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--- pipeline:utilities:sp_separate_class [2019/12/12 09:54]
shaikh
+++ pipeline:utilities:sp_separate_class [2020/01/31 11:38]
shaikh [Output]
@@ 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
+  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
@@ Line 18: / Line 18: @@
   : 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,
+  : optionally low-pass filter and/or downsample the images, and
   : optionally compute eigenimages (basis images) for each class
@@ Line 57: / Line 58: @@
   ; %%--%%shrink : Downsampling factor, e.g., 6 -> 1/6 original size. (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)
 \\
 === Advanced Parameters ===
   ; %%--%%format : Format of optional output aligned-imaged stacks. (default .mrcs)
+  ; %%--%%debug : Writes additional diagnostics for debugging. (default False)
 \\
@@ Line 66: / Line 71: @@
   ; 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
-  ; params_combined.txt : (Optional) Combined particle alignment parameters
+  ; bdb:stkclass_???: Virtual stacks of particles for each class
-  ; stack_all.bdb : Virtual stack with all particles
+  ; bdb:stkflt_???: (Optional) Virtual stacks of filtered particles for each class
-  ; stkorig_???.bdb : Virtual stacks of particles for each class
+  ; params_???.txt : (Optional) Particle alignment parameters, one file per class
-  ; stkfilt_???.bdb : (Optional) Virtual stacks of aligned and optionally filtered particles for each class
+  ; stkavgvar.hdf : (Optional) Montage of class averages and variances
-  ; stkeigen.hdf : (Optional) Montage of average, variance, and eigenimages
+  ; stkeigen.hdf : (Optional) Montage of class averages, variances, and eigenimages

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