This shows you the differences between two versions of the page.
Next revision | Previous revision Next revision Both sides next revision | ||
pipeline:utilities:sp_separate_class [2019/04/02 11:45] lusnig created |
pipeline:utilities:sp_separate_class [2019/12/12 09:48] shaikh |
||
---|---|---|---|
Line 9: | Line 9: | ||
Usage in command line: | Usage in command line: | ||
- | sp_separate_class.py input_class_avgs input_image_stack output_directory --filt=filter_radius --pxsz=pixel_size --shrink=shrink_factor --verbose | + | sp_separate_class.py input_class_avgs input_image_stack output_directory --filtrad=filter_radius --apix=pixel_size --shrink=shrink_factor |
| | ||
| | ||
Line 17: | Line 17: | ||
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__: | ||
Line 27: | Line 27: | ||
\\ __2. Apply a low-pass filter to the image stacks__: | \\ __2. Apply a low-pass filter to the image stacks__: | ||
- | sp_separate_class.py input_class_avgs input_image_stack output_directory --filt=filter_radius --pxsz=pixel_size | + | sp_separate_class.py input_class_avgs input_image_stack output_directory --filt=filter_radius --apix=pixel_size |
- | Filter radius is in units of Angstroms. If pxsz parameter is not specified, program will assume units of pixels^-1. | + | Filter radius is in units of Angstroms. If apix parameter is not specified, program will assume units of pixels^-1. |
\\ __3. Downsample output image stack__: | \\ __3. Downsample output image stack__: | ||
Line 35: | Line 35: | ||
sp_separate_class.py input_class_avgs input_image_stack output_directory --shrink=shrink_factor | sp_separate_class.py input_class_avgs input_image_stack output_directory --shrink=shrink_factor | ||
| | ||
+ | \\ __4. Apply ISAC alignments to particles__: | ||
+ | |||
+ | sp_separate_class.py input_class_avgs input_image_stack output_directory --align_isac_dir=isac_directory | ||
+ | | ||
+ | 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 | + | ; input_class_avgs : Set of 2D class averages, with particle-membership information in header. (default required string)[{{ : |
- | ; input_image_stack | + | ; input_image_stack : Particle image stack. (default required string) |
- | ; output_directory | + | ; output_directory : Directory where outputs will be written. (default required string) |
- | ; %%--%%filt : Filter radius | + | ; %%--%%filtrad |
- | ; %%--%%pxsz : Pixel size : Angstroms per pixel, might be downsampled already by ISAC2. (default None) | + | ; %%--%%apix : Angstroms per pixel, might be downsampled already by ISAC2. (default None) |
- | ; %%--%%shrink | + | ; %%--%%shrink : Downsampling factor, e.g., 6 -> 1/6 original size. (default None) |
- | ; %%--%%verbose | + | ; %%--%%align_isac_dir |
+ | ; %%--%%verbose | ||
| | ||
\\ | \\ | ||
=== Advanced Parameters === | === Advanced Parameters === | ||
+ | ; %%--%%format : Format of optional output aligned-imaged stacks. (default .mrcs) | ||
\\ | \\ | ||
===== 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??? | ||
- | ; EMAN2DB/stkclass_??? | + | ; params_combined.txt : (Optional) Combined particle alignment parameters |
- | ; EMAN2DB/ | + | ; stack_all.bdb : Virtual stack with all particles |
+ | ; stkclass_??? | ||
+ | ; stkclass_??? | ||
+ | ; stkalign_???.bdb : (Optional) | ||
+ | ; stkeigen.hdf : (Optional) Montage of average, variance, and eigenimages | ||
+ | |||
\\ | \\ | ||
+ | |||
===== Description ===== | ===== Description ===== | ||
Line 68: | Line 88: | ||
==== Developer Notes ==== | ==== Developer Notes ==== | ||
: Should allow filter types other than Gaussian low-pass | : Should allow filter types other than Gaussian low-pass | ||
- | : Should offer option to write aligned images | ||
\\ | \\ | ||
Line 80: | Line 99: | ||
\\ | \\ | ||
==== Files ==== | ==== Files ==== | ||
- | sparx/ | + | sphire/ |
\\ | \\ | ||
Line 94: | Line 113: | ||
\\ | \\ | ||
- |