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===== sxisac_post_processing =====
Beautifier: Beautify the ISAC 2D clustering result with the original pixel size.

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===== Usage =====
Usage in command lines:

  sxisac_post_processing.py  stack_file  isac_directory  class_file_name_no_dir_info --radius=particle_radius  --CTF  --single_stack_output 

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===== Typical usage =====
sxisac_post_processing.py exists only in MPI version.

  mpirun -np 32 sxisac_post_processing.py bdb:data fisac1 locres.hdf --radius=28

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===== Input =====
=== Main Parameters ===

  ; stack_file : Original image stack: Particles required to create the full-sized class averages. The images must be square (''nx''=''ny'') and the stack must be bdb format (default required string)
  ; isac_directory : Isac output directory: Name of the directory where isac was run previously. (default required string)
  ; class_file_name_no_dir_info : Isac class file name: Name of the file (no directory info) that contains the class averages. It is located in the Isac directory. (default required string)
  ; radius : Particle radius [Pixels]: There is no default radius. (default required int)
  ; CTF : Phase-flip: If set, the data will be phase-flipped using CTF information included in the image headers. (default False)
  ; single_stack_output : Single stack output: If set, only one stack for all classes will be generated. Otherwise, which is the default, one file per class will be generated. (default False) 

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===== Output =====
The output directory is created in the isac directory and has the format "post_processing_YYYY-MM-DD--HH-MM-SS". It contains all the output files "original_image_number_in_each_class_average.txt", "twoD_params_info_list.txt" and "radius_adjusted_class_averages.hdf" (one file or multiple files according to the --single_stack_output option). 

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==== Author / Maintainer ====
Horatiu Voicu and Pawel A. Penczek

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==== Files =====
sxisac_post_processing.py

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==== Maturity ====
alpha:: in development

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