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pipeline:utilities:sp_separate_class

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pipeline:utilities:sp_separate_class [2019/12/12 09:46]
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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   : write particle-membership lists for each class   : write particle-membership lists for each class
-  : write separate stacks for each class, with an option to low-pass filter and/or downsample the images, and+  : write separate stacks for each class,  
 +  : optionally low-pass filter and/or downsample the images, and
   : optionally compute eigenimages (basis images) for each class   : optionally compute eigenimages (basis images) 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)
 +  ; %%--%%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: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 +  ; 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 averagesvariances, and eigenimages
-  ; stkeigen.hdf : (Optional) Montage of averagevariance, and eigenimages+
    
  
pipeline/utilities/sp_separate_class.txt · Last modified: 2020/01/31 11:38 by shaikh