pipeline:utilities:sp_separate_class

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pipeline:utilities:sp_separate_class [2019/04/02 11:45]
lusnig created
pipeline:utilities:sp_separate_class [2019/12/12 09:54]
shaikh
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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 --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, with an option to low-pass filter and/or downsample the images, and 
-  : write separate stacks for each class, with an option to low-pass filter and/or downsample the images+  : 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)
   ​   ​
 \\ \\
 === Advanced Parameters === === Advanced Parameters ===
 +  ; %%--%%format : Format of optional output aligned-imaged stacks. (default .mrcs)
  
 \\ \\
 ===== 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 +  ; params_combined.txt : (Optional) Combined particle alignment parameters 
-  ; EMAN2DB/​stkflt_???.bdb : (Optional) ​virtual ​stacks of filtered particles for each class+  ; stack_all.bdb : Virtual stack with all particles 
 +  ; stkorig_???.bdb : Virtual stacks of particles for each class 
 +  ; stkfilt_???.bdb : (Optional) ​Virtual ​stacks of aligned and optionally ​filtered particles for each class 
 +  ; stkeigen.hdf : (Optional) Montage of average, variance, 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