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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 --align_isac_dir=isac_dir --filtrad=filter_radius --apix=pixel_size --shrink=shrink_factor --nvec=number_of_eigenimages --ctf --verbose
  
  
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===== Typical usage =====

The purpose of sp_separate_class.py is to: 

  : write particle-membership lists for each class
  : write separate stacks for each class, 
  : optionally low-pass filter and/or downsample the images, and
  : optionally compute eigenimages (basis images) for each class

\\ __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 --apix=pixel_size

Filter radius is in units of Angstroms. If apix 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
  
\\ __4. Apply ISAC alignments to particles__:

  sp_separate_class.py input_class_avgs input_image_stack output_directory --align_isac_dir=isac_directory
  
If the input class averages are ordered_class_averages.hdf, the alignments applied to the ordered class averages will be applied to the particles.

\\ __5. Compute eigenimages (basis images) for each class__:

  sp_separate_class.py input_class_avgs input_image_stack output_directory --align_isac_dir=isac_directory --nvec=number_of_eigenimages
  
The additional output, stkeigen.hdf, will contain the average, variance, and the requested number of eigenimages.

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===== Input =====
=== Main Parameters ===
  ; input_class_avgs : Set of 2D class averages, with particle-membership information in header. (default required string)[{{ :pipeline:utilities:class084.png?400|Filtered, aligned particles of TcdA1 corresponding to class #9 below}}]
  ; input_image_stack : Particle image stack. (default required string)
  ; output_directory : Directory where outputs will be written. (default required string)
  ; %%--%%filtrad : Gaussian low-pass filter radius, Angstroms if apix specified below, else pixels^-1. (default None)
  ; %%--%%apix : Angstroms per pixel, might be downsampled already by ISAC2. (default None)
  ; %%--%%shrink : Downsampling factor, e.g., 6 -> 1/6 original size. (default None)
  ; %%--%%align_isac_dir : If applying alignments, directory for ISAC output (default None)
  ; %%--%%nvec : Number of eigenimages to compute. (default None)
  ; %%--%%ctf : Applies CTF correction. (default False)
  ; %%--%%verbose : Writes additional messages to the terminal during execution. (default False)
  
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=== Advanced Parameters ===
  ; %%--%%format : Format of optional output aligned-imaged stacks. (default .mrcs)
  ; %%--%%debug : Writes additional diagnostics for debugging. (default False)

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===== Output =====
  ; classmap.txt : Class-to-particle lookup table, one file for all classes[{{ :pipeline:utilities:ave_eig75-84.png?400|For each class (from left to right): average, variance, and first 5 eigenimages}}]
  ; docclass???.txt : List of particles for each class, one file per class
  ; bdb:stkclass_??? : Virtual stacks of particles for each class
  ; bdb:stkflt_??? : (Optional) Virtual stacks of filtered particles for each class
  ; params_???.txt : (Optional) Particle alignment parameters, one file per class
  ; stkavgvar.hdf : (Optional) Montage of class averages and variances
  ; stkeigen.hdf : (Optional) Montage of class averages, variances, and eigenimages
 

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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

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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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