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pipeline:utilities:sp_separate_class

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pipeline:utilities:sp_separate_class [2019/12/12 10:31]
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+  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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   ; %%--%%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)
      
 \\ \\
 === 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)
  
 \\ \\
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   ; 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}}]   ; 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 
-  ; stkorig_???.bdb : Virtual stacks of particles for each class +  ; params_???.txt : (Optional) Particle alignment parameters, one file per class 
-  ; stkfilt_???.bdb : (Optional) Virtual stacks of aligned and optionally filtered particles for each class +  ; stkavgvar.hdf : (Optional) Montage of class averages and variances 
-  ; stkeigen.hdf : (Optional) Montage of averagevariance, and eigenimages+  ; stkeigen.hdf : (Optional) Montage of class averagesvariances, and eigenimages
    
  
pipeline/utilities/sp_separate_class.txt · Last modified: 2020/01/31 11:38 by shaikh