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pipeline:utilities:sp_separate_class [2019/09/12 16:43] shaikh [Output] |
pipeline:utilities:sp_separate_class [2020/01/31 11:32] shaikh [Usage] |
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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 |
+ | 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, |
- | : 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) | + | ; 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) | ||
- | ; %%--%%verbose : Writes additional messages to the terminal during execution. (default False) | ||
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\\ | \\ | ||
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===== Output ===== | ===== Output ===== | ||
- | ; classmap.txt : Class-to-particle lookup table, one file for all classes[{{ :pipeline:utilities:ordered_class_averages.png?400|ordered_class_averages.hdf of TcdA from ISAC}}] | + | ; 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 | ; params_combined.txt : (Optional) Combined particle alignment parameters | ||
; stack_all.bdb : Virtual stack with all particles | ; stack_all.bdb : Virtual stack with all particles | ||
- | ; stkclass_???.bdb : Virtual stacks of particles for each class | + | ; stkorig_???.bdb : Virtual stacks of particles for each class |
- | ; stkclass_???.bdb : Virtual stacks of unaligned particles for each class | + | ; stkfilt_???.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 | + | ; stkeigen.hdf : (Optional) Montage of average, variance, and eigenimages |
- | [{{ :pipeline:utilities:stkalign_029.png?400|Montage of particles from class 29, using a filter radius of 0.05 px^-1}}] | + | |
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