sparx/emdata_sparx.cpp:  changed symvol to work properly.
	  Uses rot_scale_trans	(quadratic interpolation).

2006-09-19 17:57  mhhohn

	* CMakeLists.txt:     Check the most generic boost library name
	  first (used by cctbx).

2006-09-19 17:18  zweig

	* libEM/reconstructor.cpp: change parameter name from shift_x to
	  x_shift for consistancy

2006-09-19 14:24  stevel

	* doc/latex/Makefile, programs/e2ssematch.py: ssematch runs again

2006-09-18 15:37  zweig

	* libEM/: transform.cpp, transform.h: add copy constructor to class
	  Transform3D

2006-09-18 15:36  zweig

	* libEM/: emobject.h, emobject.cpp: add new emobject type INTARRAY

2006-09-18 15:35  zweig

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: add a new
	  argument mult to nn for multiplier

2006-09-18 15:15  zweig

	* libEM/sparx/processor_sparx.h: change parameter name from shift_x
	  to x_shift for unification

2006-09-18 15:13  zweig

	* libEM/sparx/util_sparx.cpp: add x and y shift to BPCQ for wbp

2006-09-18 11:29  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2006-09-18 10:01  ppenczek

	* libEM/sparx/util_sparx.cpp:  editing mistakes corrected

2006-09-15 23:27  stevel

	* programs/e2ssematch.py: More ssematch work

2006-09-14 21:38  stevel

	* programs/e2ssematch.py: Work on ssematch

2006-09-14 18:47  cyang

	* libEM/analyzer.cpp:
	  fixed a typo in scratchfile

2006-09-14 16:37  gtang

	* libpyEM/libpyUtils2.cpp: update with create_boost_python

2006-09-14 16:36  gtang

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: remove the inline
	  from Util::bilinear(), otherwise it fails to import libpyUtils2

2006-09-14 11:20  gtang

	* libEM/sparx/analyzer_sparx.h: leave space to add comment for
	  analyzers' parameters.

2006-09-14 11:16  gtang

	* libpyEM/analyzer.pyste, libpyEM/libpyAnalyzer2.cpp,
	  libpyEM/EMAN2.py, libEM/analyzer.cpp, libEM/analyzer.h: add
	  dump_analyzers() and dump_analyzers_list() function

2006-09-13 19:52  gtang

	* libEM/sparx/analyzer_sparx.h: fix 'pca_large' Analyzer's NEW()
	  function.

2006-09-13 19:36  cyang

	* libEM/sparx/analyzer_sparx.h:
	  Added the Lanczos version of pca

2006-09-13 19:35  cyang

	* libEM/analyzer.cpp:
	  added the Lanczos version of PCA

2006-09-13 15:24  gtang

	* libEM/: hdfio.cpp, hdfio2.cpp: fix the bug EMAN2 can not read
	  old-style hdf file created by EMAN1.

2006-09-11 19:09  cyang

	* libEM/analyzer.cpp:
	  added set_params(), insert_image and analyzer()

2006-09-11 19:08  cyang

	* libEM/sparx/analyzer_sparx.h:
	  commented out set_params() and insert_image(), and placed them in
	  analyzer.cpp instead.

2006-09-11 17:22  barry

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: util_sparx.cpp

2006-09-10 16:02  gtang

	* libEM/analyzer.cpp, libEM/analyzer.h,
	  libEM/sparx/analyzer_sparx.h, libpyEM/libpyAnalyzer2.cpp,
	  libpyEM/libpyEMData2.cpp, libEM/emdata_modular.cpp,
	  libEM/emdata_modular.h: modify Analyzer interface

2006-09-10 14:59  gtang

	* libEM/reconstructor.h: fix incorrect comment

2006-09-09 14:51  gtang

	* rt/pyem/test_imageio.py: unit test for hdf file attibute
	  deletion.

2006-09-09 14:28  gtang

	* libEM/hdfio2.cpp: minor fix for image count update correctly.

2006-09-09 14:20  gtang

	* libEM/: CMakeLists.txt, sparx/periodogram.cpp: remove
	  periodogram.cpp

2006-09-09 12:44  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2006-09-09 08:33  ppenczek

	* libEM/sparx/: fundamentals.cpp, periodogram.cpp, util_sparx.cpp:
	  [no log message]

2006-09-09 08:04  ppenczek

	* libEM/sparx/: SparxIO.cpp, SparxIO.h, Tokenizer.cpp, Tokenizer.h,
	  analyzer_sparx.h, emarray.h, emconstants.h, emdata_sparx.cpp,
	  emdata_sparx.h, fourierfilter.cpp, fundamentals.cpp,
	  fundamentals.h, lapackblas.cpp, lapackblas.h, native_fft.cpp,
	  native_fft.h, normpadft.cpp, normpadft.h, periodogram.cpp,
	  processor_sparx.h, rsconvolution.cpp, tflm.cpp, util_sparx.cpp,
	  util_sparx.h: [no log message]

2006-09-08 15:27  gtang

	* libEM/: analyzer.cpp, analyzer.h: [no log message]

2006-09-08 15:22  zweig

	* libEM/sparx/fourierfilter.cpp: fix a problem: lambda should be
	  get from parameter lambda instead of voltage

2006-09-08 14:53  gtang

	* libEM/: Assert.h, aligner.cpp, aligner.h, all_imageio.h,
	  amiraio.cpp, amiraio.h, analyzer.cpp, analyzer.h, averager.cpp,
	  averager.h, byteorder.cpp, byteorder.h, cmp.cpp, cmp.h, ctf.cpp,
	  ctf.h, dm3io.cpp, dm3io.h, emcache.cpp, emcache.h, emdata.cpp,
	  emdata.h, emdata_core.cpp, emdata_core.h, emdata_io.cpp,
	  emdata_io.h, emdata_metadata.cpp, emdata_metadata.h,
	  emdata_modular.cpp, emdata_modular.h, emdata_transform.cpp,
	  emdata_transform.h, emfft.cpp, emfft.h, emimio.cpp, emimio.h,
	  emio.cpp, emio.h, emobject.cpp, emobject.h, emutil.cpp, emutil.h,
	  exception.cpp, exception.h, gatan2io.cpp, gatan2io.h,
	  geometry.cpp, geometry.h, hdfio.cpp, hdfio.h, hdfio2.cpp,
	  hdfio2.h, icosio.cpp, icosio.h, imageio.cpp, imageio.h,
	  imagicio.cpp, imagicio.h, interp.cpp, interp.h, jpegio.cpp,
	  jpegio.h, log.cpp, log.h, lstio.cpp, lstio.h, mrcio.cpp, mrcio.h,
	  pgmio.cpp, pgmio.h, pifio.cpp, pifio.h, pngio.cpp, pngio.h,
	  pointarray.cpp, pointarray.h, polardata.cpp, polardata.h,
	  portable_fileio.h, processor.cpp, processor.h, projector.cpp,
	  projector.h, quaternion.cpp, quaternion.h, reconstructor.cpp,
	  reconstructor.h, salio.cpp, salio.h, spiderio.cpp, spiderio.h,
	  sspiderio.cpp, sspiderio.h, testutil.cpp, testutil.h, tifio.cpp,
	  tifio.h, transform.cpp, transform.h, util.cpp, util.h,
	  v4l2io.cpp, v4l2io.h, vec3.h, vtkio.cpp, vtkio.h, xplorio.cpp,
	  xplorio.h, xydata.cpp, xydata.h, sparx/SparxIO.cpp,
	  sparx/analyzer_sparx.h, sparx/fundamentals.cpp,
	  sparx/normpadft.cpp, sparx/SparxIO.h, sparx/Tokenizer.cpp,
	  sparx/Tokenizer.h, sparx/emarray.h, sparx/emconstants.h,
	  sparx/emdata_sparx.cpp, sparx/emdata_sparx.h,
	  sparx/fourierfilter.cpp, sparx/fundamentals.h,
	  sparx/lapackblas.cpp, sparx/lapackblas.h, sparx/native_fft.cpp,
	  sparx/native_fft.h, sparx/normpadft.h, sparx/pca.cpp,
	  sparx/pca.h, sparx/periodogram.cpp, sparx/processor_sparx.h,
	  sparx/rsconvolution.cpp, sparx/tflm.cpp, sparx/util_sparx.cpp,
	  sparx/util_sparx.h: copyright notice

2006-09-08 14:52  stevel

	* programs/: e2skelpath.py, e2ssematch.py: skelpath working well.
	  ssematch needs more work still

2006-09-08 14:44  gtang

	* examples/: comparepairs.py, e2aligntest.py, makebigfromseq.py,
	  sortsimilar.py, telescope.py, transalignavg.py: copyright notice

2006-09-08 14:40  gtang

	* libtbx_refresh.py, test-imports.py, utils/docgen.py,
	  utils/iminfo.cpp, utils/proc2d.cpp, utils/speedtest.cpp,
	  rt/pyem/rt.py, rt/pyem/test_aligner.py, rt/pyem/test_averager.py,
	  rt/pyem/test_cmp.py, rt/pyem/test_emdata.py,
	  rt/pyem/test_imageio.py, rt/pyem/test_misc.py,
	  rt/pyem/test_processor.py, rt/pyem/test_transform.py,
	  rt/pyem/test_typeconverter.py, rt/pyem/test_utils.py,
	  rt/pyem/test_vec.py, rt/pyem/testlib.py, rt/demo/align.py,
	  rt/demo/averager.py, rt/demo/cmp.py, rt/demo/processor1.py,
	  rt/demo/processor2.py, rt/demo/processor3.py, rt/demo/project.py,
	  rt/demo/reconstruction.py, rt/demo/reconstructor.py,
	  rt/demo/tomrc.py, rt/emdata/blankimg.cpp, rt/emdata/ccf1.cpp,
	  rt/emdata/ccf2.cpp, rt/emdata/emdata_api.cpp,
	  rt/emdata/exception1.py, rt/emdata/fft.cpp,
	  rt/emdata/fft_test.cpp, rt/emdata/mem_test.cpp,
	  rt/emdata/projector_test.cpp, rt/emdata/rotate.cpp,
	  rt/emdata/rotate1.cpp, rt/emdata/rotate_phi.cpp,
	  rt/emdata/rotate_translate.cpp, rt/emdata/testalign.cpp,
	  rt/emdata/testpolardata.cpp, rt/emdata/testprocessor.cpp,
	  rt/imageio/basic.cpp, rt/imageio/imageio.cpp, pyemtbx/box.py,
	  pyemtbx/exceptions.py, pyemtbx/files.py, pyemtbx/imagetypes.py,
	  pyemtbx/options.py, programs/e2.py, programs/e2align3d.py,
	  programs/e2boxer.py, programs/e2classifykmeans.py,
	  programs/e2cmmtomrc.py, programs/e2dumplog.py,
	  programs/e2findsubunit.py, programs/e2foldfitter.py,
	  programs/e2make3d.py, programs/e2msa.py, programs/e2pdb2mrc.py,
	  programs/e2proc2d.py, programs/e2proc3d.py,
	  programs/e2project3d.py, programs/e2scannereval.py,
	  programs/e2skelpath.py, programs/e2ssematch.py,
	  programs/e2startcsym.py, programs/e2symbest.py,
	  programs/e2tilefile.py, programs/e2tomogram.py, programs/e2wx.py,
	  plugins/aligner_template.cpp, plugins/aligner_template.h,
	  plugins/averager_template.cpp, plugins/averager_template.h,
	  plugins/cmp_template.cpp, plugins/cmp_template.h,
	  plugins/io_template.cpp, plugins/io_template.h,
	  plugins/processor_template.cpp, plugins/processor_template.h,
	  plugins/projector_template.cpp, plugins/projector_template.h,
	  plugins/reconstructor_template.cpp,
	  plugins/reconstructor_template.h, libpyEM/EMAN2.py,
	  libpyEM/EMAN2_cppwrap.py, libpyEM/qtgui/emfximage.py,
	  libpyEM/qtgui/emimage.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/emimageutil.py, libpyEM/qtgui/pyshed.py,
	  libpyEM/qtgui/valslider.py, libpyEM/wxgui/wxemimage.py,
	  libpyEM/wxgui/wxemimagecanvas.py,
	  libpyEM/wxgui/wxemimageframe.py: copyright notice

2006-09-08 11:40  zhuang

	* libEM/sparx/fourierfilter.cpp: update code

2006-09-08 10:57  gtang

	* libEM/emdata.h: copyright notice

2006-09-08 01:49  stevel

	* programs/: e2skelpath.py, e2ssematch.py: skelpath is working !

2006-09-07 21:55  stevel

	* programs/e2skelpath.py: skelpath still not perfect..

2006-09-07 18:15  gtang

	* libEM/: hdfio2.cpp, hdfio2.h: fix the attribute deletion bug.

2006-09-07 11:00  stevel

	* programs/e2skelpath.py: Working on autotracing still.

2006-09-06 21:21  stevel

	* doc/latex/Makefile, programs/e2skelpath.py,
	  programs/e2ssematch.py: working on auto path tracer

2006-09-06 11:34  ppenczek

	* CMakeLists.txt:  default FFTW3=ON

2006-09-05 17:32  ppenczek

	* libEM/sparx/emdata_sparx.cpp: [no log message]

2006-09-05 14:48  ppenczek

	* libpyEM/libpyUtils2.cpp: [no log message]

2006-09-05 14:12  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, util_sparx.cpp, util_sparx.h: [no
	  log message]

2006-09-05 13:53  ppenczek

	* libpyEM/libpyUtils2.cpp: [no log message]

2006-09-05 10:47  stevel

	* libpyEM/qtgui/emimagemx.py, programs/e2boxer.py: skeletonization
	  path tracer working

2006-09-02 21:13  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, util_sparx.cpp: [no log message]

2006-09-02 17:11  ppenczek

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: [no log message]

2006-09-02 16:01  ppenczek

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: [no log message]

2006-09-02 14:38  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, util_sparx.cpp, util_sparx.h: [no
	  log message]

2006-09-01 22:49  stevel

	* doc/latex/Makefile, programs/e2skelpath.py: Chain tracing in
	  skelpath working (?)

2006-09-01 21:24  stevel

	* programs/: e2skelpath.py, e2ssematch.py: Working on backbone
	  tracing.

2006-09-01 19:40  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2006-09-01 17:51  ppenczek

	* libEM/sparx/util_sparx.cpp: 60000 in the code

2006-09-01 12:29  ppenczek

	* libEM/sparx/util_sparx.h: [no log message]

2006-08-31 22:01  stevel

	* libpyEM/qtgui/emimagemx.py, programs/e2boxer.py: Work on boxer

2006-08-30 17:58  cyang

	* libEM/sparx/pca.cpp:
	  fixed a couple bugs in Lanczos_ooc(). The out-of-core version of
	  dopca() seems to be working now.

2006-08-30 16:01  gtang

	* libEM/sparx/analyzer_sparx.h: [no log message]

2006-08-30 15:13  gtang

	* libEM/analyzer.cpp: add namespace EMAN to resolve namespace and
	  template specialization problem for gcc4.1.

2006-08-30 15:05  gtang

	* rt/pyem/test_processor.py: minor fix

2006-08-30 14:34  cyang

	* libEM/sparx/: pca.cpp, pca.h:
	  finished PCA OOC, more tests need to be done on this version

2006-08-30 14:06  gtang

	* libEM/sparx/analyzer_sparx.h: minor fix

2006-08-30 14:02  gtang

	* libEM/sparx/analyzer_sparx.h: fix for compilation error

2006-08-30 10:28  gtang

	* libEM/: hdfio2.cpp, processor.h: minor change

2006-08-30 02:21  stevel

	* programs/e2boxer.py: More boxer improvements.

2006-08-29 21:16  stevel

	* doc/latex/Makefile, libpyEM/qtgui/emimagemx.py, programs/e2.py,
	  programs/e2boxer.py, programs/e2ssematch.py: Gui work

2006-08-29 12:36  cyang

	* libEM/sparx/: pca.cpp, pca.h:
	  Modified Lanczos which now calls LAPACK tridiagonal eigensolver
	  for the projected problem.

2006-08-29 12:35  cyang

	* libEM/sparx/: lapackblas.cpp, lapackblas.h:

	  Added routines for the divide-and-conquer tridigonal eigensolver

2006-08-29 11:52  gtang

	* doc/WindowsVisualStudioDotNet2003CompilationNotes.txt: [no log
	  message]

2006-08-29 02:30  stevel

	* programs/e2ssematch.py: Added version of program that identifies
	  helices based on secondary structure prediction.

2006-08-28 18:59  barry

	* libpyEM/libpyUtils2.cpp: [no log message]

2006-08-28 18:56  barry

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: [no log message]

2006-08-28 18:51  barry

	* libEM/sparx/emdata_sparx.cpp: [no log message]

2006-08-28 02:06  stevel

	* libpyEM/qtgui/emimage.py, libpyEM/qtgui/emimage2d.py,
	  libpyEM/qtgui/emimagemx.py, programs/e2boxer.py: Work on boxer
	  GUI module.

2006-08-27 16:58  gtang

	* libEM/hdfio.cpp: for Visual Studio .NET compilation

2006-08-27 13:53  gtang

	* libEM/CMakeLists.txt: for Visual Studio .NET compilation

2006-08-26 11:52  gtang

	* libEM/processor.cpp: Fix the Visual Studio .NET compilation error

2006-08-23 18:28  gtang

	* libpyEM/: libpyUtils2.cpp, utils.pyste: exclude
	  Util::merge_peaks(), which cause trouble to import libpyUtils

2006-08-23 17:14  gtang

	* libpyEM/: libpyAligner2.cpp, libpyEMData2.cpp,
	  libpyTransform2.cpp, libpyTypeConverter2.cpp, libpyUtils2.cpp:
	  run create_boost_python, check in the changes

2006-08-23 17:12  gtang

	* libpyEM/Makefile.pyste, libpyEM/analyzer.pyste,
	  libpyEM/libpyAnalyzer2.cpp, libpyEM/SConscript, test-imports.py:
	  Add new modular class Analyzer

2006-08-23 17:09  gtang

	* libEM/CMakeLists.txt, libEM/emdata_modular.cpp,
	  libEM/emdata_modular.h, libEM/emobject.h, libpyEM/CMakeLists.txt,
	  libpyEM/EMAN2_cppwrap.py: Add new modular class Analyzer

2006-08-23 17:05  gtang

	* libEM/: sparx/analyzer_sparx.h, analyzer.cpp, analyzer.h: Add new
	  modular class Analyzer

2006-08-23 14:35  cyang

	* libEM/sparx/pca.cpp:

	  Added a vanilla version of Lanczos

2006-08-23 02:15  stevel

	* doc/latex/Makefile, libpyEM/qtgui/pyshed.py, programs/e2boxer.py:
	  More gui work

2006-08-22 22:32  stevel

	* libpyEM/qtgui/: emimage.py, pyshed.py: qt widget work

2006-08-22 17:56  cyang

	* libEM/sparx/: pca.cpp, pca.h:

	  put dopca under PCA class

2006-08-22 16:44  cyang

	* libEM/sparx/: pca.cpp, pca.h:
	  added another parameter minor changes to dopca to allow it to
	  return a subset of singular vectors

2006-08-22 14:12  stevel

	* libpyEM/CMakeLists.txt, libpyEM/qtgui/emimage.py,
	  libpyEM/qtgui/emimage3d.py, libpyEM/qtgui/pyshed.py,
	  programs/e2.py: e2 working somewhat again now.

2006-08-22 09:23  stevel

	* libpyEM/qtgui/emimage.py, programs/e2boxer.py: Boxer work.

2006-08-21 02:31  stevel

	* libpyEM/qtgui/emimage2d.py, programs/e2boxer.py: More work on QT
	  widgets, working on GUI component of e2bxoer.py

2006-08-20 03:04  stevel

	* libpyEM/qtgui/emimage2d.py, libpyEM/qtgui/emimagemx.py,
	  libpyEM/qtgui/pyshed.py, programs/e2.py: More improvements to GUI
	  widgets

2006-08-18 19:59  stevel

	* doc/latex/Makefile, libpyEM/qtgui/emimagemx.py, programs/e2.py:
	  Working on qt gui

2006-08-18 15:31  gtang

	* libEM/amiraio.cpp: get rid of uninitialized variable warning
	  message

2006-08-18 14:49  gtang

	* libEM/: tifio.cpp, tifio.h: tiff writing, not done yet

2006-08-18 12:41  stevel

	* programs/e2.py: New e2 using qt

2006-08-18 11:48  stevel

	* libpyEM/CMakeLists.txt: Minor bugfix

2006-08-18 01:33  stevel

	* libpyEM/qtgui/: emimage2d.py, pyshed.py: New e2.py almost there
	  now...

2006-08-17 21:34  stevel

	* libpyEM/: CMakeLists.txt, qtgui/pyshed.py: Fix installer problem

2006-08-17 21:22  stevel

	* libpyEM/wxgui/: ValSlider.py, __init__.py, emimage.py,
	  emimagecanvas.py, emimageframe.py, imagecontrol.py,
	  wxValSlider.py, wxemimage.py, wxemimagecanvas.py,
	  wxemimageframe.py, wximagecontrol.py: renaming files for wx

2006-08-17 20:26  stevel

	* libpyEM/qtgui/pyshed.py: Working on qt shell.

2006-08-17 10:03  stevel

	* libpyEM/qtgui/pyshed.py: Working on new qt interactive widget

2006-08-17 09:41  stevel

	* doc/latex/Makefile, libEM/emdata.cpp, libEM/processor.cpp,
	  libEM/processor.h, libpyEM/CMakeLists.txt,
	  libpyEM/qtgui/emimage2d.py, programs/e2wx.py: Beginning work on
	  QT shell, since ipython doesn't deal with QT4 yet, and lacks
	  certain useful features

2006-08-16 16:38  stevel

	* libpyEM/qtgui/emimage2d.py: All 4 shapes work in emimage2d

2006-08-15 01:03  stevel

	* programs/: e2.py, e2wx.py: Rename e2.py to e2wx.py, now a legacy
	  program. New e2.py will be QT based.

2006-08-14 10:51  stevel

	* libpyEM/qtgui/emimageutil.py: oops

2006-08-14 02:41  stevel

	* libpyEM/: EMAN2.py, qtgui/emfximage.py, qtgui/emimage.py,
	  qtgui/emimage2d.py, qtgui/emimagemx.py: GUI work. Mouse events in
	  fximage sample. Shapes in emimage2d.

2006-08-10 20:58  stevel

	* libpyEM/qtgui/emimage.py: Working on EMImage

2006-08-10 15:46  gtang

	* TODO: [no log message]

2006-08-10 10:47  gtang

	* libEM/: spiderio.cpp, spiderio.h: Fix the bug in stacked spider
	  image writing

2006-08-10 09:45  stevel

	* libpyEM/qtgui/: emfximage.py, emimage.py: More work on qt objects

2006-08-08 12:57  stevel

	* libpyEM/qtgui/emfximage.py: FXimage working. Demo only.

2006-08-08 10:09  stevel

	* libpyEM/qtgui/emfximage.py: Working on new OpenGL image widget
	  with special effects.

2006-08-07 03:02  stevel

	* libpyEM/qtgui/emimage.py: Matrix view working properly in emimage

2006-08-04 22:05  stevel

	* INSTALL, libEM/aligner.cpp, libpyEM/qtgui/emimage.py,
	  programs/e2scannereval.py: Work on qt widgets

2006-08-04 12:30  cyang

	* libEM/sparx/: lapackblas.cpp, lapackblas.h:

	  fixed the prototype for s_copy

2006-08-03 14:08  gtang

	* libEM/emdata.cpp: minor fix in DEBUG

2006-08-01 13:34  cyang

	* libEM/sparx/lapackblas.h:
	  change the prototype for s_copy to be consistent with declaration
	  in lapackblas.cpp

2006-07-31 00:46  stevel

	* doc/latex/Makefile, libEM/emdata_transform.cpp, libEM/hdfio2.cpp,
	  libpyEM/qtgui/emimage.py: emimage work

2006-07-29 02:46  stevel

	* libEM/emdata.cpp, programs/e2align3d.py: e2align3d almost working
	  again (if not well). 'rotate' bugfix

2006-07-28 10:18  gtang

	* libEM/: emdata_metadata.h, emutil.h: comment for parameter

2006-07-27 01:39  stevel

	* libpyEM/qtgui/emimage.py: Work on QT image browser.

2006-07-26 10:10  gtang

	* libEM/: imageio.cpp, emutil.cpp: made changes for compiling EMAN2
	  on Windows Visual Studio .NET

2006-07-26 10:06  gtang

	* libEM/: imagicio.cpp, pgmio.cpp, sparx/emdata_sparx.cpp,
	  util.cpp: made changes for compiling EMAN2 on Windows Visual
	  Studio .NET

2006-07-26 10:03  gtang

	* libEM/: sparx/normpadft.cpp, sparx/util_sparx.cpp,
	  sparx/util_sparx.h, emutil.h: made changes for compiling EMAN2 on
	  Windows Visual Studio .NET

2006-07-25 11:38  gtang

	* libEM/sparx/util_sparx.cpp: log2 is not for compile on Visual
	  Studio .Net

2006-07-25 02:16  stevel

	* examples/e2aligntest.py, libpyEM/qtgui/emimage.py,
	  programs/e2align3d.py, programs/e2aligntest.py,
	  programs/e2ctfplot.py, programs/e2findsubunit.py: Working on GUI.
	  Removed/moved some obsolete programs.

2006-07-24 23:51  stevel

	* doc/latex/Makefile, libEM/hdfio2.cpp, libpyEM/CMakeLists.txt,
	  libpyEM/qtgui/emimage.py, programs/e2scannereval.py: Makefile fix
	  for directory name change. Note that e2.py won't work until I
	  finish adjusting it to use QT.

2006-07-24 17:26  gtang

	* libEM/processor.h: minor fix

2006-07-24 14:14  stevel

	* libpyEM/: qtgui/emimage.py, wxgui/ValSlider.py, wxgui/emimage.py,
	  wxgui/emimagecanvas.py, wxgui/emimageframe.py,
	  wxgui/imagecontrol.py, wxgui/imagecontrol.wxg,
	  wxgui/valslider.wxg: In working on the qtgui, I took the current
	  wxpython gui and moved it to a new directory.

2006-07-23 16:53  gtang

	* rt/pyem/test_utils.py: [no log message]

2006-07-23 16:53  gtang

	* libEM/emutil.cpp: re-implement EMUtil::get_all_attributes() to
	  open stack image file only once.

2006-07-23 15:31  gtang

	* libEM/sparx/util_sparx.h: remove extra qualifier Util:: from
	  merge_peaks(), it cause compilation error on some compiler.

2006-07-21 18:46  cyang

	* libEM/CMakeLists.txt:

	  added pca.cpp

2006-07-21 18:45  cyang

	* libEM/sparx/: pca.cpp, pca.h:

	  Add PCA related functions

2006-07-21 14:21  gtang

	* rt/pyem/test_processor.py: minor modification

2006-07-21 14:18  zhuang

	* libEM/sparx/util_sparx.h: add merge_peaks

2006-07-21 12:47  zhuang

	* libEM/sparx/util_sparx.cpp: add merge_peaks to util_sparx.cpp

2006-07-21 11:52  gtang

	* rt/pyem/: test_aligner.py, test_cmp.py, test_emdata.py,
	  test_imageio.py, test_misc.py, test_processor.py, test_utils.py:
	  minor change

2006-07-21 11:06  gtang

	* libEM/sparx/util_sparx.h: remove the extra qulifier Util:: for
	  coveig(), it causes compilation failure on some compiler.

2006-07-20 19:18  cyang

	* libEM/sparx/util_sparx.cpp:
	  minor changes to coveig to clean it up

2006-07-20 18:53  cyang

	* libEM/CMakeLists.txt:
	  Update CMakeLists to include lapackblas.cpp

2006-07-20 18:52  cyang

	* libEM/sparx/: lapackblas.cpp, lapackblas.h, util_sparx.cpp,
	  util_sparx.h:
	  added LAPACK eigenvalue calculation routines for PCA

2006-07-20 15:14  gtang

	* rt/pyem/test_utils.py: unit test update

2006-07-20 12:13  gtang

	* rt/pyem/test_processor.py: unit test update

2006-07-20 01:21  stevel

	* libEM/hdfio2.cpp: Working on hdfio performance.

2006-07-19 17:44  ppenczek

	* libEM/cmp.cpp: corrected mistake with normalization in DotCmp :

2006-07-19 16:24  gtang

	* libEM/emutil.h: add some comment

2006-07-19 16:23  gtang

	* rt/pyem/test_utils.py: unit test for EMUtil class's static
	  functions

2006-07-19 14:36  gtang

	* libEM/: processor.cpp, processor.h: add a new test image
	  processor "testimage.cylinder"

2006-07-19 09:43  wjiang

	* rt/emdata/testprocessor.cpp: add to CVS

2006-07-19 09:41  wjiang

	* libEM/: processor.cpp, processor.h: add
	  GradientPlaneRemoverProcessor

2006-07-18 20:10  cyang

	* libpyEM/typeconverter.pyste:
	  added a missing ';'

2006-07-18 17:14  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2006-07-18 15:17  gtang

	* libEM/: emdata_metadata.cpp, emdata_metadata.h: add
	  EMData::get_attr_default() function, when retrieve value from a
	  non-existing attribute, return None in Python(EMObject() in C++)

2006-07-18 15:01  gtang

	* libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libpyEM/libpyEMData2.cpp, libEM/emutil.cpp: add
	  EMData::get_attr_default() function, when retrieve value from a
	  non-existing attribute, return None in Python(EMObject() in C++)

2006-07-18 15:00  gtang

	* libpyEM/: libpyTypeConverter2.cpp, typeconverter.cpp,
	  typeconverter.h, typeconverter.pyste: Implement the type
	  conersion of EMObject() to None.

2006-07-18 09:05  gtang

	* rt/pyem/: test_aligner.py, test_emdata.py: minor fix

2006-07-17 17:09  gtang

	* rt/pyem/test_utils.py: add unit test for get_all_attributes()

2006-07-17 16:27  gtang

	* libEM/: emdata_metadata.cpp, emdata_metadata.h: trivial fix

2006-07-17 16:23  gtang

	* libpyEM/libpyTypeConverter2.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/typeconverter.pyste, libEM/emutil.cpp, libEM/emutil.h:
	  for EMUtil::get_all_attributes() to get a list of values of an
	  attribute from a stack of images.

2006-07-17 14:05  ppenczek

	* libEM/sparx/fourierfilter.cpp: [no log message]

2006-07-17 11:38  gtang

	* rt/pyem/test_processor.py: unit test update

2006-07-17 11:24  gtang

	* rt/pyem/test_processor.py: unit test update

2006-07-17 10:42  gtang

	* libEM/sparx/emdata_sparx.h: remove the extra qulification
	  EMData:: for peak_ccf() and get_row()

2006-07-17 10:35  gtang

	* rt/pyem/test_utils.py: no more voea() function in Util

2006-07-16 02:53  stevel

	* libpyEM/qtgui/emimage.py: More improvements to QT image viewer.

2006-07-15 20:48  ppenczek

	* libEM/reconstructor.cpp: [no log message]

2006-07-15 19:43  ppenczek

	* libEM/: reconstructor.cpp, sparx/emdata_sparx.cpp,
	  sparx/emdata_sparx.h: [no log message]

2006-07-15 01:35  stevel

	* doc/latex/Makefile, libpyEM/qtgui/emimage.py: Working on qt
	  widgets some more.

2006-07-13 10:19  gtang

	* libEM/processor.cpp: add SHIFTProcessor to Factory

2006-07-13 07:42  ppenczek

	* libEM/: sparx/processor_sparx.h, reconstructor.cpp: [no log
	  message]

2006-07-13 02:08  stevel

	* doc/latex/Makefile, libpyEM/qtgui/emimage.py: More work on qt
	  image widget.

2006-07-12 22:09  stevel

	* doc/latex/Makefile, libpyEM/qtgui/emimage.py: Working on QT
	  widget some more.

2006-07-12 17:21  gtang

	* libEM/amiraio.cpp: add the existence check for attribute key

2006-07-12 16:57  gtang

	* libEM/imagicio.cpp: minor fix to check attribute key exist before
	  access it. Otherwise the get_attr_dict() will fail after
	  display() call.

2006-07-12 16:36  gtang

	* libEM/emdata_metadata.cpp: change for EMData's pickling support

2006-07-12 16:34  gtang

	* rt/pyem/test_emdata.py: unit test for EMData's pickling support

2006-07-12 16:30  gtang

	* rt/pyem/test_emdata.py: unit test for EMData's pickling support

2006-07-12 16:29  gtang

	* libpyEM/libpyEMData2.cpp: change for EMData's pickling support

2006-07-12 16:13  gtang

	* libpyEM/emdata.pyste: change for EMData's pickling support

2006-07-12 15:51  gtang

	* rt/pyem/test_imageio.py: unit test for PGM region IO

2006-07-12 15:50  gtang

	* rt/pyem/test_emdata.py: unit test for EMData::sqrt() function

2006-07-12 15:46  gtang

	* libEM/emdata_metadata.cpp, libEM/emdata_metadata.h,
	  libpyEM/emdata_pickle.h, libpyEM/libpyAligner2.cpp,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyTransform2.cpp: change for
	  EMData's pickling support

2006-07-12 15:44  gtang

	* libEM/emdata_core.h: minor change on inaccurate comment

2006-07-12 15:43  gtang

	* libEM/: emdata.cpp, emdata.h, emdata_core.cpp, emdata_io.cpp:
	  change for EMData's pickling support

2006-07-12 15:16  gtang

	* libEM/: ctf.cpp, ctf.h: add to_vector() and from_vector() for
	  Ctf.

2006-07-12 01:39  stevel

	* libEM/emdata_transform.cpp, libEM/emdata_transform.h,
	  libpyEM/qtgui/emimage.py, libpyEM/qtgui/valslider.py: More work
	  on QT gui.

2006-07-12 00:41  stevel

	* libEM/: emdata.cpp, emdata_transform.cpp, emdata_transform.h: New
	  histogram option in renderamp8, still work in progress.

2006-07-11 13:04  stevel

	* doc/latex/Makefile, libpyEM/CMakeLists.txt,
	  libpyEM/qtgui/emimage.py: Working on QT widgets

2006-07-10 15:00  stevel

	* doc/latex/Makefile, libEM/hdfio2.cpp, libEM/hdfio2.h,
	  libpyEM/qtgui/emimage.py, libpyEM/qtgui/qtimage.py,
	  libpyEM/qtgui/valslider.py: Work on new QT objects.

2006-07-08 22:51  stevel

	* libpyEM/qtgui/: qtimage.py, valslider.py: Add valslider

2006-07-07 21:46  stevel

	* libEM/hdfio2.cpp, libpyEM/qtgui/qtimage.py: Working on new qt
	  widgets

2006-07-07 15:03  gtang

	* libEM/emdata_metadata.cpp: throw an non-existing object exception
	  when access an non-existing key from EMData object.

2006-07-07 02:14  stevel

	* libpyEM/qtgui/qtimage.py: Begin work on QT gui widgets.

2006-07-04 06:53  ppenczek

	* libEM/sparx/emdata_sparx.cpp: [no log message]

2006-07-04 06:39  ppenczek

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h, libpyEM/libpyUtils2.cpp: [no log
	  message]

2006-07-02 21:35  zhuang

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libEM/sparx/fourierfilter.cpp, libEM/sparx/fundamentals.h,
	  libEM/sparx/processor_sparx.h, libEM/sparx/tflm.cpp,
	  libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/emdata.pyste, libpyEM/fundamentals.pyste,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyFundamentals2.cpp,
	  libpyEM/libpyGeometry2.cpp, libpyEM/libpyTransform2.cpp,
	  libpyEM/utils.pyste: Zhong, add peak_ccf and get_pow functions

2006-07-01 22:28  gtang

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/normpadft.cpp,
	  libpyEM/emdata.pyste, libpyEM/libpyEMData2.cpp, libEM/emdata.cpp,
	  libEM/emdata_core.cpp, libEM/emdata_core.h,
	  libEM/emdata_metadata.cpp: implement sqrt() function for EMData

2006-06-28 17:14  gtang

	* libEM/processor.h: fix the parameter type hidden by sub class of
	  processor issue

2006-06-26 15:46  gtang

	* libEM/: pngio.cpp, pngio.h: normalization of PNG file writing

2006-06-26 13:36  stevel

	* libEM/: all_imageio.h, emutil.cpp, hdfio2.cpp, hdfio2.h: Working
	  on HDF5 legacy support.

2006-06-24 01:38  stevel

	* libEM/: hdfio2.cpp, hdfio2.h: HDF5 mostly working now.

2006-06-23 22:05  stevel

	* doc/latex/Makefile, libEM/hdfio2.cpp, libpyEM/EMAN2.py: HDF work

2006-06-23 08:50  stevel

	* libEM/: hdfio2.cpp, hdfio2.h: More HDF work

2006-06-22 13:46  stevel

	* libEM/: all_imageio.h, emutil.cpp, hdfio2.cpp: HDF work.

2006-06-22 10:50  gtang

	* rt/emdata/fft_test.cpp: [no log message]

2006-06-22 09:20  gtang

	* rt/emdata/rotate_translate.cpp: [no log message]

2006-06-21 23:51  stevel

	* libpyEM/libpyEMData2.cpp: update for new hdf, hopefully ok

2006-06-21 23:06  stevel

	* doc/latex/Makefile, libEM/CMakeLists.txt, libEM/hdfio2.cpp,
	  libEM/hdfio2.h: More HDF work.

2006-06-20 21:23  stevel

	* libEM/CMakeLists.txt: so things compile...

2006-06-20 21:09  stevel

	* doc/latex/Makefile, libEM/CMakeLists.txt, libEM/hdfio2.cpp,
	  libEM/hdfio2.h: Working on hdf

2006-06-19 10:33  gtang

	* rt/pyem/test_emdata.py: unit test update to make sure do_ift() is
	  an out-of-place operation

2006-06-18 14:17  gtang

	* libEM/spiderio.h: spiderio.h comment correct for doxygen

2006-06-18 09:34  stevel

	* libEM/: hdfio2.cpp, hdfio2.h: Working on new HDF5.

2006-06-17 11:21  ppenczek

	* doc/latex/Makefile, libEM/emdata_transform.cpp: [no log message]

2006-06-16 16:26  stevel

	* libEM/: hdfio2.cpp, hdfio2.h: Working on new hdf

2006-06-16 15:13  gtang

	* rt/pyem/test_processor.py: unit test update

2006-06-16 15:12  gtang

	* libEM/pgmio.cpp: [no log message]

2006-06-16 15:09  stevel

	* libEM/: hdfio2.cpp, hdfio2.h: Working on new HDF io driver.

2006-06-16 15:00  gtang

	* rt/pyem/test_emdata.py: unit test update

2006-06-16 15:00  gtang

	* rt/pyem/test_imageio.py: unit test update for SPIDER image I/O

2006-06-16 11:49  gtang

	* rt/pyem/test_imageio.py: unit test update for SPIDER image I/O

2006-06-15 14:42  gtang

	* libEM/: spiderio.cpp, spiderio.h, sspiderio.cpp, sspiderio.h:
	  SPIDER I/O rewrite

2006-06-15 14:41  gtang

	* rt/pyem/test_imageio.py: unit test update for SPIDER image I/O

2006-06-14 13:33  ppenczek

	* libEM/sparx/fundamentals.cpp: Added voronoi code commented out
	  into fundamentals.cpp

2006-06-10 22:43  ppenczek

	* libEM/: emdata_transform.cpp, reconstructor.cpp,
	  sparx/fundamentals.cpp, sparx/normpadft.cpp,
	  sparx/util_sparx.cpp: fft inplace works, but not for native

2006-06-10 12:03  ppenczek

	* libEM/: emdata_transform.cpp, emfft.cpp, projector.cpp,
	  reconstructor.cpp, sparx/emdata_sparx.cpp, sparx/native_fft.cpp,
	  sparx/native_fft.h: changes in FFT! :wq

2006-06-08 18:44  mhhohn

	* libEM/emdata_metadata.h:     Removed EMData:: to avoid

	  /net/cci/hohn/tmp-rosie/installer-0.5/sparx-bin/opt/eman2/eman2-8.6.2006/libEM/emdata_metadata.h:412:
	  error: extra qualification 'EMAN::EMData::' on member
	  'del_attr_dict'

2006-06-08 17:32  stevel

	* libEM/emdata.cpp, programs/e2tilefile.py: minor fix

2006-06-07 12:04  ppenczek

	* libEM/emfft.cpp: [no log message]

2006-06-06 17:46  ppenczek

	* libEM/CMakeLists.txt:     To avoid linking error, added
	  zlib_library when using png_library.

2006-06-05 18:43  cyang

	* libEM/sparx/native_fft.cpp:
	  Added additional dimension check for 2/3-D Native FFT/IFT.
	  Terminate FFT/IFT when dimension is invalid

2006-06-05 16:52  mhhohn

	* CMakeLists.txt:     Check for most specific boost_python first.

2006-06-05 14:33  gtang

	* libEM/emfft.cpp: fix the broken of FFTW2 switch/case block issue
	  for old compiler.

2006-06-05 14:30  gtang

	* libEM/emfft.cpp: fix the broken of FFTW3 switch/case block issue
	  for old compiler.

2006-06-05 14:12  cyang

	* libEM/sparx/native_fft.cpp:
	  terminate and exit with error if the leading dimension of the
	  image is not allowed in Native FFT/IFT

2006-06-02 12:56  stevel

	* libEM/emdata.cpp: Fix radial_dist for Friedel pair.

2006-06-02 08:42  gtang

	* rt/pyem/test_emdata.py: EMData::calc_radial_dist() interface
	  changed.

2006-06-02 08:18  gtang

	* rt/emdata/rotate_translate.cpp: EMData::calc_redial_dist()
	  interface changed.

2006-06-02 02:50  stevel

	* libEM/emdata.cpp, programs/e2tilefile.py: Minor bugfix in
	  calc_radial_dist

2006-06-02 02:16  stevel

	* libpyEM/libpyEMData2.cpp: Fixed python template.

2006-06-02 02:11  stevel

	* libEM/: cmp.cpp, emdata.cpp, emdata.h, processor.cpp: Rewritten
	  calc_radial_dist, with new option for selecting amp/inten.

2006-06-01 23:24  stevel

	* doc/latex/Makefile, programs/e2tilefile.py: Working on tilefile
	  generator.

2006-06-01 09:53  stevel

	* doc/latex/Makefile, programs/e2tilefile.py: Working on tile-file
	  production

2006-06-01 09:05  gtang

	* rt/pyem/test_emdata.py: add comment

2006-06-01 08:54  gtang

	* libEM/emfft.cpp: remove the code negate the imaginary part for
	  native fft.

2006-05-31 16:44  gtang

	* libEM/emfft.cpp: minor fix

2006-05-31 16:22  gtang

	* libEM/: emdata_transform.cpp, emfft.cpp, emfft.h: FFT routines
	  debug.

2006-05-31 16:17  gtang

	* rt/emdata/: CMakeLists.txt, emdata_api.cpp, fft_test.cpp,
	  mem_test.cpp, projector_test.cpp, testpolardata.cpp: a bunch of
	  testing program.

2006-05-31 16:00  gtang

	* rt/pyem/test_emdata.py: solid unit test for FFT routine, bu tno
	  test for large image.

2006-05-31 15:59  gtang

	* rt/pyem/test_averager.py: nn4Reconstructor not work?

2006-05-31 14:12  gtang

	* libEM/emdata.cpp: comment for EMData::calc_flcf(), this function
	  is broken.

2006-05-30 17:20  ppenczek

	* libEM/reconstructor.cpp: [no log message]

2006-05-30 10:50  ppenczek

	* doc/latex/Makefile: [no log message]

2006-05-30 10:42  prb

	* libEM/sparx/: emdata_sparx.cpp, util_sparx.cpp, util_sparx.h:
	  removed some print statements that had existed for testing; that
	  is all

2006-05-30 01:56  stevel

	* libEM/processor.cpp, libEM/processor.h, programs/e2tilefile.py:
	  Tilefile work

2006-05-28 22:53  stevel

	* doc/latex/Makefile, libEM/processor.cpp, libpyEM/EMAN2.py: Fixed
	  buggy realtofft filter

2006-05-28 11:42  ppenczek

	* libEM/reconstructor.cpp, libEM/sparx/emdata_sparx.cpp,
	  libEM/sparx/emdata_sparx.h, libEM/sparx/normpadft.cpp,
	  libpyEM/emdata.pyste, libpyEM/libpyEMData2.cpp: [no log message]

2006-05-26 09:45  gtang

	* rt/pyem/test_averager.py: change unit test Pawel_back_projector
	  to nn4Reconstructor

2006-05-26 08:48  gtang

	* libEM/sparx/util_sparx.h: parameter fix for Doxygen

2006-05-26 08:27  gtang

	* doc/Doxyfile: Doxygen document support graphic class view

2006-05-26 08:24  gtang

	* libEM/sparx/emdata_sparx.h: comment fix for parameter

2006-05-25 21:07  ppenczek

	* libEM/: reconstructor.cpp, reconstructor.h: [no log message]

2006-05-25 18:51  ppenczek

	* libEM/: reconstructor.cpp, reconstructor.h,
	  sparx/emdata_sparx.cpp, sparx/emdata_sparx.h,
	  sparx/fourierfilter.cpp: [no log message]

2006-05-25 17:37  gtang

	* libEM/: emfft.cpp, emfft.h: fix the memory leak for FFTW2.

2006-05-25 16:21  gtang

	* CMakeLists.txt: make FFTW2 as default fft library for EMAN2 for
	  water's nightly build temporarily.

2006-05-25 13:33  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h, util_sparx.cpp:
	  [no log message]

2006-05-25 13:21  phani

	* libEM/reconstructor.cpp: nn4_ctfReconstructor modified

2006-05-25 12:58  ppenczek

	* libEM/: reconstructor.cpp, reconstructor.h: [no log message]

2006-05-25 12:45  phani

	* libEM/: reconstructor.cpp, reconstructor.h: nn4_ctf_Reconstructor
	  added

2006-05-25 11:30  ppenczek

	* doc/latex/Makefile, libEM/reconstructor.cpp: [no log message]

2006-05-24 22:18  ppenczek

	* libEM/: reconstructor.cpp, sparx/emdata_sparx.cpp: [no log
	  message]

2006-05-24 14:41  ppenczek

	* libEM/: processor.cpp, sparx/processor_sparx.h: [no log message]

2006-05-24 14:03  gtang

	* libEM/emutil.cpp: minor change

2006-05-24 14:00  gtang

	* CMakeLists.txt: make FFTW3 as default fft library for EMAN2.

2006-05-24 12:23  gtang

	* rt/pyem/test_processor.py: improve unit test for
	  testimage.noise.gauss

2006-05-24 11:49  gtang

	* rt/pyem/test_imageio.py: add unit test for PGM file I/O

2006-05-24 11:48  gtang

	* libEM/: processor.cpp, processor.h: add parameter "seed" for all
	  random noise related processor.

2006-05-24 11:38  gtang

	* libEM/util.cpp: remove the srand(time(0)) in Util::get_frand(),
	  the static variable seems does not work in the Python call of
	  this function.

2006-05-24 01:40  stevel

	* programs/e2tilefile.py: error checking in e2tilefile

2006-05-24 01:36  stevel

	* programs/e2tilefile.py: Tilefile working

2006-05-23 22:21  stevel

	* libEM/: emobject.h, jpegio.cpp, jpegio.h, processor.cpp,
	  processor.h: Modified random test image again.

2006-05-23 16:31  gtang

	* libEM/: processor.cpp, processor.h: reimplement
	  testimage.noise.gaussian, add parameter seed for random number
	  generator seed.

2006-05-23 16:03  ppenczek

	* libEM/: processor.cpp, sparx/processor_sparx.h,
	  sparx/util_sparx.cpp: [no log message]

2006-05-23 14:57  prb

	* libEM/sparx/emdata_sparx.cpp:   fixed even-odd issue in
	  rot_scale_trans for even sided 3d images

2006-05-23 12:11  ppenczek

	* libEM/processor.cpp: comments about noise

2006-05-23 11:32  gtang

	* libEM/: pgmio.cpp, pgmio.h: PGM file only support 8 bit.

2006-05-22 15:37  gtang

	* libEM/: imageio.cpp, imageio.h, jpegio.cpp, pgmio.cpp, pgmio.h:
	  PGM file writing support and image normalization.

2006-05-21 09:10  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2006-05-20 21:26  stevel

	* programs/e2tilefile.py: Working on new tilefile application

2006-05-20 20:44  ppenczek

	* doc/latex/Makefile, libEM/sparx/util_sparx.h: [no log message]

2006-05-20 16:07  gtang

	* libpyEM/: libpyEMData2.cpp, libpyPointArray2.cpp,
	  libpyTransform2.cpp, libpyUtils2.cpp: Again, I have to fix the
	  broken EMAN2 due to somebody checked in filesgenerated by
	  unpatched Pyste.

2006-05-20 16:02  gtang

	* libEM/emdata.cpp: put the debug output into #ifdef DEBUG

2006-05-20 15:54  gtang

	* libEM/emdata.cpp: put the debug output into #ifdef DEBUG

2006-05-20 15:20  gtang

	* rt/pyem/test_transform.py: unit test update since Phil change the
	  transform

2006-05-20 14:18  ppenczek

	* libpyEM/emdata.pyste: [no log message]

2006-05-20 14:08  ppenczek

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp, libpyEM/utils.pyste: [no log message]

2006-05-20 13:39  ppenczek

	* libEM/sparx/util_sparx.cpp: oops, previous had bugs...

2006-05-20 13:36  ppenczek

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/emdata.pyste, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyGeometry2.cpp, libpyEM/libpyPointArray2.cpp,
	  libpyEM/libpyTransform2.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/utils.pyste: [no log message]

2006-05-20 12:16  ppenczek

	* libEM/sparx/normpadft.cpp: corrected ft stuff

2006-05-19 15:52  prb

	* libEM/emdata.cpp, libEM/util.h, libEM/sparx/emdata_sparx.cpp,
	  libEM/sparx/emdata_sparx.h, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h, libpyEM/libpyEMData2.cpp:	 I created
	  a 2d/3d rotate translate program
		   rot_scale_trans in emdata_sparx.cpp
		   that uses quadrilinear interpolation
		     it calls Util::triquad
			       from util_sparx.cpp
	      It uses a  Transform3D object as a variable.

	      It will replace rot_scale_trans2D
	       as soon as the functions calling rot_scale_trans2D
		      wind up using Transform3D objects as arguments.

	     I don't think I touched anything in emdata.cpp

2006-05-19 09:47  prb

	* libEM/: transform.cpp, transform.h:	centered angles- phi, psi
	  etc now live on interval between -180 and +180 degreees

2006-05-19 08:49  gtang

	* libEM/: emdata.h, emdata_metadata.h, polardata.h, util.h,
	  sparx/emdata_sparx.h, sparx/fundamentals.h, sparx/normpadft.h,
	  sparx/util_sparx.h: Fix the warning of doxygen

2006-05-19 07:10  gtang

	* rt/pyem/test_processor.py: filter.integercyclicshift2d removed,
	  update unit test

2006-05-19 02:18  stevel

	* libpyEM/EMAN2.py: Minor additions.

2006-05-18 20:28  barry

	* libEM/sparx/util_sparx.cpp: util_sparx.cpp

2006-05-18 20:16  barry

	* libpyEM/libpyUtils2.cpp: libpyUtils2.cpp

2006-05-18 20:15  barry

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: util_sparx.cpp

2006-05-18 18:20  phani

	* libEM/: processor.cpp, processor.h: mirror processor implmention,
	  removed integercyclic2d processor

2006-05-18 18:18  phani

	* libEM/sparx/: processor_sparx.h, util_sparx.cpp: comments added
	  tocyclicshift.cpp, mirror processor included

2006-05-18 16:44  zhuang

	* libEM/sparx/util_sparx.h: Update doc

2006-05-18 16:30  phani

	* libEM/sparx/util_sparx.cpp: cyclicshift fixed

2006-05-18 15:08  zhuang

	* libEM/sparx/fourierfilter.cpp:
	  update ctf filter

2006-05-18 12:41  ppenczek

	* libEM/sparx/emdata_sparx.cpp: He, he, previous one was not
	  correct, this one is!

2006-05-18 11:51  barry

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: util_sparx.cpp

2006-05-18 11:38  barry

	* libEM/sparx/util_sparx.cpp: util_sparx.cpp

2006-05-18 11:21  gtang

	* utils/CMakeLists.txt: remove e2proc2d from install list. use
	  e2proc2d.py only.

2006-05-18 10:45  stevel

	* doc/latex/Makefile, libEM/aligner.cpp, libEM/all_imageio.h,
	  libEM/emutil.cpp, libEM/hdfio.cpp, libEM/jpegio.cpp,
	  libEM/jpegio.h, libEM/processor.cpp, libpyEM/EMAN2.py,
	  programs/e2proc2d.py: Jpeg writing support fixed. Fixed
	  indentation (hopefully correctly) on e2proc2d.py

2006-05-18 09:31  ppenczek

	* libEM/sparx/emdata_sparx.cpp: corrected center for odd images for
	  rot_scale_conv

2006-05-18 01:49  stevel

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/emutil.cpp,
	  libEM/emutil.h, libEM/jpegio.cpp, libEM/jpegio.h: Added JPEG
	  write support, broken but compiles

2006-05-17 21:06  ppenczek

	* libEM/sparx/fundamentals.cpp: fixed

2006-05-17 16:48  gtang

	* libEM/spiderio.cpp: EMUtil::process_region_io() does not work
	  with spider image stack writing.

2006-05-17 16:07  ppenczek

	* libEM/sparx/fundamentals.cpp: [no log message]

2006-05-17 12:52  gtang

	* rt/pyem/test_processor.py: add unit test for "eman1.xform.flip"
	  processor

2006-05-17 12:27  gtang

	* libEM/: processor.cpp: fix the wrongly implemented FlipProcessor

2006-05-17 12:01  gtang

	* libEM/processor.cpp: fix the wrongly implemented FlipProcessor

2006-05-17 09:54  gtang

	* libEM/sparx/fourierfilter.cpp: minor fix for back compatibility
	  of old g++ compiler. compilation failed on water.

2006-05-16 19:12  zhuang

	* libEM/sparx/fourierfilter.cpp: update fourierfilter

2006-05-16 17:25  ppenczek

	* libEM/sparx/emdata_sparx.cpp: rot_scale_trans2D fixed

2006-05-16 15:59  zhuang

	* libEM/processor.cpp, libEM/sparx/fourierfilter.cpp,
	  libEM/sparx/processor_sparx.h, libEM/sparx/util_sparx.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyGeometry2.cpp,
	  libpyEM/libpyProcessor2.cpp, libpyEM/libpyTransform2.cpp,
	  libpyEM/libpyUtils2.cpp:  fixed ctf stuff

2006-05-16 15:54  zhuang

	* libEM/sparx/util_sparx.cpp:  updated ctf program

2006-05-16 13:29  zhuang

	* libEM/: sparx/fourierfilter.cpp, sparx/processor_sparx.h,
	  processor.h: add CTF filter

2006-05-16 13:27  zhuang

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: remove ctf_img
	  from emdata_sparx.cpp and emdata_sparx.h

2006-05-16 09:32  gtang

	* libEM/spiderio.cpp: region I/O support has probelm, use non
	  region I/O support version temporarily.

2006-05-14 17:33  zhuang

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: put SPIDER ctf
	  generator ctf_img in util_sparx.cpp

2006-05-12 16:42  gtang

	* rt/pyem/test_emdata.py: unit test for EMData::amplitude() and
	  EMData::phase()

2006-05-12 16:26  gtang

	* libpyEM/libpyEMData2.cpp: implement EMData::amplitude() and
	  EMData::phase() function

2006-05-12 16:09  gtang

	* libpyEM/emdata.pyste, libEM/emdata_core.cpp, libEM/emdata_core.h:
	  implement EMData:;amplitude() and EMData::phase() functions.

2006-05-12 15:17  gtang

	* rt/pyem/test_emdata.py: new unit test for divide by zero
	  exception

2006-05-12 15:16  gtang

	* rt/pyem/test_transform.py: fix several unit test failure.

2006-05-12 14:27  gtang

	* libEM/emdata_core.cpp: throw exception for zero pixel in image
	  division operation.

2006-05-12 12:00  barry

	* libEM/sparx/emdata_sparx.cpp: emdata_sparx.cpp

2006-05-11 22:13  zhuang

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h:  Zhong

2006-05-11 12:30  gtang

	* rt/pyem/test_emdata.py: add unit test for
	  EMData::process(Processor)

2006-05-11 12:17  gtang

	* libEM/: emdata_modular.cpp, emdata_modular.h:
	  EMData::process(Processor *) EMData::process_inplace(Processor *)

2006-05-11 12:16  gtang

	* libpyEM/: libpyEMData2.cpp, libpyTransform2.cpp: run
	  create_boost_python for EMData::process(Processor *),
	  EMData::process_inplace(Processor *), EMData::ctf_img().

2006-05-11 11:52  gtang

	* libpyEM/emdata.pyste: set return policy for EMData::ctf_img()

2006-05-10 20:45  zhuang

	* libEM/sparx/emdata_sparx.cpp: C Zhong, SPIDER ctf_img get rid of
	  warnings VS:
	  ----------------------------------------------------------------------

2006-05-09 23:06  zhuang

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: SPIDER ctf

2006-05-09 17:21  prb

	* libEM/emdata.cpp, libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp:	i) fixed a degree/radian problem in
	  emdata
	   ii) added XYZ convention

2006-05-08 18:11  gtang

	* rt/pyem/test_emdata.py: add test cases for EMData::del_attr()
	  EMData::del_attr_dict()

2006-05-08 14:32  prb

	* libEM/transform.cpp:	patched some pesky things, always returns
	  positive degrees for EMAN, SPIDER

2006-05-07 12:26  gtang

	* libpyEM/: libpyEMData2.cpp, libpyGeometry2.cpp,
	  libpyTransform2.cpp, libpyUtils2.cpp: implement image attributes
	  deletion

2006-05-07 11:38  gtang

	* libEM/: emdata_metadata.cpp, emdata_metadata.h: implement
	  deletion of attributes.

2006-05-07 11:16  gtang

	* libEM/: emdata_metadata.cpp, emdata_metadata.h, emobject.h:
	  implement deletion of attributes.

2006-05-07 10:31  gtang

	* libEM/emdata_core.cpp: avoid devide by zero for image division.

2006-05-06 14:16  gtang

	* libEM/: emdata_metadata.cpp, emdata_metadata.h:
	  EMData::set_attr_dict() update the attribute dictionary instead
	  of replace it with new dictionary.

2006-05-04 22:20  prb

	* libEM/transform.cpp:	 Need to touch things up so that SPIDER
	  always returns positive angles.

2006-05-04 17:37  phani

	* libpyEM/libpyUtils2.cpp: libpyutils

2006-05-04 17:29  phani

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: BPCQ

2006-05-04 11:59  stevel

	* doc/: EMAN2.0.big.jpg, doc.html, index.html, latex/Makefile: Add
	  webpage links to docs.

2006-05-04 00:32  stevel

	* programs/e2tomogram.py: Trivial fix to e2tomogram.

2006-05-03 11:54  gtang

	* libEM/emfft.cpp: ACML 1D fft/ift finished.

2006-05-03 11:14  gtang

	* rt/pyem/test_aligner.py, libEM/aligner.cpp, libEM/aligner.h:
	  RTFSlowest Aligner eliminated.

2006-05-03 10:52  gtang

	* rt/pyem/test_aligner.py: [no log message]

2006-05-03 10:43  gtang

	* libEM/cmp.h: add the 'keepzero' parameter to SqEuclidean cmp to
	  make RTFSlowest aligner consistent.

2006-05-03 09:58  gtang

	* rt/pyem/test_processor.py: processor unit test update for
	  testimage.sinewave

2006-05-02 14:47  gtang

	* libEM/: pngio.cpp, pngio.h, emdata_io.cpp: fix the segmentation
	  fault for PNG file writing.

2006-05-01 21:38  phani

	* libEM/sparx/util_sparx.cpp: phani

2006-05-01 18:04  cyang

	* libEM/sparx/util_sparx.cpp:
	  added some error checking in infomask

2006-05-01 18:02  cyang

	* libEM/sparx/util_sparx.cpp:
	  added error check

2006-05-01 16:50  gtang

	* libpyEM/libpyEMData2.cpp: remove the redundant conjugate()
	  function. cconj() did the same thing.

2006-05-01 16:35  gtang

	* libEM/: emdata_core.cpp, emdata_core.h: remove the redundant
	  conjugate() function. cconj() did the same thing.

2006-05-01 16:30  barry

	* libEM/sparx/util_sparx.cpp: util_sparx.cpp

2006-05-01 14:07  cyang

	* libEM/projector.cpp:
	  fixed a bug in ChaoProjector (should pass &dm(1,j) instead of dm
	  to fwdpj3 and bckpj3)

2006-05-01 12:05  barry

	* libpyEM/: libpyEMData2.cpp, libpyGeometry2.cpp,
	  libpyTransform2.cpp, libpyUtils2.cpp: libpyUtils2.cpp

2006-05-01 11:47  barry

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: util_sparx.cpp

2006-04-29 12:30  gtang

	* libEM/emdata.cpp: fix the incorrect implementation of
	  EMAN::operator-(float, EMData*) and EMAN::operator/(float,
	  EMData*).

2006-04-28 15:58  gtang

	* libEM/emutil.cpp: throw more meaningful exception for writing to
	  unsupported image file format.

2006-04-27 21:49  ppenczek

	* libEM/cmp.cpp: [no log message]

2006-04-27 19:45  cyang

	* libEM/projector.cpp:
	  Set the default center in PawelProjector::backproject3d to
	  (nx/2,ny/2,nz/2) instead of (nx/2+1,ny/2+1,nz/2+1) to be
	  consistent with PawelProjector::project3d

2006-04-27 13:58  cyang

	* libEM/projector.cpp:
	  added the missing ret->done_data() in ChaoProjector::project3d

2006-04-27 13:41  cyang

	* libEM/projector.cpp:

	  replaced callocs with news, and replaced delete with
	  EMDeleteArray some other minor cleanups

2006-04-27 13:40  cyang

	* libEM/emutil.h:

	  Added two inline clean delete functions EMDeletePtr and
	  EMDeleteArray

2006-04-26 14:59  gtang

	* libEM/projector.cpp: remove dgr_to_rad to fix broken projector
	  because all angle use degree now.

2006-04-26 13:19  cyang

	* libEM/projector.cpp:
	  removed dgr_to_rad from Pawel backproject3d

2006-04-26 11:30  ppenczek

	* libEM/projector.cpp: [no log message]

2006-04-25 21:49  gtang

	* libpyEM/: libpyEMData2.cpp, libpyGeometry2.cpp,
	  libpyTransform2.cpp: make sure libpy*.cpp work.

2006-04-25 20:55  prb

	* libEM/transform.cpp:	corrected a factor of 2

2006-04-25 20:19  ppenczek

	* libEM/projector.cpp: [no log message]

2006-04-25 19:15  mhhohn

	* test-imports.py:     low-level import test

2006-04-25 19:14  mhhohn

	* libpyEM/SConscript:	  libpyTypeConverter2 and  libpyEMData2
	  need extra files.

2006-04-25 19:13  cyang

	* libpyEM/: emdata.pyste, libpyEMData2.cpp, libpyProjector2.cpp,
	  projector.pyste:
	  Added Python exposure to backproject

2006-04-25 19:11  cyang

	* plugins/: projector_template.cpp, projector_template.h:
	  Added backproject

2006-04-25 19:10  cyang

	* libEM/: emdata_modular.cpp, emdata_modular.h, projector.cpp,
	  projector.h:
	  Added Pawel backprojector, Chao projector, backprojector defined
	  a new backproject method

2006-04-25 19:03  mhhohn

	* libtbx_refresh.py: [no log message]

2006-04-25 19:00  mhhohn

	* libtbx_refresh.py:	 configuration.

2006-04-25 18:46  mhhohn

	* SConscript: [no log message]

2006-04-25 18:05  mhhohn

	* libpyEM/SConscript: [no log message]

2006-04-25 18:03  ppenczek

	* libEM/polardata.cpp: commented out log2 call in last section

2006-04-25 17:49  barry

	* libEM/sparx/util_sparx.cpp: util_sparx.cpp

2006-04-25 17:48  mhhohn

	* libEM/SConscript: [no log message]

2006-04-25 17:33  mhhohn

	* libtbx_config: [no log message]

2006-04-25 17:25  mhhohn

	* libEM/SConscript, SConscript:     added.

2006-04-25 17:03  barry

	* libpyEM/: libpyEMData2.cpp, libpyGeometry2.cpp,
	  libpyTransform2.cpp, libpyUtils2.cpp: libpyEMData2.cpp

2006-04-25 16:59  ppenczek

	* libEM/cmp.cpp: [no log message]

2006-04-25 16:10  barry

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h, util_sparx.cpp,
	  util_sparx.h: util_sparx.cpp

2006-04-25 15:33  gtang

	* libEM/cmp.cpp: give EMData* mask=0; will cause lots of
	  segmentation fault, turn it back to original. But this is bug
	  anyway.

2006-04-25 13:52  gtang

	* libpyEM/: libpyEMData2.cpp, libpyGeometry2.cpp,
	  libpyTransform2.cpp: add EMData::conjugate() function.

2006-04-25 12:30  gtang

	* libEM/: emdata_core.cpp, emdata_core.h: implement conjugate()
	  operation for complex image.

2006-04-25 11:38  gtang

	* libEM/cmp.cpp: get rid of the warning message for uninitialized
	  variable.

2006-04-24 18:59  phani

	* libpyEM/: libpyUtils2.cpp, utils.pyste: cyclicshif

2006-04-24 18:59  phani

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: cyclicshift

2006-04-24 15:58  zhuang

	* libEM/sparx/emdata_sparx.h: add comments to peak_search

2006-04-24 14:46  barry

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: util_sparx.cpp

2006-04-24 10:55  gtang

	* libEM/emfft.cpp: make native_fft complex part sign compatible
	  with FFTW.

2006-04-24 09:47  gtang

	* rt/pyem/test_cmp.py, libEM/aligner.h, programs/e2boxer.py,
	  utils/speedtest.cpp, rt/emdata/rotate_translate.cpp,
	  examples/comparepairs.py, examples/sortsimilar.py: change
	  "variance" cmp to "SqEuclidean".

2006-04-23 15:40  ppenczek

	* libEM/cmp.h: [no log message]

2006-04-23 10:54  ppenczek

	* libEM/: cmp.cpp, cmp.h: [no log message]

2006-04-22 19:25  ppenczek

	* libEM/polardata.cpp: [no log message]

2006-04-22 18:14  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2006-04-22 06:32  prb

	* libEM/transform.cpp:	 Everything now in degrees.

2006-04-21 14:53  barry

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: util_sparx.cpp

2006-04-21 10:23  barry

	* libEM/sparx/util_sparx.cpp: util_sparx.cpp

2006-04-21 09:52  barry

	* libEM/sparx/util_sparx.cpp: util_sparx.cpp

2006-04-20 21:31  ppenczek

	* libpyEM/libpyUtils2.cpp, libpyEM/utils.pyste, doc/EMAN2.pdf,
	  doc/EMAN2.ps, doc/latex/EMAN2.lot, libEM/sparx/util_sparx.cpp,
	  libEM/sparx/util_sparx.h: [no log message]

2006-04-20 20:49  barry

	* libpyEM/: libpyEMData2.cpp, libpyUtils2.cpp, utils.pyste:
	  utils.pyste

2006-04-20 20:48  barry

	* libEM/sparx/: util_sparx.h, util_sparx.cpp: util_sparx.cpp

2006-04-20 19:24  mhhohn

	* libEM/sparx/emdata_sparx.cpp: changed includes to	#include
	  <gsl/gsl_sf_bessel.h>     #include <gsl/gsl_errno.h>

2006-04-20 19:20  mhhohn

	* libEM/emdata.cpp:	fixed
		  #include <gsl/gsl_sf_bessel.h>
		  #include <gsl/gsl_errno.h>

2006-04-20 19:17  zhuang

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: peak_search add
	  constant image case

2006-04-20 16:19  gtang

	* libEM/projector.h: more fix for projector's parameters.

2006-04-20 15:45  gtang

	* libEM/projector.h: Define the parameter needed for "pawel"
	  projector

2006-04-20 15:25  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, util_sparx.cpp: [no log message]

2006-04-20 15:15  prb

	* libEM/transform.cpp: Made some small changes to set_pretrans etc.

2006-04-20 13:55  ppenczek

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyUtils2.cpp: [no log message]

2006-04-20 13:20  ppenczek

	* libEM/sparx/: util_sparx.cpp, fourierfilter.cpp: [no log message]

2006-04-20 08:58  prb

	* libEM/transform.cpp:	   debugging small errors in inverse method
	  call

2006-04-19 18:03  ppenczek

	* libEM/sparx/emdata_sparx.cpp: [no log message]

2006-04-19 17:07  barry

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: [no log message]

2006-04-19 17:02  barry

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: [no log message]

2006-04-19 16:20  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h, util_sparx.cpp:
	  [no log message]

2006-04-19 15:54  gtang

	* libEM/: processor.cpp, processor.h: finish 'testimage.sinewave'
	  for 1D/2D/3D.

2006-04-19 15:21  zhuang

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: zhong add
	  comments to peak_search

2006-04-19 15:03  ppenczek

	* libpyEM/: libpyEMData2.cpp, libpyUtils2.cpp, utils.pyste: [no log
	  message]

2006-04-19 14:53  ppenczek

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: [no log message]

2006-04-19 14:51  barry

	* libpyEM/: libpyEMData2.cpp, libpyUtils2.cpp, utils.pyste:
	  utils.pyste

2006-04-19 14:46  barry

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: util_sparx.cpp

2006-04-19 14:21  ppenczek

	* libEM/sparx/util_sparx.cpp, libEM/sparx/util_sparx.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/utils.pyste: [no log message]

2006-04-19 10:37  phani

	* libpyEM/utils.pyste: comment

2006-04-19 10:19  phani

	* libpyEM/libpyUtils2.cpp: comment

2006-04-18 16:58  phani

	* libEM/sparx/util_sparx.cpp: eyebies

2006-04-18 16:43  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2006-04-18 16:35  phani

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: eyebies

2006-04-18 15:35  barry

	* libEM/sparx/util_sparx.h: util_sparx.h

2006-04-18 15:17  gtang

	* libEM/emdata_metadata.h: minor fix

2006-04-18 14:37  barry

	* libEM/sparx/util_sparx.cpp: util_sparx.cpp

2006-04-18 13:23  gtang

	* libEM/: polardata.cpp, tifio.cpp: get rid of the warning message

2006-04-18 12:23  barry

	* libpyEM/: libpyEMData2.cpp, libpyGeometry2.cpp,
	  libpyPointArray2.cpp, libpyTransform2.cpp, libpyUtils2.cpp,
	  utils.pyste: utils.pyste

2006-04-18 12:23  barry

	* libEM/sparx/util_sparx.h: util_sparx.cpp

2006-04-17 20:46  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2006-04-17 20:37  ppenczek

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyGeometry2.cpp,
	  libpyEM/libpyPointArray2.cpp, libpyEM/libpyTransform2.cpp,
	  libpyEM/libpyUtils2.cpp: [no log message]

2006-04-17 18:33  cyang

	* libEM/sparx/SparxIO.cpp:
	  Check for SPIDER comments lines (lines starts with ';') and skip
	  these lines when reading a SPIDER document file.

2006-04-17 17:27  gtang

	* libEM/processor.h, libEM/processor.cpp,
	  rt/pyem/test_processor.py: 2D image support for eman1.bilateral
	  processor.

2006-04-17 12:18  ppenczek

	* libEM/sparx/util_sparx.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyUtils2.cpp, libpyEM/utils.pyste: Various additions

2006-04-17 11:49  barry

	* libEM/sparx/util_sparx.cpp: util_sparx.cpp

2006-04-17 11:39  barry

	* libEM/sparx/util_sparx.h: util_sparx.cpp

2006-04-17 10:40  ppenczek

	* libEM/sparx/util_sparx.cpp: [no log message]

2006-04-14 18:36  gtang

	* libEM/processor.h, rt/pyem/test_averager.py: unit test update due
	  to parameters check.

2006-04-14 16:57  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, util_sparx.cpp, util_sparx.h:
	  failed completely

2006-04-14 16:48  gtang

	* rt/pyem/test_aligner.py: unit test update due to parameters
	  check.

2006-04-14 16:34  gtang

	* rt/pyem/test_cmp.py: unit test update due to parameters check.

2006-04-14 16:29  gtang

	* libpyEM/libpyEMData2.cpp: give default Dict() for cmp()

2006-04-14 16:26  gtang

	* rt/pyem/: test_averager.py, test_cmp.py: unit test update due to
	  parameters check.

2006-04-14 16:10  gtang

	* libEM/emdata_modular.h: give default Dict() for cmp()

2006-04-14 14:04  ppenczek

	* libEM/sparx/emdata_sparx.cpp: more stuff

2006-04-14 13:27  barry

	* libpyEM/libpyEMData2.cpp: [no log message]

2006-04-14 12:51  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h, util_sparx.cpp:
	  More stuff

2006-04-14 11:23  barry

	* libEM/sparx/emdata_sparx.cpp: barry

2006-04-14 10:37  barry

	* libEM/sparx/util_sparx.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyGeometry2.cpp, libpyEM/libpyTransform2.cpp,
	  libpyEM/libpyUtils2.cpp: [no log message]

2006-04-14 09:41  barry

	* libEM/sparx/emdata_sparx.cpp: barry

2006-04-13 18:53  cyang

	* libEM/sparx/: Tokenizer.h, Tokenizer.cpp:
	  removed #ifdef 0

2006-04-13 18:38  cyang

	* libEM/sparx/SparxIO.h:
	  added // after #endif

2006-04-13 18:38  cyang

	* libEM/sparx/SparxIO.cpp:
	  initialized data to zero

2006-04-13 18:34  cyang

	* libpyEM/utils.pyste:
	  Add python interface to the TFList for reading SPARX Text File.

2006-04-13 18:04  barry

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: barry

2006-04-13 17:45  ppenczek

	* libEM/sparx/emdata_sparx.cpp: rot_scale_conv

2006-04-13 16:42  ppenczek

	* libEM/sparx/emdata_sparx.cpp: [no log message]

2006-04-13 16:36  gtang

	* libpyEM/: libpyAligner2.cpp, libpyAverager2.cpp, libpyCmp2.cpp,
	  libpyEMData2.cpp, libpyEMObject2.cpp, libpyGeometry2.cpp,
	  libpyPointArray2.cpp, libpyPolarData2.cpp, libpyProcessor2.cpp,
	  libpyProjector2.cpp, libpyReconstructor2.cpp,
	  libpyTransform2.cpp, libpyTypeConverter2.cpp, libpyUtils2.cpp:
	  fix the broken type conversion in libpy*.cpp

2006-04-13 16:16  gtang

	* libEM/sparx/emdata_sparx.cpp: fix for broken on older c++
	  compiler.

2006-04-13 16:13  gtang

	* libEM/sparx/emdata_sparx.cpp: fix for broken on older c++
	  compiler.

2006-04-13 15:53  gtang

	* libEM/aligner.cpp, libEM/aligner.h, libEM/processor.h,
	  rt/pyem/test_aligner.py: parameter check

2006-04-13 14:42  gtang

	* libEM/emutil.cpp: [no log message]

2006-04-13 11:05  barry

	* libEM/sparx/emdata_sparx.h: barry

2006-04-13 10:25  ppenczek

	* libEM/sparx/SparxIO.cpp, libEM/sparx/SparxIO.h,
	  libEM/sparx/Tokenizer.cpp, libEM/sparx/Tokenizer.h,
	  libEM/sparx/normpadft.cpp, libEM/sparx/normpadft.h,
	  libpyEM/libpyAligner2.cpp, libpyEM/libpyAverager2.cpp,
	  libpyEM/libpyCmp2.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyEMObject2.cpp, libpyEM/libpyGeometry2.cpp,
	  libpyEM/libpyPointArray2.cpp, libpyEM/libpyPolarData2.cpp,
	  libpyEM/libpyProcessor2.cpp, libpyEM/libpyProjector2.cpp,
	  libpyEM/libpyReconstructor2.cpp, libpyEM/libpyTransform2.cpp,
	  libpyEM/libpyTypeConverter2.cpp, libpyEM/libpyUtils2.cpp: [no log
	  message]

2006-04-13 10:08  barry

	* libEM/sparx/emdata_sparx.cpp: barry

2006-04-12 17:13  cyang

	* libEM/CMakeLists.txt:
	  Added sparx/Tokenizer.cpp and sparx/SparxIO.cpp to the source
	  list

2006-04-12 17:12  cyang

	* libEM/sparx/: SparxIO.cpp, SparxIO.h, Tokenizer.cpp, Tokenizer.h:

	  Add utilities for reading SPARX Text Files

2006-04-12 16:07  gtang

	* rt/pyem/test_processor.py: unit test update due to parameters
	  check.

2006-04-12 15:20  phani

	* libEM/sparx/util_sparx.cpp: phani added infomask and im_diff

2006-04-12 14:47  gtang

	* libEM/: processor.h, processor.cpp: [no log message]

2006-04-11 17:49  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: Maybe works

2006-04-11 17:14  gtang

	* libEM/: emobject.h, exception.h, processor.h: check parameter for
	  processor, etc modular class, if it's not defined throw an
	  exception.

2006-04-11 16:05  zhuang

	* libEM/sparx/emdata_sparx.cpp: peak_search vector float ix->
	  vector integer

2006-04-11 12:06  ppenczek

	* libEM/sparx/fourierfilter.cpp: [no log message]

2006-04-11 11:02  gtang

	* rt/pyem/test_emdata.py: unit test update for EMData::rotavg()

2006-04-10 22:23  stevel

	* doc/latex/Makefile, libEM/processor.cpp, libEM/processor.h,
	  programs/e2foldfitter.py, programs/e2pdb2mrc.py: Program
	  improvements.

2006-04-10 18:14  gtang

	* libpyEM/: libpyEMData2.cpp, libpyTransform2.cpp: run
	  create_boost_python for Pawel's change.

2006-04-10 13:06  ppenczek

	* libEM/sparx/: rsconvolution.cpp, util_sparx.cpp: see what happens

2006-04-10 13:02  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: I doubt it works

2006-04-10 12:55  gtang

	* rt/emdata/rotate_translate.cpp: remove sparx_util.h/cpp

2006-04-10 12:49  gtang

	* libpyEM/: libpyEMData2.cpp, libpyFundamentals2.cpp,
	  libpyTypeConverter2.cpp, libpyUtils2.cpp: run create_boost_python
	  for remove Peak() SparxUtil() and move peak_search() to EMData()

2006-04-10 12:40  gtang

	* libpyEM/: typeconverter.h, typeconverter.pyste: remove
	  sparx_util.h

2006-04-10 12:31  gtang

	* libEM/sparx/emdata_sparx.cpp: add new function peak_search
	  --Zhong Huang

2006-04-10 12:24  gtang

	* libpyEM/utils.pyste: set return policy for Util::im_diff()

2006-04-10 12:19  gtang

	* libEM/: CMakeLists.txt, sparx/sparx_util.cpp, sparx/sparx_util.h:
	  remove sparx_util.h/cpp

2006-04-10 12:13  gtang

	* libpyEM/fundamentals.pyste: get rid of Peak and SparxUtil class.

2006-04-10 12:12  gtang

	* libpyEM/typeconverter.pyste: get rid of Peak() class,use Pixel
	  instead

2006-04-10 12:09  gtang

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: move
	  peak_search() to EMData class as member function.

2006-04-10 12:05  gtang

	* libEM/sparx/: sparx_util.cpp, sparx_util.h: change Peak to Pixel
	  in peak_search()

	  Zhong

2006-04-10 11:29  zhuang

	* libEM/sparx/: sparx_util.cpp, sparx_util.h: peak_search done

2006-04-09 22:05  ppenczek

	* libEM/: emdata.cpp, emdata.h, sparx/emdata_sparx.cpp,
	  sparx/emdata_sparx.h, sparx/fundamentals.h,
	  sparx/rsconvolution.cpp, sparx/util_sparx.cpp: more cleanup,
	  started rcvsp, but did not finish...

2006-04-09 18:46  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: rotational
	  average wors for 2D and 3D sh: wq: command not found

2006-04-09 18:02  ppenczek

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: merged

2006-04-09 16:06  ppenczek

	* libEM/projector.cpp: just fixing line alignment ;

2006-04-08 22:33  ppenczek

	* libEM/: emdata.h, emdata_transform.cpp, emdata_transform.h,
	  util.cpp, util.h, sparx/util_sparx.cpp, sparx/util_sparx.h: [no
	  log message]

2006-04-08 22:19  ppenczek

	* libEM/sparx/: normpadft.cpp, normpadft.h: [no log message]

2006-04-07 18:56  barry

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h:  barry

2006-04-07 17:11  phani

	* libEM/sparx/util_sparx.cpp: [no log message]

2006-04-07 16:12  phani

	* libEM/sparx/: util_sparx.cpp, util_sparx.h: [no log message]

2006-04-07 13:33  barry

	* libpyEM/libpyEMData2.cpp: [no log message]

2006-04-07 12:48  barry

	* libEM/sparx/: emdata_sparx.cpp, emdata_sparx.h: [no log message]

2006-04-06 18:21  ppenczek

	* libEM/sparx/emdata_sparx.cpp, libEM/sparx/emdata_sparx.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyTransform2.cpp,
	  libpyEM/libpyTypeConverter2.cpp, libpyEM/libpyUtils2.cpp: [no log
	  message]

2006-04-06 14:40  gtang

	* rt/pyem/test_processor.py: improve unit test for
	  'eman1.bilateral'

2006-04-06 14:29  gtang

	* libEM/processor.cpp: make 'eman1.bilateral' not crash on 2D
	  image.

2006-04-06 13:59  gtang

	* libEM/sparx/00_README_ADDING_NEW_CODE: [no log message]

2006-04-06 10:50  gtang

	* libEM/: CMakeLists.txt, emdata_core.h, emdata_io.h,
	  emdata_metadata.h, emdata_modular.h, emdata_transform.h,
	  util.cpp, util.h, sparx/util_sparx.cpp, sparx/util_sparx.h: split
	  util.h/cpp, add util_sparx.h/cpp.

2006-04-05 19:40  gtang

	* libEM/: CMakeLists.txt, emdata.cpp, emdata.h, emdata_core.cpp,
	  emdata_core.h, emdata_io.cpp, emdata_io.h, emdata_metadata.cpp,
	  emdata_metadata.h, emdata_modular.cpp, emdata_modular.h,
	  emdata_transform.cpp, emdata_transform.h, sparx/emdata_sparx.cpp,
	  sparx/emdata_sparx.h: Split emdata.h/cpp files: emdata_io.h/cpp
	  emdata_metadata.h/cpp emdata_transform.h/cpp emdata_core.h/cpp
	  emdata_sparx.h/cpp

2006-04-05 10:29  gtang

	* libEM/: emfft.cpp, emfft.h: ACML fft, still half way.

2006-04-04 16:10  gtang

	* rt/emdata/rotate_translate.cpp: test code for peak_search()

2006-04-04 12:06  gtang

	* libpyEM/libpyFundamentals2.cpp: add new function peak_search
	  --Zhong Huang

2006-04-04 11:47  gtang

	* libEM/sparx/: sparx_util.cpp, sparx_util.h: add new function
	  peak_search --Zhong Huang

2006-04-04 11:39  gtang

	* libpyEM/CMakeLists.txt, libpyEM/Makefile.pyste,
	  libpyEM/fundamentals.pyste, libpyEM/sparxutil.pyste,
	  libEM/sparx/sparx_util.cpp, libEM/sparx/sparx_util.h: add new
	  function peak_search --Zhong Huang

2006-04-04 11:36  gtang

	* libpyEM/typeconverter.pyste: add new function peak_search --Zhong
	  Huang

2006-04-03 20:54  gtang

	* libpyEM/: typeconverter.h, typeconverter.pyste: add new function
	  peak_search --Zhong Huang

2006-04-03 20:33  gtang

	* libEM/sparx/sparx_util.h: add new function peak_search --Zhong
	  Huang

2006-04-03 20:27  gtang

	* libpyEM/: Makefile.pyste, sparxutil.pyste: add new function
	  peak_search --Zhong Huang

2006-04-03 20:23  gtang

	* libpyEM/CMakeLists.txt, libpyEM/Makefile.pyste,
	  libpyEM/emdata.pyste, libpyEM/sparxutil.pyste,
	  libEM/sparx/sparx_util.cpp, libEM/sparx/sparx_util.h: add new
	  function peak_search --Zhong Huang

2006-04-03 14:36  gtang

	* libEM/CMakeLists.txt: add new function peak_search --Zhong Huang

2006-04-03 14:27  gtang

	* libEM/sparx/sparx_util.cpp, libEM/sparx/sparx_util.h,
	  libEM/sparx/util.cpp, libEM/sparx/util.h, libpyEM/emdata.pyste:
	  add new function peak_search --Zhong Huang

2006-04-03 11:53  ppenczek

	* libEM/CMakeLists.txt: [no log message]

2006-04-03 10:41  zhuang

	* libEM/sparx/: util.cpp, util.h: [no log message]

2006-03-31 15:15  gtang

	* libEM/: transform.cpp, transform.h: fix the
	  Transform3D.set_rotation() pass a python Dictionary parameter
	  bug.

2006-03-31 14:38  gtang

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp: fix the Transform3D.set_rotation()
	  pass a python Dictionary parameter bug.

2006-03-23 10:27  gtang

	* programs/golem: move out the small golem script.

2006-03-22 22:12  gtang

	* rt/CMakeLists.txt: move APTEST directory to sparx/Golem

2006-03-22 17:58  gtang

	* libpyEM/libpyUtils2.cpp: run create_boost_python after create
	  sparx sub directory in libEM.

2006-03-22 17:14  gtang

	* libEM/CMakeLists.txt, libEM/emdata.h, libEM/emfft.cpp,
	  libEM/processor.cpp, libEM/util.h, libpyEM/fundamentals.pyste,
	  libpyEM/libpyFundamentals2.cpp: move Pawel group's code to sparx
	  sub directory in libEM.

2006-03-22 16:47  gtang

	* libEM/CMakeLists.txt, libEM/emdata.h, libEM/emfft.cpp,
	  libEM/processor.cpp, libEM/processor.h, libEM/util.h,
	  libEM/sparx/CMakeLists.txt, libEM/sparx/emarray.h,
	  libEM/sparx/emconstants.h, libEM/sparx/fourierfilter.cpp,
	  libEM/sparx/fundamentals.cpp, libEM/sparx/fundamentals.h,
	  libEM/sparx/native_fft.cpp, libEM/sparx/native_fft.h,
	  libEM/sparx/normpadft.cpp, libEM/sparx/periodogram.cpp,
	  libEM/sparx/processor_sparx.h, libEM/sparx/rsconvolution.cpp,
	  libEM/sparx/tflm.cpp, libpyEM/Makefile.pyste,
	  libpyEM/fundamentals.pyste, libpyEM/libpyFundamentals2.cpp: move
	  Pawel group's code to sparx sub directory in libEM.

2006-03-21 17:17  gtang

	* doc/CMakeLists.txt: doc directory for Golem moved in from
	  eman2/doc/Golem

2006-03-21 17:01  gtang

	* libpyEM/CMakeLists.txt: move Golem out to the sparx project.

2006-03-19 16:56  gtang

	* CMakeLists.txt: ACML(AMD Core Math Library) fft, only 1D
	  available now.

2006-03-18 17:14  gtang

	* libEM/emfft.h: ACML(AMD Core Math Library) fft, only 1D available
	  now.

2006-03-18 16:05  gtang

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/emfft.cpp, libEM/emfft.h,
	  libpyEM/emdata_wrapitems.cpp, libpyEM/typeconverter.cpp,
	  libpyEM/typeconverter.h: ACML(AMD Core Math Library) fft, only 1D
	  available now.

2006-03-13 16:57  gtang

	* doc/latex/goals.tex: filter -> processor

2006-03-11 17:19  gtang

	* libEM/aligner.cpp, libEM/aligner.h, libEM/averager.cpp,
	  libEM/averager.h, libEM/cmp.cpp, libEM/cmp.h, libEM/emobject.h,
	  libEM/processor.cpp, libEM/processor.h, libEM/projector.cpp,
	  libEM/projector.h, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libpyEM/aligner.pyste,
	  libpyEM/averager.pyste, libpyEM/cmp.pyste,
	  libpyEM/libpyAligner2.cpp, libpyEM/libpyAverager2.cpp,
	  libpyEM/libpyCmp2.cpp, libpyEM/libpyProcessor2.cpp,
	  libpyEM/libpyProjector2.cpp, libpyEM/libpyReconstructor2.cpp,
	  libpyEM/processor.pyste, libpyEM/projector.pyste,
	  libpyEM/reconstructor.pyste: dump modular class(processor,
	  aligner, ...etc.) info as a dictionary {name:[list]}, for future
	  Pyhthon introspection programming.

2006-03-11 11:17  gtang

	* libpyEM/: CMakeLists.txt, EMAN2.py, EMAN2_cppwrap.py,
	  Makefile.pyste, libpyFilter2.cpp, libpyProcessor2.cpp: change
	  libpyFilter2.cpp -> libpyProcessor2.cpp

2006-03-10 20:21  gtang

	* libEM/emdata.cpp, libEM/emdata.h, libEM/processor.cpp,
	  libEM/processor.h, libpyEM/emdata.pyste,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyFilter2.cpp,
	  libpyEM/processor.pyste: The EMData::process() not process image
	  out of place. It will return a EMData object as result, the
	  original image will not be changed.

2006-03-10 17:22  gtang

	* examples/comparepairs.py, examples/makebigfromseq.py,
	  examples/sortsimilar.py, examples/transalignavg.py,
	  libEM/aligner.cpp, libEM/cmp.cpp, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/pointarray.cpp, libEM/processor.cpp,
	  libEM/processor.h, libEM/projector.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyFilter2.cpp, plugins/processor_template.cpp,
	  plugins/processor_template.h, programs/e2align3d.py,
	  programs/e2boxer.py, programs/e2classifykmeans.py,
	  programs/e2findsubunit.py, programs/e2foldfitter.py,
	  programs/e2make3d.py, programs/e2msa.py, programs/e2pdb2mrc.py,
	  programs/e2proc2d.py, programs/e2proc3d.py,
	  programs/e2project3d.py, programs/e2scannereval.py,
	  programs/e2tomogram.py, rt/demo/filter1.py, rt/demo/filter2.py,
	  rt/demo/filter3.py, rt/demo/processor1.py, rt/demo/processor2.py,
	  rt/demo/processor3.py, rt/emdata/emdata_api.cpp,
	  rt/emdata/rotate_translate.cpp, rt/pyem/test_aligner.py,
	  rt/pyem/test_averager.py, rt/pyem/test_cmp.py,
	  rt/pyem/test_emdata.py, rt/pyem/test_misc.py,
	  rt/pyem/test_processor.py, rt/pyem/test_utils.py,
	  utils/proc2d.cpp, utils/speedtest.cpp: change current
	  EMData::process() function name to EMData::process_inplace(). The
	  EMData::process() will become a out of place function call.

2006-03-10 16:22  gtang

	* libpyEM/emdata.pyste: add policy to new function
	  EMData::FH2Real()

2006-03-10 16:12  gtang

	* doc/adding_processor.txt: change file name filter -> processor

2006-03-09 14:19  gtang

	* libEM/emfft.cpp: code cleaning

2006-03-09 12:36  gtang

	* libEM/emdata.cpp: native FFT already done normalization by
	  itself, no need to do it in EMData::do_ift().

2006-03-09 12:34  gtang

	* rt/pyem/test_emdata.py: update unit test for do_fft()/do_ift(),
	  make sure after fft and ift, we get the original iamge data.

2006-03-08 18:34  gtang

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/emfft.cpp,
	  libEM/emfft.h: native fft code fron Chao incoporate into EMAN2.

2006-03-07 11:31  gtang

	* rt/pyem/: test_emdata.py, test_imageio.py, test_misc.py,
	  test_processor.py, test_transform.py, test_typeconverter.py,
	  test_utils.py, test_vec.py, testlib.py: change #!/bin/env to
	  #!/usr/bin/env

2006-03-07 09:57  dmann

	* doc/latex/python-scripts.tex: Missing documentation file added

2006-03-06 23:07  gtang

	* libpyEM/: libpyUtils2.cpp, utils.pyste: remove TwoDTestFunck,
	  etc. from utils.pyste to fix the broken EMAN2 compilation.

2006-03-05 15:19  prb

	* libEM/util.cpp: tidied utils.cpp

2006-03-05 14:36  prb

	* libEM/util.h, .cdtproject, .project, libEM/util.cpp: Changed
	  TwoDTestFunc so that the func, function in Fourier space,
	  projection and projection in Fourier space are all called from a
	  single function with a flag.

2006-03-05 10:10  wjiang

	* programs/: e2.py, e2align3d.py, e2aligntest.py, e2boxer.py,
	  e2cmmtomrc.py, e2ctfplot.py, e2dumplog.py, e2foldfitter.py,
	  e2pdb2mrc.py, e2proc2d.py, e2proc3d.py, e2project3d.py,
	  e2scannereval.py, e2startcsym.py, e2symbest.py, e2tomogram.py:
	  change /bin/env to /usr/bin/env

2006-03-05 00:52  stevel

	* programs/: e2boxer.py, e2classifykmeans.py: Working on new 2D
	  boxing method.

2006-03-03 14:56  gtang

	* CMakeLists.txt, doc/CMakeLists.txt: install /doc when make
	  install.

2006-03-03 10:59  prb

	* libEM/emdata.cpp, libEM/emdata.h, libEM/transform.cpp,
	  libEM/transform.h, libEM/util.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyTransform2.cpp, rt/CMakeLists.txt:   minor changes

2006-03-02 09:42  stevel

	* programs/e2align3d.py: Improved image viewer.

2006-03-01 17:31  gtang

	* CMakeLists.txt: install python unit test files to EMAN2/test
	  directory

2006-03-01 16:38  gtang

	* rt/emdata/testpolardata.cpp: minor bug fix for polardata test

2006-03-01 16:38  gtang

	* CMakeLists.txt: add target "test", so we can run make test to
	  invoke unit test for EMAN2

2006-03-01 16:37  gtang

	* rt/: CMakeLists.txt, pyem/CMakeLists.txt: install python unit
	  test files to EMAN2/test directory

2006-03-01 15:00  gtang

	* rt/pyem/test_emdata.py: add unit test for log() and log10() of
	  EMData

2006-03-01 12:58  gtang

	* libEM/emdata.cpp: logrithm math function for EMData

2006-03-01 12:36  gtang

	* libpyEM/: libpyEMData2.cpp, libpyPolarData2.cpp: EMData logrithm
	  math function.

2006-03-01 11:42  gtang

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/emdata.pyste: logrithm
	  math function for EMData

2006-02-26 19:20  ppenczek

	* libEM/emdata.h: defaults for FourInter added

2006-02-22 09:54  gtang

	* libEM/polardata.cpp: Fix the compilation error on water. make it
	  compatible with old compiler.

2006-02-21 16:33  gtang

	* libEM/polardata.cpp: PolarData implementation

2006-02-21 15:08  gtang

	* CMakeLists.txt: mark DJBFFT as advanced option

2006-02-21 14:11  gtang

	* rt/emdata/testpolardata.cpp, libpyEM/libpyPolarData2.cpp,
	  libEM/polardata.cpp, libEM/polardata.h: PolarData implementation

2006-02-14 13:38  prb

	* libEM/emdata.cpp, libEM/emdata.h, libEM/util.cpp, libEM/util.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/utils.pyste:	  Created a family of test functions
	  (cosine waves modulated by Gaussians) which have a nice
	  analytical form,
	     and for which it is easy to calculate, analytically, the
	  projections.

2006-02-13 16:57  gtang

	* rt/pyem/test_emdata.py, rt/pyem/test_processor.py,
	  rt/pyem/test_utils.py, libEM/testutil.cpp: unit test update

2006-02-10 20:01  gtang

	* libEM/emdata.cpp, libEM/mrcio.cpp, libEM/spiderio.cpp,
	  rt/pyem/test_emdata.py: replace attribute 'is_ri' with
	  'is_complex_ri'

2006-02-10 12:25  ppenczek

	* libEM/emdata.cpp: [no log message]

2006-02-09 16:58  gtang

	* libEM/emdata.cpp: debuging for EMData::FourInterpol()

2006-02-09 15:03  ppenczek

	* libEM/emdata.cpp: [no log message]

2006-02-08 12:31  gtang

	* libEM/polardata.h: PolarData implementation

2006-02-08 12:12  gtang

	* libEM/polardata.cpp: $Id$

2006-02-08 12:03  gtang

	* libEM/polardata.cpp: PolarData implementation

2006-02-08 11:48  gtang

	* libEM/: polardata.h: PolarData implementation

2006-02-08 11:43  gtang

	* libEM/polardata.h: PolarData implementation

2006-02-08 11:39  gtang

	* libEM/polardata.h: PolarData implementation

2006-02-08 11:21  gtang

	* libEM/polardata.h: PolarData implementation.

2006-02-08 11:16  gtang

	* libEM/polardata.h: PolarData implementation.

2006-02-07 18:14  gtang

	* rt/emdata/testpolardata.cpp: c++ testing code for PolarData
	  class.

2006-02-07 18:13  gtang

	* libEM/polardata.h: PolarData implementation.

2006-02-07 18:10  gtang

	* libEM/: polardata.h: PolarData implementation.

2006-02-07 18:06  gtang

	* libEM/: polardata.h: PolarData implementation.

2006-02-07 18:02  gtang

	* libEM/polardata.h: PolarData implementation.

2006-02-07 17:22  gtang

	* libpyEM/libpyPolarData2.cpp: PolarData implementation.

2006-02-07 17:08  gtang

	* libpyEM/polardata.pyste, libEM/polardata.cpp, libEM/polardata.h:
	  PolarData implementation.

2006-02-06 16:59  gtang

	* rt/emdata/: CMakeLists.txt, testpolardata.cpp: c++ testing code
	  for PolarData class.

2006-02-06 16:58  gtang

	* libEM/CMakeLists.txt, libEM/polardata.cpp, libEM/polardata.h,
	  libpyEM/CMakeLists.txt, libpyEM/EMAN2_cppwrap.py,
	  libpyEM/Makefile.pyste, libpyEM/libpyPolarData2.cpp,
	  libpyEM/polardata.pyste: Introduce PolarData, a specialized image
	  class for storing the results of a transform to polar
	  coordinates.

2006-02-04 21:43  gtang

	* libEM/emdata.h: fix the infamous null value created problem when
	  access a nonexisting key in attr_dict, for broken unit test in
	  hdf file IO.

2006-02-03 21:45  ppenczek

	* libEM/emdata.cpp: Almost works, except for fft

2006-02-03 21:17  gtang

	* libEM/emdata.cpp: minor fix for hdf file writing.

2006-02-03 21:00  gtang

	* libEM/emdata.cpp: minor fix for hdf file writing.

2006-02-03 14:50  gtang

	* libEM/hdfio.cpp: hdf file can write/read arbitrary attributes for
	  int/float/string. Previously, it just handle some predefined
	  attribute.

2006-02-01 09:54  gtang

	* libpyEM/: emdata.pyste, libpyEMData2.cpp: run create_boost_python
	  for EMData::FourInterPol --Grant Tang--

2006-02-01 09:46  ppenczek

	* libpyEM/emdata.pyste: [no log message]

2006-02-01 09:24  gtang

	* libpyEM/: libpyAligner2.cpp, libpyCmp2.cpp, libpyEMData2.cpp,
	  libpyFilter2.cpp, libpyGeometry2.cpp, libpyPointArray2.cpp,
	  libpyProjector2.cpp, libpyTransform2.cpp,
	  libpyTypeConverter2.cpp, libpyUtils2.cpp: I run
	  create_boost_python on NCMI server, which use all the Pyste thing
	  from old blake server.  --Grant Tang--

2006-02-01 09:18  gtang

	* libpyEM/: emdata.pyste, typeconverter.pyste, utils.pyste: change
	  these pyste files back since create_boost_python can run on NCMI
	  server now.

2006-02-01 08:53  ppenczek

	* libEM/: emdata.cpp, emdata.h: [no log message]

2006-02-01 08:34  ppenczek

	* libEM/: emdata.cpp, emdata.h: [no log message]

2006-01-31 23:20  stevel

	* libpyEM/libpyTypeConverter2.cpp: Temporary fix for typeconverter
	  problem with pyste

2006-01-31 20:14  stevel

	* libpyEM/: emdata.pyste, libpyEMData2.cpp,
	  libpyTypeConverter2.cpp: Pyste update

2006-01-31 14:16  gtang

	* libpyEM/: emdata.pyste, typeconverter.pyste, utils.pyste:
	  Temprarily solution for Pyste on blake server.  After done with
	  create_boost_python script, please add these lines into
	  libpyTypeConverter2.cpp:

	  #include <typeconverter.h>

	  BOOST_PYTHON_MODULE(libpyTypeConverter2) {	 class_<
	  EMAN::EMNumPy, boost::noncopyable >("EMNumPy", no_init)
	  .def("em2numpy", &EMAN::EMNumPy::em2numpy)
	  .def("numpy2em", &EMAN::EMNumPy::numpy2em)
	  .staticmethod("em2numpy")	    .staticmethod("numpy2em")	  ;

2006-01-31 02:02  stevel

	* libEM/: emdata.cpp, emdata.h: Complex flags now dictionary
	  attributes. New images default to RI not AP.

2006-01-30 18:15  ppenczek

	* libEM/util.cpp: [no log message]

2006-01-30 11:47  ppenczek

	* libEM/util.cpp: [no log message]

2006-01-29 15:02  ppenczek

	* libEM/: emdata.cpp, emdata.h: [no log message]

2006-01-29 10:19  ppenczek

	* libEM/emdata.h: [no log message]

2006-01-29 10:03  ppenczek

	* libEM/emdata.cpp: [no log message]

2006-01-28 20:27  ppenczek

	* libEM/emdata.cpp: obsolete comments from fft removed, should
	  somebody need them, please go back to the previous version

2006-01-28 19:14  ppenczek

	* libEM/emdata.cpp: removed setting to zero of padded area, it
	  should not be necessary, but who knows?

2006-01-28 01:55  stevel

	* libEM/util.h, libpyEM/emdata.pyste: Minor fix.

2006-01-28 01:06  stevel

	* libEM/util.cpp, libEM/util.h, libpyEM/libpyUtils2.cpp: Bugfixes
	  in svd

2006-01-27 00:39  stevel

	* libEM/: util.cpp, util.h: svdcmp using gsl

2006-01-26 17:36  ppenczek

	* libpyEM/: libpyTypeConverter2.cpp, libpyUtils2.cpp: reactivated
	  K-B stuff

2006-01-25 18:23  grant

	* doc/: EMAN2.pdf, EMAN2.ps, latex/EMAN2.lot:
	  libpyEM/Golem/projection.py

2006-01-25 15:23  ppenczek

	* libEM/emdata.cpp: changed rotation direction in fouriergridrot2d

2006-01-25 11:19  grant

	* libpyEM/util_wrapitems.h: remove extraneous line

2006-01-25 10:41  ppenczek

	* libEM/: util.cpp, util.h: and now works in two different ways

2006-01-24 22:33  ppenczek

	* libEM/: util.cpp, util.h: doesn work but complies

2006-01-23 15:08  grant

	* libEM/: util.cpp, util.h: Fixed up Util::Crosrng_ms wrapper to
	  use Steve's Dict hack.

2006-01-23 14:50  grant

	* libEM/util.cpp: remove debugging code in Util::crosrng_e

2006-01-23 14:20  grant

	* libEM/util.cpp, libEM/util.h, libpyEM/Makefile.pyste,
	  libpyEM/libpyTransform2.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/typeconverter.h, libpyEM/util_wrapitems.h,
	  libpyEM/utils.pyste: Util.{h,cpp} now has a Crosrng_e method that
	  wraps Util::crosrng_e and returns a
	  boost::tuple<double,float,int>.  When there's a working
	  boost::tuple to python tuple converter working this code should
	  work without changes.  Meanwhile, I've added in libpyEM/ a
	  util_wrapitems.h file that does the conversion to a python tuple
	  explicitly.  Unfortunately, I ran into a problem with pyste
	  inasmuch as it doesn't seem to know how to explicitly mark a
	  method as a static method, so I've hacked the
	  libpyEM/Makefile.pyste to explicitly sed the generated
	  libpyUtils2.cpp file.  Ugh!  Better solutions gratefully
	  accepted.

2006-01-23 02:03  stevel

	* libEM/emdata.cpp, libpyEM/EMAN2.py: New footprint routine
	  working.

2006-01-20 14:51  ppenczek

	* libEM/: util.cpp, util.h:
	  temp

2006-01-20 14:26  gtang

	* libEM/emdata.cpp: a.calc_ccf(a) a.calc_ccf(None)  will both
	  calculate autocorrelation

	  a.calc_mutual_correlation(a) a.calc_mutual_correlation(None)
	  will both calculate self_correlation

2006-01-20 14:24  ppenczek

	* libEM/util.cpp, libEM/util.h, libpyEM/libpyUtils2.cpp: more
	  stuff, Pawel.

2006-01-19 18:49  ppenczek

	* libEM/util.cpp, libEM/util.h, libpyEM/libpyUtils2.cpp,
	  libpyEM/utils.pyste: more pawel's effort

2006-01-19 18:14  ppenczek

	* libEM/emdata.cpp, libEM/util.cpp, libEM/util.h,
	  libpyEM/libpyAligner2.cpp, libpyEM/libpyCmp2.cpp,
	  libpyEM/libpyFilter2.cpp, libpyEM/libpyPointArray2.cpp,
	  libpyEM/libpyProjector2.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/utils.pyste: pawel's new effort

2006-01-16 01:28  stevel

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/CMakeLists.txt,
	  libpyEM/emdata.pyste, libpyEM/libpyEMData2.cpp,
	  programs/e2proc2d.py: make_footprint

2006-01-12 14:44  grant

	* libEM/emdata.cpp: updates

2006-01-07 11:20  stevel

	* examples/makebigfromseq.py: New example for astronomy

2005-12-19 14:50  grant

	* libEM/util.h: fix doc error; thanks to Chao

2005-12-15 23:18  stevel

	* examples/telescope.py, programs/e2.py: FFT support in image
	  display, and weak references used.

2005-12-15 01:48  stevel

	* libEM/processor.cpp: Work on gui

2005-12-12 19:17  stevel

	* libEM/: processor.cpp, processor.h: Working on amp weighting
	  processor.

2005-12-12 09:47  gtang

	* rt/pyem/: test_emdata.py: unit test update

2005-12-12 09:43  gtang

	* rt/pyem/test_emdata.py: unit test update

2005-12-12 09:37  gtang

	* rt/pyem/test_processor.py: unit test update

2005-12-11 12:25  stevel

	* libEM/processor.cpp, libEM/processor.h, programs/e2.py: Various
	  fixes.

2005-12-09 02:25  stevel

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/CMakeLists.txt,
	  programs/e2.py: Working on more controls for image GUI

2005-12-08 10:17  stevel

	* examples/transalignavg.py, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/processor.cpp, libEM/processor.h, libEM/util.cpp,
	  libEM/util.h, libpyEM/CMakeLists.txt, programs/e2.py: Workign on
	  new EMAN2 gui.

2005-12-07 09:04  gtang

	* libEM/transform.cpp: minor fix for water.3dem.bioch.bcm.tmc

2005-12-07 00:05  stevel

	* programs/e2.py: Beginning of an EMAN2 GUI.

2005-12-06 15:00  gtang

	* libEM/Assert.h, libEM/byteorder.h, libEM/ctf.h, libEM/dm3io.cpp,
	  libEM/emcache.h, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emobject.cpp, libEM/hdfio.cpp, libEM/imagicio.cpp,
	  libEM/interp.h, libEM/log.h, libEM/lstio.cpp, libEM/mrcio.cpp,
	  libEM/pgmio.cpp, libEM/portable_fileio.h, libEM/processor.cpp,
	  libEM/processor.h, libEM/testutil.cpp, libEM/tifio.cpp,
	  libEM/transform.cpp, libEM/util.cpp, libEM/util.h,
	  libEM/v4l2io.cpp, libEM/vec3.h, libEM/vtkio.cpp,
	  libEM/xydata.cpp, libEM/hdfio.h, libEM/log.cpp,
	  rt/emdata/blankimg.cpp, rt/emdata/fft.cpp, rt/emdata/rotate.cpp,
	  rt/emdata/rotate_phi.cpp, rt/imageio/basic.cpp,
	  rt/imageio/imageio.cpp, utils/proc2d.cpp, utils/speedtest.cpp:
	  header inclusion cleaning, substitute #include <*.h> with
	  #include <c*>

2005-12-05 18:05  gtang

	* libEM/: pointarray.h, processor.cpp, projector.cpp,
	  reconstructor.cpp, tifio.cpp, util.cpp, util.h: header inclusion
	  cleaning

2005-12-05 18:02  gtang

	* libEM/: emdata.cpp, emdata.h, exception.cpp, hdfio.cpp,
	  pngio.cpp: header inclusion cleaning

2005-12-05 16:24  grant

	* libEM/: emdata.cpp, util.cpp: Fix broken periodic boundary
	  conditions in Util::quadri

2005-12-02 21:06  stevel

	* examples/transalignavg.py: New demo

2005-12-02 20:05  stevel

	* examples/telescope.py, libEM/v4l2io.cpp, libEM/v4l2io.h:
	  Telescope work

2005-12-02 16:47  gtang

	* libEM/emdata.cpp: minor fix, misuse 'or', should be '||'

2005-12-02 16:42  gtang

	* libEM/projector.cpp: minor fix, misuse 'or', should be '||'

2005-12-01 14:50  gtang

	* INSTALL: delete untrue comment.

2005-12-01 01:05  stevel

	* libEM/: v4l2io.cpp, v4l2io.h: v4l2 with webcams. Lots of
	  hardcoded options at the moment.

2005-11-30 17:54  grant

	* libpyEM/: emdata.pyste, libpyEMData2.cpp: Remove unnecessary
	  all_imageio.h include, since boost.python and png.h have an
	  unfortunate setjmp.h include order problem

2005-11-30 16:50  grant

	* libEM/emdata.cpp: trivial changes

2005-11-30 15:27  grant

	* libEM/emdata.cpp, libEM/emdata.h, libEM/projector.cpp,
	  libEM/projector.h, libEM/util.cpp, libEM/util.h,
	  libpyEM/emdata.pyste, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyGeometry2.cpp, libpyEM/libpyReconstructor2.cpp,
	  libpyEM/libpyTransform2.cpp, libpyEM/libpyUtils2.cpp: Fourier
	  gridding projections added

2005-11-30 14:37  grant

	* libEM/: emdata.cpp, emdata.h: add array offset guards in some
	  EMData methods; fix broken 3-d padded image centering; fix broken
	  3-d fft shuffling; fix broken 3-D cmplx method; add a helper
	  script to Golem/utilities to generate an image from a
	  simply-formatted text file

2005-11-29 09:40  gtang

	* libEM/hdfio.cpp: still hdf version issue, blake use hdf 1.4.5 to
	  compile EMAN2.

2005-11-29 01:39  stevel

	* examples/telescope.py, libEM/v4l2io.cpp, libEM/v4l2io.h:
	  Telescope mods.

2005-11-28 11:30  gtang

	* libEM/hdfio.cpp: make EMAN2 compilable with hdf5 1.6.5

2005-11-22 16:39  stevel

	* libEM/v4l2io.cpp: Trivial

2005-11-22 10:47  gtang

	* INSTALL: hdf5 1.6.4 is supported now.

2005-11-22 10:41  gtang

	* libEM/hdfio.h: H5 version already defined in H5pulic.h

2005-11-22 10:30  gtang

	* libEM/: hdfio.cpp, hdfio.h: a temporary solution to deal with hdf
	  1.6.3 and 1.6.4 version incompatibility problem.

2005-11-22 02:16  stevel

	* libEM/: hdfio.cpp, v4l2io.cpp, v4l2io.h: V4L2 input working, at
	  least in certain cases.

2005-11-21 17:03  gtang

	* libEM/processor.cpp: minor update to testimage.scurve

2005-11-21 15:32  stevel

	* libEM/v4l2io.cpp: Work on v4l reader

2005-11-21 11:38  stevel

	* CMakeLists.txt, libEM/all_imageio.h, libEM/emutil.cpp,
	  libEM/hdfio.cpp, libEM/v4l2io.cpp, libpyEM/libpyUtils2.cpp,
	  pyemtbx/imagetypes.py: v4l2 better

2005-11-21 11:17  prb

	* libEM/emdata.cpp, libpyEM/Makefile.pyste,
	  libpyEM/libpyReconstructor2.cpp, libpyEM/libpyUtils2.cpp: I only
	  touched emdata.cpp; I removed MArray2D in the Fourier Harmonic
	  sections of code

2005-11-21 09:03  stevel

	* CMakeLists.txt: v4l flag

2005-11-21 09:00  stevel

	* libEM/: CMakeLists.txt, all_imageio.h, emutil.cpp, emutil.h,
	  hdfio.cpp, v4l2io.cpp, v4l2io.h: New video4linux2 support.
	  Untested, but compiles.

2005-11-20 15:52  gtang

	* rt/pyem/test_averager.py: unit test update, no
	  ReverseGriddingReconstructor any more.

2005-11-18 14:48  grant

	* libEM/: cmp.cpp, emdata.cpp, emdata.h, processor.cpp,
	  projector.cpp, reconstructor.cpp, reconstructor.h, util.cpp: Fix
	  almost all code using MArray or MCArray.

2005-11-16 13:29  grant

	* libpyEM/emdata_wrapitems.py: Removing old python wrapper file

2005-11-15 16:21  grant

	* CMakeLists.txt, libEM/emdata.h: Add compile-time optional bounds
	  checking to EMData's operator() and .cmplx

2005-11-15 11:54  grant

	* libpyEM/CMakeLists.txt, libpyEM/EMAN2_cppwrap.py,
	  libpyEM/emdata.pyste, libpyEM/emdata_wrapitems.cpp,
	  libpyEM/emdata_wrapitems.h, libpyEM/libpyEMData2.cpp,
	  rt/pyem/test_emdata.py: New __getitem__ and __setitem__ wrappers
	  for EMData

2005-11-14 23:58  stevel

	* programs/e2boxer.py: Option fix

2005-11-10 09:15  gtang

	* libEM/: util.cpp, projector.cpp, processor.cpp: make explicit
	  type conversion to suppress warnings in Visual Studio

2005-11-07 13:40  gtang

	* rt/pyem/test_misc.py: unit test update

2005-11-07 11:54  eman1

	* libpyEM/libpyEMData2.cpp: fix the default argument issue for
	  EMData::FH2F().

2005-11-07 11:44  gtang

	* rt/pyem/test_emdata.py: unit test update

2005-11-06 14:23  prb

	* libEM/emdata.cpp, libEM/emdata.h, libEM/transform.cpp,
	  libEM/transform.h, libpyEM/libpyTransform2.cpp: Just some small
	  changes: added finger, and get magnitude methods.

2005-11-04 12:44  dmann

	* doc/: EMAN2.dvi, EMAN2.pdf, EMAN2.ps, latex/EMAN2.tex,
	  latex/TOC.tex, latex/e2align3d.tex, latex/e2aligntest.tex,
	  latex/e2boxer.tex, latex/e2cmmtomrc.tex, latex/e2dumplog.tex,
	  latex/e2foldfitter.tex, latex/e2make3d.tex, latex/e2pdb2mrc.tex,
	  latex/e2proc2d.tex, latex/e2proc3d.tex, latex/e2project3d.tex,
	  latex/e2scannereval.tex, latex/e2symbest.tex,
	  latex/e2tomogram.tex: Added documentation for most of the python
	  scripts located in the programs directory

2005-11-04 12:07  dmann

	* programs/: e2align3d.py, e2aligntest.py, e2boxer.py,
	  e2cmmtomrc.py, e2foldfitter.py, e2pdb2mrc.py, e2scannereval.py,
	  e2tomogram.py: Removed an extra "Usage: " from the usage string
	  for OptionParser

2005-11-03 16:37  dmann

	* doc/latex/: make3d.tex, project3d.tex: Documentation for new
	  scripts

2005-11-03 16:36  dmann

	* doc/latex/TOC.tex, doc/latex/adding-components.tex,
	  doc/latex/misc-developers-guide.tex, programs/e2make3d.py:
	  Documentation update

2005-11-02 13:00  dmann

	* programs/e2make3d.py: Forgot to turn on the logger

2005-11-02 12:55  dmann

	* programs/: e2make3d.py, e2project3d.py: Initial versions of
	  make3d and project3d

2005-10-31 14:03  dmann

	* libEM/: projector.cpp, projector.h: Fixed bugs in
	  GaussFFTProjector

2005-10-28 15:09  grant

	* libEM/CMakeLists.txt, libpyEM/fundamentals.pyste,
	  libpyEM/libpyFundamentals2.cpp: Zhong's first addition, still in
	  progress

2005-10-25 16:28  dmann

	* libEM/projector.cpp: changed the "standard" projector to accept
	  angles instead of radians and fixed the rotation matrix

2005-10-24 16:32  gtang

	* libEM/util.h: no isinff() and isnanf() on Mac OS, use old way to
	  judge good float.

2005-10-24 16:25  gtang

	* libEM/: util.h: no isinff() and isnanf() on Mac OS, use old way
	  to judge good float.

2005-10-20 17:18  gtang

	* libEM/processor.cpp: minor fix for exception catch

2005-10-20 17:17  gtang

	* rt/pyem/test_processor.py: unit test update for new processor

2005-10-17 16:28  grant

	* libEM/emdata.cpp, libEM/processor.cpp, libEM/processor.h,
	  libEM/transform.h, libEM/util.cpp, libpyEM/libpyFilter2.cpp,
	  libpyEM/libpyTransform2.cpp: Added integer shift processor

2005-10-17 11:05  ppenczek

	* libEM/emdata.cpp: fsc corrected

2005-10-14 10:55  gtang

	* CMakeLists.txt: turn on more warning message whrn ENABLE_DEBUG is
	  ON for GCC.

2005-10-11 13:46  grant

	* libEM/emdata.cpp, libEM/util.cpp, libEM/util.h,
	  libpyEM/libpyUtils2.cpp: gridding now (mostly) works, but boy is
	  it ugly

2005-10-11 10:53  gtang

	* libEM/: emdata.cpp, aligner.cpp: put the printf message in DEBUG
	  mode, this make unit test output cleaner

2005-10-11 10:53  gtang

	* rt/pyem/: test_emdata.py, test_averager.py: testing code update

2005-10-10 18:36  grant

	* libEM/emdata.cpp, libEM/emdata.h, libEM/util.cpp, libEM/util.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyUtils2.cpp: Gridding still
	  broken

2005-10-10 11:49  gtang

	* rt/pyem/test_processor.py: testing code update

2005-10-07 13:26  dmann

	* doc/EMAN2.pdf, doc/EMAN2.ps, libEM/reconstructor.cpp: Fixed issue
	  with rotation matrix and FourierReconstructor class

2005-10-06 09:07  dmann

	* libEM/: processor.cpp, processor.h: Added a new processor to
	  normalize CCD images

2005-10-05 17:41  gtang

	* libEM/util.cpp: fix compilation error and warning on Window
	  visual studio platform.

2005-10-05 17:26  gtang

	* libEM/emdata.cpp: fix compilation error and warning on Window
	  visual studio platform.

2005-10-05 17:06  gtang

	* libEM/processor.cpp: fix compilation error and warning on Window
	  visual studio platform.

2005-10-05 17:01  gtang

	* libEM/processor.cpp: fix compilation error and warning on Window
	  visual studio platform.

2005-10-05 16:31  gtang

	* libEM/cmp.cpp: fix compilation error on Window visual studio
	  platform.

2005-10-05 15:56  gtang

	* libEM/: util.cpp, emdata.cpp: fix compilation error on Window
	  visual studio platform.

2005-10-05 15:41  gtang

	* libEM/emdata.cpp: fix compilation error on Window visual studio
	  platform.

2005-10-05 15:31  gtang

	* libEM/: emdata.cpp, processor.cpp: fix compilation error on
	  Window visual studio platform.

2005-10-05 15:12  gtang

	* libEM/emdata.cpp: fix compilation error on Window visual studio
	  platform.

2005-10-05 14:42  gtang

	* libEM/util.h: fix compilation error on Window visual studio
	  platform.

2005-10-05 14:34  gtang

	* libEM/util.h: fix compilation error on Window visual studio
	  platform.

2005-10-05 13:56  gtang

	* libEM/util.h: keep the old implementation of goodf() for Windows
	  platform.  isinff() and isnanf() is not supported on Windows.

2005-10-04 17:32  grant

	* libEM/emdata.cpp: window_center fix

2005-10-04 11:35  gtang

	* libEM/util.h: change goodf() implementation to utilize isinff()
	  and isnanf(), the old implementation cause problem on Fedora Core
	  64 bit system.

2005-10-04 09:54  grant

	* libEM/cmp.h, libEM/emdata.cpp, libEM/emdata.h,
	  libpyEM/libpyEMData2.cpp: add image complex conjugation

2005-10-03 10:49  grant

	* libEM/cmp.cpp, libEM/cmp.h, libEM/emdata.cpp, libEM/emdata.h,
	  libpyEM/libpyEMData2.cpp: added EMData::masked_stats and
	  CMP::CccCmp

2005-09-30 15:53  dmann

	* doc/: EMAN2.pdf, EMAN2.ps, latex/Makefile: Documentation update

2005-09-30 15:17  dmann

	* libEM/reconstructor.cpp: Fixed problem limiting image size

2005-09-29 15:37  dmann

	* doc/EMAN2.pdf, doc/EMAN2.ps, doc/latex/adding-components.tex,
	  doc/latex/adding-documentation.tex, doc/latex/coding-style.tex,
	  doc/latex/exceptions.tex, doc/latex/frame-work-testing.tex,
	  doc/latex/help-opt-prog-inst.tex, doc/latex/install.tex,
	  doc/latex/logger.tex, doc/latex/misc-developers-guide.tex,
	  doc/latex/using-cvs.tex, libEM/emdata.cpp: fixed bug in
	  documentation and in EMData::get_clip()

2005-09-29 12:14  gtang

	* rt/pyem/test_emdata.py: add unit test for modifided
	  window_center()

2005-09-29 11:37  grant

	* libEM/emdata.cpp, libEM/emdata.h, libEM/reconstructor.cpp,
	  libpyEM/emdata.pyste, libpyEM/libpyEMData2.cpp: gridding closer
	  to working; changed window_padded to window_center and made the
	  method less stupid

2005-09-29 10:58  dmann

	* libEM/geometry.cpp, libEM/geometry.h, libpyEM/libpyGeometry2.cpp:
	  Added 1D Region support

2005-09-21 11:55  dmann

	* doc/latex/: Makefile, TOC.tex, adding-components.tex,
	  adding-documentation.tex, coding-style.tex, exceptions.tex,
	  frame-work-testing.tex, help-opt-prog-inst.tex, install.tex,
	  logger.tex, misc-developers-guide.tex, using-cvs.tex: doc update

2005-09-21 10:11  gtang

	* CMakeLists.txt: suppress the warning message in Mac OSX.

2005-09-19 17:27  grant

	* libEM/emdata.cpp: gridding stuff still in progress

2005-09-19 17:07  grant

	* libEM/emdata.cpp, libEM/emdata.h, libEM/processor.cpp,
	  libpyEM/emdata.pyste, libpyEM/libpyEMData2.cpp,
	  rt/pyem/test_emdata.py: fixed fft_shuffle method and added unit
	  tests

2005-09-19 14:20  grant

	* libEM/util.cpp, libEM/util.h, libpyEM/emdata.pyste,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyUtils2.cpp: KB window
	  update which allows for different units in the tabulation

2005-09-15 18:18  grant

	* libEM/: all_imageio.h, emdata.cpp, emdata.h: more gridding; still
	  almost certainly broken

2005-09-15 11:04  eman1

	* libpyEM/: libpyEMData2.cpp, libpyTransform2.cpp: fix the default
	  argument handling problem in Python.

2005-09-14 20:15  grant

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/libpyEMData2.cpp: new
	  convenience function: EMData::center_padded

2005-09-14 16:23  prb

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp: put back the inverse method

2005-09-14 15:38  prb

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp:	added a transpose method

2005-09-14 11:16  gtang

	* libEM/cmp.cpp: fix a warning message convert double to int

2005-09-13 17:17  dmann

	* doc/: EMAN2.pdf, EMAN2.ps: Doc. update

2005-09-13 17:16  dmann

	* doc/EMAN2.pdf, doc/EMAN2.ps, doc/latex/TOC.tex,
	  doc/latex/adding-documentation.tex,
	  doc/latex/development-policy-faq.tex, doc/latex/exceptions.tex,
	  doc/latex/logger.tex, doc/latex/misc-developers-guide.tex,
	  libEM/processor.h: Documentation update

2005-09-13 16:23  grant

	* libEM/emdata.cpp: bug fix

2005-09-12 15:59  dmann

	* doc/: EMAN2.pdf, EMAN2.ps, latex/adding-documentation.tex: forgot
	  to add a section

2005-09-12 15:39  dmann

	* doc/: EMAN2.pdf, EMAN2.ps, latex/EMAN2.tex, latex/TOC.tex,
	  latex/adding-documentation.tex, latex/misc-developers-guide.tex,
	  latex/rm_preamble.py: Another update to the doc files

2005-09-12 15:36  grant

	* libEM/transform.h: Transform3D ctor fix

2005-09-11 14:39  prb

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp: PRB added a get_rotation method to
	  pull out the matrix directly.

2005-09-09 13:50  grant

	* libEM/: emdata.cpp, reconstructor.h: reconstructor fix and
	  gridding (still in progress)

2005-09-09 13:44  prb

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp:	PRB added a constructor and a set
	  rotation: so that one can enter the transformation
	   matrix directly.

2005-09-08 17:05  dmann

	* doc/latex/: distutils.sty, manual.cls, manual.tex, pypaper.sty,
	  python.ist, python.sty: don't need these anymore

2005-09-08 16:59  dmann

	* doc/latex/: EMAN2.tex, exceptions.tex, goals.tex,
	  image-header-attribs.tex, install.tex: fixed some layout issues

2005-09-08 16:47  gtang

	* rt/pyem/test_averager.py: unit test for reconstructor

2005-09-08 16:43  gtang

	* libEM/reconstructor.cpp: add ReverseGriddingReconstructor to
	  factory

2005-09-08 16:20  dmann

	* doc/latex/: EMAN2.tex, Makefile, adding-components.tex,
	  coding-style.tex, exceptions.tex, frame-work-testing.tex,
	  image-header-attribs.tex, misc-developers-guide.tex: removed all
	  components of python style doc

2005-09-08 16:20  gtang

	* libEM/reconstructor.cpp: default symmetry for
	  PawelBackProjectionReconstructor is "c1"

2005-09-08 10:05  grant

	* libEM/util.cpp: forgot to remove spurious #include

2005-09-07 09:27  dmann

	* doc/EMAN2.pdf: pdf version of doc

2005-09-07 08:48  dmann

	* doc/: EMAN2.dvi, EMAN2.ps: updated docs

2005-09-06 12:39  dmann

	* doc/latex/hyperref.perl: file needed for proper LaTex to html
	  conversion

2005-09-06 10:27  dmann

	* makedoc.sh, doc/eman2doc.h: Added a few links

2005-09-06 10:26  dmann

	* doc/latex/: EMAN2.tex, Makefile, exceptions.tex,
	  image-header-attribs.tex: Added a few links and a doc file

2005-09-06 10:02  dmann

	* doc/eman2doc.h: [no log message]

2005-09-03 17:22  gtang

	* rt/pyem/: test_averager.py, test_emdata.py: unit test update

2005-09-02 17:19  grant

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/emdata.pyste,
	  libpyEM/libpyEMData2.cpp: gridding rotations still in progress,
	  and broken

2005-09-02 14:35  dmann

	* doc/latex/reference-manual.tex: fixed a link

2005-09-02 13:47  dmann

	* doc/EMAN2.ps: ps version of the doc so far

2005-09-02 13:38  dmann

	* doc/latex/: EMAN2.lot, EMAN2.tex, Makefile, abstract.tex,
	  adding-components.tex, coding-style.tex,
	  development-policy-faq.tex, dirs.tex, distutils.sty,
	  exceptions.tex, factory-classes.tex, fancyhdr.sty, fncychap.sty,
	  goals.tex, help-opt-prog-inst.tex, index.tex, install.tex,
	  ltxmarkup.sty, manual.cls, manual.tex, misc-developers-guide.tex,
	  processors.tex, pypaper.sty, python.ist, python.sty,
	  reference-manual.tex: doc files

2005-09-02 13:34  dmann

	* doc/EMAN2.dvi: documentation file

2005-09-01 14:48  gtang

	* rt/pyem/test_aligner.py: unit test for aligner

2005-09-01 13:23  gtang

	* rt/pyem/test_cmp.py: unit test update

2005-09-01 11:11  gtang

	* rt/pyem/test_cmp.py: finish unit test for cmp

2005-09-01 10:36  gtang

	* rt/pyem/: test_processor.py, test_cmp.py: unit test update

2005-09-01 09:47  gtang

	* rt/pyem/test_utils.py: unit test update

2005-08-31 23:49  stevel

	* programs/e2boxer.py: Support farfocus option

2005-08-31 21:40  stevel

	* programs/e2boxer.py: trivial

2005-08-31 20:52  stevel

	* programs/e2boxer.py: work on boxer

2005-08-31 17:30  gtang

	* rt/pyem/test_emdata.py: unit test update

2005-08-31 15:38  grant

	* libEM/emdata.cpp: real fix of get_attr_header breakage

2005-08-31 11:13  stevel

	* libEM/: cmp.cpp, emdata.cpp: Implement matched filter. Fixed
	  calc_radial... for complex images.

2005-08-31 10:33  gtang

	* libEM/processor.cpp: comment out a printf message.

2005-08-31 10:28  eman1

	* libpyEM/: libpyEMData2.cpp, libpyGeometry2.cpp,
	  libpyTransform2.cpp: run create_boost_python again to fix the
	  default argument handling fail.--Grant Tang

2005-08-31 02:05  stevel

	* programs/e2boxer.py: oops

2005-08-30 22:59  grant

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/emdata.pyste,
	  libpyEM/libpyEMData2.cpp: more work in progress

2005-08-30 14:48  gtang

	* rt/pyem/test_processor.py: finish unit test for processor

2005-08-29 17:16  gtang

	* rt/pyem/test_processor.py: continue on unit test for processor

2005-08-29 17:15  gtang

	* libEM/processor.cpp: add exception and couple of bug fix

2005-08-29 12:12  dmann

	* doc/developer-guide.html: [no log message]

2005-08-29 10:04  gtang

	* libEM/: transform.h, util.h, vec3.h: label testing status

2005-08-28 17:32  gtang

	* rt/pyem/: test_filter.py, test_processor.py: unit test for
	  processor

2005-08-28 17:32  gtang

	* rt/emdata/rotate_translate.cpp: testing code

2005-08-28 16:03  gtang

	* libEM/processor.h: fix the implementation error in
	  SigmaProcessor.

2005-08-27 10:48  gtang

	* libEM/emdata.h: fix a typo is_complex to is_complex_x in
	  set_complex()

2005-08-26 18:01  grant

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyGeometry2.cpp, libpyEM/libpyTransform2.cpp: fixed
	  broken get_attr_dict, I hope

2005-08-26 16:10  eman1

	* libpyEM/: libpyEMData2.cpp, libpyUtils2.cpp: run
	  create_boost_python, fix teh broken libpy*.cpp not handle default
	  argument.  --Grant Tang

2005-08-26 15:45  gtang

	* libEM/emdata.h, libEM/processor.h, rt/pyem/test_filter.py: change
	  filter name and parameter to small case.

2005-08-26 13:46  grant

	* libEM/util.cpp, libEM/util.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyUtils2.cpp: Updated Util::KaiserBessel to handle
	  more parameters

2005-08-26 12:15  grant

	* libEM/cmp.cpp: Commented out lines defining unused variables

2005-08-25 20:34  grant

	* libEM/: emdata.cpp, emdata.h: work in progress

2005-08-25 17:40  gtang

	* rt/pyem/test_filter.py: unit test for processor

2005-08-25 17:27  gtang

	* libEM/processor.h: fix an implementation error in
	  CollapseProcessor

2005-08-25 15:58  grant

	* libEM/: emdata.cpp, emdata.h, spiderio.cpp, spiderio.h,
	  sspiderio.cpp: Change spider I/O to handle complex (even and odd)
	  images

2005-08-25 11:29  gtang

	* rt/pyem/rt.sh: unit test update

2005-08-25 11:28  gtang

	* rt/pyem/rt.py: regression test script, run all python unit test
	  under current directory.

2005-08-25 11:11  gtang

	* rt/pyem/test_transform.py: unit test update

2005-08-25 11:08  gtang

	* libEM/transform.cpp: to_identity() make diagonal element 1, rest
	  0.

2005-08-25 10:57  gtang

	* rt/pyem/test_filter.py: unit test update

2005-08-25 10:42  gtang

	* rt/pyem/: testImage.py, test_imageio.py, test_misc.py: unit test
	  update

2005-08-24 18:39  eman1

	* libpyEM/libpyUtils2.cpp: run create boost python for modified
	  util.pyste --Grant Tang

2005-08-24 18:08  gtang

	* libpyEM/utils.pyste: exclude functions not callable in Python

2005-08-24 18:06  gtang

	* rt/pyem/test_utils.py: unit test for Util class

2005-08-24 17:08  grant

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/EMAN2_cppwrap.py,
	  libpyEM/emdata.pyste, libpyEM/emdata_wrapitems.py,
	  libpyEM/libpyEMData2.cpp: Add new subscripting support for emdata
	  objects in both c++ and python

2005-08-24 16:09  gtang

	* rt/pyem/: test_utils.py, test_typeconverter.py: unit test for
	  type converter

2005-08-24 16:03  gtang

	* rt/pyem/test_emdata.py: unit test for EMData

2005-08-24 16:02  gtang

	* rt/pyem/test_typeconverter.py: unit test for type converter

2005-08-24 16:01  gtang

	* libpyEM/typeconverter.cpp: fix the broken EMNumPy::numpy2em()

2005-08-24 14:30  dmann

	* INSTALL, doc/INSTALL, doc/developer-guide.html: [no log message]

2005-08-24 12:30  gtang

	* rt/pyem/test_transform.py: unit test for Transform3D class

2005-08-24 12:29  gtang

	* rt/pyem/test_vec.py: unit test for Vec3i and Vec3f class

2005-08-24 11:51  gtang

	* rt/pyem/test_transform.py: unit test for Transform3D class

2005-08-23 11:44  gtang

	* libEM/emdata.h: put some testing status label on

2005-08-23 10:33  gtang

	* libEM/emdata.h: minor fix to comment

2005-08-22 16:03  eman1

	* libpyEM/libpyUtils2.cpp: remove two functions, one in Util, one
	  in EMUtil to make EMAN2 compilable with boost 1.33.0

2005-08-22 15:46  gtang

	* libpyEM/utils.pyste: exclude two functions to make EMAN2
	  compilable with boost 1.33.0

2005-08-22 15:41  gtang

	* rt/pyem/test_emdata.py: unit test for EMData class almost
	  finished now.

2005-08-22 15:40  gtang

	* libEM/emdata.h: minor fix to comment

2005-08-22 14:45  gtang

	* libEM/emdata.h: minor fix to comment

2005-08-21 18:05  gtang

	* rt/emdata/rotate_translate.cpp: some testing code.

2005-08-21 17:46  gtang

	* libpyEM/emdata.pyste: fix problem in some functions in EMData
	  class: power(), real(), imag(), real2complex()

2005-08-21 17:37  gtang

	* rt/pyem/test_emdata.py: unit test for EMData

2005-08-21 17:36  gtang

	* libEM/: emdata.cpp, emdata.h: fix problem in some functions in
	  EMData class: power(), real(), imag(), real2complex()

2005-08-21 15:51  eman1

	* libpyEM/libpyEMData2.cpp: run create_boost_python. --Grant Tang

2005-08-21 15:23  gtang

	* libEM/emdata.cpp: fix problem in some functions in EMData class:
	  power(), real(), imag(), real2complex()

2005-08-21 15:15  gtang

	* libpyEM/emdata.pyste, libEM/emdata.h, libEM/emdata.cpp: fix
	  problem in some functions in EMData class: power(), real(),
	  imag(), real2complex()

2005-08-20 13:27  gtang

	* rt/pyem/test_emdata.py: unit test for EMData

2005-08-20 13:17  gtang

	* libEM/emdata.cpp: fix some routines forget to set is_complex_x
	  flag

2005-08-20 12:21  gtang

	* libEM/emdata.h: fix an error in set_value_at()

2005-08-19 16:20  gtang

	* rt/pyem/test_emdata.py: unit test for EMData

2005-08-19 10:15  eman1

	* libpyEM/: libpyEMData2.cpp, libpyTransform2.cpp: run
	  creat_boost_python

2005-08-18 14:47  gtang

	* rt/pyem/test_emdata.py: unit test for EMData

2005-08-18 14:37  gtang

	* rt/pyem/test_emdata.py: unit test for EMData

2005-08-18 14:35  gtang

	* libEM/: emdata.cpp, emdata.h: rewrite calc_az_dist() function,
	  make it return vector<float> instead of taking float * as
	  argument. and make corresponding change to function call of this
	  function.

2005-08-18 11:17  gtang

	* libEM/emdata.h: add comment for cut_slice(), claim exception.

2005-08-17 16:17  gtang

	* libEM/emdata.h: fix comment for dot(), exception throwed in
	  function.

2005-08-17 15:30  gtang

	* libEM/: emdata.cpp, emdata.h: minor fix for calc_flcf()

2005-08-17 12:31  gtang

	* libEM/: emdata.cpp, emdata.h: rewrite and debug calc_hist(),
	  return a vector<float>

2005-08-17 12:22  grant

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/libpyTransform2.cpp:
	  minor fsc/frc update

2005-08-17 10:44  ppenczek

	* libEM/emdata.cpp: change term zero in FSC

2005-08-16 17:22  ppenczek

	* libpyEM/libpyEMData2.cpp: [no log message]

2005-08-16 16:46  ppenczek

	* libEM/: emdata.h, emdata.cpp: new fsc

2005-08-15 11:34  prb

	* libEM/transform.cpp: fixed a few things in set_rotation given a
	  pair of vectors

2005-08-14 18:17  gtang

	* rt/pyem/test_emdata.py: unit test code for EMData

2005-08-14 18:08  eman1

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyTransform2.cpp: rewrite calc_hist() function to
	  return vector<float>, run pyste. --Grant Tang

2005-08-14 00:00  stevel

	* examples/sortsimilar.py, libEM/cmp.cpp, programs/e2boxer.py:
	  e2boxer working pretty reliably. Still false negatives, but very
	  few false positives

2005-08-12 17:04  prb

	* libEM/: emdata.h, transform.cpp, transform.h: added a new
	  Transform3d constructor that yields a 3d rotation given a pair of
	  unit vectors and their rotated counterparts.

2005-08-12 15:27  stevel

	* libEM/cmp.cpp: new optvariance option

2005-08-12 15:03  gtang

	* libEM/emdata.h: minor fix to comment

2005-08-12 13:56  gtang

	* libEM/emdata.h: minor fix to comment

2005-08-12 09:03  stevel

	* examples/sortsimilar.py, programs/e2boxer.py,
	  programs/e2dumplog.py: Work on boxer again.

2005-08-11 21:50  stevel

	* libEM/cmp.cpp: oops

2005-08-11 21:35  stevel

	* examples/comparepairs.py, examples/sortsimilar.py, libEM/cmp.cpp,
	  libEM/cmp.h: New option in variance comparison. Changed default
	  weight in mean phase error.

2005-08-11 19:46  gtang

	* rt/pyem/test_emdata.py: unit test code for EMData

2005-08-10 17:24  gtang

	* rt/pyem/test_emdata.py: unit test code for EMData

2005-08-10 14:37  grant

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/emdata.pyste,
	  libpyEM/libpyEMData2.cpp: Make kaiser-bessel windowing/gridding
	  stuff a bit more flexible.

2005-08-10 11:18  grant

	* libEM/emdata.cpp: Whoops, forgot to put rot_trans2D back together

2005-08-10 11:16  gtang

	* rt/emdata/rotate_translate.cpp: debugging code

2005-08-10 10:39  gtang

	* rt/emdata/rotate_translate.cpp: some debugging code

2005-08-10 10:23  grant

	* libpyEM/: fundamentals.pyste, libpyFundamentals2.cpp: Add
	  info_mask to Golem to get statistics under a mask, and fix
	  equalsize's visability in python

2005-08-10 02:18  stevel

	* examples/00README, examples/comparepairs.py,
	  examples/sortsimilar.py, programs/e2boxer.py: More e2boxer work.
	  New examples directory for small (commented) scripts

2005-08-09 21:54  grant

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/libpyEMData2.cpp:
	  Change EMData::rot_scale_trans2D to rotate all slices in a
	  volume, making Steve happy(er) [sic]

2005-08-09 21:27  grant

	* libEM/emdata.cpp, libEM/emdata.h, libEM/util.cpp, libEM/util.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyUtils2.cpp: Rewrote
	  EMData::rot_scale_trans2D and Util::quadri to be zero-based and
	  actually correct this time

2005-08-09 01:26  stevel

	* libEM/emdata.cpp, programs/e2boxer.py: rot_scale_trans_2D ->
	  radians

2005-08-08 17:21  grant

	* libEM/emdata.cpp: Hopefully fix do_fft_inplace memory issue

2005-08-08 14:56  grant

	* libEM/: emdata.cpp, emdata.h: doc fixes and exception throws
	  suggested by Grant T

2005-08-08 13:55  gtang

	* libEM/emdata.cpp: do_fft() and do_fft_inplace() throw exception
	  when apply to complex image.

2005-08-08 12:36  grant

	* libEM/: emdata.cpp, emdata.h: minor fix

2005-08-08 09:56  grant

	* libpyEM/libpyEMData2.cpp: pyste update

2005-08-08 09:50  grant

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/emdata.pyste,
	  libpyEM/libpyEMData2.cpp: Add rotation that uses bilinear
	  interpolation.  Need to make the interpolation scheme
	  'pluggable'.

2005-08-08 09:00  prb

	* libpyEM/libpyUtils2.cpp: got rid of the overloaded atan2

2005-08-08 08:24  prb

	* libEM/emdata.cpp, libEM/util.h, libpyEM/libpyUtils2.cpp: changed
	  my patch to the atan2(int, int) issue.  Changed all arguments to
	  floats instead of overloading atan2.

2005-08-08 02:22  stevel

	* libpyEM/EMAN2.py, programs/e2boxer.py, programs/e2dumplog.py:
	  Work on boxer. Added logging for command-line programs.

2005-08-07 17:17  gtang

	* rt/pyem/test_emdata.py: unit test code for EMData

2005-08-07 11:49  eman1

	* libpyEM/: emdata.pyste, libpyEMData2.cpp, libpyTransform2.cpp:
	  add policy for EMData::real2FH() and EMData::FH2F().	fix
	  compilation error.

2005-08-07 11:01  gtang

	* libEM/util.h: fix for warning. let atan2(int, int) not make
	  recursive call.

2005-08-06 14:13  prb

	* libpyEM/: libpyEMData2.cpp, libpyUtils2.cpp:
	  These are my boost changes from blake (that result from FH2F
	  Real2FH)

2005-08-06 13:15  prb

	* libEM/: emdata.cpp, util.h: minor changes: overloaded atan2 to
	  accept ints.

2005-08-06 09:30  gtang

	* libEM/emdata.h: add comment to remind user about the MArray2D and
	  MArray3D's subscription order.

2005-08-05 17:52  prb

	* libEM/: emdata.cpp, util.cpp:
	  patched spline_mat; fixed sqrt(int) to sqrt(float)

2005-08-05 17:00  gtang

	* rt/pyem/test_emdata.py: unit test code for EMData

2005-08-05 14:35  prb

	* libEM/: emdata.cpp, emdata.h, processor.cpp, util.cpp, util.h:
	  Added the real2FH commands (real image to Fourier Harmonic image)
	  and FH2F (Fourier Harmonic image to Fourier-shuffled image).
	  Here is a typical "round-trip"

	  *************************************************************

	   int Size=31; // must be an odd-number
	   EMData* e = new EMData;
	    e.set_size(Size,Size,1);
	    e.set_value_at(2,3,1.0);
	   // we just created an odd image, e.

	   EMData* FH= e-> real2FH(4); // 4 is the amount of oversampling
	  //   we just represented e in the FH basis

	   EMData* FFT = FH-> FH2F(Size,4); // but this FFT is shuffled
	   FFT->process("eman1.xform.fourierorigin"); // now its the usual
	  2d FFT
	  //  we took the FH image and put it to F space.

	   EMData* eRecon= FFT-> do_ift();
	  // now eRecon and e are nearly identical

	  ********************************************************************

	  The time of the round trip is given more or less by the ->
	  real2FH() step.

2005-08-05 10:28  grant

	* libpyEM/CMakeLists.txt, programs/CMakeLists.txt, programs/golem,
	  programs/sparx: Replace 'Sparx' with 'Golem'.  NOTE: need to run
	  cmake before recompiling.

2005-08-03 18:49  grant

	* libEM/emdata.cpp, libEM/emdata.h, libEM/transform.h,
	  libpyEM/emdata.pyste, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyGeometry2.cpp, libpyEM/libpyPointArray2.cpp,
	  libpyEM/libpyTransform2.cpp, libpyEM/libpyUtils2.cpp: Added
	  gridding rotational convolution

2005-08-02 17:35  grant

	* libpyEM/: libpyEMData2.cpp, libpyFilter2.cpp,
	  libpyPointArray2.cpp, libpyUtils2.cpp: pyste update

2005-08-02 17:34  grant

	* libEM/: emdata.cpp, emdata.h: remove unnecessary code

2005-08-02 17:33  grant

	* libEM/processor.h: New fourier filter wrappers

2005-08-02 17:33  grant

	* libEM/: util.cpp, util.h: Add some utility window functors

2005-08-02 16:34  gtang

	* rt/emdata/rotate_translate.cpp: add testing code

2005-08-02 16:15  gtang

	* libEM/emdata.cpp: fix insert_clip() 3D issue, it works
	  incorrectly for 3D before.

2005-08-02 16:14  gtang

	* rt/pyem/: test_emdata.py, test_misc.py: add more unit test code

2005-07-31 18:37  gtang

	* rt/pyem/: test_emdata.py, test_filter.py: improve unittest

2005-07-29 16:11  gtang

	* rt/pyem/test_emdata.py: correct some errors in this unittest
	  because of the code change

2005-07-27 16:16  gtang

	* doc/: developer-guide.html, development_policy_faq.html: document
	  refresh and add comment for testing group tags

2005-07-27 10:04  eman1

	* libpyEM/: libpyEMData2.cpp, libpyUtils2.cpp: run
	  create_boost_python on blake to accommodate pawel's new change.

2005-07-27 06:16  prb

	* libEM/: emdata.cpp, emdata.h, processor.cpp, util.cpp: I moved
	  PRBs shuffle (for FFTs of square odd images) from emdata to the
	  processor section.

2005-07-26 08:44  prb

	* libEM/: emdata.cpp, util.cpp, util.h: I added a spline utility,
	  that is needed for the FH calls.  Nothing was added to
	  emdata.cpp.	    PRB

2005-07-25 11:41  gtang

	* libEM/: emimio.cpp, emio.cpp: support image file size >2G, make
	  off_t conversion explicit

2005-07-25 10:06  gtang

	* libEM/mrcio.cpp: fix the mrc image size <2G problem.

2005-07-24 12:21  prb

	* libEM/: emdata.cpp, util.cpp, util.h: I added a Radialize
	  command: which lists the sorted lengths of the integer lattice
	  sites of a square sided image of size Size. This needed a sort
	  command (sort_mat) like in Matlab, which carries along a
	  Permutation Matrix: PRB

2005-07-22 15:17  gtang

	* rt/emdata/rotate_translate.cpp: for debugging purpose.

2005-07-21 18:27  grant

	* libEM/emdata.cpp, libEM/emdata.h, libEM/processor.cpp,
	  libEM/processor.h, libpyEM/emdata.pyste,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyFilter2.cpp: Added simpler
	  rotational average

2005-07-21 11:43  grant

	* libEM/emdata.cpp, libEM/emdata.h, libEM/util.cpp, libEM/util.h,
	  libpyEM/libpyUtils2.cpp: wrapper addition

2005-07-20 11:38  grant

	* libpyEM/libpyUtils2.cpp: KB pyste update

2005-07-20 11:36  grant

	* libEM/: util.cpp, util.h: more KaiserBessel methods

2005-07-20 10:18  gtang

	* libEM/processor.cpp: explicit cast to get rid of two warnings.

2005-07-20 10:09  grant

	* libEM/util.h, libpyEM/libpyEMData2.cpp, libpyEM/libpyUtils2.cpp:
	  add debugging method to the KaiserBessel class

2005-07-19 13:43  grant

	* libEM/emdata.cpp, libEM/emdata.h, libEM/util.cpp, libEM/util.h,
	  libpyEM/emdata.pyste, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyTransform2.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/processor.pyste: add a KaiserBessel window class

2005-07-19 12:04  gtang

	* libEM/emdata.cpp: fix the complex image division bug

2005-07-19 10:52  gtang

	* libEM/emutil.cpp: dump_dict eliminate "UNKNOWN" type to avoid
	  exception.

2005-07-18 09:24  gtang

	* plugins/: CMakeLists.txt, filter_template.cpp, filter_template.h,
	  processor_template.cpp, processor_template.h: change file name
	  from filter->processor

2005-07-16 10:03  gtang

	* libEM/CMakeLists.txt, libEM/aligner.cpp, libEM/emdata.cpp,
	  libEM/processor.cpp, libEM/processor.h, libpyEM/Makefile.pyste,
	  libpyEM/emdata.pyste, libpyEM/filter.pyste,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyFilter2.cpp,
	  libpyEM/processor.pyste, plugins/filter_template.h,
	  rt/imageio/basic.cpp: change file name from filter->processor

2005-07-15 15:48  gtang

	* rt/emdata/rotate_translate.cpp: some testing code for my own use

2005-07-15 15:34  gtang

	* libEM/emdata.cpp: fix a bug, check if the key exist in attr_dict
	  before get value from it.

2005-07-15 12:21  gtang

	* libEM/emobject.h: temp fix for operator []

2005-07-15 08:51  gtang

	* libEM/emobject.h: when get value by key from Dict, first check if
	  this key exist, if not, throw an exception

2005-07-14 22:03  stevel

	* programs/e2boxer.py: round and round we go

2005-07-14 17:23  prb

	* libEM/: emdata.cpp, emdata.h: added a shuffle command for FFTs
	  resulting from FFTing real odd square images PRB needs this to
	  make later Fourier Harmonic code easy to program.

2005-07-14 09:13  stevel

	* programs/e2boxer.py: Sigh...

2005-07-14 00:30  stevel

	* libEM/cmp.cpp, libEM/emdata.cpp, programs/e2boxer.py: Working on
	  boxer

2005-07-13 13:35  stevel

	* libpyEM/libpyEMData2.cpp: trivial pyste rerun

2005-07-13 13:33  stevel

	* libEM/cmp.cpp, libEM/cmp.h, libEM/emdata.cpp, libEM/emdata.h,
	  programs/e2boxer.py: A number of changes related to comparisons.
	  Broken for a few minutes.

2005-07-13 12:12  gtang

	* utils/proc2d.cpp: print out exception message

2005-07-13 10:45  gtang

	* libEM/exception.cpp: add a return, optimize the ouput of
	  exception

2005-07-12 11:54  stevel

	* libEM/cmp.cpp: Fixed phasecmp for new FFT convention.

2005-07-12 01:53  stevel

	* libEM/cmp.cpp, libEM/cmp.h, programs/e2boxer.py: Fixed
	  optvariance problem. More work on e2boxer.

2005-07-11 21:37  stevel

	* programs/: e2boxer.py, e2scannereval.py: Playing with boxer some
	  more. Fixed e2scannereval.

2005-07-11 09:09  stevel

	* libEM/cmp.cpp, libEM/cmp.h, programs/e2boxer.py: More work on
	  e2boxer

2005-07-10 19:29  grant

	* libEM/emdata.cpp, programs/sparx: Some flags weren't getting
	  copied in EMData::copy() and copy_header().  Should we have this
	  stuff in the header/dictionary instead of a flag of bits?

2005-07-10 14:31  gtang

	* libEM/emutil.cpp: sort out the header inclusion.

2005-07-10 13:55  gtang

	* libEM/aligner.cpp, libEM/all_imageio.h, libEM/amiraio.cpp,
	  libEM/amiraio.h, libEM/averager.cpp, libEM/averager.h,
	  libEM/cmp.cpp, libEM/ctf.cpp, libEM/ctf.h, libEM/dm3io.cpp,
	  libEM/dm3io.h, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emimio.cpp, libEM/emimio.h, libEM/emio.cpp, libEM/emio.h,
	  libEM/emobject.cpp, libEM/emobject.h, libEM/emutil.cpp,
	  libEM/emutil.h, libEM/gatan2io.cpp, libEM/gatan2io.h,
	  libEM/hdfio.cpp, libEM/icosio.cpp, libEM/icosio.h,
	  libEM/imageio.cpp, libEM/imageio.h, libEM/imagicio.cpp,
	  libEM/imagicio.h, libEM/log.cpp, libEM/lstio.cpp, libEM/lstio.h,
	  libEM/mrcio.cpp, libEM/mrcio.h, libEM/pgmio.cpp, libEM/pgmio.h,
	  libEM/pifio.cpp, libEM/pifio.h, libEM/pngio.cpp, libEM/pngio.h,
	  libEM/pointarray.cpp, libEM/pointarray.h, libEM/projector.cpp,
	  libEM/projector.h, libEM/quaternion.h, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libEM/salio.cpp, libEM/salio.h,
	  libEM/spiderio.cpp, libEM/spiderio.h, libEM/sspiderio.cpp,
	  libEM/testutil.cpp, libEM/testutil.h, libEM/tifio.cpp,
	  libEM/tifio.h, libEM/transform.cpp, libEM/transform.h,
	  libEM/util.cpp, libEM/util.h, libEM/vtkio.cpp, libEM/vtkio.h,
	  libEM/xplorio.cpp, libEM/xplorio.h, plugins/io_template.cpp,
	  plugins/io_template.h, utils/iminfo.cpp, utils/proc2d.cpp,
	  utils/speedtest.cpp: sort out the header inclusion.

2005-07-07 15:37  stevel

	* libEM/cmp.h, programs/e2boxer.py: trivial

2005-07-07 13:44  gtang

	* doc/eman2doc.h: testing group definition.

2005-07-07 09:21  gtang

	* libEM/: aligner.h, emdata.h: Document the new parameter
	  cmp_params for aligner class.

2005-07-07 01:18  stevel

	* programs/e2boxer.py: Still optimizing boxer. Alignment issues
	  still ?

2005-07-07 01:07  stevel

	* libpyEM/EMAN2.py, programs/e2boxer.py, utils/speedtest.cpp:
	  Removed import Sparx from EMAN2. Done immediately to eliminate
	  filter problem, but this also should not return. import Sparx may
	  import EMAN2, but not the other way around.

2005-07-06 21:19  stevel

	* utils/speedtest.cpp: valgrind option

2005-07-06 15:16  grant

	* libEM/emdata.cpp, libEM/util.cpp, libEM/util.h,
	  libpyEM/libpyUtils2.cpp: added Kaiser-Bessel window and possibly
	  fixed a valgrind error in do_ift

2005-07-06 10:49  eman1

	* libpyEM/: libpyEMData2.cpp, libpyTransform2.cpp: run
	  create_boost_python on blake.

2005-07-06 09:34  gtang

	* libEM/aligner.h: bug fix for compilation error on blake

2005-07-05 15:25  gtang

	* libEM/aligner.cpp, libEM/aligner.h, libEM/emdata.cpp,
	  libEM/emdata.h, libpyEM/libpyAligner2.cpp,
	  plugins/aligner_template.cpp, plugins/aligner_template.h: modify
	  the aligner class(es) so they take not only the name of the cmp
	  routine to invoke, but also a dictionary of options for the
	  comparator

2005-07-05 14:01  gtang

	* programs/e2boxer.py: change comparator name to lower case

2005-07-05 12:07  gtang

	* plugins/projector_template.h: change projector's name to lower
	  case

2005-07-05 12:07  gtang

	* plugins/filter_template.h: processor's name to lower case

2005-07-05 12:07  gtang

	* plugins/reconstructor_template.h: change reconstructor name to
	  lower case

2005-07-05 12:04  gtang

	* libEM/projector.h, rt/pyem/test_emdata.py: change projector's
	  name to lower case

2005-07-05 11:46  gtang

	* doc/developer-guide.html, libEM/reconstructor.h,
	  rt/demo/reconstructor.py: change reconstructor name to lower case

2005-07-05 11:13  uid32057

	* libEM/averager.h, libEM/emobject.h, libEM/projector.h,
	  rt/demo/averager.py: change averager name to lower case

2005-07-05 10:50  uid32057

	* libEM/aligner.cpp, libEM/pointarray.cpp, plugins/cmp_template.h,
	  programs/e2align3d.py, programs/e2aligntest.py,
	  programs/e2foldfitter.py, rt/demo/cmp.py, rt/pyem/test_filter.py,
	  utils/speedtest.cpp: change comparator name to lower case

2005-07-05 10:37  uid32057

	* libEM/aligner.cpp, libEM/aligner.h, plugins/aligner_template.h,
	  plugins/averager_template.h, programs/e2boxer.py,
	  rt/demo/align.py, rt/emdata/testalign.cpp, utils/proc2d.cpp,
	  utils/speedtest.cpp: change aligner name to lower case

2005-07-05 01:34  stevel

	* libEM/: aligner.h, cmp.cpp: Work on comparitors.

2005-07-02 01:36  stevel

	* programs/e2foldfitter.py: New scurve test image used for 2D
	  alignment testing.

2005-07-01 15:18  uid2314

	* libEM/emdata.cpp, libEM/emdata.h, libEM/util.cpp, libEM/util.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyFilter2.cpp: Added a
	  real-space phase shift, some new Fourier filters, a pure
	  (non-random) Gaussian model generator, and some minor fixes

2005-07-01 10:09  gtang

	* rt/emdata/emdata_api.cpp: get rid of a warning

2005-06-30 15:54  gtang

	* utils/proc2d.cpp: new EMData::translate() ask for this little fix

2005-06-30 15:53  gtang

	* rt/emdata/rotate_translate.cpp: add code for testing of
	  EMData::translate()

2005-06-30 15:52  gtang

	* libEM/: emdata.cpp, emdata.h: fix the EMData::translate()

2005-06-29 10:19  gtang

	* rt/CMakeLists.txt: rt directory changed

2005-06-29 10:18  gtang

	* rt/imageio/basic.cpp: filter -> processor name conversion

2005-06-27 14:09  gtang

	* rt/emdata/CMakeLists.txt: eliminate shared memory functionalility
	  in EMData

2005-06-27 13:42  grant

	* libEM/util.cpp, libEM/util.h, libpyEM/libpyUtils2.cpp:
	  Documentation fix that somehow ended up with me rewriting the
	  core of the routine.	Since boost multi_array's know their sizes
	  and starting values, we may as well use that info.

2005-06-27 12:37  gtang

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/typeconverter.cpp: eliminate shared memory
	  functionalility in EMData

2005-06-27 12:24  gtang

	* rt/emdata/shared_data.cpp: eliminate shared memory
	  functionalility in EMData

2005-06-27 11:47  gtang

	* libEM/: emdata.h, transform.h: fix in comment for Doxygen
	  documentation generation.

2005-06-27 11:27  gtang

	* doc/developer-guide.html: minor changes

2005-06-27 11:16  gtang

	* doc/developer-guide.html: minor changes

2005-06-27 10:23  gtang

	* doc/eman2doc.h: filter -> processor name conversion

2005-06-26 15:02  gtang

	* programs/e2proc2d.py: make processor name self-consistent

2005-06-26 14:36  gtang

	* doc/: processors.html, processor_groups.html: filter -> processor
	  name conversion

2005-06-26 14:24  gtang

	* doc/developer-guide.html, libEM/emdata.cpp, libEM/pointarray.cpp,
	  libEM/projector.cpp, rt/demo/filter1.py, rt/demo/filter2.py,
	  utils/proc2d.cpp, utils/speedtest.cpp: make processor name
	  self-consistent

2005-06-25 16:48  gtang

	* utils/docgen.py: filter -> processor name conversion

2005-06-25 16:43  gtang

	* utils/docgen.py: filter -> processor name conversion

2005-06-25 16:15  gtang

	* doc/: developer-guide.html, eman2doc.h: filter -> processor name
	  conversion

2005-06-25 15:30  gtang

	* libEM/: emdata.cpp, emdata.h, emobject.h: filter -> processor
	  name conversion

2005-06-24 17:15  gtang

	* utils/speedtest.cpp: eliminate parent of EMData from EMAN2

2005-06-24 16:34  gtang

	* libEM/aligner.cpp, libEM/aligner.h, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/projector.cpp, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, programs/e2symbest.py, utils/proc2d.cpp,
	  libpyEM/emdata.pyste, libpyEM/libpyEMData2.cpp: eliminate parent
	  of EMData from EMAN2

2005-06-24 12:18  grant

	* libpyEM/: EMAN2.py, EMAN2_cppwrap.py: Split out c++ wrappers so
	  that they may be imported independently

2005-06-23 18:14  grant

	* libEM/util.h, libpyEM/CMakeLists.txt, libpyEM/Sparx.py: Changed
	  Sparx.py to a package

2005-06-23 14:57  eman1

	* libpyEM/libpyEMData2.cpp: run pyste on blake. Grant Tang

2005-06-23 14:24  stevel

	* libEM/: cmp.cpp, cmp.h, emdata.h: Fixing buggy comparison
	  routines

2005-06-23 14:08  gtang

	* libpyEM/: filter.pyste, libpyFilter2.cpp: filter -> processor
	  name conversion

2005-06-23 14:01  gtang

	* libpyEM/filter.pyste, libpyEM/libpyFilter2.cpp, utils/docgen.py:
	  filter -> processor name conversion

2005-06-23 13:33  gtang

	* doc/developer-guide.html, doc/development_policy_faq.html,
	  libEM/averager.h, libEM/emdata.h, libEM/emobject.h,
	  libEM/pointarray.cpp, libEM/projector.h, libEM/reconstructor.h,
	  libpyEM/EMAN2.py, plugins/filter_template.h,
	  programs/e2align3d.py, programs/e2findsubunit.py,
	  programs/e2foldfitter.py, programs/e2msa.py,
	  programs/e2proc2d.py, programs/e2proc3d.py,
	  programs/e2scannereval.py, programs/e2tomogram.py,
	  rt/demo/filter1.py, rt/demo/filter2.py, rt/demo/filter3.py,
	  rt/emdata/emdata_api.cpp, rt/imageio/basic.cpp, utils/docgen.py,
	  TODO: filter -> processor name conversion

2005-06-23 12:01  ppenczek

	* libpyEM/Sparx.py:  Addded three functions, window2d, ramp, and
	  welch_pw2.
	   Fixed two filters.

2005-06-22 12:50  grant

	* libpyEM/Sparx.py: Fix to use python parse_spider_fname

2005-06-22 12:40  grant

	* libEM/util.cpp, libEM/util.h, libpyEM/libpyUtils2.cpp: removed
	  c++ parse_spider_fname

2005-06-22 12:26  grant

	* libpyEM/Sparx.py: parse_spider_fname rewritten in python

2005-06-19 22:53  stevel

	* libEM/cmp.cpp, libEM/emdata.cpp, programs/e2boxer.py,
	  programs/e2pdb2mrc.py: Working on boxer again

2005-06-16 21:29  gtang

	* utils/proc2d.cpp: eman1.Bilateral -> eman1.bilateral

2005-06-16 11:36  grant

	* libEM/CMakeLists.txt, libEM/emdata.cpp,
	  libpyEM/fundamentals.pyste, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyFundamentals2.cpp, libpyEM/libpyGeometry2.cpp,
	  libpyEM/libpyTransform2.cpp: added circulant real-space
	  convolution; may end up moving the location once we have it
	  debugged

2005-06-14 15:35  gtang

	* libEM/emdata.cpp: fix last time check in mistake, if shared
	  memory, just rdata=0

2005-06-13 17:38  gtang

	* libEM/aligner.cpp, libEM/averager.cpp, libEM/cmp.cpp,
	  libEM/dm3io.cpp, libEM/emcache.cpp, libEM/emcache.h,
	  libEM/emdata.cpp, libEM/emobject.h, libEM/emutil.cpp,
	  libEM/hdfio.cpp, libEM/icosio.cpp, libEM/mrcio.cpp,
	  libEM/pifio.cpp, libEM/pngio.cpp, libEM/pointarray.cpp,
	  libEM/projector.cpp, libEM/reconstructor.cpp, libEM/spiderio.cpp,
	  libEM/testutil.cpp, libEM/util.cpp, libEM/vtkio.cpp,
	  rt/emdata/ccf1.cpp, rt/emdata/ccf2.cpp, rt/emdata/emdata_api.cpp,
	  rt/emdata/rotate.cpp, rt/emdata/rotate1.cpp,
	  rt/emdata/rotate_phi.cpp, rt/emdata/rotate_translate.cpp,
	  rt/emdata/shared_data.cpp, rt/emdata/testalign.cpp,
	  rt/imageio/basic.cpp, rt/imageio/imageio.cpp, utils/iminfo.cpp,
	  utils/proc2d.cpp, utils/speedtest.cpp: try to fix double free()
	  bug, make sure all delete() and free() follow the safe way: check
	  if the pointer is zero, then delete/free, the assign the pointer
	  to zero.

2005-06-11 00:28  stevel

	* libpyEM/: EMAN2.py, filter.pyste, libpyFilter2.cpp:
	  dump_processors

2005-06-10 23:39  stevel

	* libEM/emdata.cpp, programs/e2boxer.py: Fixed rot footprints due
	  to filter fix. e2boxer centers and sorts properly

2005-06-09 22:35  lpeng

	* libEM/: emdata.cpp, hdfio.cpp: fixed warning for unused variables

2005-06-09 14:11  stevel

	* libEM/emdata.cpp: Fixed eman1 Fourier filters. They were
	  completely broken. Also changed the convention to use 0-0.5 as
	  the filter parameter, matching what I think Pawel/Grant were
	  doing.

2005-06-08 14:08  grant

	* libEM/emdata.cpp: z fix

2005-06-05 10:40  lpeng

	* libEM/util.h: change param [in]/[out] style

2005-06-05 10:13  lpeng

	* INSTALL, README, doc/Doxyfile, doc/coding_style.html: update the
	  documents on doxygen and pyste issues

2005-06-04 12:08  lpeng

	* libpyEM/: libpyAligner2.cpp, libpyAverager2.cpp, libpyCmp2.cpp,
	  libpyEMData2.cpp, libpyEMObject2.cpp, libpyFilter2.cpp,
	  libpyGeometry2.cpp, libpyPointArray2.cpp, libpyProjector2.cpp,
	  libpyReconstructor2.cpp, libpyTransform2.cpp, libpyUtils2.cpp:
	  regenerate libpyEM files using patched pyste

2005-06-04 12:06  lpeng

	* rt/pyem/: test_defaultargs.py, test_emdata.py,
	  test_typeconverter.py, test_utils.py: add/change tests

2005-06-03 16:00  ppenczek

	* libpyEM/Sparx.py: new functions

2005-06-03 11:57  ppenczek

	* libpyEM/Sparx.py: new functions

2005-06-03 10:47  grant

	* libEM/: emdata.cpp, emdata.h: fixes and additions

2005-06-03 10:18  grant

	* libpyEM/Sparx.py: now w/ filter wrapper

2005-06-02 20:14  stevel

	* libEM/aligner.cpp, programs/e2boxer.py, programs/e2tomogram.py:
	  Fixed e2tomogram for new fft routines.

2005-06-02 18:48  ppenczek

	* libpyEM/Sparx.py: [no log message]

2005-06-02 18:00  ppenczek

	* libpyEM/Sparx.py: [no log message]

2005-06-01 22:00  lpeng

	* libpyEM/libpyEMData2.cpp: remove boost::noncopyable manually

2005-06-01 13:04  gtang

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/emfft.cpp: add djbfft
	  support for power of 2 fft transform.

2005-05-31 22:18  lpeng

	* rt/pyem/: test_typeconverter.py, test_utils.py, test_vec.py:
	  update test cases

2005-05-31 22:17  lpeng

	* libEM/: geometry.h, vec3.h: add copy constructor for pyste
	  purpose

2005-05-31 09:15  eman1

	* libpyEM/: libpyCmp2.cpp, libpyEMData2.cpp, libpyEMObject2.cpp,
	  libpyFilter2.cpp, libpyProjector2.cpp, libpyReconstructor2.cpp,
	  libpyTransform2.cpp, libpyUtils2.cpp: boost python wrap for
	  set_value_at()  --Grant Tang

2005-05-30 01:58  stevel

	* libEM/aligner.cpp: Fixed translational alignment with new CCF
	  routines.

2005-05-29 23:49  stevel

	* libEM/emdata.cpp: Fixed 2D rotations.

2005-05-28 11:06  lpeng

	* rt/pyem/test_defaultargs.py: simple test for default args

2005-05-27 10:04  gtang

	* libEM/: emdata.cpp, spiderio.cpp: fix calloc minor error,
	  calloc(numberOfElements, sizeOfElements)

2005-05-26 16:48  grant

	* libEM/emdata.cpp: minor fix

2005-05-26 14:14  stevel

	* libEM/: emutil.cpp, hdfio.cpp: Fixed problem with hdfio error
	  when creating file then writing 2nd image.  There are still
	  resource leaks in hdfio.cpp Fixed e2boxer to work with Pawel's
	  new correlation routines.

2005-05-26 11:36  stevel

	* programs/e2boxer.py: e2boxer needs to handle new CCF routine

2005-05-26 11:15  gtang

	* libEM/emdata.h: bounds-checking for set_value_at()

2005-05-25 20:38  ppenczek

	* libEM/emdata.cpp: corrected fft normalization

2005-05-25 13:24  grant

	* libEM/emdata.cpp: rot_scale_trans2D fix

2005-05-25 13:04  grant

	* libpyEM/libpyEMData2.cpp: pyste update

2005-05-25 13:03  grant

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/emdata.pyste:
	  rot_scale_trans2D fixes

2005-05-25 09:14  gtang

	* libEM/log.cpp: fix a warning, print time_t as long int, %ld

2005-05-24 17:13  grant

	* libpyEM/libpyEMData2.cpp: pyste update

2005-05-24 17:12  grant

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/emdata.pyste: new
	  rotation_translation_scale method

2005-05-24 15:52  grant

	* libEM/: util.cpp, util.h: add triquadratic interpolation

2005-05-24 00:01  lpeng

	* libEM/emdata.cpp, libEM/hdfio.cpp, libEM/log.h,
	  libEM/projector.cpp, libEM/salio.cpp, libEM/spiderio.cpp,
	  libEM/testutil.cpp, libEM/testutil.h, libEM/transform.cpp,
	  libEM/util.cpp, libEM/util.h, libpyEM/libpyUtils2.cpp: fix
	  windows warnings/errors

2005-05-23 17:15  grant

	* libpyEM/: emdata.pyste, libpyEMData2.cpp: pyste again

2005-05-23 17:10  grant

	* libpyEM/libpyEMData2.cpp: yet another libpyEMData2.cpp hack

2005-05-23 17:02  grant

	* libpyEM/: emdata.pyste, libpyEMData2.cpp: pyste update

2005-05-23 17:01  grant

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/libpyEMData2.cpp: depad
	  fixes

2005-05-23 16:51  grant

	* libpyEM/: emdata.pyste, libpyEMData2.cpp: pyste update

2005-05-23 16:42  grant

	* libpyEM/Sparx.py: post-whitespace-debacle fix

2005-05-23 16:42  grant

	* libEM/: emdata.cpp, emdata.h, projector.cpp, reconstructor.cpp,
	  reconstructor.h, transform.cpp, transform.h, util.cpp, util.h:
	  hopefully fixed correlation/convolution bug; put various changes
	  back in after the great whitespace repo reversion

2005-05-22 01:56  stevel

	* libEM/emdata.cpp, programs/e2boxer.py: self_correlation in
	  calc_ccf

2005-05-19 22:21  lpeng

	* libEM/reconstructor.cpp: comment out unused vars

2005-05-19 22:20  lpeng

	* libEM/exception.h: add some comments

2005-05-18 18:04  grant

	* libEM/transform.cpp, libpyEM/Sparx.py: symmetrization fixes

2005-05-17 22:48  lpeng

	* libEM/emdata.cpp: use 'else if' instead of 'if' in EMData::sub

2005-05-17 22:47  lpeng

	* rt/pyem/: test_emdata.py, test_filter.py: update test cases for
	  updated APIs

2005-05-17 17:46  grant

	* libpyEM/libpyEMData2.cpp: ugly hack to get libpyEMData2.cpp to
	  compile

2005-05-17 17:39  grant

	* libpyEM/: emdata.pyste, libpyEMData2.cpp, libpyTransform2.cpp,
	  libpyUtils2.cpp: pyste update

2005-05-17 17:33  grant

	* libEM/emdata.cpp, libEM/emdata.h, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libEM/transform.cpp, libEM/transform.h,
	  libEM/util.cpp, libEM/util.h, libpyEM/Sparx.py: added
	  symmetrization to the PawelBackProjectionReconstructor, along
	  with helper functions, all of which compile but are probably
	  broken

2005-05-17 10:14  grant

	* libEM/reconstructor.cpp: code cleaning

2005-05-17 09:53  ppenczek

	* libpyEM/Sparx.py: remove npad from arguments and hardwire into
	  do_reconstruction

2005-05-16 23:25  lpeng

	* libEM/emdata.cpp, libEM/emfft.cpp, libEM/emfft.h,
	  rt/emdata/CMakeLists.txt, rt/emdata/fft.cpp,
	  rt/emdata/shared_data.cpp, rt/emdata/testalign.cpp: fix fftw
	  cache issue

2005-05-16 19:07  ppenczek

	* libEM/: util.cpp, reconstructor.cpp: maybe changed something

2005-05-16 18:12  gtang

	* libEM/emdata.cpp: add update_stat() for several new functions in
	  EMData.

2005-05-16 16:52  grant

	* libEM/emdata.cpp: whoops, angle off-by-one error fix

2005-05-16 16:45  grant

	* libpyEM/: Sparx.py, libpyEMData2.cpp: nasty hack to get
	  libpyEMData2.cpp to compile

2005-05-16 16:40  grant

	* libpyEM/: emdata.pyste, libpyEMData2.cpp: fix policy errors

2005-05-16 16:32  grant

	* libpyEM/: libpyEMData2.cpp, libpyTransform2.cpp, libpyUtils2.cpp:
	  pyste update

2005-05-16 16:27  grant

	* libEM/: emdata.cpp, emdata.h, reconstructor.cpp, reconstructor.h,
	  transform.h: now using Transform3D objects sensibly in
	  PawelBackProjectionReconstructor

2005-05-16 15:03  grant

	* libEM/: emdata.cpp, emdata.h, reconstructor.cpp: remove in-situ
	  windowing from do_fft_inplace

2005-05-15 11:45  lpeng

	* libEM/emdata.cpp: run to_zero() after set_size()

2005-05-14 12:02  gtang

	* libEM/: emdata.cpp, emdata.h, exception.h: arithmatic operation
	  for complex image.  get real and imaginary part of a complex
	  image.  create a complex image by a real image.

2005-05-13 18:23  grant

	* libEM/: emdata.cpp, reconstructor.cpp: reconstructor fixes

2005-05-13 11:32  prb

	* libEM/transform.cpp: Made minor changes so that the Euler angles
	  in SPIDER corresponding to the identity come out to be
	  phi=theta=psi=0

2005-05-12 14:19  grant

	* rt/demo/model.tcp: test model

2005-05-12 14:18  grant

	* rt/demo/reconstruction.py: new sample

2005-05-12 13:43  grant

	* libEM/projector.cpp, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libpyEM/Sparx.py, libpyEM/libpyUtils2.cpp:
	  general cleanups and a completely fictitious alignment script

2005-05-11 14:27  grant

	* libpyEM/Sparx.py: handly projection function

2005-05-11 13:39  grant

	* libEM/reconstructor.cpp, libpyEM/Sparx.py: reconstructor fixes

2005-05-11 09:39  grant

	* libEM/: emdata.h, emutil.cpp: fixes for gcc using -pedantic

2005-05-11 09:05  lpeng

	* libEM/emdata.cpp: fix memory leak in Factory methods

2005-05-11 09:05  lpeng

	* libEM/transform.cpp: comment out unused var

2005-05-11 09:05  lpeng

	* rt/emdata/ccf2.cpp: fix calc_ccf() api change

2005-05-10 14:30  gtang

	* rt/pyem/testImage.py: if specify input image, apply test image to
	  input.

2005-05-10 10:56  grant

	* libpyEM/libpyUtils2.cpp: pyste update

2005-05-10 10:52  grant

	* libEM/util.h: add default arguments

2005-05-10 10:45  grant

	* libpyEM/libpyUtils2.cpp: pyste update

2005-05-10 10:43  grant

	* libEM/emdata.cpp, libEM/util.cpp, libEM/util.h,
	  libpyEM/utils.pyste: fixes

2005-05-10 10:31  grant

	* libpyEM/libpyUtils2.cpp: pyste update

2005-05-10 10:29  grant

	* libEM/util.cpp, libEM/util.h, libpyEM/utils.pyste: angle util
	  fixes

2005-05-10 10:09  grant

	* libEM/: util.cpp, util.h: add angle util

2005-05-09 18:56  ppenczek

	* libEM/: projector.h, projector.cpp: Working PawelProject

2005-05-09 14:01  grant

	* libpyEM/libpyEMData2.cpp: update

2005-05-09 13:56  grant

	* libEM/: CMakeLists.txt, aligner.cpp, emdata.cpp, emdata.h:
	  calc_ccf fixes to use existing correlation function

2005-05-08 16:57  ppenczek

	* libEM/emdata.cpp: I am not sure I changed anything

2005-05-08 13:51  gtang

	* rt/pyem/testImage.py: a simple script to create test images

2005-05-06 16:45  grant

	* libpyEM/: libpyAligner2.cpp, libpyAverager2.cpp, libpyCmp2.cpp,
	  libpyEMData2.cpp, libpyEMObject2.cpp, libpyFilter2.cpp,
	  libpyGeometry2.cpp, libpyPointArray2.cpp, libpyProjector2.cpp,
	  libpyReconstructor2.cpp, libpyTransform2.cpp,
	  libpyTypeConverter2.cpp, libpyUtils2.cpp: update .cpp files on
	  blake

2005-05-06 16:26  grant

	* libpyEM/: filter.pyste, libpyFilter2.cpp: unhiding the Processor
	  class

2005-05-06 13:16  grant

	* libEM/reconstructor.cpp: default constructor broke ipython; oops!

2005-05-06 12:50  grant

	* libpyEM/EMAN2.py: Fixed broken include

2005-05-05 16:05  grant

	* libpyEM/Sparx.py: added reconstruction

2005-05-05 15:46  grant

	* libpyEM/: emdata.pyste, libpyEMData2.cpp, libpyFundamentals2.cpp,
	  libpyUtils2.cpp: update

2005-05-05 15:37  grant

	* libEM/: emdata.h, reconstructor.cpp, reconstructor.h, util.h:
	  reconstructor added, but not yet tested

2005-05-04 16:45  grant

	* libEM/: emdata.cpp, emdata.h, reconstructor.cpp, reconstructor.h:
	  working on a reconstructor; not yet done

2005-05-04 13:06  grant

	* libEM/: util.cpp, util.h: added printMatI3D function

2005-05-04 12:25  grant

	* libpyEM/libpyEMData2.cpp: new method in emdata

2005-05-04 12:23  grant

	* libEM/: emdata.cpp, emdata.h: add print_image method

2005-05-04 09:21  grant

	* libpyEM/fundamentals.pyste: add missing fundamentals.pyste

2005-05-03 22:54  lpeng

	* libpyEM/create_boost_python: add option -f

2005-05-03 14:23  grant

	* libpyEM/libpyFundamentals2.cpp: adding file; oops!

2005-05-03 13:49  grant

	* libEM/transform.h, libpyEM/libpyTransform2.cpp: replace print
	  method w/ printme method for the time being

2005-05-03 11:57  grant

	* libpyEM/: CMakeLists.txt, Makefile.pyste, libpyAligner2.cpp,
	  libpyAverager2.cpp, libpyCmp2.cpp, libpyEMData2.cpp,
	  libpyEMObject2.cpp, libpyFilter2.cpp, libpyFundamentals.cpp,
	  libpyGeometry2.cpp, libpyPointArray2.cpp, libpyProjector2.cpp,
	  libpyReconstructor2.cpp, libpyTransform2.cpp,
	  libpyTypeConverter2.cpp, libpyUtils2.cpp: Now using pyste for
	  libpyFundamentals2.cpp

2005-05-01 10:01  lpeng

	* libEM/: Assert.h, aligner.h, imageio.h, mrcio.h: add some
	  comments

2005-04-30 21:51  lpeng

	* INSTALL: upgrade software version information

2005-04-30 21:43  lpeng

	* rt/pyem/test_emdata.py: add test_statistics

2005-04-30 18:00  lpeng

	* libpyEM/: libpyAligner2.cpp, libpyAverager2.cpp, libpyCmp2.cpp,
	  libpyEMData2.cpp, libpyFilter2.cpp, libpyPointArray2.cpp,
	  libpyTransform2.cpp, libpyUtils2.cpp: touch all *.pyste and
	  re-run create_boost_python

2005-04-30 17:59  lpeng

	* libpyEM/filter.pyste: change Filter to Processor

2005-04-30 17:58  lpeng

	* rt/: emdata/rotate_translate.cpp, pyem/test_emdata.py,
	  pyem/test_filter.py, pyem/test_imageio.py, pyem/test_misc.py,
	  pyem/test_transform.py, pyem/test_typeconverter.py,
	  pyem/test_vec.py: rename Transform to Transform3D; filter to
	  process

2005-04-29 14:12  prb

	* libEM/aligner.cpp, libEM/cmp.h, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/hdfio.cpp, libEM/pointarray.cpp, libEM/pointarray.h,
	  libEM/projector.cpp, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libEM/transform.cpp, libEM/transform.h,
	  libpyEM/EMAN2.py, libpyEM/libpyAligner2.cpp,
	  libpyEM/libpyAverager2.cpp, libpyEM/libpyCmp2.cpp,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyPointArray2.cpp,
	  libpyEM/libpyReconstructor2.cpp, libpyEM/libpyTransform2.cpp,
	  libpyEM/transform.pyste, plugins/reconstructor_template.cpp,
	  plugins/reconstructor_template.h, pyemtbx/imagetypes.py,
	  utils/proc2d.cpp: Modified Transform3D class and lines in other
	  programs to be consistent.

2005-04-28 11:03  grant

	* libEM/emdata.cpp: whoops, left efence in; now removed

2005-04-28 11:02  grant

	* libEM/emdata.cpp: minor fixo

2005-04-27 15:44  grant

	* libpyEM/Sparx.py: fix printing to be a bit nicer

2005-04-27 15:43  grant

	* libEM/emdata.cpp: Fixed broken pad_fft in forward padding.

2005-04-25 23:26  lpeng

	* rt/: emdata/emdata_api.cpp, pyem/test_typeconverter.py: add more
	  tests; fix compilatio changing EMData::filter() to
	  EMData::process()

2005-04-24 17:24  lpeng

	* libEM/: imageio.h, sspiderio.h: add more documentation

2005-04-22 15:45  grant

	* libEM/: emdata.cpp, util.h: put padding in image attributes; misc
	  fixes

2005-04-22 13:06  grant

	* libpyEM/Makefile.pyste: Fixed non-Posix head -1

2005-04-22 11:58  ppenczek

	* libpyEM/Sparx.py: not ready yet

2005-04-22 01:36  stevel

	* libEM/emdata.cpp, programs/e2boxer.py: Quick patch to make ccf's
	  work again until Pawel's new routine is in place.

2005-04-21 15:20  grant

	* libEM/: CMakeLists.txt, emdata.cpp, util.cpp: moved
	  parse_spider_fname into util.h

2005-04-21 12:22  ppenczek

	* libEM/emdata.h: add default arguments to set_size

2005-04-21 11:44  gtang

	* libEM/emdata.cpp: fix EMData::div() bug.  should be rdata[i] /= f
	  instead of rdata[i] *= f

2005-04-20 15:34  grant

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/libpyFundamentals.cpp:
	  Modify EMData::do_ift_inplace to shrink the data array, removing
	  the fft extension along x

2005-04-20 10:58  grant

	* libEM/CMakeLists.txt, libEM/exception.h, libEM/util.h,
	  libpyEM/libpyUtils2.cpp: Added routine to parse spider-format
	  filename strings

2005-04-18 17:04  grant

	* libpyEM/Sparx.py: more helper funcs

2005-04-18 15:46  grant

	* programs/sparx: fix broken try

2005-04-17 17:21  gtang

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emobject.h, libEM/projector.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyFilter2.cpp, plugins/filter_template.cpp,
	  plugins/filter_template.h, utils/proc2d.cpp, utils/speedtest.cpp:
	  Rename Filter to Process

2005-04-17 10:45  lpeng

	* libEM/: emutil.cpp, emutil.h: rename euler_convention to
	  euler_type for consist

2005-04-15 18:28  ppenczek

	* libEM/emdata.cpp: flipping of FFT removed, old code may not work

2005-04-15 16:00  ppenczek

	* libpyEM/Sparx.py: Yet another version

2005-04-15 15:26  ppenczek

	* libpyEM/Sparx.py: Yet another version

2005-04-15 11:39  grant

	* programs/sparx: report if ipython not installed

2005-04-15 11:37  grant

	* programs/: CMakeLists.txt, sparx: Added a quick script to launch
	  ipython as an interactive sparx/eman2 shell.

2005-04-15 11:33  ppenczek

	* libpyEM/Sparx.py: new version of statistics with comments

2005-04-14 23:52  lpeng

	* libEM/: emdata.cpp, emdata.h: operators change: return new EMData
	  object instead of change on old ones

2005-04-14 23:51  lpeng

	* rt/pyem/: test_emdata.py, testlib.py: operator tests

2005-04-14 23:50  lpeng

	* rt/emdata/CMakeLists.txt: remove spider2.cpp

2005-04-14 16:43  ppenczek

	* libpyEM/: EMAN2.py, Sparx.py: helper functions

2005-04-13 22:15  lpeng

	* doc/developer-guide.html: rename Wrapper to EMNumPy

2005-04-12 14:04  grant

	* libpyEM/libpyFilter2.cpp: Need two different base fourierfilter
	  functions for python object ownership to be sensible.

2005-04-12 10:38  grant

	* libEM/CMakeLists.txt, libpyEM/libpyFilter2.cpp: extremely
	  preliminary fourierfilter stuff added for testing

2005-04-11 22:54  lpeng

	* libEM/amiraio.cpp, libEM/dm3io.cpp, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/emimio.cpp, libEM/emio.cpp,
	  libEM/emutil.cpp, libEM/emutil.h, libEM/gatan2io.cpp,
	  libEM/hdfio.cpp, libEM/icosio.cpp, libEM/imageio.h,
	  libEM/imagicio.cpp, libEM/lstio.cpp, libEM/mrcio.cpp,
	  libEM/pgmio.cpp, libEM/pifio.cpp, libEM/pngio.cpp,
	  libEM/salio.cpp, libEM/spiderio.cpp, libEM/spiderio.h,
	  libEM/sspiderio.cpp, libEM/sspiderio.h, libEM/tifio.cpp,
	  libEM/vtkio.cpp, libEM/xplorio.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyUtils2.cpp, libpyEM/utils.pyste,
	  plugins/io_template.cpp: filestoragetype is added to
	  write_image() for imageio classes and EMData::write_image()

2005-04-09 00:22  stevel

	* programs/e2boxer.py: Working!

2005-04-08 13:47  grant

	* libpyEM/EMAN2.py: Added libpyFundamentals to the list of imports
	  for now.  Again, this may well be unceremoniously yanked in the
	  future.

2005-04-08 13:40  grant

	* libpyEM/: CMakeLists.txt, libpyFundamentals.cpp: Adding for now
	  so that we can do testing.  May be unceremoniously yanked when we
	  shuffle around this code to place it appropriately into EMAN2.

2005-04-08 13:39  grant

	* libEM/: CMakeLists.txt, emdata.h: Fixes to fourierproduct stuff,
	  and (for the moment, anyway) connecting it to the build process.

2005-04-08 11:39  stevel

	* libEM/emdata.cpp: Fix broken convolution routine.

2005-04-04 17:26  grant

	* libEM/: emdata.cpp, emdata.h: pushing initial fourier stuff
	  upstream

2005-04-04 02:33  stevel

	* libEM/aligner.cpp, libEM/emdata.cpp, libpyEM/EMAN2.py,
	  programs/e2boxer.py: Working on e2boxer. Memory leaks, alignment
	  parameters, etc.

2005-04-03 23:59  lpeng

	* rt/: emdata/CMakeLists.txt, emdata/image_overwrite.cpp,
	  pyem/test_emdata.py: remove obsolete tests; add new tests

2005-04-02 00:44  stevel

	* CMakeLists.txt, libEM/emdata.cpp, programs/e2boxer.py: Plugged
	  some memory leaks.

2005-04-01 20:56  stevel

	* libpyEM/: libpyAverager2.cpp, libpyCmp2.cpp, libpyEMData2.cpp,
	  libpyFilter2.cpp, libpyPointArray2.cpp, libpyProjector2.cpp,
	  libpyReconstructor2.cpp, libpyTransform2.cpp,
	  libpyTypeConverter2.cpp, libpyUtils2.cpp: Backed out some bad
	  pyste changes

2005-04-01 14:30  stevel

	* libEM/emdata.cpp: Memory leak work

2005-03-31 16:05  stevel

	* libEM/aligner.h, libEM/cmp.cpp, libEM/emdata.cpp, libEM/emdata.h,
	  libpyEM/emdata.pyste, libpyEM/libpyEMData2.cpp,
	  programs/e2boxer.py: Fixing memory leaks

2005-03-30 14:35  gtang

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/pointarray.cpp,
	  libEM/projector.cpp, rt/demo/filter1.py, rt/demo/filter2.py,
	  rt/pyem/test_filter.py, rt/pyem/test_misc.py,
	  utils/speedtest.cpp: again, change filter name to add "eman1."
	  prefix

2005-03-29 17:23  gtang

	* programs/e2align3d.py, programs/e2boxer.py,
	  programs/e2findsubunit.py, programs/e2foldfitter.py,
	  programs/e2msa.py, programs/e2pdb2mrc.py, programs/e2proc2d.py,
	  programs/e2scannereval.py, programs/e2tomogram.py,
	  utils/proc2d.cpp: add "eman1." prefix to filter names

2005-03-29 16:44  gtang

	* programs/e2boxer.py: fix a syntax error in line 151

2005-03-29 11:38  stevel

	* plugins/aligner_template.h: Back out bad change.

2005-03-29 10:28  ppenczek

	* libEM/aligner.cpp, libEM/aligner.h, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/emutil.cpp, libEM/spiderio.cpp,
	  libEM/spiderio.h, libpyEM/filter.pyste,
	  libpyEM/libpyAverager2.cpp, libpyEM/libpyCmp2.cpp,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyFilter2.cpp,
	  libpyEM/libpyProjector2.cpp, libpyEM/libpyReconstructor2.cpp,
	  libpyEM/libpyTypeConverter2.cpp, libpyEM/libpyUtils2.cpp,
	  plugins/aligner_template.h: incorporate from HEAD

2005-03-29 10:24  ppenczek

	* libEM/: aligner.cpp, aligner.h, emdata.cpp, emdata.h, emutil.cpp,
	  spiderio.cpp, spiderio.h: Incorporated fixes

2005-03-28 23:41  lpeng

	* libEM/emutil.cpp, libEM/spiderio.cpp, libpyEM/Makefile.pyste,
	  utils/iminfo.cpp: fixed a Spider read_header bug

2005-03-28 16:57  ppenczek

	* libpyEM/Makefile.pyste: whoops, wrong branch

2005-03-28 16:56  ppenczek

	* libpyEM/Makefile.pyste: quick fix

2005-03-28 16:44  ppenczek

	* libEM/: emdata.cpp, emdata.h, spiderio.cpp, spiderio.h: updates
	  from head

2005-03-28 09:52  ppenczek

	* libEM/: emdata.cpp, util.h: use std::max instead of our max0

2005-03-27 23:17  lpeng

	* libEM/aligner.cpp, libEM/aligner.h, libEM/emdata.cpp,
	  libEM/emdata.h, libpyEM/libpyAligner2.cpp,
	  plugins/aligner_template.h, utils/speedtest.cpp: fix filtername
	  issue for MaskSharp; fix Aligner API default arg issue

2005-03-27 19:23  ppenczek

	* libEM/: CMakeLists.txt, emdata.cpp: More fourierfilter fixes

2005-03-25 09:58  grant

	* libEM/: CMakeLists.txt, emdata.cpp: Reverted to (hopefully)
	  working code.

2005-03-24 18:33  ppenczek

	* libEM/: emdata.cpp, emdata.h, util.h: fixes

2005-03-24 16:22  ppenczek

	* libEM/emdata.cpp: corrected statistics

2005-03-23 21:34  ppenczek

	* libEM/: CMakeLists.txt, emdata.cpp: New correlation stuff and
	  some minor fixes.

2005-03-22 22:26  lpeng

	* TODO, rt/emdata/CMakeLists.txt, rt/pyem/test_emdata.py,
	  rt/pyem/test_imageio.py, utils/iminfo.cpp: more tests

2005-03-22 22:26  lpeng

	* libEM/: spiderio.cpp, spiderio.h: add single-image overwriting
	  support

2005-03-21 15:04  grant

	* libEM/: projector.cpp, spiderio.cpp, spiderio.h, util.cpp,
	  util.h: update from HEAD and incorporation of my patches

2005-03-21 08:46  stevel

	* programs/e2findsubunit.py: New program

2005-03-19 11:56  stevel

	* programs/e2cmmtomrc.py: New program

2005-03-17 23:38  lpeng

	* rt/imageio/: CMakeLists.txt, ctf.cpp, test_hdfio.cpp: remove old
	  tests

2005-03-17 23:36  lpeng

	* libEM/: spiderio.cpp, spiderio.h: fixed a spider read problem

2005-03-14 21:48  lpeng

	* rt/: emdata/CMakeLists.txt, emdata/locations.cpp,
	  emdata/radial_dist.cpp, pyem/test_emdata.py,
	  pyem/test_imageio.py: add more tests

2005-03-06 22:09  lpeng

	* TODO, libpyEM/aligner.pyste, libpyEM/libpyAligner2.cpp,
	  rt/pyem/test_imageio.py: fix python CTF EMData::set_ctf() issue.
	  This function can be used in python now

2005-03-06 17:43  lpeng

	* libEM/emdata.h, libEM/testutil.cpp, rt/emdata/CMakeLists.txt,
	  rt/emdata/cmp.cpp, rt/emdata/compleximg.cpp,
	  rt/emdata/exception1.cpp, rt/emdata/getclip.cpp,
	  rt/emdata/marray.cpp, rt/emdata/setvalue.cpp,
	  rt/pyem/test_emdata.py, rt/pyem/test_filter.py: add more tests

2005-03-02 23:34  lpeng

	* TODO, doc/header_naming.html, libEM/emdata.h, libEM/emutil.cpp,
	  libEM/emutil.h, libEM/hdfio.cpp, libEM/hdfio.h,
	  libEM/imagicio.cpp, libEM/testutil.cpp, libpyEM/libpyUtils2.cpp:
	  improve HdfIO: ctfit/euler attributes

2005-03-02 23:33  lpeng

	* rt/: imageio/test_hdfio.cpp, pyem/test_imageio.py: add more tests
	  on HDF imageio

2005-02-27 17:12  lpeng

	* libEM/aligner.h, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emutil.h, libEM/lstio.h, libEM/util.h,
	  libpyEM/libpyEMData2.cpp: add more comments; change write_lst()
	  api

2005-02-27 16:11  lpeng

	* libEM/byteorder.cpp, libEM/byteorder.h, libEM/spiderio.cpp,
	  libEM/sspiderio.cpp, rt/imageio/test_hdfio.cpp: move the spider
	  byteorder checking to a func

2005-02-27 12:05  lpeng

	* TODO, libEM/spiderio.cpp, libEM/sspiderio.cpp,
	  libEM/testutil.cpp, rt/pyem/test_imageio.py, rt/pyem/testlib.py:
	  fix spider endian check using EMAN1 way

2005-02-26 15:50  lpeng

	* rt/imageio/test_hdfio.cpp: add a new hdfio test

2005-02-24 23:35  lpeng

	* CMakeLists.txt, TODO, libEM/emdata.cpp, libEM/emutil.cpp,
	  rt/imageio/CMakeLists.txt: change ImageIO caching to be an
	  optional CMake flag, with default=off

2005-02-24 23:13  lpeng

	* libEM/: hdfio.cpp, hdfio.h: migrated Wen's bugfix in EMAN1 to
	  EMAN2

2005-02-23 22:05  lpeng

	* rt/pyem/rt.sh: to run all programs

2005-02-22 23:15  lpeng

	* libpyEM/typeconverter.h, rt/pyem/test_emdata.py: more tests on
	  multi_array

2005-02-20 23:00  lpeng

	* TODO, libEM/aligner.cpp, libEM/emdata.cpp,
	  libpyEM/libpyTypeConverter2.cpp, libpyEM/typeconverter.cpp,
	  libpyEM/typeconverter.h, libpyEM/typeconverter.pyste,
	  rt/imageio/CMakeLists.txt, rt/pyem/test_emdata.py,
	  rt/pyem/test_imageio.py: add typeconverter method to convert
	  multi_array from c++ to python Numeric array

2005-02-20 14:15  lpeng

	* rt/: imageio/emio.py, imageio/imagic1.cpp, imageio/mrc.cpp,
	  pyem/test_filter.py, pyem/test_imageio.py: more imagicio test

2005-02-19 19:35  lpeng

	* rt/pyem/test_filter.py: add more filter tests

2005-02-19 18:56  lpeng

	* rt/pyem/: test_imageio.py, test_transform.py, test_utils.py,
	  testlib.py: more tests

2005-02-18 18:38  lpeng

	* libEM/testutil.cpp: add more on EMObject tests

2005-02-18 18:37  lpeng

	* libpyEM/: libpyTypeConverter2.cpp, typeconverter.h,
	  typeconverter.pyste: add: string->EMObject transparently

2005-02-18 18:36  lpeng

	* rt/pyem/: test_filter.py, test_imageio.py, test_misc.py,
	  test_transform.py, test_typeconverter.py, test_utils.py: remove
	  EMObject and get_debug_image()

2005-02-17 00:13  lpeng

	* libEM/log.cpp, libEM/log.h, libEM/testutil.cpp, libEM/testutil.h,
	  libpyEM/emobject.pyste, libpyEM/libpyEMObject2.cpp,
	  libpyEM/libpyTypeConverter2.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/typeconverter.cpp, libpyEM/typeconverter.h,
	  libpyEM/typeconverter.pyste, rt/pyem/test_emdata.py,
	  rt/pyem/test_misc.py, rt/pyem/test_typeconverter.py,
	  rt/pyem/testlib.py: hide EMObject in boost python: a user will
	  use the native type directly

2005-02-15 01:46  stevel

	* libEM/aligner.cpp: Commit partial conversion to out-of-place
	  operation, before switching back again

2005-02-15 00:02  lpeng

	* TODO, libEM/aligner.cpp, libEM/aligner.h, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/emobject.cpp, libEM/emobject.h,
	  libEM/projector.h, libEM/testutil.cpp, libEM/testutil.h,
	  libpyEM/emdata.pyste, libpyEM/emobject.pyste,
	  libpyEM/libpyAligner2.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyEMObject2.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/typeconverter.cpp, libpyEM/typeconverter.h,
	  libpyEM/utils.pyste, plugins/aligner_template.cpp,
	  plugins/aligner_template.h, rt/imageio/badfilename.py,
	  rt/imageio/clip.py, rt/pyem/test_emdata.py, rt/pyem/test_misc.py,
	  rt/pyem/test_typeconverter.py, utils/proc2d.cpp,
	  utils/speedtest.cpp: aligner classes: make EMData* to_image
	  explicit

2005-02-14 12:02  wjiang

	* libEM/: emdata.cpp, emdata.h, exception.h: add 1.5x shrink
	  support in mean_shrink()

2005-02-14 01:32  stevel

	* libEM/: aligner.cpp, emdata.cpp, emdata.h, projector.cpp,
	  projector.h, transform.cpp: Changed EMAN euler order convention
	  to az,alt,phi. Fixed bug in transformation.

2005-02-13 22:21  stevel

	* libEM/aligner.cpp, libEM/emdata.cpp, libpyEM/EMAN2.py,
	  programs/e2boxer.py: Fixed some aligner problems. More to come.

2005-02-13 01:40  stevel

	* libEM/aligner.cpp, programs/e2boxer.py: More filter naming fixes.

2005-02-12 02:32  stevel

	* programs/e2boxer.py: Work on e2boxer. Bugfixes in filter naming

2005-02-11 02:07  stevel

	* libEM/aligner.cpp, libEM/emdata.cpp, programs/e2boxer.py: Fixed
	  problems with filter name change.

2005-02-09 22:24  lpeng

	* rt/pyem/test_utils.py: python unit tests

2005-02-09 22:24  lpeng

	* libEM/emcache.cpp, libEM/emutil.cpp, libEM/emutil.h,
	  libEM/imagicio.cpp, libEM/testutil.cpp, libEM/testutil.h,
	  libEM/util.cpp, libpyEM/emobject.pyste,
	  libpyEM/libpyEMObject2.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/typeconverter.h, pyemtbx/imagetypes.py,
	  rt/CMakeLists.txt, rt/emdata/blankimg.cpp,
	  rt/imageio/CMakeLists.txt, rt/imageio/append.cpp,
	  rt/imageio/mrc.py, rt/imageio/region.cpp,
	  rt/imageio/writetwice.cpp, rt/pyem/test_imageio.py,
	  rt/pyem/test_misc.py, rt/pyem/test_vec.py, rt/pyem/testlib.py:
	  add more unit tests using python unit tests

2005-02-07 16:03  stevel

	* programs/: e2boxer.py, e2tomogram.py: Work on boxer

2005-02-07 02:01  stevel

	* libEM/emobject.cpp, programs/e2boxer.py: Working a bit on
	  autoboxing

2005-02-07 01:20  stevel

	* libpyEM/: libpyAligner2.cpp, libpyAverager2.cpp, libpyCmp2.cpp,
	  libpyEMObject2.cpp, libpyProjector2.cpp, libpyReconstructor2.cpp:
	  Update pyste regen.

2005-02-07 01:16  stevel

	* libEM/aligner.cpp, libEM/aligner.h, libEM/averager.h,
	  libEM/cmp.h, libEM/emobject.cpp, libEM/emobject.h,
	  libEM/projector.h, libEM/reconstructor.h,
	  plugins/aligner_template.h, plugins/averager_template.h,
	  plugins/cmp_template.h, plugins/projector_template.h,
	  plugins/reconstructor_template.h: Added descriptions to all
	  modular classes similar to filters.

2005-02-06 02:01  stevel

	* programs/: e2align3d.py, e2boxer.py, e2foldfitter.py, e2msa.py,
	  e2pdb2mrc.py, e2proc2d.py, e2scannereval.py, e2tomogram.py:
	  Massive filter renaming.

2005-02-05 02:19  stevel

	* libEM/emdata.h, libpyEM/libpyEMData2.cpp: trivial

2005-02-05 02:13  stevel

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/EMAN2.py,
	  programs/e2boxer.py: New option in add.

2005-01-31 09:49  lpeng

	* rt/CMakeLists.txt: remove utils dir

2005-01-30 12:15  lpeng

	* TODO, doc/coding_style.html, doc/testing.html, libEM/amiraio.cpp,
	  libEM/ctf.cpp, libEM/emdata.h, libEM/emutil.cpp,
	  libEM/imagicio.cpp, libEM/imagicio.h, libEM/log.cpp,
	  libEM/lstio.cpp, libEM/salio.cpp, libEM/testutil.cpp,
	  libEM/testutil.h, libEM/util.cpp, libEM/util.h,
	  libEM/xplorio.cpp, libEM/xydata.cpp, libpyEM/emdata.pyste,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyUtils2.cpp,
	  rt/CMakeLists.txt, rt/imageio/region.cpp, utils/proc2d.cpp: more
	  doc changes; more testing

2005-01-30 12:14  lpeng

	* rt/pyem/: rt, test_emdata.py, test_filter.py, test_imageio.py,
	  test_misc.py, test_transform.py, test_typeconverter.py,
	  test_vec.py, testlib.py: tests in python unittest format

2005-01-30 12:12  lpeng

	* rt/pyem/: ccf1.py, ccf2.py, converter.py, defaultargs.py,
	  emobject.py, exception.py, exception2.py, filter1.py, help.py,
	  imageio1.py, imageio_caching.py, imagicio.py, marray.py,
	  namedclass.py, numpy.py, numpy2.py, operators.py, overloads.py,
	  pixel.py, pixel2.py, project1.py, rotate.py, rotate_translate.py,
	  rotation.py, testlib.py, transvec.py, typeconverter.py, vec1.py,
	  vec2.py, vec3.py: remove tests not in py unittest framework

2005-01-27 12:52  grant

	* libEM/: emdata.cpp, emdata.h: Nascent in-place fft stuff

2005-01-25 17:09  grant

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/emdata.pyste,
	  libpyEM/libpyEMData2.cpp: minor renames

2005-01-24 20:12  ppenczek

	* libEM/: emdata.cpp, emdata.h: fft boost.python fixes

2005-01-24 16:32  grant

	* libEM/: emdata.cpp, emdata.h: fix my fft mistake wrt boost.python

2005-01-24 15:29  grant

	* libEM/: emdata.cpp, emdata.h: windum w/ better docs and no
	  boost.python issues

2005-01-21 23:05  lpeng

	* TODO, libEM/emutil.cpp, libEM/emutil.h, libEM/testutil.cpp,
	  libEM/xplorio.cpp, libEM/xplorio.h, libpyEM/emdata.pyste,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyUtils2.cpp,
	  rt/imageio/region.cpp: more region writing support; libpyEM
	  updates

2005-01-21 16:52  grant

	* libEM/: emdata.cpp, emdata.h: new methods

2005-01-21 12:18  grant

	* libEM/: emdata.cpp, emfft.cpp, emfft.h: add some new functions

2005-01-20 10:02  grant

	* libEM/: emdata.cpp, emdata.h: added some reconstruction helper
	  methods

2005-01-16 22:17  lpeng

	* TODO, libEM/emio.cpp, libEM/emio.h, libEM/hdfio.cpp,
	  libEM/hdfio.h, libEM/imageio.cpp, libEM/imageio.h,
	  libEM/imagicio.cpp, libEM/imagicio.h, libEM/mrcio.cpp,
	  libEM/mrcio.h, libEM/pgmio.cpp, libEM/vtkio.cpp,
	  libEM/xplorio.cpp, libEM/xplorio.h, rt/imageio/region.cpp: more
	  region writing support

2005-01-14 17:34  grant

	* libEM/emdata.cpp: fft w/ odd nx seems to be working now

2005-01-14 16:20  grant

	* libEM/: emdata.cpp, emdata.h: Use fortran storage order in
	  get_*view() member functions; fft tweaks.

2005-01-13 00:24  lpeng

	* libEM/Assert.h, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/hdfio.cpp, libEM/pointarray.cpp, libEM/spiderio.cpp,
	  libEM/testutil.cpp, libEM/testutil.h, libEM/transform.cpp,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyUtils2.cpp,
	  rt/imageio/imageio.cpp, rt/imageio/region.cpp: more tests; remove
	  useless get_data() call

2005-01-12 15:44  grant

	* libEM/: emdata.h, mrcio.cpp, projector.cpp: Pawel Projector
	  updates

2005-01-11 17:22  ppenczek

	* libEM/: projector.cpp, projector.h: Fixed up PawelProjector
	  (which apparently never worked in eman2).

2005-01-09 20:48  eman

	* CMakeLists.txt, libEM/CMakeLists.txt: add jpeg

2005-01-09 14:29  lpeng

	* TODO: more tasks

2005-01-09 14:27  lpeng

	* rt/: imageio/CMakeLists.txt, imageio/append.cpp,
	  imageio/region.cpp, pyem/imagicio.py, pyem/typeconverter.py: more
	  rt

2005-01-09 14:25  lpeng

	* libpyEM/: libpyEMData2.cpp, libpyEMObject2.cpp,
	  libpyTypeConverter2.cpp, typeconverter.h, typeconverter.pyste:
	  converter for array->emobject

2005-01-09 14:24  lpeng

	* libEM/: cmp.cpp, emdata.cpp, emdata.h, emobject.cpp, emobject.h,
	  imageio.cpp, imagicio.cpp, mrcio.cpp, pifio.cpp,
	  reconstructor.cpp, spiderio.cpp, spiderio.h, sspiderio.cpp,
	  testutil.cpp, testutil.h: fix spiderio and imagicio append err

2005-01-08 23:17  lpeng

	* TODO, libEM/emdata.cpp, libEM/emdata.h, libEM/imageio.cpp,
	  libEM/mrcio.cpp, libEM/pifio.cpp, libEM/spiderio.cpp,
	  libEM/spiderio.h, libEM/sspiderio.cpp, libEM/testutil.cpp,
	  libEM/testutil.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyPointArray2.cpp, libpyEM/libpyUtils2.cpp,
	  rt/emdata/ccf2.cpp, rt/emdata/compleximg.cpp,
	  rt/emdata/emdata_api.cpp, rt/emdata/exception1.cpp,
	  rt/emdata/image_overwrite.cpp, rt/emdata/locations.cpp,
	  rt/emdata/marray.cpp, rt/emdata/rotate.cpp,
	  rt/emdata/rotate_phi.cpp, rt/emdata/rotate_translate.cpp,
	  rt/emdata/shared_data.cpp, rt/imageio/imagic1.cpp,
	  rt/imageio/region.cpp, rt/pyem/rt: more region writing

2005-01-05 20:34  lpeng

	* TODO, libEM/amiraio.cpp, libEM/byteorder.h, libEM/dm3io.cpp,
	  libEM/emdata.cpp, libEM/emdata.h, libEM/emimio.cpp,
	  libEM/emio.cpp, libEM/emutil.h, libEM/gatan2io.cpp,
	  libEM/geometry.cpp, libEM/geometry.h, libEM/hdfio.cpp,
	  libEM/hdfio.h, libEM/icosio.cpp, libEM/imageio.cpp,
	  libEM/imageio.h, libEM/imagicio.cpp, libEM/imagicio.h,
	  libEM/lstio.cpp, libEM/mrcio.cpp, libEM/pgmio.cpp,
	  libEM/pifio.cpp, libEM/pifio.h, libEM/spiderio.cpp,
	  libEM/tifio.cpp, libEM/util.h, libEM/vtkio.h, libEM/xplorio.cpp,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyGeometry2.cpp,
	  rt/imageio/region.cpp, utils/iminfo.cpp: more imageio region
	  writing support

2005-01-03 10:07  lpeng

	* rt/pyem/overloads.py: to test func overloading in boost py

2005-01-03 10:06  lpeng

	* TODO, libEM/aligner.cpp, libEM/aligner.h, libEM/amiraio.cpp,
	  libEM/amiraio.h, libEM/ctf.cpp, libEM/ctf.h, libEM/dm3io.cpp,
	  libEM/dm3io.h, libEM/emcache.cpp, libEM/emcache.h,
	  libEM/emdata.cpp, libEM/emdata.h, libEM/emimio.cpp,
	  libEM/emimio.h, libEM/emio.cpp, libEM/emio.h, libEM/emobject.h,
	  libEM/emutil.cpp, libEM/emutil.h, libEM/gatan2io.cpp,
	  libEM/gatan2io.h, libEM/geometry.h, libEM/hdfio.cpp,
	  libEM/hdfio.h, libEM/icosio.cpp, libEM/icosio.h,
	  libEM/imageio.cpp, libEM/imageio.h, libEM/lstio.cpp,
	  libEM/lstio.h, libEM/mrcio.cpp, libEM/mrcio.h, libEM/pgmio.cpp,
	  libEM/pgmio.h, libEM/pifio.cpp, libEM/pifio.h, libEM/pngio.cpp,
	  libEM/pngio.h, libEM/pointarray.cpp, libEM/pointarray.h,
	  libEM/salio.cpp, libEM/salio.h, libEM/spiderio.cpp,
	  libEM/spiderio.h, libEM/sspiderio.cpp, libEM/sspiderio.h,
	  libEM/transform.h, libEM/vec3.h, libEM/vtkio.cpp, libEM/vtkio.h,
	  libEM/xplorio.cpp, libEM/xplorio.h, libEM/xydata.cpp,
	  libEM/xydata.h, libpyEM/Makefile.pyste,
	  libpyEM/libpyAligner2.cpp, libpyEM/libpyAverager2.cpp,
	  libpyEM/libpyCmp2.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyEMObject2.cpp, libpyEM/libpyFilter2.cpp,
	  libpyEM/libpyPointArray2.cpp, libpyEM/libpyProjector2.cpp,
	  libpyEM/libpyReconstructor2.cpp, libpyEM/libpyTransform2.cpp,
	  plugins/aligner_template.cpp, plugins/aligner_template.h,
	  plugins/io_template.cpp, plugins/io_template.h,
	  rt/emdata/marray.cpp, rt/imageio/region.cpp, rt/pyem/ccf2.py,
	  rt/pyem/rt: change string to 'const string&'

2005-01-02 11:45  lpeng

	* TODO, libpyEM/libpyEMData2.cpp, libpyEM/libpyUtils2.cpp: boost
	  multi_array

2005-01-02 11:43  lpeng

	* rt/: emdata/CMakeLists.txt, emdata/emdata_api.cpp,
	  emdata/locations.cpp, emdata/marray.cpp, emdata/rotate.cpp,
	  emdata/rotate_translate.cpp, pyem/marray.py: boost multi_array
	  test

2005-01-02 11:42  lpeng

	* rt/imageio/region.cpp: region tests

2005-01-02 11:42  lpeng

	* libEM/: emdata.cpp, emdata.h, emutil.cpp, imagicio.cpp,
	  mrcio.cpp, util.cpp, util.h: add get_view()

2004-12-23 21:51  lpeng

	* libpyEM/EMAN2.py: add class overview docs

2004-12-23 21:23  lpeng

	* libpyEM/aligner.pyste, libpyEM/libpyAligner2.cpp,
	  libpyEM/libpyTypeConverter2.cpp, libpyEM/typeconverter.cpp,
	  libpyEM/typeconverter.h, libpyEM/typeconverter.pyste,
	  rt/pyem/ccf1.py, rt/pyem/converter.py: rename Wrapper to EMNumPy

2004-12-23 15:33  stevel

	* programs/: e2foldfitter.py, e2tomogram.py: Tomogram work.

2004-12-22 21:57  lpeng

	* libpyEM/EMAN2.py, rt/pyem/help.py: add some docs

2004-12-22 21:49  stevel

	* programs/e2tomogram.py: Working on tomography.

2004-12-22 21:23  lpeng

	* doc/developer-guide.html: update docs

2004-12-22 21:14  lpeng

	* rt/demo/reconstructor.py: simple dummy reconstruction

2004-12-22 21:13  lpeng

	* TODO, libEM/reconstructor.cpp, libpyEM/libpyReconstructor2.cpp,
	  libpyEM/reconstructor.pyste: fixed a boost python memory problem
	  with Reconstructor wrap

2004-12-21 21:57  lpeng

	* libpyEM/aligner.pyste, libpyEM/averager.pyste, libpyEM/cmp.pyste,
	  libpyEM/libpyAligner2.cpp, libpyEM/libpyAverager2.cpp,
	  libpyEM/libpyCmp2.cpp, libpyEM/libpyProjector2.cpp,
	  libpyEM/libpyReconstructor2.cpp, libpyEM/projector.pyste,
	  libpyEM/reconstructor.pyste, rt/demo/align.py, utils/docgen.py:
	  fixed some issues with boost python

2004-12-21 20:50  lpeng

	* libEM/emdata.cpp: fixed a problem in make_rotational_print()

2004-12-20 22:02  lpeng

	* TODO, doc/coding_style.html, doc/cvshowto.html,
	  doc/developer-guide.html, libpyEM/filter.pyste,
	  libpyEM/libpyFilter2.cpp, utils/docgen.py: rename filters

2004-12-20 21:55  lpeng

	* rt/pyem/: ccf1.py, ccf2.py, converter.py, defaultargs.py,
	  filter1.py, imageio1.py, imageio_caching.py, namedclass.py,
	  pixel.py, project1.py, rotate.py, rotate_translate.py,
	  rotation.py, rt, testlib.py, typeconverter.py: fixed rt test
	  errors

2004-12-20 20:30  lpeng

	* libEM/aligner.cpp, libEM/emdata.h, libEM/pointarray.cpp,
	  libEM/reconstructor.cpp, libpyEM/libpyEMData2.cpp,
	  utils/proc2d.cpp: EMData::get_rotation() changed to
	  get_transform()

2004-12-19 14:54  lpeng

	* libEM/testutil.cpp, libpyEM/libpyTypeConverter2.cpp,
	  libpyEM/typeconverter.h, libpyEM/typeconverter.pyste,
	  rt/pyem/emobject.py, rt/pyem/emobject2.py, rt/pyem/rt,
	  rt/pyem/typeconverter.py: add XYData->EMObject implicit type
	  conversion

2004-12-19 12:05  lpeng

	* libEM/testutil.cpp, libEM/testutil.h, libpyEM/libpyUtils2.cpp,
	  libpyEM/typeconverter.h, rt/pyem/typeconverter.py: use tests
	  fixed another type converter bug in Dict

2004-12-19 11:30  lpeng

	* TODO, libEM/emobject.cpp, libEM/emobject.h, libEM/geometry.cpp,
	  libEM/geometry.h, libEM/testutil.cpp, libpyEM/libpyEMObject2.cpp,
	  libpyEM/libpyGeometry2.cpp, rt/pyem/emobject.py,
	  rt/pyem/emobject2.py, rt/pyem/pixel2.py, rt/pyem/rt,
	  rt/pyem/testlib.py, rt/pyem/typeconverter.py, rt/pyem/vec1.py,
	  rt/pyem/vec2.py, rt/pyem/vec3.py: more type converter tests

2004-12-18 18:06  lpeng

	* libEM/: testutil.cpp, testutil.h: remove comments

2004-12-18 18:03  lpeng

	* libEM/testutil.cpp, libEM/testutil.h, libpyEM/typeconverter.h,
	  rt/pyem/typeconverter.py: fixed a big bug in std::map<> related
	  type converters

2004-12-18 17:10  lpeng

	* libEM/testutil.cpp, libEM/testutil.h,
	  libpyEM/libpyTypeConverter2.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/typeconverter.pyste, rt/pyem/typeconverter.py: more type
	  converter tests

2004-12-18 09:36  lpeng

	* libEM/testutil.cpp, libEM/testutil.h, libpyEM/libpyUtils2.cpp,
	  rt/pyem/typeconverter.py: more test cases

2004-12-18 07:57  lpeng

	* rt/emdata/: cmp.cpp, rotate_translate.cpp: fixed errors caused by
	  changing of API

2004-12-18 07:44  lpeng

	* libpyEM/: libpyTypeConverter2.cpp, typeconverter.pyste: add more
	  std::map related type converters

2004-12-18 01:50  stevel

	* libpyEM/libpyTransform2.cpp: repyste

2004-12-18 01:28  stevel

	* utils/proc2d.cpp: Trivial

2004-12-18 01:22  stevel

	* libEM/: aligner.cpp, emdata.cpp, reconstructor.cpp,
	  transform.cpp, transform.h: Transform map() -> Dict()

2004-12-16 22:46  lpeng

	* libEM/CMakeLists.txt, libEM/emutil.cpp, libEM/emutil.h,
	  libEM/testutil.cpp, libEM/testutil.h, libEM/util.cpp,
	  libEM/util.h, libpyEM/Makefile.pyste, libpyEM/libpyUtils2.cpp,
	  libpyEM/transform.pyste, libpyEM/typeconverter.h,
	  libpyEM/utils.pyste, pyemtbx/imagetypes.py: add more test utils

2004-12-16 22:44  lpeng

	* rt/: emdata/ccf2.cpp, emdata/compleximg.cpp,
	  emdata/exception1.cpp, emdata/image_overwrite.cpp,
	  emdata/rotate_phi.cpp, emdata/rotate_translate.cpp,
	  emdata/shared_data.cpp, imageio/badfilename.py, imageio/emio.py,
	  imageio/imagic1.cpp, pyem/ccf1.py, pyem/ccf2.py,
	  pyem/defaultargs.py, pyem/emobject.py, pyem/exception.py,
	  pyem/filter1.py, pyem/imageio1.py, pyem/imageio_caching.py,
	  pyem/namedclass.py, pyem/numpy.py, pyem/pixel.py,
	  pyem/project1.py, pyem/rotate.py, pyem/rotate_translate.py,
	  pyem/rt, pyem/typeconverter.py, pyem/vec1.py, pyem/vec2.py: write
	  more tests for typeconverter testing

2004-12-16 20:35  lpeng

	* libEM/CMakeLists.txt, libEM/quaternion.cpp, libEM/quaternion.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyTransform2.cpp,
	  libpyEM/transform.pyste: remove matrix.h/matrix.cpp, replaced by
	  new transform.h/transform.cpp

2004-12-16 20:22  lpeng

	* TODO, libEM/CMakeLists.txt, libEM/emdata.h, libEM/projector.cpp,
	  libEM/reconstructor.cpp, libEM/reconstructor.h,
	  plugins/reconstructor_template.cpp,
	  plugins/reconstructor_template.h: remove rotation.h/rotation.cpp
	  because they are replaced by the new transform.h/cpp

2004-12-16 02:29  stevel

	* libEM/transform.cpp: Oops.

2004-12-16 02:25  stevel

	* libEM/transform.cpp, libEM/transform.h, libpyEM/EMAN2.py:
	  Transform inversion works (I think). Fixed bug in one of the
	  set_rotation routines, but non-EMAN formats may be buggy still.

2004-12-15 21:57  lpeng

	* TODO: more things to do

2004-12-15 21:36  lpeng

	* libEM/emutil.cpp, libpyEM/CMakeLists.txt, libpyEM/EMAN2.py,
	  libpyEM/Makefile.pyste, libpyEM/aligner.pyste, libpyEM/cmp.pyste,
	  libpyEM/emdata.pyste, libpyEM/libpyAligner2.cpp,
	  libpyEM/libpyCmp2.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyTransform2.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/transform.pyste, libpyEM/typeconverter.h,
	  libpyEM/utils.pyste, rt/pyem/emobject.py, rt/pyem/project1.py:
	  arrange pyste files for faster compilation; fixed type converter
	  problem for emobject->emdata

2004-12-15 21:35  lpeng

	* libpyEM/: libpyTypeConverter2.cpp, typeconverter.pyste: move type
	  converter stuff from libpyUtil2 to here

2004-12-15 20:10  lpeng

	* libEM/transform.cpp, libpyEM/CMakeLists.txt,
	  libpyEM/Makefile.pyste, libpyEM/aligner.pyste,
	  libpyEM/averager.pyste, libpyEM/cmp.pyste, libpyEM/emdata.pyste,
	  libpyEM/filter.pyste, libpyEM/libpyAligner2.cpp,
	  libpyEM/libpyAverager2.cpp, libpyEM/libpyCmp2.cpp,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyFilter2.cpp,
	  libpyEM/libpyProjector2.cpp, libpyEM/libpyReconstructor2.cpp,
	  libpyEM/libpyTransform2.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/projector.pyste, libpyEM/pylist.cpp, libpyEM/pylist.h,
	  libpyEM/reconstructor.pyste, libpyEM/typeconverter.cpp,
	  libpyEM/typeconverter.h, libpyEM/utils.pyste,
	  rt/pyem/project1.py: rename pylist.h/.cpp to typeconverter.h/.cpp

2004-12-15 01:34  stevel

	* libpyEM/EMAN2.py, programs/e2tomogram.py: Minor changes

2004-12-15 01:29  stevel

	* libEM/: pointarray.cpp, transform.h, vec3.h: adding some
	  convenience functions

2004-12-14 23:00  lpeng

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/pointarray.cpp, libEM/pointarray.h,
	  libEM/reconstructor.cpp, libEM/transform.cpp, libEM/transform.h,
	  TODO, libpyEM/libpyEMData2.cpp, libpyEM/libpyPointArray2.cpp,
	  libpyEM/libpyTransform2.cpp, libpyEM/transform.pyste,
	  utils/proc2d.cpp: new Transform compiles again

2004-12-14 20:50  lpeng

	* libEM/: transform.cpp, transform.h: implement get_nsym(),
	  get_sym()

2004-12-14 07:43  lpeng

	* libEM/: transform.cpp, transform.h: add iterator to transform

2004-12-14 02:00  stevel

	* libEM/: emdata.cpp, pointarray.cpp, pointarray.h, transform.cpp,
	  transform.h: Many updates for new Transform. Still not complete.
	  Still won't compile.

2004-12-14 00:15  stevel

	* libEM/: transform.cpp, vec3.h: Minor fixes.

2004-12-13 20:38  lpeng

	* rt/pyem/rotation.py: rotation euler angle tests

2004-12-13 02:07  stevel

	* libEM/: transform.cpp, transform.h: Fixed some math problems in
	  new Transform

2004-12-12 21:02  lpeng

	* libEM/: CMakeLists.txt, emdata.cpp, emdata.h, transform.cpp,
	  transform.h: more code adapted for the new Transform API

2004-12-12 19:33  lpeng

	* libEM/: CMakeLists.txt, pointarray.cpp, quaternion.cpp,
	  quaternion.h, transform.cpp, transform.h: add new transformation
	  API

2004-12-12 10:29  lpeng

	* libpyEM/libpyEMData2.cpp: better formats

2004-12-12 10:28  lpeng

	* rt/: imageio/emio.py, pyem/emobject.py: more tests

2004-12-12 00:46  stevel

	* libEM/: pointarray.cpp, pointarray.h: Additions for derivative
	  calculations.

2004-12-11 15:42  lpeng

	* TODO, libEM/emutil.cpp, libpyEM/emdata.pyste,
	  libpyEM/libpyEMData2.cpp, libpyEM/pylist.h, rt/demo/cmp.py: fixed
	  pyem EMData -> EMObject transparently

2004-12-11 15:06  lpeng

	* libEM/emobject.h, libEM/emutil.cpp, libEM/emutil.h, libEM/util.h,
	  libEM/vec3.h, libpyEM/emdata.pyste, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyTransform2.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/pylist.h, rt/demo/filter3.py: remove XYZ_to/from_python
	  duplicate code; add emobject_farray_from_python

2004-12-11 00:10  stevel

	* CMakeLists.txt, libEM/pointarray.cpp, libEM/pointarray.h:
	  pointarray optimization compiles, but certainly doesn't work.

2004-12-10 21:57  lpeng

	* libEM/aligner.cpp, libEM/cmp.cpp, libEM/cmp.h, libEM/emdata.cpp,
	  libEM/emdata.h, libpyEM/libpyCmp2.cpp, plugins/cmp_template.cpp,
	  plugins/cmp_template.h, utils/speedtest.cpp: change Cmp::cmp():
	  add EMData* with as a fixed parameter

2004-12-09 22:12  lpeng

	* doc/: develop_system_setup.html, developer-guide.html: add
	  compiling of eman2 and set up login shell

2004-12-09 21:46  lpeng

	* rt/pyem/project1.py: test projection

2004-12-09 21:03  lpeng

	* rt/pyem/transvec.py: test vector = vector * transform

2004-12-09 21:02  lpeng

	* libEM/transform.h, libpyEM/libpyTransform2.cpp: add vector =
	  vector * transform

2004-12-09 19:28  stevel

	* libEM/projector.cpp, libpyEM/EMAN2.py: Fixed Standard projector.

2004-12-09 18:09  lpeng

	* INSTALL: add more details

2004-12-08 01:52  stevel

	* CMakeLists.txt, programs/e2tomogram.py: New tomogram option
	  working.

2004-12-07 21:41  lpeng

	* libEM/exception.h: add some comments

2004-12-07 21:38  lpeng

	* doc/exception_faq.html: exception introduction

2004-12-07 19:34  lpeng

	* libEM/emdata.cpp: remove some unnecessary err msg printing

2004-12-07 19:32  lpeng

	* rt/pyem/: ccf1.py, ccf2.py: more tests

2004-12-07 02:16  stevel

	* programs/e2tomogram.py: More tomo alignment work.

2004-12-06 21:38  lpeng

	* doc/developer-guide.html, libpyEM/pylist.h: more docs

2004-12-06 21:08  lpeng

	* INSTALL: update boost python

2004-12-06 21:02  lpeng

	* libpyEM/libpyUtils2.cpp, libpyEM/pylist.h, libpyEM/utils.pyste,
	  INSTALL, README, TODO, doc/develop_system_setup.html,
	  libEM/util.cpp, rt/pyem/numpy2.py: switch from numarray to
	  Numeric numpy

2004-12-06 20:18  lpeng

	* rt/: imageio/badfilename.py, pyem/ccf1.py, pyem/ccf2.py,
	  pyem/defaultargs.py, pyem/exception.py, pyem/exception2.py,
	  pyem/filter1.py, pyem/imageio1.py, pyem/imageio_caching.py,
	  pyem/namedclass.py, pyem/numpy.py, pyem/numpy2.py, pyem/pixel.py,
	  pyem/rotate.py, pyem/rotate_translate.py: change the way to find
	  the path of the test images

2004-12-06 20:04  lpeng

	* libEM/: salio.cpp, util.cpp: add more exception handling

2004-12-06 19:25  lpeng

	* TODO: more items are done

2004-12-05 19:52  lpeng

	* libEM/emdata.cpp: fixed a bug in
	  EMData::calc_fourier_shell_correlation(), which was fixed first
	  by Wen in EMAN1 EMData::fsc() on 11/29/04

2004-12-05 16:17  lpeng

	* CMakeLists.txt, INSTALL: updated python support

2004-12-05 15:25  lpeng

	* CMakeLists.txt, INSTALL: INSTALL

2004-12-05 10:54  lpeng

	* INSTALL, doc/develop_system_setup.html: update docs on how to
	  install Numeric python

2004-12-05 10:34  lpeng

	* INSTALL, libpyEM/libpyUtils2.cpp, libpyEM/pylist.h,
	  libpyEM/utils.pyste, rt/pyem/numpy.py, rt/pyem/numpy2.py: change
	  Numeric.array to numarray

2004-12-05 08:43  lpeng

	* rt/emdata/exception1.cpp: add more tests for exceptions

2004-12-05 08:31  lpeng

	* libEM/reconstructor.cpp: fixed type conversion warnings for pow()

2004-12-05 07:34  lpeng

	* doc/development_policy_faq.html: first version from Steve
	  formatted by liwei

2004-12-02 21:17  stevel

	* libEM/pngio.h: trivia

2004-12-01 23:29  stevel

	* libEM/emdata.cpp: Fixes for render_amp8

2004-11-30 20:43  lpeng

	* rt/emdata/: CMakeLists.txt, image_overwrite.cpp, shared_data.cpp:
	  to test EMData::set_shared_data()

2004-11-30 20:30  lpeng

	* TODO, libpyEM/libpyEMData2.cpp, libpyEM/libpyPointArray2.cpp,
	  libpyEM/libpyTransform2.cpp, libpyEM/pylist.cpp: add support to
	  Numerc.array->EMData object, both share the same data block
	  memory

2004-11-30 20:29  lpeng

	* rt/: emdata/exception1.cpp, emdata/image_overwrite.cpp,
	  emdata/rotate_translate.cpp, imageio/imagic1.cpp,
	  imageio/region.cpp, imageio/writetwice.cpp, pyem/numpy.py,
	  pyem/numpy2.py: more numpy rt

2004-11-30 20:29  lpeng

	* doc/developer-guide.html: more development howto docs

2004-11-30 02:08  stevel

	* libEM/emdata.cpp, libEM/emdata.h, programs/e2tomogram.py: Quick
	  patch to temporarily fix e2tomogram.

2004-11-29 22:45  stevel

	* libEM/emdata.cpp, libEM/exception.cpp, libEM/exception.h,
	  libEM/pointarray.cpp, utils/iminfo.cpp, utils/proc2d.cpp:
	  Exception->E2Exception

2004-11-29 22:09  lpeng

	* libEM/: emdata.cpp, emdata.h, pointarray.cpp: add
	  set_shared_data() to EMData

2004-11-29 14:21  stevel

	* libEM/emdata.h: trivial

2004-11-29 14:17  stevel

	* libEM/emdata.cpp: render_amp8 fix now working

2004-11-29 13:20  stevel

	* libpyEM/libpyPointArray2.cpp: regen boost

2004-11-29 12:46  stevel

	* libEM/: emdata.cpp, emdata.h, emutil.h, exception.h,
	  pointarray.cpp, projector.cpp, projector.h: Renderamp8 fix for
	  rgb. Work on projections.

2004-11-29 10:03  stevel

	* CMakeLists.txt, libEM/pointarray.cpp, libEM/pointarray.h: Working
	  on pointarray functionality,this version may not compile with
	  opt++.

2004-11-28 14:14  lpeng

	* libpyEM/libpyUtils2.cpp, libpyEM/pylist.cpp, libpyEM/pylist.h,
	  libpyEM/utils.pyste, rt/pyem/numpy.py: fixed the em2numpy
	  completely

2004-11-28 11:35  lpeng

	* libpyEM/libpyUtils2.cpp, libpyEM/pylist.cpp, libpyEM/pylist.h,
	  rt/pyem/numpy.py: improved em2numpy2() for efficient memory
	  usage; still have a problem: it is column-major(like fortran)
	  instead of row-major

2004-11-27 20:12  lpeng

	* libEM/exception.h: add more comments

2004-11-27 18:18  lpeng

	* doc/: coding_style.html, cvshowto.html,
	  develop_system_setup.html: add more details

2004-11-27 15:46  lpeng

	* doc/: coding_style.html, cvshowto.html: first version

2004-11-27 15:37  lpeng

	* doc/developer-guide.html: updates on LOG

2004-11-27 15:37  lpeng

	* doc/develop_system_setup.html: first version

2004-11-26 02:37  stevel

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/emdata.pyste,
	  libpyEM/libpyEMData2.cpp, programs/e2tomogram.py: render_amp8
	  works. Hope no mem leak

2004-11-25 13:24  stevel

	* libEM/emdata.cpp, libEM/emdata.h, libEM/imagicio.cpp,
	  libEM/imagicio.h, programs/e2tomogram.py: Tomography work. New
	  imagic writing routine.

2004-11-24 21:34  lpeng

	* libEM/emutil.cpp: add exception handling

2004-11-24 21:34  lpeng

	* rt/imageio/imagic1.cpp: add more test case for imagic

2004-11-24 16:00  stevel

	* libEM/imagicio.cpp, programs/e2tomogram.py: more tomogram work.

2004-11-24 01:14  stevel

	* programs/e2tomogram.py: Working on tomogram software some more.

2004-11-23 21:53  lpeng

	* TODO, libEM/imagicio.cpp, libEM/imagicio.h,
	  rt/imageio/CMakeLists.txt, rt/imageio/imagic1.cpp,
	  rt/imageio/writetwice.cpp: fixed some imagic image writing issues

2004-11-23 16:22  stevel

	* programs/: e2ctfplot.py, e2tomogram.py: work on tomography.

2004-11-23 01:58  stevel

	* libEM/emdata.cpp, programs/e2tomogram.py: Bug fix memory leak,
	  working on tomography alignment.

2004-11-22 22:29  lpeng

	* libEM/imageio.h: add appending and insertion policy

2004-11-22 16:15  stevel

	* programs/e2tomogram.py: Work on e2tomogram.py

2004-11-22 15:52  stevel

	* libEM/emcache.cpp, libEM/emdata.cpp, libEM/emutil.cpp,
	  libEM/imagicio.cpp, programs/e2tomogram.py: Few file writing
	  fixes.

2004-11-22 14:17  stevel

	* programs/: e2scannereval.py, e2tomogram.py: Scanner evaluation
	  update.

2004-11-22 02:04  stevel

	* libEM/pointarray.cpp, libEM/pointarray.h, libEM/vec3.h,
	  libpyEM/libpyPointArray2.cpp, libpyEM/libpyTransform2.cpp,
	  programs/e2align3d.py, programs/e2tomogram.py: Beginning of
	  tomography program. Additions to pointarray.

2004-11-21 21:00  lpeng

	* TODO, libEM/exception.cpp, libEM/exception.h,
	  libpyEM/emobject.pyste, libpyEM/factory.pyste,
	  libpyEM/libpyEMData2.cpp, libpyEM/pyexception.cpp,
	  libpyEM/pyexception.h, pyemtbx/exceptions.py,
	  rt/pyem/exception2.py: boost python exception support

2004-11-21 10:04  lpeng

	* CMakeLists.txt: add win32-specific PNG/ZLIB support

2004-11-21 10:03  lpeng

	* libEM/: aligner.cpp, emdata.cpp, emutil.cpp, pifio.cpp, vec3.h:
	  remove type conversion warning in windows

2004-11-20 14:48  lpeng

	* libpyEM/: emdata.pyste, libpyEMData2.cpp: more converter classes

2004-11-20 14:47  lpeng

	* TODO: more items

2004-11-20 06:55  lpeng

	* libEM/emdata.cpp: restore hand opt in get_fft_amplitude()

2004-11-19 21:43  lpeng

	* TODO: more items

2004-11-18 21:49  lpeng

	* libEM/emdata.cpp, libEM/emdata.h, libEM/exception.cpp,
	  libEM/exception.h, libpyEM/libpyUtils2.cpp,
	  rt/emdata/CMakeLists.txt, rt/emdata/exception1.cpp,
	  rt/emdata/exception1.py: better exception handling

2004-11-18 15:31  wjiang

	* libpyEM/libpyEMData2.cpp: add get_fft_amplitude() and
	  get_fft_phase()

2004-11-18 14:29  wjiang

	* libpyEM/emdata.pyste: add get_fft_amplitude() and get_fft_phase()

2004-11-18 14:23  wjiang

	* libEM/: emdata.cpp, emdata.h: add functions: get_fft_amplitude()
	  and get_fft_phase()

2004-11-18 13:29  wjiang

	* programs/e2msa.py: add to cvs

2004-11-17 22:51  lpeng

	* libEM/: emio.cpp, emutil.cpp, emutil.h, icosio.cpp, icosio.h,
	  salio.cpp: add region write in imageio

2004-11-17 22:50  lpeng

	* TODO: more items

2004-11-17 20:20  lpeng

	* rt/emdata/: CMakeLists.txt, compleximg.cpp: test complex image
	  output

2004-11-17 07:54  lpeng

	* libEM/: emdata.h, vec3.h: document change

2004-11-17 07:54  lpeng

	* TODO: more items

2004-11-17 01:39  stevel

	* libEM/emdata.cpp, programs/e2pdb2mrc.py,
	  programs/e2scannereval.py: Fixed bug in insert_clip. New Real2FFT
	  filter. Added e2scannereval.py.

2004-11-15 20:08  lpeng

	* programs/e2pdb2mrc.py: remove FloatPoint; rename GaussMask to
	  MaskGauss

2004-11-14 20:43  lpeng

	* TODO, plugins/aligner_template.cpp, plugins/io_template.cpp,
	  plugins/projector_template.cpp,
	  plugins/reconstructor_template.cpp: imageio changes; remove
	  warnings on windows

2004-11-14 20:42  lpeng

	* rt/pyem/: ccf1.py, ccf2.py: test EMData::calc_ccf

2004-11-14 20:41  lpeng

	* rt/: emdata/CMakeLists.txt, emdata/ccf1.cpp, emdata/ccf2.cpp,
	  emdata/rotate_translate.cpp, pyem/vec1.py: more tests

2004-11-14 20:40  lpeng

	* libEM/: all_imageio.h, amiraio.cpp, averager.cpp, averager.h,
	  cmp.cpp, ctf.cpp, ctf.h, dm3io.cpp, emimio.cpp, emio.cpp,
	  emobject.cpp, emutil.cpp, exception.h, gatan2io.cpp, geometry.h,
	  hdfio.cpp, icosio.cpp, imageio.cpp, imageio.h, imagicio.cpp,
	  interp.cpp, interp.h, log.cpp, lstio.cpp, mrcio.cpp, mrcio.h,
	  pgmio.cpp, pifio.cpp, pifio.h, pngio.cpp, reconstructor.cpp,
	  salio.cpp, spiderio.cpp, sspiderio.cpp, tifio.cpp, util.cpp,
	  util.h, vtkio.cpp, xplorio.cpp, xplorio.h: ImageIO classes
	  improvements: use exception to replace error code; region write

2004-11-14 16:40  lpeng

	* libEM/: emdata.cpp, emdata.h, transform.h: Vec3 template ->
	  Vec3i/Vec3f classes

2004-11-14 16:37  lpeng

	* libpyEM/: emdata.pyste, emobject.pyste, libpyEMData2.cpp,
	  libpyEMObject2.cpp, libpyGeometry2.cpp, libpyTransform2.cpp,
	  libpyUtils2.cpp, pylist.h, transform.pyste: change Vec3 template
	  to 2 classes Vec3i/Vec3f; define python converter from list/tuple
	  to Vec3i/Vec3f

2004-11-14 12:18  lpeng

	* libEM/vec3.h, utils/proc2d.cpp, utils/speedtest.cpp: change Vec3
	  <> to Vec3i/Vec3f

2004-11-14 12:16  lpeng

	* libEM/: aligner.cpp, pointarray.cpp, projector.cpp, projector.h,
	  quaternion.cpp, quaternion.h, transform.cpp, transform.h: change
	  Vec3<> to Vec3i/Vec3f; fixed many warnings inarnings on windows

2004-11-14 02:53  stevel

	* programs/e2foldfitter.py: foldfitter.

2004-11-14 02:27  stevel

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyTransform2.cpp, programs/e2align3d.py,
	  programs/e2foldfitter.py: More fixes for e2foldfitter.py, incl
	  library changes.

2004-11-12 01:36  stevel

	* libEM/emdata.cpp, libEM/vec3.h, programs/e2align3d.py,
	  programs/e2foldfitter.py: Bugfix CCF and a couple of filters.
	  Work on e2align3d.py

2004-11-10 20:02  lpeng

	* libEM/emdata.cpp: type conversion to avoid warning; change in
	  copy()

2004-11-10 19:59  lpeng

	* libEM/emdata.h: change enum for EMData flags; change var name
	  'mult' to something else

2004-11-10 10:26  lpeng

	* CMakeLists.txt, libEM/CMakeLists.txt: fixed issues on windows
	  installation

2004-11-10 10:26  lpeng

	* INSTALL: add more details

2004-11-10 10:25  lpeng

	* README: add file structure

2004-11-06 21:03  lpeng

	* libpyEM/Makefile.pyste, libpyEM/cmp.pyste, libpyEM/libpyCmp2.cpp,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyTransform2.cpp,
	  libpyEM/libpyUtils2.cpp, libpyEM/pylist.h,
	  libpyEM/transform.pyste, plugins/io_template.cpp,
	  plugins/io_template.h, programs/e2proc3d.py, utils/proc2d.cpp:
	  imageio and transform change

2004-11-06 21:01  lpeng

	* rt/: emdata/rotate_phi.cpp, pyem/vec3.py: more rt

2004-11-06 20:59  lpeng

	* libEM/: CMakeLists.txt, amiraio.cpp, dm3io.cpp, emcache.cpp,
	  emdata.h, emimio.cpp, emimio.h, emio.cpp, emio.h, emobject.cpp,
	  emobject.h, emutil.cpp, emutil.h, exception.h, gatan2io.cpp,
	  hdfio.cpp, hdfio.h, icosio.cpp, imageio.cpp, imageio.h,
	  imagicio.cpp, imagicio.h, log.cpp, log.h, lstio.cpp, lstio.h,
	  mrcio.cpp, pgmio.cpp, pifio.cpp, pifio.h, pngio.cpp,
	  reconstructor.cpp, salio.cpp, spiderio.cpp, spiderio.h,
	  sspiderio.cpp, sspiderio.h, tifio.cpp, util.h, vtkio.cpp,
	  vtkio.h, xplorio.cpp: fixed many imageio problem: caching,
	  header/data separation

2004-11-06 20:45  lpeng

	* rt/: emdata/CMakeLists.txt, emdata/rotate1.cpp,
	  imageio/CMakeLists.txt, imageio/region.cpp,
	  imageio/writetwice.cpp, pyem/rotate.py: add more unit tests

2004-11-06 20:45  lpeng

	* libEM/: quaternion.cpp, quaternion.h, transform.cpp, transform.h,
	  vec3.h: split transform.h/cpp into multiple files; each file has
	  a class

2004-11-06 13:44  lpeng

	* TODO: more items to do

2004-11-05 15:11  lpeng

	* libpyEM/libpyTransform2.cpp: fixed a bug

2004-11-05 15:02  lpeng

	* libEM/projector.cpp: rename get_vector to get_row

2004-11-05 15:00  lpeng

	* libEM/: transform.cpp, transform.h: fixed a problem in Vec3
	  operations

2004-11-05 15:00  lpeng

	* libEM/emdata.cpp: rotate_translate(): odd size image problem
	  fixed

2004-11-05 12:07  lpeng

	* libEM/imageio.h: is_single_image_format() added to imageio

2004-11-05 12:00  lpeng

	* libEM/: util.cpp, util.h: add is_file_exist()

2004-11-05 11:59  lpeng

	* libEM/: emdata.cpp, emdata.h, transform.cpp, transform.h: fixed a
	  problem in transform scaling factor

2004-11-03 16:28  lpeng

	* README: readme

2004-11-03 14:22  stevel

	* programs/e2align3d.py: New program. not functional yet

2004-11-01 18:16  lpeng

	* TODO, doc/header_naming.html, libEM/emdata.cpp, libEM/mrcio.cpp,
	  libEM/mrcio.h, programs/e2startcsym.py, programs/e2symbest.py:
	  more python code

2004-11-01 08:25  lpeng

	* programs/e2startcsym.py: added e2symbest.py

2004-10-29 11:09  lpeng

	* programs/e2symbest.py: add more code

2004-10-28 09:43  lpeng

	* doc/header_naming.html, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/lstio.cpp: add LST write support

2004-10-27 21:10  lpeng

	* libEM/emutil.cpp, libEM/emutil.h, libpyEM/libpyUtils2.cpp,
	  libpyEM/utils.pyste, programs/e2symbest.py: ImageSort added to
	  emutil.h/cpp

2004-10-26 19:36  lpeng

	* libEM/emutil.cpp, libEM/emutil.h, libEM/pointarray.cpp,
	  programs/e2proc2d.py, programs/e2startcsym.py,
	  programs/e2symbest.py, pyemtbx/files.py: start to port startcsym
	  from eman1 to eman2

2004-10-26 07:22  lpeng

	* libpyEM/libpyEMData2.cpp: restore back converter test

2004-10-25 09:29  lpeng

	* rt/pyem/vec2.py: simple test for Vec and Matrix

2004-10-23 07:47  lpeng

	* TODO, libEM/amiraio.cpp, libEM/amiraio.h, libEM/dm3io.cpp,
	  libEM/dm3io.h, libEM/emcache.cpp, libEM/emcache.h,
	  libEM/emdata.cpp, libEM/emdata.h, libEM/emimio.cpp,
	  libEM/emimio.h, libEM/emio.cpp, libEM/emio.h, libEM/emobject.cpp,
	  libEM/emutil.cpp, libEM/exception.h, libEM/gatan2io.cpp,
	  libEM/gatan2io.h, libEM/hdfio.cpp, libEM/hdfio.h,
	  libEM/icosio.cpp, libEM/icosio.h, libEM/imageio.cpp,
	  libEM/imageio.h, libEM/imagicio.cpp, libEM/lstio.cpp,
	  libEM/lstio.h, libEM/mrcio.cpp, libEM/mrcio.h, libEM/pgmio.cpp,
	  libEM/pgmio.h, libEM/pifio.cpp, libEM/pifio.h, libEM/pngio.cpp,
	  libEM/pngio.h, libEM/salio.cpp, libEM/salio.h,
	  libEM/spiderio.cpp, libEM/spiderio.h, libEM/sspiderio.cpp,
	  libEM/tifio.cpp, libEM/tifio.h, libEM/util.cpp, libEM/vtkio.cpp,
	  libEM/vtkio.h, libEM/xplorio.cpp, libEM/xplorio.h,
	  libpyEM/libpyEMData2.cpp, rt/demo/cmp.py: imageio classes
	  changes: more docs; image_index is_3d check; separate header/data
	  read/write; add EXITFUNC;

2004-10-19 11:54  lpeng

	* TODO, libEM/emdata.cpp, rt/emdata/CMakeLists.txt,
	  rt/emdata/rotate_translate.cpp, rt/pyem/rotate_translate.py:
	  fixed a problem in rotate_translate()

2004-10-19 11:26  lpeng

	* libEM/util.cpp: fixed a buffer overflow in get_line_from_string()

2004-10-18 17:22  lpeng

	* TODO, libEM/emcache.cpp, libEM/emdata.cpp, libEM/mrcio.cpp,
	  rt/imageio/writetwice.cpp: fixed part of imageio caching problem

2004-10-15 15:33  lpeng

	* libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp: update spider euler angle
	  conventions

2004-10-14 16:06  lpeng

	* libEM/emcache.cpp, libEM/mrcio.cpp, rt/emdata/getclip.cpp,
	  rt/emdata/locations.cpp, rt/imageio/CMakeLists.txt,
	  rt/imageio/mrc.cpp, rt/imageio/writetwice.cpp,
	  rt/pyem/imageio_caching.py: remove caching for image write

2004-10-14 15:02  lpeng

	* libEM/amiraio.cpp, libEM/dm3io.cpp, libEM/emdata.cpp,
	  libEM/emimio.cpp, libEM/emio.cpp, libEM/gatan2io.cpp,
	  libEM/hdfio.cpp, libEM/icosio.cpp, libEM/imageio.h,
	  libEM/imagicio.cpp, libEM/lstio.cpp, libEM/mrcio.cpp,
	  libEM/pgmio.cpp, libEM/pifio.cpp, libEM/pngio.cpp,
	  libEM/salio.cpp, libEM/spiderio.cpp, libEM/tifio.cpp,
	  libEM/vtkio.cpp, libEM/xplorio.cpp, libpyEM/libpyUtils2.cpp,
	  plugins/io_template.cpp, rt/pyem/imageio_caching.py: add imageio
	  flush

2004-10-14 13:24  lpeng

	* libEM/: icosio.cpp, imagicio.cpp, mrcio.cpp, pifio.cpp,
	  spiderio.cpp, vtkio.cpp, xplorio.cpp: add fflush() back to
	  imageio subclass

2004-10-14 13:22  lpeng

	* TODO, libEM/emdata.cpp, libEM/icosio.cpp, libEM/imagicio.cpp,
	  libEM/mrcio.cpp, libEM/pifio.cpp, libEM/spiderio.cpp,
	  libEM/vtkio.cpp, libEM/xplorio.cpp, libpyEM/pylist.h,
	  rt/pyem/imageio_caching.py, rt/pyem/namedclass.py,
	  rt/pyem/vec1.py: convert IntSize,FloatSize,IntPoint,FloatPoint to
	  be tuple in python side

2004-10-13 14:47  lpeng

	* doc/header_naming.html: more header attrs: micrograph_id,
	  particle locations etc

2004-10-13 14:39  lpeng

	* TODO, libEM/transform.cpp, libEM/transform.h,
	  libpyEM/libpyTransform2.cpp, rt/pyem/vec1.py: rename get_value()
	  to get_as_list()

2004-10-13 09:56  lpeng

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/emdata.pyste,
	  libpyEM/libpyEMData2.cpp, rt/pyem/namedclass.py: change
	  get_rotated_clip() so that const XX& is used

2004-10-13 01:13  stevel

	* libEM/: emdata.cpp, icosio.cpp, imagicio.cpp, mrcio.cpp,
	  pifio.cpp, spiderio.cpp, vtkio.cpp, xplorio.cpp: Flush output
	  files on write.

2004-10-12 16:18  lpeng

	* libEM/emdata.cpp, libEM/emutil.cpp, libEM/geometry.cpp,
	  libEM/geometry.h, libEM/mrcio.cpp, libEM/pointarray.cpp,
	  libEM/transform.cpp, libpyEM/geometry.pyste,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyGeometry2.cpp,
	  libpyEM/libpyPointArray2.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/pylist.h, rt/pyem/vec1.py: change
	  IntSize,FloatSize,IntPoint,FloatPoint access approach; convert
	  them to list on python part;

2004-10-12 11:13  lpeng

	* TODO: 037 is fixed

2004-10-11 11:35  lpeng

	* TODO: more stuff

2004-10-10 23:54  stevel

	* libEM/emdata.cpp: sigh

2004-10-10 23:24  stevel

	* libEM/emdata.cpp: trivial

2004-10-10 22:07  stevel

	* libEM/emdata.cpp: Minor fix

2004-10-10 21:20  stevel

	* libEM/emdata.cpp: Working on foldfitter

2004-10-08 01:58  stevel

	* programs/: e2aligntest.py, e2foldfitter.py: Foldfitter work

2004-10-07 22:02  stevel

	* programs/e2foldfitter.py: mdk 10.1 specific bug ?

2004-10-06 01:39  stevel

	* libpyEM/Simplex.py, programs/e2foldfitter.py: Work on foldfitter,
	  Gnu Python simplex minimizer

2004-10-01 16:20  lpeng

	* programs/: e2proc2d.py, e2proc3d.py: use metavar for better help
	  string

2004-10-01 14:56  lpeng

	* CMakeLists.txt, libEM/emutil.cpp, libEM/log.cpp, libEM/log.h,
	  libEM/mrcio.cpp, libpyEM/EMAN2.py, programs/CMakeLists.txt,
	  programs/e2proc2d.py, pyemtbx/CMakeLists.txt, pyemtbx/box.py,
	  pyemtbx/imagetypes.py, pyemtbx/options.py: move some functions
	  from EMAN2.py to pyemtbx

2004-10-01 14:27  lpeng

	* pyemtbx/__init__.py: initial; empty

2004-10-01 14:22  lpeng

	* pyemtbx/CMakeLists.txt: first version

2004-10-01 13:34  lpeng

	* programs/e2proc2d.py: use metavar for options

2004-09-30 11:33  lpeng

	* doc/header_naming.html: add MRC specific labels

2004-09-30 11:22  lpeng

	* INSTALL: add quick-install and advanced install

2004-09-30 11:12  lpeng

	* CMakeLists.txt, INSTALL, libEM/emutil.cpp, libEM/emutil.h,
	  libpyEM/CMakeLists.txt: add PYTHON_LIBRARY for non-win32
	  platforms

2004-09-29 17:06  lpeng

	* doc/header_naming.html: first version. more are coming.

2004-09-29 16:18  lpeng

	* programs/e2proc2d.py: fixed a bug in clip

2004-09-29 16:18  lpeng

	* programs/e2boxer.py: fixed filter names

2004-09-29 15:31  lpeng

	* TODO, libEM/emobject.cpp: change error msg to be more meaningful

2004-09-28 15:02  lpeng

	* TODO: TODO

2004-09-28 14:57  lpeng

	* libEM/emfft.h, libEM/log.cpp, utils/speedtest.cpp: filter name
	  change

2004-09-28 14:53  lpeng

	* TODO: more changes

2004-09-27 18:36  stevel

	* programs/e2aligntest.py: trivial

2004-09-27 16:03  lpeng

	* TODO, libEM/emdata.cpp, libEM/emdata.h, libEM/exception.h,
	  libpyEM/libpyEMData2.cpp: more docs; remove 'name'

2004-09-27 12:09  lpeng

	* libEM/: emdata.cpp, emdata.h: more comments

2004-09-27 11:50  lpeng

	* rt/pyem/imageio1.py: test same image read by 2 EMData obj

2004-09-27 11:48  lpeng

	* libEM/emdata.h: more docs

2004-09-26 01:23  stevel

	* programs/e2aligntest.py: Sigh...

2004-09-26 00:49  stevel

	* programs/e2aligntest.py: Test.

2004-09-23 12:17  lpeng

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/libpyEMData2.cpp: more
	  docs; add more exceptions

2004-09-22 13:06  lpeng

	* libEM/cmp.cpp, libEM/cmp.h, libEM/emdata.cpp, libEM/emdata.h,
	  libpyEM/emdata.pyste, libpyEM/libpyEMData2.cpp, libpyEM/pylist.h,
	  rt/demo/cmp.py, rt/demo/filter1.py: more docs; in EMData::cmp(),
	  change 'Dict&' to 'const Dict&' for params

2004-09-21 14:53  lpeng

	* INSTALL, TODO, libEM/aligner.h, libEM/averager.h, libEM/cmp.h,
	  libEM/emdata.cpp, libEM/emdata.h, libEM/exception.h,
	  libEM/imageio.h, libEM/projector.h, libEM/reconstructor.h,
	  libEM/transform.cpp, libEM/transform.h, libpyEM/libpyEMData2.cpp:
	  more and better docs

2004-09-21 10:24  lpeng

	* TODO: more done

2004-09-20 15:57  lpeng

	* rt/demo/averager.py: more rt

2004-09-20 13:19  lpeng

	* doc/developer-guide.html: change filter naming; log usage

2004-09-20 13:10  lpeng

	* rt/emdata/: CMakeLists.txt, rotate.cpp: add rotatation test to
	  EMData

2004-09-19 21:22  lpeng

	* libEM/amiraio.cpp, libEM/dm3io.cpp, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/emimio.cpp, libEM/emio.cpp,
	  libEM/emobject.h, libEM/gatan2io.cpp, libEM/hdfio.cpp,
	  libEM/icosio.cpp, libEM/imageio.h, libEM/imagicio.cpp,
	  libEM/lstio.cpp, libEM/mrcio.cpp, libEM/pgmio.cpp,
	  libEM/pifio.cpp, libEM/pngio.cpp, libEM/pointarray.cpp,
	  libEM/salio.cpp, libEM/spiderio.cpp, libEM/sspiderio.cpp,
	  libEM/sspiderio.h, libEM/tifio.cpp, libEM/vtkio.cpp,
	  libEM/xplorio.cpp, plugins/io_template.cpp: rename more filters

2004-09-19 21:21  lpeng

	* libpyEM/: CMakeLists.txt, EMAN2.py, Makefile.pyste,
	  aligner.pyste, averager.pyste, cmp.pyste, create_boost_python,
	  emobject.pyste, filter.pyste, geometry.pyste, libpyAligner2.cpp,
	  libpyAverager2.cpp, libpyCmp2.cpp, libpyEMData2.cpp,
	  libpyEMObject2.cpp, libpyFactory2.cpp, libpyFilter2.cpp,
	  libpyGeometry2.cpp, libpyProjector2.cpp, libpyReconstructor2.cpp,
	  libpyTransform2.cpp, libpyUtils2.cpp, pointarray.pyste,
	  projector.pyste, pylist.h, reconstructor.pyste, transform.pyste:
	  rearrange pyste file and Makefile structure

2004-09-16 16:11  stevel

	* programs/e2foldfitter.py: Working on foldfitter

2004-09-16 11:00  stevel

	* programs/: e2foldfitter.py, e2proc2d.py: Working on foldfitter.

2004-09-14 23:08  lpeng

	* libEM/: emdata.cpp, projector.cpp, reconstructor.cpp,
	  transform.cpp: fix (alt,az,phi) -> 3x3 matrix problem

2004-09-14 15:13  lpeng

	* libEM/emdata.cpp, libEM/emdata.h, libEM/projector.cpp,
	  utils/docgen.py: change some filter class names so that more
	  generic words come first

2004-09-14 01:22  stevel

	* libEM/emdata.cpp, libEM/geometry.cpp, programs/e2foldfitter.py:
	  Fixed problem with rotate, still broken. Fixed bug in sorting
	  Pixels.

2004-09-13 17:51  lpeng

	* TODO: add more items

2004-09-13 17:19  lpeng

	* libpyEM/emdata.pyste, libpyEM/geometry.pyste,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyGeometry2.cpp,
	  rt/pyem/pixel.py: add Pixel to boost python

2004-09-11 12:41  lpeng

	* TODO: add write-region todo

2004-09-11 12:39  lpeng

	* libEM/: emcache.cpp, emdata.cpp, emdata.h, hdfio.cpp,
	  imageio.cpp, imageio.h, mrcio.cpp, spiderio.cpp: add a WRITE_ONLY
	  mode to imageio

2004-09-11 08:22  wjiang

	* libpyEM/libpyPointArray2.cpp: sync to the updated PointArray
	  class

2004-09-11 00:17  wjiang

	* libEM/: pointarray.cpp, pointarray.h: move all optimization
	  related code into seperate directory

2004-09-11 00:12  wjiang

	* CMakeLists.txt: move TAO config to tao directory

2004-09-09 17:22  lpeng

	* libEM/: emcache.cpp, hdfio.cpp, imageio.cpp, mrcio.cpp: add mrc
	  file size truncation when overwriting

2004-09-08 22:36  lpeng

	* libpyEM/CMakeLists.txt: change debug flag to null. this greatly
	  shortened the linkted the link time

2004-09-08 21:43  lpeng

	* libEM/emutil.cpp, libEM/util.cpp, libEM/util.h,
	  libEM/xplorio.cpp, libEM/xplorio.h, programs/e2proc2d.py: add
	  xplor image read

2004-09-07 21:34  lpeng

	* libEM/emutil.cpp, libEM/icosio.cpp, libEM/icosio.h, libEM/log.h,
	  libEM/util.cpp, utils/iminfo.cpp: fixed image format problems;
	  exception handling in iminfo

2004-09-02 16:33  lpeng

	* INSTALL: change fftw config options

2004-09-01 17:05  lpeng

	* libEM/: emobject.cpp, exception.h: more exceptions

2004-08-31 20:46  lpeng

	* CMakeLists.txt, libEM/emdata.cpp, libEM/exception.cpp,
	  libEM/exception.h, libEM/log.cpp, libEM/log.h, libEM/lstio.cpp,
	  libEM/mrcio.cpp, libEM/util.cpp, libEM/util.h: better log and
	  exception

2004-08-31 17:30  lpeng

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/emdata.h,
	  libpyEM/libpyEMData2.cpp, utils/speedtest.cpp: fix EMData::cmp()

2004-08-31 17:30  lpeng

	* rt/emdata/: cmp.cpp, image_overwrite.cpp: change exception dump

2004-08-28 01:42  stevel

	* programs/e2pdb2mrc.py: apix fix

2004-08-23 08:39  lpeng

	* TODO, libEM/aligner.h, libEM/averager.h, libEM/cmp.h,
	  libEM/emdata.cpp, libEM/emobject.h, libEM/emutil.h,
	  libEM/exception.cpp, libEM/exception.h, libEM/projector.h,
	  libEM/reconstructor.cpp, libEM/reconstructor.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyFactory2.cpp,
	  libpyEM/libpyPointArray2.cpp, libpyEM/libpyUtils2.cpp,
	  plugins/reconstructor_template.cpp,
	  plugins/reconstructor_template.h: more docs; better exception
	  classes

2004-08-12 22:35  lpeng

	* utils/docgen.py:
	  add usage and purpose on comments

2004-08-12 22:31  lpeng

	* doc/INSTALL, doc/eman2doc.h, libpyEM/EMAN2.py,
	  libpyEM/libpyFactory2.cpp, plugins/filter_template.h,
	  utils/docgen.py: for better filter manuals

2004-08-12 21:12  lpeng

	* TODO, libEM/emdata.cpp, libEM/emdata.h, libEM/emfft.cpp,
	  libEM/emfft.h, libpyEM/emdata.pyste, libpyEM/factory.pyste,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyFactory2.cpp,
	  libpyEM/sparx.cpp, libpyEM/sparx.h, rt/emdata/fft.cpp,
	  utils/CMakeLists.txt, utils/docgen.py: change filter docs from
	  comments into get_desc()

2004-08-11 22:01  stevel

	* libpyEM/: Makefile.pyste, libpyEMData2.cpp, libpyUtils2.cpp:
	  pointarray additions

2004-08-11 21:46  stevel

	* libpyEM/: EMAN2.py, Makefile.pyste: Add pointarray support for
	  python

2004-08-11 19:06  wjiang

	* libEM/: pointarray.cpp, pointarray.h: fixed conditional include
	  for nfft and opt++

2004-08-11 11:21  wjiang

	* libpyEM/libpyPointArray2.cpp: add to CVS

2004-08-11 11:21  wjiang

	* libpyEM/CMakeLists.txt: add support to pointarray

2004-08-11 11:16  wjiang

	* CMakeLists.txt: add support to nfft, optpp

2004-08-11 11:16  wjiang

	* libEM/CMakeLists.txt: add support to pointarray.h/.cpp

2004-08-11 11:14  wjiang

	* libpyEM/pointarray.pyste, libEM/pointarray.cpp,
	  libEM/pointarray.h: add to CVS

2004-08-07 06:52  lpeng

	* libEM/emdata.cpp, libEM/emdata.h, libEM/transform.h,
	  rt/emdata/getclip.cpp: default transformation: identity matrix

2004-08-06 21:15  lpeng

	* TODO, libEM/dm3io.cpp, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emio.cpp, libEM/emutil.cpp, libEM/gatan2io.cpp,
	  libEM/geometry.cpp, libEM/geometry.h, libEM/hdfio.cpp,
	  libEM/icosio.cpp, libEM/imageio.cpp, libEM/imageio.h,
	  libEM/imagicio.cpp, libEM/mrcio.cpp, libEM/pgmio.cpp,
	  libEM/pifio.cpp, libEM/pngio.cpp, libEM/salio.cpp,
	  libEM/spiderio.cpp, libEM/tifio.cpp, libEM/vtkio.cpp,
	  libpyEM/geometry.pyste, libpyEM/libpyGeometry2.cpp: Geometry:
	  Size class changed to IntSize and FloatSize; Region uses float
	  origin and float size

2004-08-05 22:19  lpeng

	* libEM/emdata.cpp, libEM/geometry.h, rt/emdata/CMakeLists.txt,
	  rt/emdata/getclip.cpp: fixed get_clip() error

2004-08-03 10:44  lpeng

	* libEM/: transform.cpp, transform.h: fixed matrix mult and div
	  errors

2004-08-03 06:54  lpeng

	* INSTALL, doc/Doxyfile, doc/developer-guide.html, libEM/imageio.h,
	  libEM/spiderio.h, libEM/sspiderio.h, libpyEM/libpyEMData2.cpp,
	  utils/docgen.py: more documents are added

2004-08-02 23:50  wjiang

	* libEM/transform.cpp: fixed Rotation::set_angle() rotation matrix
	  error

2004-08-02 22:01  wjiang

	* libEM/: transform.cpp, transform.h: fixed Matrix3f and Matrix4f
	  operator *= and Matrix4f::get_matrix3()

2004-08-02 16:14  wjiang

	* libEM/emdata.cpp: add 2D support to insert_scaled_sum

2004-07-31 14:12  lpeng

	* TODO, libpyEM/libpyEMData2.cpp, libpyEM/libpyUtils2.cpp,
	  rt/emdata/CMakeLists.txt, rt/emdata/image_overwrite.cpp,
	  rt/emdata/locations.cpp, rt/pyem/defaultargs.py: fixed a bug in
	  pyste. re-created python wrapper

2004-07-30 07:54  lpeng

	* utils/docgen.py: add time info

2004-07-30 07:53  lpeng

	* TODO: filter document generator script

2004-07-30 07:23  lpeng

	* utils/docgen.py: for filters document

2004-07-29 01:22  stevel

	* libEM/emdata.h, programs/e2boxer.py: Trivial

2004-07-28 18:58  stevel

	* libpyEM/EMAN2.py, programs/e2boxer.py: Working on boxer

2004-07-28 18:51  lpeng

	* libEM/: aligner.cpp, averager.cpp, cmp.cpp, projector.cpp,
	  reconstructor.cpp: fixed some namespace issues

2004-07-28 07:40  lpeng

	* doc/developer-guide.html, libpyEM/factory.pyste,
	  libpyEM/geometry.pyste, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyFactory2.cpp, libpyEM/libpyGeometry2.cpp,
	  plugins/filter_template.h: spacing_row/col/sec changed to
	  apix_x/y/z; Point<> changed to IntPoint,FloatPoint

2004-07-28 07:40  lpeng

	* libEM/: averager.cpp, emdata.cpp, emdata.h, emobject.cpp,
	  emobject.h, geometry.cpp, geometry.h, hdfio.cpp, mrcio.cpp,
	  pifio.cpp, vtkio.cpp: spacing_row/col/sec changed to apix_x/y/z;
	  Point<> changed to IntPoint, FloatPoint

2004-07-28 02:00  stevel

	* programs/e2boxer.py: New program. Still working on it.

2004-07-27 22:36  lpeng

	* TODO: more stuff

2004-07-27 15:04  stevel

	* libEM/emdata.cpp, libpyEM/EMAN2.py, programs/e2pdb2mrc.py:
	  e2pdb2mrc.py works !

2004-07-27 01:31  stevel

	* programs/e2pdb2mrc.py: Ready for first test.

2004-07-26 13:56  stevel

	* programs/e2pdb2mrc.py: New program, still work in progress

2004-07-26 02:28  stevel

	* CMakeLists.txt, libEM/emdata.cpp, libpyEM/libpyEMData2.cpp,
	  programs/e2foldfitter.py, programs/foldfitter.py: Misc work.

2004-07-25 11:58  lpeng

	* TODO, doc/developer-guide.html, libEM/aligner.cpp,
	  libEM/amiraio.cpp, libEM/averager.cpp, libEM/ctf.cpp,
	  libEM/dm3io.cpp, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emimio.cpp, libEM/emio.cpp, libEM/emobject.cpp,
	  libEM/emutil.cpp, libEM/exception.cpp, libEM/gatan2io.cpp,
	  libEM/geometry.cpp, libEM/geometry.h, libEM/hdfio.cpp,
	  libEM/icosio.cpp, libEM/imageio.cpp, libEM/imagicio.cpp,
	  libEM/log.cpp, libEM/log.h, libEM/lstio.cpp, libEM/mrcio.cpp,
	  libEM/pgmio.cpp, libEM/pifio.cpp, libEM/pngio.cpp,
	  libEM/projector.cpp, libEM/reconstructor.cpp, libEM/salio.cpp,
	  libEM/spiderio.cpp, libEM/sspiderio.cpp, libEM/tifio.cpp,
	  libEM/transform.cpp, libEM/util.cpp, libEM/vtkio.cpp,
	  libEM/xplorio.cpp, libEM/xydata.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyGeometry2.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/utils.pyste, plugins/io_template.cpp,
	  rt/emdata/CMakeLists.txt, rt/emdata/emdata_api.cpp,
	  rt/emdata/locations.cpp, rt/imageio/imageio.cpp,
	  rt/imageio/mrc.cpp, utils/iminfo.cpp, utils/proc2d.cpp: change
	  the way to call Log: use macro LOGERR etc

2004-07-24 09:18  lpeng

	* rt/emdata/emdata_api.cpp: include EMData.h from EMAN1

2004-07-23 22:15  stevel

	* programs/foldfitter.py: New program doesn't work yet

2004-07-23 15:38  stevel

	* libEM/emdata.cpp, rt/emdata/emdata_api.cpp: Working on new
	  function

2004-07-23 13:46  stevel

	* libpyEM/: libpyEMData2.cpp, libpyFactory2.cpp,
	  libpyGeometry2.cpp, libpyUtils2.cpp: reran Pyste

2004-07-23 13:37  stevel

	* libpyEM/emdata.pyste: Need to try pyste on blake.

2004-07-23 12:33  stevel

	* libEM/: emdata.cpp, emdata.h, geometry.h: New functions.

2004-07-23 08:40  lpeng

	* doc/developer-guide.html: rename guide.html to
	  developer-guide.html

2004-07-23 08:10  lpeng

	* rt/emdata/CMakeLists.txt: add EMAN1 inc/lib search to emdata_api

2004-07-22 21:18  lpeng

	* rt/: emdata/CMakeLists.txt, emdata/emdata_api.cpp,
	  pyem/exception.py: add more EMData filter tests

2004-07-22 18:44  lpeng

	* TODO: initial one

2004-07-21 18:10  lpeng

	* libpyEM/: CMakeLists.txt, Makefile.pyste, factory.pyste: fixed
	  flags not availabe under windows vc

2004-07-21 17:44  lpeng

	* libEM/: emobject.cpp, emobject.h, imageio.h, imagicio.cpp,
	  imagicio.h, interp.h, mrcio.cpp, mrcio.h, projector.cpp,
	  reconstructor.cpp, reconstructor.h, spiderio.cpp, spiderio.h,
	  transform.cpp, transform.h, util.cpp, util.h: more docs; floating
	  point fix

2004-07-20 11:45  lpeng

	* libEM/: emdata.cpp, emdata.h: more documents

2004-07-20 08:37  lpeng

	* libEM/: aligner.cpp, averager.cpp, byteorder.h, cmp.cpp, ctf.cpp:
	  fix floating point default types

2004-07-19 20:43  stevel

	* CMakeLists.txt, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyFactory2.cpp, libpyEM/libpyGeometry2.cpp,
	  libpyEM/libpyUtils2.cpp, libpyEM/pylist.cpp: Various compilation
	  problems

2004-07-13 16:50  lpeng

	* INSTALL, makedoc.sh, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emutil.h, libEM/exception.h, libEM/imageio.h,
	  libEM/mrcio.h, libpyEM/create_boost_python,
	  libpyEM/libpyEMData2.cpp: add more documentations and exceptions

2004-07-12 14:44  lpeng

	* libEM/CMakeLists.txt, libEM/averager.h, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/emobject.h, libEM/emutil.h,
	  libEM/exception.cpp, libEM/exception.h, libEM/imageio.h,
	  libEM/mrcio.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyFactory2.cpp, rt/emdata/blankimg.cpp,
	  rt/emdata/fft.cpp, rt/emdata/setvalue.cpp,
	  rt/imageio/imageio.cpp: define exceptions to handle errors

2004-07-12 10:57  lpeng

	* CMakeLists.txt, INSTALL, libEM/averager.h, libEM/ctf.h,
	  libEM/interp.cpp, libEM/pifio.cpp, libEM/salio.cpp,
	  libEM/spiderio.cpp, libEM/util.cpp, libEM/util.h,
	  libEM/vtkio.cpp: fixed double->float convert warnings

2004-07-08 16:25  lpeng

	* libEM/: emdata.cpp, emdata.h: more documentation

2004-07-07 09:28  lpeng

	* libpyEM/pylist.cpp: index error fixed

2004-07-06 13:11  lpeng

	* CMakeLists.txt, libpyEM/CMakeLists.txt: more sgi fix

2004-07-06 11:24  lpeng

	* libpyEM/CMakeLists.txt: more fixed on SGI

2004-07-06 10:50  lpeng

	* CMakeLists.txt, libEM/averager.cpp, libEM/emobject.h,
	  utils/proc2d.cpp, utils/speedtest.cpp: fixed some warnings found
	  on SGI

2004-06-30 16:41  lpeng

	* CMakeLists.txt: win32 support: search python inc path

2004-06-29 10:58  lpeng

	* libpyEM/pylist.cpp: added back

2004-06-29 10:57  lpeng

	* libpyEM/pylist.cpp: remove pylist.cpp for testing

2004-06-29 10:33  lpeng

	* libpyEM/pylist.cpp: define wrapper functions

2004-06-28 14:54  lpeng

	* CMakeLists.txt, libpyEM/CMakeLists.txt, libpyEM/Makefile.pyste,
	  libpyEM/libpyFactory2.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/pylist.h, libpyEM/utils.pyste, rt/pyem/numpy.py: added
	  numeric python array support

2004-06-28 11:22  lpeng

	* libpyEM/pylist.h: numpy support

2004-06-24 14:43  lpeng

	* libEM/: averager.cpp, averager.h: averager: add_image_list()

2004-06-23 15:01  lpeng

	* CMakeLists.txt, INSTALL, libEM/averager.cpp, libEM/averager.h,
	  libEM/emdata.h, libpyEM/factory.pyste, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyFactory2.cpp, plugins/averager_template.cpp,
	  plugins/averager_template.h: change averager interface to:
	  add_image(), finish()

2004-06-23 10:12  lpeng

	* libpyEM/: pylist.h, sparx.cpp, sparx.h:
	  initial design; hasn't compiled and tested yet

2004-06-17 18:36  lpeng

	* CMakeLists.txt, INSTALL: add FFTWDIR and GSLDIR in default search
	  path

2004-06-11 16:12  lpeng

	* libEM/aligner.cpp, libEM/aligner.h, libEM/log.h, libEM/mrcio.cpp,
	  libEM/mrcio.h, libEM/util.cpp, libEM/util.h,
	  libpyEM/libpyUtils2.cpp: more documentations

2004-06-11 14:04  lpeng

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/emdata.pyste,
	  libpyEM/libpyEMData2.cpp, rt/pyem/filter1.py, utils/iminfo.cpp:
	  add more docs; remove bool->EMObject in libpyEM

2004-06-11 10:57  lpeng

	* CMakeLists.txt, libEM/emobject.cpp, libEM/emobject.h,
	  libpyEM/CMakeLists.txt, utils/proc2d.cpp:
	  minor changes; space changes in emobject.h/cpp to fix 'indent''s
	  bad formats

2004-06-09 00:30  wjiang

	* libEM/emdata.cpp: misc changes to conform to EMAN1 behavior and
	  make fitctf2.py work

2004-06-08 11:43  lpeng

	* libEM/emobject.h, libEM/exception.h, libpyEM/Makefile.pyste,
	  libpyEM/factory.pyste, libpyEM/libpyFactory2.cpp,
	  rt/pyem/exception.py: rename RangeMask to RangeThreshold in
	  filter

2004-06-07 08:59  lpeng

	* indentcode.sh, purifycode.sh:
	  change file names

2004-06-07 08:57  lpeng

	* plugins/: aligner_template.cpp, aligner_template.h,
	  averager_template.cpp, averager_template.h, cmp_template.cpp,
	  cmp_template.h, filter_template.cpp, filter_template.h,
	  io_template.cpp, io_template.h, projector_template.cpp,
	  projector_template.h, reconstructor_template.cpp,
	  reconstructor_template.h: purified using indent

2004-06-03 16:49  lpeng

	* makedoc.sh, purifycode.sh, libEM/aligner.cpp, libEM/aligner.h,
	  libEM/amiraio.cpp, libEM/amiraio.h, libEM/averager.cpp,
	  libEM/averager.h, libEM/byteorder.cpp, libEM/byteorder.h,
	  libEM/cmp.cpp, libEM/cmp.h, libEM/ctf.cpp, libEM/ctf.h,
	  libEM/dm3io.cpp, libEM/dm3io.h, libEM/emcache.cpp,
	  libEM/emcache.h, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/emfft.cpp, libEM/emfft.h, libEM/emimio.cpp, libEM/emimio.h,
	  libEM/emio.cpp, libEM/emio.h, libEM/emobject.cpp,
	  libEM/emobject.h, libEM/emutil.cpp, libEM/emutil.h,
	  libEM/gatan2io.cpp, libEM/gatan2io.h, libEM/geometry.cpp,
	  libEM/geometry.h, libEM/hdfio.cpp, libEM/hdfio.h,
	  libEM/icosio.cpp, libEM/icosio.h, libEM/imageio.cpp,
	  libEM/imageio.h, libEM/imagicio.cpp, libEM/imagicio.h,
	  libEM/interp.cpp, libEM/interp.h, libEM/log.cpp, libEM/log.h,
	  libEM/lstio.cpp, libEM/lstio.h, libEM/mrcio.cpp, libEM/mrcio.h,
	  libEM/pgmio.cpp, libEM/pgmio.h, libEM/pifio.cpp, libEM/pifio.h,
	  libEM/pngio.cpp, libEM/pngio.h, libEM/portable_fileio.h,
	  libEM/projector.cpp, libEM/projector.h, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libEM/salio.cpp, libEM/salio.h,
	  libEM/spiderio.cpp, libEM/spiderio.h, libEM/sspiderio.cpp,
	  libEM/sspiderio.h, libEM/tifio.cpp, libEM/tifio.h,
	  libEM/transform.cpp, libEM/transform.h, libEM/util.cpp,
	  libEM/util.h, libEM/vtkio.cpp, libEM/vtkio.h, libEM/xplorio.cpp,
	  libEM/xplorio.h, libEM/xydata.cpp, libEM/xydata.h: fix code
	  indention problem in libEM: use tabs only

2004-06-03 11:33  lpeng

	* CMakeLists.txt, libEM/CMakeLists.txt, libpyEM/CMakeLists.txt,
	  plugins/CMakeLists.txt: fixed some option bugs in CMakeLists.txt

2004-06-02 16:48  lpeng

	* CMakeLists.txt, libEM/aligner.cpp, libEM/aligner.h,
	  libEM/averager.cpp, libEM/averager.h, libEM/cmp.cpp, libEM/cmp.h,
	  libEM/emdata.cpp, libEM/emdata.h, libEM/emobject.h,
	  libEM/emutil.cpp, libEM/emutil.h, libEM/projector.cpp,
	  libEM/projector.h, libEM/reconstructor.cpp,
	  libEM/reconstructor.h, libpyEM/CMakeLists.txt, libpyEM/EMAN2.py,
	  libpyEM/Makefile.pyste, libpyEM/factory.pyste,
	  libpyEM/filter.pyste, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyFactory2.cpp, libpyEM/libpyFilter2.cpp,
	  libpyEM/libpyUtils2.cpp, plugins/aligner_template.h,
	  plugins/averager_template.h, plugins/cmp_template.h,
	  plugins/filter_template.h, plugins/projector_template.h,
	  plugins/reconstructor_template.h, rt/demo/averager.py,
	  rt/imageio/basic.cpp: change Factory implementation and its name
	  in python

2004-06-02 15:16  lpeng

	* plugins/: CMakeLists.txt, aligner_template.cpp,
	  aligner_template.h, averager_template.cpp, averager_template.h,
	  cmp_template.cpp, cmp_template.h, filter_template.cpp,
	  filter_template.h, io_template.cpp, io_template.h,
	  projector_template.cpp, projector_template.h,
	  reconstructor_template.cpp, reconstructor_template.h: rename
	  'ext' to 'plugins'

2004-06-02 11:19  lpeng

	* libEM/: CMakeLists.txt, projector.cpp, projector.h: SGI MIPSpro:
	  cannot define type(struct,class) in a function

2004-06-02 10:43  lpeng

	* libpyEM/libpyEMData2.cpp: updated

2004-06-02 10:13  lpeng

	* libEM/aligner.cpp, libEM/ctf.cpp, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/emutil.h, libEM/projector.cpp,
	  libEM/projector.h, libEM/util.cpp, rt/imageio/basic.cpp,
	  utils/proc2d.cpp, utils/speedtest.cpp: remove with_fft in
	  EMData::copy()

2004-06-01 16:54  lpeng

	* libEM/: averager.cpp, emdata.cpp, spiderio.cpp: fixed variables
	  whose memory should be initialized to be zero using calloc in
	  eman1

2004-06-01 11:47  lpeng

	* CMakeLists.txt, libEM/log.cpp: windows support

2004-06-01 11:45  lpeng

	* rt/imageio/clip.py: test for image clip

2004-06-01 11:44  lpeng

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/emdata.cpp,
	  libEM/log.cpp, libEM/lstio.cpp, libpyEM/CMakeLists.txt,
	  libpyEM/factory.pyste, libpyEM/libpyFactory2.cpp: added for
	  windows (VC & MinGW) support

2004-05-28 16:00  lpeng

	* libEM/emdata.cpp, rt/emdata/CMakeLists.txt,
	  rt/emdata/radial_dist.cpp: fixed uninitialized memory problem in
	  calc_radial_dist()

2004-05-28 15:02  lpeng

	* libEM/emdata.cpp, rt/imageio/mrc.cpp: fixed a bug in get_clip()

2004-05-28 13:50  lpeng

	* CMakeLists.txt, libEM/emdata.h, libEM/emobject.cpp,
	  libEM/log.cpp, libEM/mrcio.cpp, rt/imageio/mrc.py: getenv(HOME)
	  won't work for windows

2004-05-27 10:19  lpeng

	* libEM/emdata.cpp, libEM/emdata.h, rt/imageio/mrc.cpp:
	  emdata.get_clip(): pad 0 if larger than image

2004-05-27 09:23  lpeng

	* libEM/emdata.cpp, libEM/emdata.h, libEM/transform.h,
	  rt/imageio/mrc.cpp: fixed get_clip()

2004-05-26 16:10  lpeng

	* rt/imageio/ctf.cpp: testing ctf read/write

2004-05-26 15:08  lpeng

	* libEM/hdfio.cpp, libEM/mrcio.cpp, rt/imageio/CMakeLists.txt,
	  rt/imageio/mrc.cpp: HDF IO: after read/write CTF, cur_dataset
	  need to be updated

2004-05-26 14:35  lpeng

	* libEM/emutil.cpp: fix a bug in determining image types

2004-05-26 12:17  lpeng

	* libEM/averager.cpp, libEM/ctf.cpp, libEM/ctf.h, libEM/emutil.h,
	  libpyEM/libpyUtils2.cpp: fixed ctf::compute_1d() so that it uses
	  image size instead of image as the arg

2004-05-26 11:41  lpeng

	* libEM/emcache.cpp, libEM/emcache.h, libEM/emutil.cpp,
	  libEM/imageio.h, rt/imageio/mrc.py: improved imageio caching: add
	  caching of file open rw mode

2004-05-26 10:04  lpeng

	* libEM/: imageio.h, reconstructor.h: more documentation for
	  templates in 'ext' subdir

2004-05-26 09:23  lpeng

	* CMakeLists.txt, INSTALL:
	  more documentation on INSTALL; more c++ flags in CMake

2004-05-25 16:17  lpeng

	* libEM/amiraio.cpp, libEM/byteorder.cpp, libEM/byteorder.h,
	  libEM/dm3io.cpp, libEM/dm3io.h, libEM/emimio.cpp, libEM/emio.cpp,
	  libEM/emobject.h, libEM/gatan2io.cpp, libEM/hdfio.cpp,
	  libEM/icosio.cpp, libEM/imageio.h, libEM/imagicio.cpp,
	  libEM/lstio.cpp, libEM/mrcio.cpp, libEM/pgmio.cpp,
	  libEM/pifio.cpp, libEM/pngio.cpp, libEM/salio.cpp,
	  libEM/spiderio.cpp, libEM/sspiderio.cpp, libEM/sspiderio.h,
	  libEM/tifio.cpp, libEM/util.cpp, libEM/vtkio.cpp,
	  libEM/xplorio.cpp, libpyEM/libpyUtils2.cpp: change names of some
	  api; add reverse byteorder in api level;

2004-05-25 14:35  lpeng

	* libpyEM/libpyEMData2.cpp: [no log message]

2004-05-24 16:49  lpeng

	* libpyEM/EMAN2.py, libpyEM/Makefile.pyste, libpyEM/emdata.pyste,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyUtils2.cpp,
	  programs/e2proc2d.py, programs/e2proc3d.py: e2proc3d.py is almost
	  done; need more tests

2004-05-24 14:27  lpeng

	* programs/: e2proc2d.py, e2proc3d.py:
	  remove e2proc3d.py temporarily

2004-05-24 13:39  fang

	* libpyEM/libpyEMData2.cpp: no message

2004-05-24 13:22  lpeng

	* libEM/emdata.cpp, libEM/emdata.h, libEM/emutil.cpp,
	  libEM/emutil.h, libEM/mrcio.cpp, programs/e2proc3d.py: more
	  proc3d stuff

2004-05-24 10:24  lpeng

	* libEM/emobject.cpp, libEM/emobject.h, libEM/mrcio.cpp,
	  libpyEM/libpyFactory2.cpp, rt/imageio/CMakeLists.txt,
	  rt/imageio/mrc.cpp, rt/imageio/mrc.py: improve MRC IO so that any
	  label can be added through python

2004-05-23 12:27  lpeng

	* rt/demo/filter3.py: more filters for tests

2004-05-23 12:26  lpeng

	* libEM/mrcio.cpp: added 'ext' directory for user-extensions

2004-05-20 15:22  lpeng

	* CMakeLists.txt, libEM/CMakeLists.txt, libpyEM/CMakeLists.txt:
	  create filter template for user-defined filters

2004-05-20 12:42  lpeng

	* libEM/lstio.cpp, rt/demo/averager.py, rt/demo/project.py:
	  averager demo in python

2004-05-20 12:17  lpeng

	* libEM/emdata.cpp, libEM/emdata.h, libpyEM/CMakeLists.txt,
	  libpyEM/emdata.pyste, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyUtils2.cpp, libpyEM/pyem.cpp, libpyEM/pyem.h,
	  libpyEM/utils.pyste: remove retired pyem.h(cpp)

2004-05-20 11:08  lpeng

	* libEM/emobject.cpp, libEM/emobject.h, libEM/emutil.h,
	  libEM/util.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyFactory2.cpp, libpyEM/libpyUtils2.cpp,
	  rt/imageio/basic.cpp: add functions to dump a factory

2004-05-19 16:28  lpeng

	* libEM/CMakeLists.txt, libEM/emobject.cpp, libEM/emobject.h,
	  libpyEM/libpyEMData2.cpp: fixed a python implicit converter bug

2004-05-19 16:04  lpeng

	* libEM/transform.h: implicit converter in EMObject

2004-05-19 16:04  lpeng

	* libpyEM/: emdata.pyste, libpyEMData2.cpp: add implicit converter

2004-05-19 16:04  lpeng

	* rt/demo/: filter1.py, filter2.py:
	  for testing

2004-05-19 15:23  fang

	* libEM/transform.h: no message

2004-05-19 15:22  lpeng

	* rt/demo/align.py:
	  for testing only

2004-05-19 15:21  lpeng

	* libEM/aligner.cpp, libEM/averager.cpp, libEM/averager.h,
	  libEM/cmp.cpp, libEM/emobject.h, libEM/hdfio.cpp,
	  libpyEM/factory.pyste, libpyEM/libpyFactory2.cpp,
	  rt/imageio/basic.cpp: simplify EMObject usage again: EMData*,
	  XYData*, string

2004-05-19 14:20  lpeng

	* libEM/aligner.cpp, libEM/amiraio.cpp, libEM/averager.cpp,
	  libEM/averager.h, libEM/cmp.cpp, libEM/ctf.cpp, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/emio.cpp, libEM/emobject.h,
	  libEM/emutil.cpp, libEM/hdfio.cpp, libEM/icosio.cpp,
	  libEM/imagicio.cpp, libEM/mrcio.cpp, libEM/pgmio.cpp,
	  libEM/pifio.cpp, libEM/pngio.cpp, libEM/projector.cpp,
	  libEM/projector.h, libEM/reconstructor.cpp, libEM/spiderio.cpp,
	  libEM/vtkio.cpp, libEM/xplorio.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyFactory2.cpp, rt/demo/filter1.py,
	  rt/imageio/basic.cpp, rt/imageio/imageio.cpp, utils/proc2d.cpp,
	  utils/speedtest.cpp: simplify EMObject usage: remove get_int(),
	  get_float(), get_double()

2004-05-19 10:57  lpeng

	* libEM/: emdata.cpp, emimio.cpp: remove EMObject() wrapper when
	  used in filter param dict

2004-05-19 10:54  lpeng

	* libEM/: aligner.cpp, cmp.cpp, ctf.cpp, dm3io.cpp, emdata.cpp,
	  emio.cpp, emobject.h, gatan2io.cpp, hdfio.cpp, icosio.cpp,
	  imagicio.cpp, mrcio.cpp, pgmio.cpp, pifio.cpp, pngio.cpp,
	  projector.cpp, salio.cpp, spiderio.cpp, tifio.cpp, vtkio.cpp:
	  remove EMObject() wrapper when used in filter param dict

2004-05-19 09:44  lpeng

	* rt/: demo/filter1.py, demo/tomrc.py, pyem/converter.py,
	  pyem/filter1.py, pyem/operators.py: more tests

2004-05-19 09:29  lpeng

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/emobject.h: add
	  filter template

2004-05-18 17:27  lpeng

	* CMakeLists.txt, libEM/ctf.cpp, libEM/emdata.cpp, libEM/emdata.h,
	  libEM/log.cpp, libEM/lstio.cpp, libEM/mrcio.cpp,
	  libEM/projector.cpp, libpyEM/libpyEMData2.cpp, rt/emdata/fft.cpp,
	  utils/CMakeLists.txt, utils/proc2d.cpp, utils/speedtest.cpp:
	  remove gimme_fft();

2004-05-18 15:21  wjiang

	* libEM/emdata.cpp: fixed calc_radial_dist() function for angular
	  wedge: use intensity instead of amplitude

2004-05-18 14:27  lpeng

	* CMakeLists.txt, libpyEM/libpyEMData2.cpp,
	  programs/CMakeLists.txt, programs/e2proc3d.py,
	  programs/iminfo.cpp, programs/proc2d.cpp, programs/speedtest.cpp,
	  utils/iminfo.cpp, utils/proc2d.cpp, utils/speedtest.cpp: more
	  filters are defined from proc3d; also, move *.cpp to 'utils'
	  directory

2004-05-17 16:55  lpeng

	* programs/e2proc3d.py: more proc3d migration

2004-05-17 12:33  lpeng

	* libEM/emdata.cpp, libEM/emdata.h, programs/e2proc2d.py,
	  programs/e2proc3d.py: move more filters from proc3d to Filter
	  factory

2004-05-14 14:33  lpeng

	* libEM/aligner.cpp, libEM/aligner.h, libEM/emdata.cpp,
	  libEM/emdata.h, libEM/projector.cpp, libEM/reconstructor.cpp,
	  libEM/transform.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyGeometry2.cpp, programs/e2proc3d.py,
	  programs/proc2d.cpp, programs/speedtest.cpp:
	  change the api on rotate_translate(). remove set_rlign_params(),
	  set_talign_params() etc

2004-05-07 13:11  lpeng

	* programs/e2proc2d.py, programs/e2proc3d.py, libEM/emdata.cpp,
	  libEM/emdata.h: add proc3d

2004-05-07 12:55  lpeng

	* programs/e2proc2d.py: complete; need more tests

2004-05-06 11:07  lpeng

	* programs/e2proc2d.py: add arbitrary orders; add options
	  docstrings; need to check average_nimg

2004-05-05 11:34  lpeng

	* programs/e2proc2d.py: try to use arbitrary options orders; not
	  working yet

2004-05-04 16:46  lpeng

	* libEM/averager.cpp, libEM/cmp.cpp, libEM/util.cpp, libEM/util.h,
	  libpyEM/EMAN2.py, libpyEM/libpyUtils2.cpp, programs/e2proc2d.py,
	  programs/proc2d.cpp: moved more filters from proc2d to Filter
	  system. Made a primitive e2proc2d.py

2004-05-04 09:17  lpeng

	* libEM/cmp.h, libEM/ctf.h, libEM/emdata.h, libEM/projector.h,
	  libEM/reconstructor.h, libEM/transform.h,
	  programs/CMakeLists.txt, programs/e2proc2d.py,
	  programs/proc2d.cpp: more documentation

2004-04-30 16:01  lpeng

	* libEM/emdata.cpp, libEM/emdata.h, libEM/xydata.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyUtils2.cpp: move several
	  filters from proc2d to Filter system

2004-04-30 16:00  lpeng

	* programs/: e2proc2d.py, proc2d.cpp, speedtest.cpp: [no log
	  message]

2004-04-30 11:13  lpeng

	* libEM/CMakeLists.txt, libEM/ctf.h, libEM/emcache.h,
	  libEM/emfft.h, libEM/emio.h, libEM/interp.h, libEM/util.h,
	  libEM/xydata.h, libpyEM/filter.pyste, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyFilter2.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/utils.pyste: more documentation

2004-04-30 10:19  lpeng

	* programs/speedtest.cpp: fixed a bug in speedtest

2004-04-29 17:32  lpeng

	* programs/speedtest.cpp: make eman1 api to eman2 api in speedtest

2004-04-29 17:10  lpeng

	* libEM/aligner.cpp, libEM/emdata.cpp, libEM/emfft.cpp,
	  libEM/mrcio.cpp, libEM/projector.cpp, programs/speedtest.cpp: fix
	  bugs in alignment

2004-04-29 12:15  lpeng

	* libEM/: emdata.h, emio.cpp, interp.cpp, util.cpp, util.h: made
	  some changes for windows support

2004-04-29 12:02  lpeng

	* libEM/byteorder.h: documentation

2004-04-29 11:55  fang

	* libEM/emdata.h: no message

2004-04-29 11:46  fang

	* libEM/xydata.cpp: no message

2004-04-29 11:43  fang

	* libEM/: salio.cpp, transform.cpp, util.cpp, util.h, xplorio.cpp:
	  no message

2004-04-29 11:40  fang

	* libEM/: lstio.cpp, pifio.cpp, projector.h: no message

2004-04-29 11:36  fang

	* libEM/: amiraio.cpp, ctf.h, imagicio.cpp, log.cpp: no message

2004-04-29 10:29  lpeng

	* libEM/: aligner.h, averager.h, cmp.h, geometry.h, imageio.h,
	  projector.h, reconstructor.h, transform.h: more documentation

2004-04-29 09:04  lpeng

	* makedoc.sh: add some print-out info

2004-04-28 16:47  lpeng

	* libEM/: emfft.h, lstio.cpp, util.cpp: remove some unused includes

2004-04-28 15:33  lpeng

	* libEM/: aligner.h, cmp.h, emobject.h, projector.h: documentation

2004-04-28 13:42  lpeng

	* makedoc.sh, doc/Doxyfile: doxygen support

2004-04-28 11:52  lpeng

	* rt/: emdata/CMakeLists.txt, emdata/blankimg.C,
	  emdata/blankimg.cpp, emdata/cmp.C, emdata/cmp.cpp, emdata/fft.C,
	  emdata/fft.cpp, emdata/setvalue.C, emdata/setvalue.cpp,
	  imageio/CMakeLists.txt, imageio/basic.C, imageio/basic.cpp,
	  imageio/imageio.C, imageio/imageio.cpp: rename file ext from .C
	  to .cpp

2004-04-28 11:46  lpeng

	* libpyEM/: CMakeLists.txt, pyem.C, pyem.cpp: rename .C to .cpp

2004-04-28 11:45  lpeng

	* libEM/: CMakeLists.txt, aligner.cpp, amiraio.cpp, averager.cpp,
	  byteorder.cpp, cmp.cpp, ctf.cpp, dm3io.cpp, emcache.cpp,
	  emdata.cpp, emfft.cpp, emimio.cpp, emio.cpp, emutil.cpp,
	  gatan2io.cpp, geometry.cpp, hdfio.cpp, icosio.cpp, imageio.cpp,
	  imagicio.cpp, interp.cpp, log.cpp, lstio.cpp, mrcio.cpp,
	  pgmio.cpp, pifio.cpp, pngio.cpp, projector.cpp,
	  reconstructor.cpp, salio.cpp, spiderio.cpp, sspiderio.cpp,
	  tifio.cpp, transform.cpp, util.cpp, vtkio.cpp, xplorio.cpp,
	  xydata.cpp: rename file ext from .C to .cpp

2004-04-28 11:41  lpeng

	* CMakeLists.txt, libEM/aligner.h: fix bugs found by speedtest

2004-04-28 11:40  lpeng

	* programs/: CMakeLists.txt, iminfo.C, iminfo.cpp, proc2d.C,
	  proc2d.cpp, speedtest.C, speedtest.cpp:
	  rename .C to .cpp

2004-04-27 15:54  lpeng

	* programs/speedtest.C: [no log message]

2004-04-27 15:52  lpeng

	* CMakeLists.txt, libEM/aligner.h, libEM/emfft.h, libEM/emobject.h,
	  libEM/geometry.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyGeometry2.cpp, programs/CMakeLists.txt,
	  programs/proc2d.C: fixed some bugs found by rewriting speedtest

2004-04-26 13:31  lpeng

	* libEM/: aligner.h, projector.h, reconstructor.h: documentations

2004-04-26 10:25  lpeng

	* libEM/emdata.h, libpyEM/libpyEMData2.cpp: create more filters
	  from emdata functions

2004-04-26 09:53  lpeng

	* libEM/emdata.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyUtils2.cpp, programs/proc2d.C: create more filters
	  from emdata functions

2004-04-26 09:06  lpeng

	* libEM/: log.h, util.h: add eman1 log mechanism

2004-04-23 14:20  lpeng

	* libEM/: emdata.h, projector.h:
	  combine gaussfftprojectors

2004-04-23 11:05  lpeng

	* libEM/emdata.h, libpyEM/libpyEMData2.cpp, programs/proc2d.C: [no
	  log message]

2004-04-22 11:54  lpeng

	* libEM/emdata.h, libpyEM/emdata.pyste, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyUtils2.cpp:
	  more documentation

2004-04-21 16:35  lpeng

	* libEM/cmp.h, libEM/projector.h, libEM/reconstructor.h,
	  rt/emdata/CMakeLists.txt, rt/emdata/cmp.C:
	  fixed a couple of name issues and bugs

2004-04-21 14:15  lpeng

	* programs/proc2d.C: [no log message]

2004-04-20 14:47  lpeng

	* programs/proc2d.C:
	  add rfilter and usage info

2004-04-20 13:54  lpeng

	* libEM/hdfio.h, programs/proc2d.C:
	  fixed some bugs found by proc2d

2004-04-20 11:12  lpeng

	* libEM/util.h, programs/proc2d.C: make proc2d.C compiles first

2004-04-20 09:58  lpeng

	* libEM/aligner.h, libEM/emdata.h, libEM/util.h,
	  libpyEM/libpyEMData2.cpp, libpyEM/libpyUtils2.cpp,
	  programs/proc2d.C: [no log message]

2004-04-18 15:26  lpeng

	* programs/proc2d.C: test eman2 only

2004-04-15 15:37  lpeng

	* libEM/ctf.h, libEM/emdata.h, libEM/emobject.h, libEM/emutil.h,
	  libpyEM/libpyUtils2.cpp: [no log message]

2004-04-15 09:36  lpeng

	* libEM/: ctf.h, emdata.h:
	  new filter types

2004-04-14 12:43  lpeng

	* libEM/: xydata.h, aligner.h, amiraio.h, averager.h, cmp.h, ctf.h,
	  dm3io.h, emcache.h, emfft.h, emimio.h, emio.h, emobject.h,
	  emutil.h, gatan2io.h, geometry.h, hdfio.h, icosio.h, imageio.h,
	  imagicio.h, interp.h, log.h, lstio.h, mrcio.h, pgmio.h, pifio.h,
	  pngio.h, portable_fileio.h, projector.h, reconstructor.h,
	  salio.h, spiderio.h, sspiderio.h, tifio.h, transform.h, util.h,
	  vtkio.h, xplorio.h: add CVS Id

2004-04-14 10:45  lpeng

	* libEM/emdata.h:
	  add CVS $Id$

2004-04-14 09:52  lpeng

	* libEM/aligner.h, libEM/cmp.h, libEM/dm3io.h, libEM/emdata.h,
	  libEM/geometry.h, libEM/log.h, libEM/projector.h,
	  libEM/reconstructor.h, libEM/transform.h, libEM/util.h,
	  libpyEM/CMakeLists.txt, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyUtils2.cpp, programs/CMakeLists.txt,
	  programs/iminfo.C, rt/emdata/blankimg.C, rt/emdata/setvalue.C:
	  change get_x() to get_xsize() for more meaningful name; same to
	  get_y(), get_z()

2004-04-13 12:39  lpeng

	* libEM/log.h:
	  add some comments and usage

2004-04-13 11:04  lpeng

	* libpyEM/: EMAN2.py, e2EMAN.py: [no log message]

2004-04-13 10:22  lpeng

	* INSTALL:
	  simplify INSTALL, especially CMake installation part

2004-04-12 16:48  lpeng

	* libEM/emdata.h, libpyEM/libpyEMData2.cpp:
	  more filters are defined

2004-04-01 16:02  lpeng

	* libEM/emdata.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyFilter2.cpp:
	  move normalize methods from emdata class to filters

2004-04-01 09:08  lpeng

	* libpyEM/emdata.pyste, libpyEM/factory.pyste,
	  libpyEM/filter.pyste, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyFactory2.cpp, libpyEM/libpyFilter2.cpp,
	  rt/pyem/filter1.py:
	  remove useless 'log.h' in .pyste files

2004-03-30 16:38  lpeng

	* libEM/emdata.h, libEM/util.h, libpyEM/libpyEMData2.cpp,
	  programs/iminfo.C:
	  change some names: average->mean, std->sigma()

2004-03-30 11:22  lpeng

	* libEM/emdata.h, libpyEM/libpyEMData2.cpp:
	  added more functions: get_skewness, etc

2004-03-30 08:49  lpeng

	* libpyEM/libpyEMData2.cpp:
	  remove fft_slice()

2004-03-29 11:17  lpeng

	* libEM/emdata.h:
	  remove ift_slice()

2004-03-26 11:53  lpeng

	* libEM/emfft.h, libpyEM/libpyEMData2.cpp:
	  get_dim() changed to get_ndim()

2004-03-26 08:29  lpeng

	* libEM/: emdata.h, emfft.h:
	  fix a problem in set_size() which causes do_ift() doesn't work

2004-03-25 14:29  lpeng

	* rt/emdata/fft.C:
	  more

2004-03-25 13:54  lpeng

	* rt/emdata/fft.C:
	  fixed a bug in mrc write: flip phase was not correct

2004-03-25 12:11  lpeng

	* libEM/util.h, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyGeometry2.cpp, libpyEM/libpyUtils2.cpp:
	  more changes

2004-03-24 16:08  lpeng

	* libEM/: emdata.h, mrcio.h, util.h:
	  fixed ap2ri() partially in mrc. need a good fix in other places
	  also

2004-03-24 14:36  lpeng

	* libEM/emdata.h, libEM/mrcio.h, libpyEM/create_boost_python,
	  libpyEM/libpyEMData2.cpp, rt/emdata/fft.C:
	  1) remove pixel_size for square pixel; use spacing_row/col/sec
	  instead.  2) fixed a bug partiall in write mrc complex image.
	  need further work to	  remove the bug totally

2004-03-23 13:45  lpeng

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/emfft.h,
	  rt/emdata/fft.C:
	  1) test fftw lib; 2) enable user to choose which fftw version to
	  use in ccmake

2004-03-23 11:26  lpeng

	* rt/emdata/fft.C:
	  create grid mrc for testing

2004-03-23 10:27  lpeng

	* libEM/transform.h:
	  make some functions inline for better performance

2004-03-22 12:40  lpeng

	* CMakeLists.txt, libEM/emdata.h, libEM/transform.h,
	  libpyEM/geometry.pyste, libpyEM/libpyGeometry2.cpp:
	  template version of Vec3.  optimized project3d

2004-03-19 15:25  lpeng

	* libpyEM/: pyemdata.h, types.txt:
	  useless now

2004-03-19 15:24  lpeng

	* libEM/util.h, libpyEM/CMakeLists.txt, libpyEM/Makefile.pyste,
	  libpyEM/create_boost_python, libpyEM/emdata.pyste,
	  libpyEM/libpyEMData.cpp, libpyEM/libpyEMData2.cpp,
	  libpyEM/libpyFactory.cpp, libpyEM/libpyFactory2.cpp,
	  libpyEM/libpyFilter.cpp, libpyEM/libpyFilter2.cpp,
	  libpyEM/libpyGeometry.cpp, libpyEM/libpyGeometry2.cpp,
	  libpyEM/libpyUtils.cpp, libpyEM/libpyUtils2.cpp,
	  libpyEM/run_pyste, libpyEM/types.txt, rt/imageio/imageio.C:
	  1. add some windows support to solve functions not existing in
	  windows; 2. boost python: check in the right files.

2004-03-19 10:27  lpeng

	* libEM/: CMakeLists.txt, emobject.h, util.h:
	  put everything in emobject.C to emobject.h; add set_log_level()
	  to util

2004-03-19 10:13  lpeng

	* rt/emdata/: CMakeLists.txt, fft.C:
	  fft test

2004-03-18 16:29  lpeng

	* libEM/transform.h:
	  fix a memory problem in Matrix3f and Matrix4f.

2004-03-18 14:35  lpeng

	* CMakeLists.txt, libEM/portable_fileio.h:
	  remove sizeof(off_t) check

2004-03-18 12:12  lpeng

	* libEM/: aligner.h, averager.h, cmp.h, emfft.h, projector.h,
	  reconstructor.h:
	  fix some template declaration problems when using explicity
	  specification; pass the IBM VisualAgeC++ compiler

2004-03-18 10:39  lpeng

	* libEM/: CMakeLists.txt, emdata.h, transform.h:
	  template<> and 'friend' fix

2004-03-17 11:09  lpeng

	* CMakeLists.txt, libEM/util.h, libEM/xydata.h,
	  rt/emdata/blankimg.C:
	  change 'int' to 'size_t' at necessary places

2004-03-16 16:49  lpeng

	* CMakeLists.txt:
	  srfftw.h

2004-03-16 15:35  lpeng

	* CMakeLists.txt, libEM/portable_fileio.h:
	  change largefile support to a simplified python-way.

2004-03-15 16:02  lpeng

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/byteorder.h,
	  libEM/ctf.h, libEM/dm3io.h, libEM/emdata.h, libEM/emio.h,
	  libEM/emobject.h, libEM/emutil.h, libEM/imagicio.h,
	  libEM/mrcio.h, libEM/portable_fileio.h, libEM/xydata.h,
	  libpyEM/CMakeLists.txt, libpyEM/EMAN.py, libpyEM/Makefile.pyste,
	  libpyEM/e2EMAN.py, libpyEM/libpyEMData.cpp,
	  libpyEM/libpyFactory.cpp, libpyEM/libpyFilter.cpp,
	  libpyEM/libpyGeometry.cpp, libpyEM/libpyUtils.cpp,
	  programs/CMakeLists.txt, rt/emdata/CMakeLists.txt,
	  rt/imageio/CMakeLists.txt, rt/pyem/filter1.py:
	  use 'size_t' and 'off_t' at proper place to improve portability.
	  change CMakeLists.txt for eman2 naming

2004-03-12 17:07  lpeng

	* libEM/ctf.h, libpyEM/libpyUtils.cpp, libpyEM/pyem.pyste:
	  ctf implemntations: make sure EMAN1 code is copied

2004-03-11 14:44  lpeng

	* libEM/emdata.h, libEM/imageio.h, libEM/spiderio.h,
	  libEM/sspiderio.h, libpyEM/libpyFactory.cpp,
	  libpyEM/libpyUtils.cpp, rt/pyem/filter1.py:
	  change map<string, EMObject> to Dict; they are equivalent anyway

2004-03-11 11:49  lpeng

	* libEM/ctf.h, libEM/emobject.h, rt/pyem/filter1.py:
	  fixed a bug in boost python support

2004-03-11 11:30  lpeng

	* libpyEM/: emdata.pyste, factory.pyste, filter.pyste, libpyEM.cpp,
	  libpyEMData.cpp, libpyFilter.cpp, libpyUtils.cpp:
	  updated

2004-03-09 16:35  lpeng

	* CMakeLists.txt, libEM/emdata.h, libEM/pgmio.h, libEM/vtkio.h:
	  compiled on SGI. found many warnings and errors

2004-03-09 13:38  lpeng

	* libEM/transform.h, libpyEM/libpyGeometry.cpp:
	  interpolate() in Quaternion and Rotation

2004-03-08 14:21  lpeng

	* INSTALL, libpyEM/CMakeLists.txt, libpyEM/EMAN.py,
	  libpyEM/Makefile.pyste, libpyEM/emdata.pyste,
	  libpyEM/factory.pyste, libpyEM/filter.pyste,
	  libpyEM/geometry.pyste, libpyEM/libpyEMData.cpp,
	  libpyEM/libpyFactory.cpp, libpyEM/libpyFilter.cpp,
	  libpyEM/libpyGeometry.cpp, libpyEM/libpyUtils.cpp,
	  libpyEM/run_pyste, libpyEM/utils.pyste:
	  split boost python wrappers into 5 modules to speed up
	  compilation time.  this result to 45% time reduction

2004-03-08 13:19  lpeng

	* libEM/emobject.h:
	  interpolate: empty implementation

2004-03-08 13:07  lpeng

	* CMakeLists.txt:
	  add 64 support

2004-03-05 16:52  lpeng

	* libEM/transform.h, libpyEM/libpyEM.cpp, libpyEM/pyem.h,
	  libpyEM/pyem.pyste:
	  boost python support

2004-03-04 16:15  lpeng

	* libEM/aligner.h, libEM/averager.h, libEM/cmp.h, libEM/emobject.h,
	  libEM/projector.h, libEM/reconstructor.h, libpyEM/libpyEM.cpp,
	  libpyEM/pyem.pyste:
	  redefine factory class. make it a template to simplify code

2004-03-02 12:36  lpeng

	* libEM/: spiderio.h, sspiderio.h, tifio.h, transform.h, util.h,
	  vtkio.h, xplorio.h, xydata.h:
	  indent

2004-03-02 12:19  lpeng

	* libEM/: amiraio.h, averager.h, emdata.h, emimio.h, imageio.h,
	  pifio.h, pngio.h, portable_fileio.h, projector.h,
	  reconstructor.h, salio.h, xydata.h:
	  indent

2004-03-02 10:01  lpeng

	* libEM/: interp.h, log.h, lstio.h, mrcio.h, pgmio.h:
	  indent

2004-03-02 09:45  lpeng

	* libEM/: gatan2io.h, geometry.h, hdfio.h, icosio.h, imageio.h,
	  imagicio.h:
	  indent

2004-03-01 21:31  lpeng

	* libEM/exception.h:
	  indent

2004-03-01 21:18  lpeng

	* libEM/: emobject.h, emutil.h:
	  indent

2004-03-01 20:40  lpeng

	* libEM/: emfft.h, emimio.h, emio.h:
	  indent

2004-03-01 20:25  lpeng

	* libEM/: dm3io.h, emcache.h:
	  indent

2004-03-01 20:16  lpeng

	* libEM/: aligner.h, amiraio.h, averager.h, byteorder.h, cmp.h,
	  ctf.h:
	  indent

2004-03-01 11:00  lpeng

	* libEM/emdata.h:
	  indent; arrange function positions

2004-02-27 16:22  lpeng

	* libEM/averager.h, libEM/emdata.h, libpyEM/libpyEM.cpp,
	  libpyEM/pyem.pyste:
	  fix several problems: setup4slice, make_image_median() etc

2004-02-27 08:53  lpeng

	* libpyEM/libpyEM.cpp:
	  make_image_median

2004-02-26 16:11  lpeng

	* libEM/: emdata.h, emutil.h:
	  minor changes

2004-02-24 14:13  lpeng

	* libpyEM/CMakeLists.txt:
	  more indent on amiraio.C

2004-02-23 17:35  lpeng

	* libEM/emdata.h, libEM/emutil.h, libEM/imageio.h,
	  libpyEM/libpyEM.cpp, libpyEM/pyem.pyste:
	  libpyem, api arrangement in libem

2004-02-23 10:36  lpeng

	* libEM/emdata.h:
	  more functions

2004-02-20 15:53  lpeng

	* libEM/cmp.h, libEM/ctf.h, libEM/emdata.h, libEM/emutil.h,
	  libEM/reconstructor.h, libEM/util.h, libpyEM/libpyEM.cpp,
	  libpyEM/run_pyste:
	  more functions

2004-02-19 10:56  lpeng

	* libEM/emdata.h:
	  more functions

2004-02-18 11:11  lpeng

	* libEM/: CMakeLists.txt, xydata.h:
	  XYData is done

2004-02-17 15:56  lpeng

	* libEM/: ctf.h, emdata.h, xydata.h:
	  ctf curve calculation

2004-02-17 11:04  lpeng

	* libEM/util.h: [no log message]

2004-02-13 15:33  lpeng

	* libEM/averager.h, libEM/emobject.h, libpyEM/libpyEM.cpp,
	  libpyEM/pyem.pyste: get_EMData() renamed to get_emdata()

2004-02-13 14:20  lpeng

	* CMakeLists.txt, libEM/emfft.h, libEM/util.h: portability changes

2004-02-10 14:20  lpeng

	* libEM/: CMakeLists.txt, averager.h:
	  averagers.

2004-02-10 11:46  lpeng

	* libEM/dm3io.h, libEM/emdata.h, libEM/emobject.h,
	  libEM/gatan2io.h, libEM/imageio.h, libEM/imagicio.h,
	  rt/imageio/imageio.C: [no log message]

2004-02-09 16:51  lpeng

	* libEM/averager.h:
	  not completed yet

2004-01-29 15:37  lpeng

	* CMakeLists.txt, libEM/averager.h, libEM/emdata.h:
	  averager

2004-01-28 11:48  lpeng

	* libEM/: emdata.h, portable_fileio.h:
	  more functions and largefile support

2004-01-27 12:14  lpeng

	* libEM/emdata.h:
	  (un)cut_slice()

2004-01-26 14:06  lpeng

	* libEM/: emdata.h, util.h:
	  more functions: commonlines etc

2004-01-23 16:26  lpeng

	* libEM/emdata.h:
	  more functions

2004-01-20 16:43  lpeng

	* libEM/: emdata.h, util.h: [no log message]

2004-01-15 13:40  lpeng

	* CMakeLists.txt:
	  make 'make install' work. fix image type check bug in mrc

2004-01-14 15:11  lpeng

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/amiraio.h,
	  libEM/dm3io.h, libEM/emdata.h, libEM/emfft.h, libEM/emimio.h,
	  libEM/emio.h, libEM/emutil.h, libEM/gatan2io.h, libEM/hdfio.h,
	  libEM/icosio.h, libEM/imageio.h, libEM/imagicio.h, libEM/lstio.h,
	  libEM/mrcio.h, libEM/pgmio.h, libEM/pifio.h, libEM/pngio.h,
	  libEM/salio.h, libEM/spiderio.h, libEM/tifio.h, libEM/vtkio.h,
	  libEM/xplorio.h:
	  fix a bug in is_valid() for EM and MRC image format

2004-01-13 13:36  lpeng

	* libEM/emdata.h:
	  more functions

2004-01-13 11:41  lpeng

	* CMakeLists.txt, INSTALL, libEM/CMakeLists.txt, libEM/emfft.h:
	  make fftw3 compile

2004-01-12 11:52  lpeng

	* libEM/: emdata.h, geometry.h:
	  more functions to EMData

2004-01-07 11:45  lpeng

	* libEM/emdata.h:
	  calc_az_dist()

2004-01-02 17:11  lpeng

	* libEM/emdata.h:
	  more functions

2003-12-18 14:51  lpeng

	* libEM/: CMakeLists.txt, emdata.h, emfft.h:
	  add support for fftw3. not compiled, not tested yet

2003-12-18 12:08  lpeng

	* libEM/emdata.h:
	  add fft support; compiles

2003-12-18 10:44  lpeng

	* libEM/CMakeLists.txt, libEM/emdata.h, libEM/emfft.h,
	  CMakeLists.txt: [no log message]

2003-12-16 11:27  lpeng

	* libEM/emdata.h:
	  more functions

2003-12-14 15:36  lpeng

	* libEM/emdata.h:
	  more functions

2003-12-12 13:24  lpeng

	* libEM/reconstructor.h: [no log message]

2003-12-11 15:28  lpeng

	* libEM/: CMakeLists.txt, emdata.h, reconstructor.h, util.h:
	  3d reconstruction classes defined in reconstructor.h(C).
	  implementation is just a copy of code from EMAN1. need further
	  redesign and clean up later.

2003-12-09 16:33  lpeng

	* libEM/: CMakeLists.txt, aligner.h, emdata.h, interp.h,
	  projector.h, util.h:
	  projectors, not handling slice operations yet. some magic numbers
	  not handled neatly yet

2003-12-05 12:05  lpeng

	* libpyEM/: libpyEM.cpp, pyem.pyste, types.txt:
	  update pyem.pyste and make python compiles.

2003-12-04 16:19  lpeng

	* libEM/emdata.h:
	  basic library compiles but pyem not.

2003-11-24 10:35  lpeng

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/cmp.h,
	  libEM/emdata.h, libEM/emobject.h, libEM/projector.h,
	  libEM/util.h:
	  projectors

2003-11-07 13:36  lpeng

	* CMakeLists.txt, libEM/dm3io.h, libEM/emcache.h: change for alpha
	  compilation

2003-11-07 13:13  lpeng

	* libEM/: aligner.h, dm3io.h, emobject.h:
	  small changes

2003-11-05 18:06  mhhohn

	* ChangeLog:	 Newly added.

2003-11-05 18:06  mhhohn

	* CMakeLists.txt:	    - there is no provision in
	  eman2/CMakeLists.txt
			for user-defined root directories, e.g.
			    FIND_PATH(BOOST_INCLUDE_PATH boost/python.hpp
						      $ENV{HOME}/include
						      /usr/local/include
						      /usr/include)

		      - $ENV{GSLDIR} gives a way for custom gsl locations,
			but for boost...

		  Thus, I added the use of a generic EMAN2_PREFIX,
	  analogous to the
		  --prefix option in configure.

		  For boost (the headers), I added EMAN2_BOOST_DIST, which
	  should
		  point to the top-level boost directory.

		  Lastly, I had emacs re-indent the file...

2003-11-04 11:46  lpeng

	* libpyEM/: libpyEM.cpp, pyem.pyste:
	  updated pyem

2003-11-04 10:53  lpeng

	* libEM/emcache.h:
	  fix "assert" problem

2003-11-03 14:18  lpeng

	* CMakeLists.txt, libEM/aligner.h, libEM/emdata.h, libEM/util.h:
	  alignments

2003-10-31 16:00  lpeng

	* libEM/byteorder.h:
	  Id again

2003-10-31 15:58  lpeng

	* libEM/byteorder.h:
	  'Id' for CVS

2003-10-29 17:04  lpeng

	* libEM/: aligner.h, cmp.h, emdata.h, emobject.h, transform.h,
	  util.h:
	  more code for alignment

2003-10-22 16:51  lpeng

	* libEM/transform.h, rt/CMakeLists.txt:
	  fixed several bugs

2003-10-21 12:12  wjiang

	* INSTALL: hello, man

2003-10-21 11:48  lpeng

	* INSTALL: [no log message]

2003-10-20 20:23  lpeng

	* INSTALL: test

2003-10-20 20:20  lpeng

	* INSTALL: cmake

2003-10-16 14:54  lpeng

	* libEM/transform.h:
	  better names

2003-10-16 14:40  lpeng

	* libEM/transform.h:
	  transform stuff

2003-10-14 15:07  lpeng

	* libEM/: emdata.h, emobject.h, transform.h:
	  filters

2003-10-08 15:40  lpeng

	* libEM/transform.h:
	  Rotation class

2003-10-07 17:31  lpeng

	* libEM/util.h:
	  changed fixed bugs

2003-10-07 17:31  lpeng

	* CMakeLists.txt:
	  changed

2003-10-07 09:29  lpeng

	* rt/emdata/setvalue.C:
	  new

2003-10-07 09:27  lpeng

	* libEM/: aligner.h, cmp.h, geometry.h, projector.h:
	  added

2003-10-06 15:35  lpeng

	* libEM/: CMakeLists.txt, transform.h:
	  quaternion class

2003-10-02 15:36  lpeng

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/transform.h:
	  added Matrix support in transform.h(C)

2003-10-01 15:11  lpeng

	* libEM/: emdata.h, util.h:
	  cmparator

2003-10-01 13:25  lpeng

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/emdata.h,
	  libEM/emutil.h, libEM/transform.h, libEM/util.h:
	  aligner and comparator

2003-09-30 14:23  lpeng

	* CMakeLists.txt, libEM/CMakeLists.txt, libEM/amiraio.h,
	  libEM/byteorder.h, libEM/ctf.h, libEM/emcache.h, libEM/emdata.h,
	  libEM/emimio.h, libEM/emio.h, libEM/emobject.h, libEM/emutil.h,
	  libEM/exception.h, libEM/gatan2io.h, libEM/hdfio.h,
	  libEM/icosio.h, libEM/imageio.h, libEM/imagicio.h, libEM/log.h,
	  libEM/lstio.h, libEM/mrcio.h, libEM/pgmio.h, libEM/pifio.h,
	  libEM/pngio.h, libEM/portable_fileio.h, libEM/salio.h,
	  libEM/spiderio.h, libEM/sspiderio.h, libEM/tifio.h,
	  libEM/transform.h, libEM/util.h, libEM/vtkio.h, libEM/xplorio.h,
	  libEM/xydata.h, rt/emdata/CMakeLists.txt:
	  changes: 1) header file '#ifndef' tag changed. 2) inline
	  functions in emobject.h; 3) cache 'nx, ny, nz' in EMData class,
	  which greatly improves performance for set_value_at() etc.

2003-09-30 09:57  lpeng

	* libpyEM/libpyEM.cpp, libpyEM/pyem.pyste, rt/pyem/filter1.py:
	  adapt new changes in Filter to boost python

2003-09-29 16:24  lpeng

	* libEM/emcache.h, libEM/emdata.h, libEM/emobject.h, libEM/util.h,
	  libpyEM/libpyEM.cpp, libpyEM/pyem.pyste:
	  redesign the filter system

2003-09-23 14:38  lpeng

	* rt/CMakeLists.txt:
	  ready for simple filter test

2003-09-23 13:57  lpeng

	* libEM/CMakeLists.txt, libEM/emdata.h, libEM/transform.h,
	  libEM/util.h, libpyEM/CMakeLists.txt, libpyEM/pylist.C:
	  added some filters

2003-09-17 16:04  lpeng

	* libEM/emcache.h, rt/imageio/imageio.C:
	  fixed a lst io bug

2003-09-16 09:50  lpeng

	* libEM/dm3io.h, programs/iminfo.C, rt/imageio/imageio.C:
	  fixed a dm3 bug

2003-09-15 17:39  lpeng

	* rt/imageio/imageio.C:
	  a bug in spider write

2003-09-15 16:12  lpeng

	* rt/emdata/: CMakeLists.txt, blankimg.C:
	  to test writing a blank image

2003-09-15 16:11  lpeng

	* libEM/emdata.h, rt/CMakeLists.txt, rt/imageio/imageio.C:
	  fixed a set_size() problem in EMData

2003-09-15 15:12  lpeng

	* libEM/emdata.h, rt/imageio/imageio.C:
	  move set_size() to public in EMData class

2003-09-15 14:59  lpeng

	* libEM/emcache.h, rt/imageio/basic.C, rt/imageio/imageio.C:
	  fixed more bugs

2003-09-15 14:06  lpeng

	* CMakeLists.txt, INSTALL, libEM/byteorder.h, libEM/emdata.h,
	  libEM/hdfio.h, libEM/imageio.h, libEM/imagicio.h, libEM/mrcio.h,
	  libpyEM/pylist.h, rt/imageio/imageio.C, rt/imageio/mrc.C:
	  fixed several issues found in SGI

2003-09-15 09:32  lpeng

	* CMakeLists.txt:
	  inhibit warnings

2003-09-12 14:57  lpeng

	* libEM/emdata.h, rt/pyem/operators.py:
	  operators

2003-09-12 13:49  lpeng

	* libEM/emdata.h, libpyEM/libpyEM.cpp:
	  operators support in EMData

2003-09-11 14:34  lpeng

	* libEM/emdata.h, libEM/emobject.h, libEM/emutil.h,
	  libpyEM/CMakeLists.txt, libpyEM/libpyEM.cpp, libpyEM/pylist.C,
	  libpyEM/pylist.h, programs/iminfo.C, rt/imageio/basic.C,
	  rt/imageio/imageio.C, rt/pyem/converter.py:
	  convert map<string, EMObject> to Dict

2003-09-11 10:57  lpeng

	* libEM/emdata.h, libpyEM/libpyEM.cpp, libpyEM/pyem.C,
	  libpyEM/pyem.h, libpyEM/pyem.pyste, libpyEM/pylist.h:
	  add wrapper functions around read_images_by_XXX()

2003-09-11 09:57  lpeng

	* libEM/emdata.h, libEM/hdfio.h, libpyEM/libpyEM.cpp,
	  libpyEM/pyem.C, libpyEM/pyem.h, libpyEM/pyem.pyste,
	  libpyEM/pylist.h, programs/iminfo.C, rt/pyem/converter.py:
	  boost python support: added map/vector type converters to/from
	  python

2003-09-09 17:13  lpeng

	* libEM/emdata.h, programs/CMakeLists.txt:
	  cmake problems

2003-09-08 14:44  lpeng

	* libpyEM/: CMakeLists.txt, EMAN.py:
	  added EMAN.py

2003-09-08 13:45  lpeng

	* libEM/emdata.h, libEM/util.h, libpyEM/pyem.C:
	  boost python works now

2003-09-08 12:34  lpeng

	* CMakeLists.txt, libEM/emdata.h, libpyEM/CMakeLists.txt,
	  libpyEM/libpyEM.cpp, libpyEM/pyem.C, libpyEM/pyem.h,
	  libpyEM/pyem.pyste, libpyEM/pyemdata.h, libpyEM/pylist.C,
	  libpyEM/pylist.h, libpyEM/run_pyste:
	  python support; compiles

2003-09-04 11:12  lpeng

	* libEM/ctf.h, libEM/emdata.h, libEM/hdfio.h, libEM/log.h,
	  programs/iminfo.C, rt/imageio/imageio.C:
	  better ctf

2003-09-04 09:52  lpeng

	* libEM/: CMakeLists.txt, ctf.h, emdata.h, emobject.h, hdfio.h,
	  imageio.h:
	  ctf support for hdfio

2003-09-03 15:23  lpeng

	* CMakeLists.txt, config.h, libEM/CMakeLists.txt, libEM/hdfio.h,
	  libEM/pngio.h, libEM/tifio.h:
	  make png, hdf, tif optional

2003-08-27 13:32  lpeng

	* CMakeLists.txt, config.h, libEM/CMakeLists.txt, libEM/amiraio.h,
	  libEM/byteorder.h, libEM/dm3io.h, libEM/emcache.h,
	  libEM/emdata.h, libEM/emimio.h, libEM/emio.h, libEM/emobject.h,
	  libEM/emutil.h, libEM/exception.h, libEM/gatan2io.h,
	  libEM/hdfio.h, libEM/icosio.h, libEM/imageio.h, libEM/imagicio.h,
	  libEM/log.h, libEM/lstio.h, libEM/mrcio.h, libEM/pgmio.h,
	  libEM/pifio.h, libEM/pngio.h, libEM/portable_fileio.h,
	  libEM/salio.h, libEM/spiderio.h, libEM/sspiderio.h,
	  libEM/tifio.h, libEM/transform.h, libEM/util.h, libEM/vtkio.h,
	  libEM/xplorio.h, libEM/xydata.h, programs/CMakeLists.txt,
	  programs/iminfo.C, rt/CMakeLists.txt, rt/imageio/CMakeLists.txt,
	  rt/imageio/basic.C, rt/imageio/imageio.C, rt/imageio/mrc.C:
	  from water

2003-08-27 13:32  lpeng

	* CMakeLists.txt, config.h, libEM/CMakeLists.txt, libEM/amiraio.h,
	  libEM/byteorder.h, libEM/dm3io.h, libEM/emcache.h,
	  libEM/emdata.h, libEM/emimio.h, libEM/emio.h, libEM/emobject.h,
	  libEM/emutil.h, libEM/exception.h, libEM/gatan2io.h,
	  libEM/hdfio.h, libEM/icosio.h, libEM/imageio.h, libEM/imagicio.h,
	  libEM/log.h, libEM/lstio.h, libEM/mrcio.h, libEM/pgmio.h,
	  libEM/pifio.h, libEM/pngio.h, libEM/portable_fileio.h,
	  libEM/salio.h, libEM/spiderio.h, libEM/sspiderio.h,
	  libEM/tifio.h, libEM/transform.h, libEM/util.h, libEM/vtkio.h,
	  libEM/xplorio.h, libEM/xydata.h, programs/CMakeLists.txt,
	  programs/iminfo.C, rt/CMakeLists.txt, rt/imageio/CMakeLists.txt,
	  rt/imageio/basic.C, rt/imageio/imageio.C, rt/imageio/mrc.C:
	  Initial revision

