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pipeline:utilities:sp_separate_class [2019/04/02 11:46]
lusnig [Output] 		pipeline:utilities:sp_separate_class [2020/01/31 11:38]
shaikh [Output]
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 Usage in command line: 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+  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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 The purpose of sp_separate_class.py is to:  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 
-  : write particle-membership lists for each class, and +  : write separate stacks for each class,  
-  : write separate stacks for each class, with an option to low-pass filter and/or downsample the images+  : 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__: \\ __1. Standard usage: create separate stacks for each class__:
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 \\ __2. Apply a low-pass filter to the image stacks__: \\ __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+  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 pxsz parameter is not specified, program will assume units of pixels^-1.+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__: \\ __3. Downsample output image stack__:
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   sp_separate_class.py input_class_avgs input_image_stack output_directory --shrink=shrink_factor   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.
 +
 \\ \\
 ===== Input ===== ===== Input =====
 === Main Parameters === === Main Parameters ===
-  ; input_class_avgs : Input class averages : Set of 2D class averages, with particle-membership information in header. (default required string) +  ; 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 : Input particles : Particle image stack. (default required string) +  ; input_image_stack : Particle image stack. (default required string) 
-  ; output_directory : Output directory : Directory where outputs will be written. (default required string) +  ; 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) +  ; %%--%%filtrad : Gaussian low-pass filter radius, Angstroms if apix specified below, else pixels^-1. (default None) 
-  ; %%--%%pxsz : Pixel size : Angstroms per pixel, might be downsampled already by ISAC2. (default None) +  ; %%--%%apix : 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) +  ; %%--%%shrink : Downsampling factor, e.g., 6 -> 1/6 original size. (default None) 
-  ; %%--%%verbose : Verbose : Writes additional messages to the terminal during execution. (default False)+  ; %%--%%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)
      
 \\ \\
 === Advanced Parameters === === Advanced Parameters ===
 +  ; %%--%%format : Format of optional output aligned-imaged stacks. (default .mrcs)
 +  ; %%--%%debug : Writes additional diagnostics for debugging. (default False)
  
 \\ \\
 ===== Output ===== ===== Output =====
-  ; classmap.txt : Class-to-particle lookup table, one file for all classes+  ; 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   ; docclass???.txt : List of particles for each class, one file per class
-  ; EMAN2DB/stkclass_???.bdb : Virtual stacks of particles for each class +  ; bdb:stkclass_???: Virtual stacks of particles for each class 
-  ; EMAN2DB/stkflt_???.bdb : Optional) virtual stacks of filtered 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
    
 +
 \\ \\
 +
 ===== Description ===== ===== Description =====
  
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 ==== Developer Notes ==== ==== Developer Notes ====
   : Should allow filter types other than Gaussian low-pass   : Should allow filter types other than Gaussian low-pass
-  : Should offer option to write aligned images 
  
 \\ \\
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 \\ \\
 ==== Files ==== ==== Files ====
-sparx/bin/sp_separate_class.py+sphire/bin/sp_separate_class.py
  
 \\ \\
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 \\ \\
- 
pipeline/utilities/sp_separate_class.txt · Last modified: 2020/01/31 11:38 by shaikh

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