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pipeline:utilities:sp_separate_class [2019/12/11 18:58]
shaikh
pipeline:utilities:sp_separate_class [2020/01/31 11:32]
shaikh [Usage]
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 Usage in command line: Usage in command line:
  
-  sp_separate_class.py input_class_avgs input_image_stack output_directory --filtrad=filter_radius --apix=pixel_size --shrink=shrink_factor --align_isac_dir=isac_directory --format=stack_format --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 
 +  sp_separate_class.py input_class_avgs input_image_stack output_directory --filtrad=filter_radius --apix=pixel_size --shrink=shrink_factor --align_isac_dir=isac_directory --format=stack_format
      
      
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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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 \\ __5. Compute eigenimages (basis images) for each class__: \\ __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_factors+  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. The additional output, stkeigen.hdf, will contain the average, variance, and the requested number of eigenimages.
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 ===== Input ===== ===== Input =====
 === Main Parameters === === 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 particles of TcdA1 corresponding to class #9 below}}]+  ; 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)   ; input_image_stack : Particle image stack. (default required string)
   ; output_directory : Directory where outputs will be written. (default required string)   ; output_directory : Directory where outputs will be written. (default required string)
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   ; %%--%%shrink : Downsampling factor, e.g., 6 -> 1/6 original size. (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)   ; %%--%%align_isac_dir : If applying alignments, directory for ISAC output (default None)
-  ; %%--%%verbose : Writes additional messages to the terminal during execution. (default False) 
      
 \\ \\
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 \\ \\
 ===== Output ===== ===== Output =====
-  ; classmap.txt : Class-to-particle lookup table, one file for all classes[{{ :pipeline:utilities:ave_eig75-84.png?400|For 10 classes (from left to right): average, variance, and 5 eigenimages}}]+  ; 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
   ; params_combined.txt : (Optional) Combined particle alignment parameters   ; params_combined.txt : (Optional) Combined particle alignment parameters
   ; stack_all.bdb : Virtual stack with all particles   ; stack_all.bdb : Virtual stack with all particles
-  ; stkclass_???.bdb : Virtual stacks of particles for each class +  ; stkorig_???.bdb : Virtual stacks of particles for each class 
-  ; stkclass_???.bdb : Virtual stacks of unaligned particles for each class +  ; stkfilt_???.bdb : (Optional) Virtual stacks of aligned and optionally filtered particles for each class 
-  ; stkalign_???.bdb : (Optional) Virtual stacks of aligned and optionally filtered particles for each class+  ; stkeigen.hdf : (Optional) Montage of average, variance, and eigenimages
    
  
pipeline/utilities/sp_separate_class.txt · Last modified: 2020/01/31 11:38 by shaikh