pipeline:utilities:sp_separate_class

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pipeline:utilities:sp_separate_class [2019/09/12 16:45]
shaikh
pipeline:utilities:sp_separate_class [2020/01/31 11:38] (current)
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 --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
   ​   ​
   ​   ​
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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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   ​   ​
 If the input class averages are ordered_class_averages.hdf,​ the alignments applied to the ordered class averages will be applied to the particles. 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 : Set of 2D class averages, with particle-membership information in header. (default required string)[{{ :​pipeline:​utilities:​ordered_class_averages.png?400|ordered_class_averages.hdf ​of TcdA from ISAC}}]+  ; 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)
 +  ; %%--%%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)   ; %%--%%verbose : Writes additional messages to the terminal during execution. (default False)
   ​   ​
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 === Advanced Parameters === === Advanced Parameters ===
   ; %%--%%format : Format of optional output aligned-imaged stacks. (default .mrcs)   ; %%--%%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[{{ :​pipeline:​utilities:​stkalign_029.png?400|Montage of particles from class 29using a filter radius of 0.05 px^-1}}]+  ; 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): averagevariance, 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 +  ; bdb:​stkclass_???​ : Virtual stacks of particles for each class 
-  ; stack_all.bdb : Virtual stack with all particles +  ; bdb:stkflt_??? : (Optional) ​Virtual stacks of filtered ​particles for each class 
-  ; stkclass_???​.bdb : Virtual stacks of particles for each class +  ; params_???.txt : (Optional) ​Particle alignment parameters, one file per class 
-  ; stkclass_???.bdb : Virtual stacks of unaligned ​particles for each class +  ; stkavgvar.hdf : (Optional) Montage ​of class averages ​and variances 
-  ; stkalign_???.bdb : (Optional) ​Virtual stacks ​of aligned ​and optionally filtered particles for each class+  ; stkeigen.hdf : (Optional) Montage of class averages, variances, and eigenimages
    
  
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  • Last modified: 2019/09/12 16:45
  • by shaikh