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--- pipeline:utilities:sp_separate_class [2019/12/12 09:48]
shaikh
+++ pipeline:utilities:sp_separate_class [2019/12/12 09:53]
shaikh
@@ Line 9: / Line 9: @@
 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 --filtrad=filter_radius --apix=pixel_size --shrink=shrink_factor --align_isac_dir=isac_directory --format=stack_format
@@ Line 57: / Line 57: @@
   ; %%--%%shrink : Downsampling factor, e.g., 6 -> 1/6 original size. (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)
 \\
@@ Line 69: / Line 68: @@
   ; params_combined.txt : (Optional) Combined particle alignment parameters
   ; 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

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