pipeline:utilities:sp_separate_class

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pipeline:utilities:sp_separate_class [2019/09/12 16:08]
shaikh
pipeline:utilities:sp_separate_class [2019/12/11 18:58]
shaikh
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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_factors
 +  ​
 +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)+  ; 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_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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 \\ \\
 ===== 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 10 classes (from left to right): average, variance, and 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
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   ; stkalign_???​.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
    
 +
 \\ \\
 +
 ===== Description ===== ===== Description =====
  
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  • pipeline/utilities/sp_separate_class.txt
  • Last modified: 2020/01/31 11:38
  • by shaikh