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pipeline:utilities:sp_separate_class [2019/12/12 09:48] 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 | + | sp_separate_class.py input_class_avgs input_image_stack output_directory |
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: write particle-membership lists for each class | : write particle-membership lists for each class | ||
- | : write separate stacks for each class, | + | : write separate stacks for each class, |
+ | : optionally | ||
: optionally compute eigenimages (basis images) for each class | : optionally compute eigenimages (basis images) for each class | ||
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\\ __5. Compute eigenimages (basis images) for each class__: | \\ __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 | + | sp_separate_class.py input_class_avgs input_image_stack output_directory --align_isac_dir=isac_directory --nvec=number_of_eigenimages |
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The additional output, stkeigen.hdf, | The additional output, stkeigen.hdf, | ||
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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) | ; %%--%%verbose : Writes additional messages to the terminal during execution. (default False) | ||
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=== 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) | ||
\\ | \\ | ||
===== 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 | + | ; bdb: |
- | ; stack_all.bdb : Virtual stack with all particles | + | ; bdb:stkflt_??? : (Optional) |
- | ; stkclass_??? | + | ; params_???.txt : (Optional) |
- | ; stkclass_???.bdb : Virtual stacks of unaligned | + | ; stkavgvar.hdf : (Optional) Montage |
- | ; stkalign_???.bdb : (Optional) | + | ; stkeigen.hdf : (Optional) Montage of class averages, variances, and eigenimages |
- | ; stkeigen.hdf : (Optional) Montage of average, variance, and eigenimages | + | |