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Both sides previous revision Previous revision Next revision | Previous revision Next revision Both sides next revision | ||
pipeline:utilities:sp_separate_class [2019/09/12 16:45] shaikh |
pipeline:utilities:sp_separate_class [2019/12/12 09:48] shaikh |
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The purpose of sp_separate_class.py is to: | The purpose of sp_separate_class.py is to: | ||
- | | + | : 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, 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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| | ||
If the input class averages are ordered_class_averages.hdf, | If the input class averages are ordered_class_averages.hdf, | ||
+ | |||
+ | \\ __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, | ||
\\ | \\ | ||
===== 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)[{{ : |
; 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[{{ : |
; docclass??? | ; docclass??? | ||
; params_combined.txt : (Optional) Combined particle alignment parameters | ; params_combined.txt : (Optional) Combined particle alignment parameters | ||
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; stkclass_??? | ; stkclass_??? | ||
; stkalign_??? | ; stkalign_??? | ||
+ | ; stkeigen.hdf : (Optional) Montage of average, variance, and eigenimages | ||