= Name =
e2boxer_old - Particle Picking: Manual and automatic particle picking.

= Usage =

''usage in command line''

e2boxer_old.py  input_micrograph_list  --boxsize=BOXSIZE  --write_dbbox  --write_ptcls  --exclude_edges  --force  --format=FORMAT  --norm=NORM  --invert  --suffix=SUFFIX  --dbls=DBLS  --autoboxer=AUTOBOXER  --ppid=PPID  --gui  --verbose=n  --gauss_autoboxer=GAUSS_AUTOBOXER  --do_ctf=DO_CTF  --cter  --indir=INDIR  --nameroot=NAMEROOT  --micsuffix=MICSUFFIX  --wn=WN  --Cs=CS  --voltage=VOLTAGE  --ac=AC  --kboot=KBOOT  --debug  --apix=APIX

=== Typical usage ===

e2boxer_old exists in non-MPI version.

    Start the e2boxer_old GUI with a list of micrographs

    e2boxer_old.py micrographs_number*


== Input ==

    input_micrograph_list:: Input micrographs: Wild cards (e.g. *) can be used to specify a list of micrographs. Not recommended if the number is very large. (default required string)

    boxsize:: Box size [Pixels]: (default -1)

    * The remaining parameters are optional. Normally you will not touch this.
    write_dbbox:: Write coordinate files: (default False)
    write_ptcls:: Write particle images: (default False)
    exclude_edges:: Exclude edge images: Exclude particles extending outside the micrograph: (default False)
    force:: Force overwrite: (default False)
    format:: Particle image format: Format of the output particles images. (default hdf)
    norm:: Particle normalization: Normalization processor applied to the final particle images: (default normalize.edgemean)
    invert:: Invert contrast: (default False)
    suffix:: Particle name suffix: Suffix used for the name of the output images and coordinates. (default _ptcls)
    dbls:: data base list storage, used by the workflow: (default none)
    autoboxer:: a key of the swarm_boxers dict in the local directory, used by the workflow: (default none)
    ppid:: Set PPID: Sets the PPID of the process. (default -1)
    gui:: dummy option; used in even older version of e2boxer_old: (default True)
    verbose:: Verbose: Accepted values 0-9. (default 0)
    gauss_autoboxer:: Sample autoboxed image: Gets the parameters used for autoboxing from the EMANDB. It requires the name of a micrograph used for automatic boxing previously. (default none)
    do_ctf:: name of file whose ctf estimation parameters should be used for automatic ctf estimation: (default none)
    cter:: CTF estimation using cter: (default False)
    indir:: directory containing micrographs to be processed: (default current directory)
    nameroot:: prefix of micrographs to be processed: (default none)
    micsuffix:: a string denoting micrograph type: (default none)
    wn:: size of window to use: (default 256)
    Cs:: Spherical aberration [mm]: (default 2.0)
    voltage:: Microscope voltage [kV]: (default 300.0)
    ac:: Amplitude contrast: (default 10.0)
    kboot:: kboot: (default 16)
    debug:: Debug mode: (default False)
    apix:: Pixel size [A]: (default -1.0)



== Output ==
The program creates the directory automatically in the micrograph directory.


= Description =

= Author / Maintainer =
EMAN2 Group

= Keywords =
    category 1:: APPLICATIONS

= Files =
e2boxer_old.py

= See also =

= Maturity =
No Bugs known so far.
