= Name =
sxpipeline_isac_substack - Create Stack Subset: Create virtual subset stack consisting from accounted particles by retrieving original image numbers listed in ISAC output average stack. The command also saves a list text file containing the retrieved original image numbers.


= Usage =

''usage in command line''

sxpipeline_isac_substack.py  stack  isac_averages  output_directory  --skip_create_substack
isac_averages  

=== Typical usage ===

sxpipeline_isac_substack.py does not support MPI. 

''' sxpipeline_isac_substack.py  bdb:test3  class_averages_generation_3.hdf  outdir_isac_substack '''


== Input ==
    stack:: Input image stack: Specify original particle image stack use for input of the ISAC process. (default required string)
    isac_averages:: ISAC class file name: Input ISAC class averages. Each class average should contain original image numbers of the associated particle members. (default required string)
    
	skip_create_substack:: Skip substack creation: Use this option to skip creation of the virtual substack. (default False)

    * The remaining parameters are optional.

== Output ==
    output_directory:: Output directory: The results will be written here. This directory will be created automatically and it must not exist previously. (default required string)


= Description =

= Method =

= Reference =


= Author / Maintainer =
Toshio Moriya

= Keywords =
 category 1:: APPLICATIONS

= Files =
sparx/bin/sxpipeline_isac_substack.py

= See also =
[[sxisac]]

= Maturity =
 alpha::     under development

= Bugs =
Under development
