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===== sp_separate_class =====
Separate Into Classes : Separates stacks of particle images into stacks for each class.

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===== Usage =====

Usage in command line:

  sp_separate_class.py input_class_avgs input_image_stack output_directory --filt=filter_radius --pxsz=pixel_size --shrink=shrink_factor --verbose
  
  
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===== Typical usage =====

The purpose of sp_separate_class.py is to: 

  : extract particle-membership information from a stack of class averages
  : write particle-membership lists for each class, and
  : write separate stacks for each class, with an option to low-pass filter and/or downsample the images

\\ __1. Standard usage: create separate stacks for each class__:

  sp_separate_class.py input_class_avgs input_image_stack output_directory 

\\ __2. Apply a low-pass filter to the image stacks__:

  sp_separate_class.py input_class_avgs input_image_stack output_directory --filt=filter_radius --pxsz=pixel_size

Filter radius is in units of Angstroms. If pxsz parameter is not specified, program will assume units of pixels^-1.

\\ __3. Downsample output image stack__:

  sp_separate_class.py input_class_avgs input_image_stack output_directory --shrink=shrink_factor
  
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===== Input =====
=== Main Parameters ===
  ; input_class_avgs : Input class averages : Set of 2D class averages, with particle-membership information in header. (default required string)
  ; input_image_stack : Input particles : Particle image stack. (default required string)
  ; output_directory : Output directory : Directory where outputs will be written. (default required string)
  ; %%--%%filt : Filter radius : Gaussian low-pass filter radius, Angstroms if pxsz specified below, else pixels^-1. (default None)
  ; %%--%%pxsz : Pixel size : Angstroms per pixel, might be downsampled already by ISAC2. (default None)
  ; %%--%%shrink : Downsampling factor : Downsampling factor, e.g., 6 -> 1/6 original size. (default None)
  ; %%--%%verbose : Verbose : Writes additional messages to the terminal during execution. (default False)
  
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=== Advanced Parameters ===

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===== Output =====
  ; classmap.txt : Class-to-particle lookup table, one file for all classes
  ; docclass???.txt : List of particles for each class, one file per class
  ; EMAN2DB/stkclass_???.bdb : Virtual stacks of particles for each class
  ; EMAN2DB/stkflt_???.bdb : (Optional) virtual stacks of filtered particles for each class
 
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===== Description =====

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==== Method ====

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==== Reference ====

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==== Developer Notes ====
  : Should allow filter types other than Gaussian low-pass
  : Should offer option to write aligned images

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==== Author / Maintainer ====
Tapu Shaikh

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==== Keywords ====
Category 1:: APPLICATIONS

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==== Files ====
sphire/bin/sp_separate_class.py

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==== See also ====

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==== Maturity ====
Beta:: Under evaluation and testing. Please let us know if there are any bugs.

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==== Bugs ====
There are no known bugs so far.

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