pipeline:utilities:sp_separate_class

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Separate Into Classes : Separates stacks of particle images into stacks for each class.


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


The purpose of sp_separate_class.py is to:

: extract particle-membership information from a stack of class averages
: write particle-membership lists for each class, and
: write separate stacks for each class, with an option to low-pass filter and/or downsample the images


1. Standard usage: create separate stacks for each class:

sp_separate_class.py input_class_avgs input_image_stack output_directory 


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

Filter radius is in units of Angstroms. If pxsz parameter is not specified, program will assume units of pixels^-1.


3. Downsample output image stack:

sp_separate_class.py input_class_avgs input_image_stack output_directory --shrink=shrink_factor


Main Parameters

input_class_avgs
Input class averages
Set of 2D class averages, with particle-membership information in header. (default required string)
input_image_stack
Input particles
Particle image stack. (default required string)
output_directory
Output directory
Directory where outputs will be written. (default required string)
--filt
Filter radius
Gaussian low-pass filter radius, Angstroms if pxsz specified below, else pixels^-1. (default None)
--pxsz
Pixel size
Angstroms per pixel, might be downsampled already by ISAC2. (default None)
--shrink
Downsampling factor
Downsampling factor, e.g., 6 → 1/6 original size. (default None)
--verbose
Verbose
Writes additional messages to the terminal during execution. (default False)


Advanced Parameters


classmap.txt
Class-to-particle lookup table, one file for all classes
docclass???.txt
List of particles for each class, one file per class
EMAN2DB/stkclass_???.bdb
Virtual stacks of particles for each class
EMAN2DB/stkflt_???.bdb
Optional) virtual stacks of filtered particles for each class





: Should allow filter types other than Gaussian low-pass
: Should offer option to write aligned images


Tapu Shaikh


Category 1:: APPLICATIONS


sparx/bin/sp_separate_class.py



Beta:: Under evaluation and testing. Please let us know if there are any bugs.


There are no known bugs so far.


  • pipeline/utilities/sp_separate_class.1554198383.txt.gz
  • Last modified: 2019/04/02 11:46
  • by lusnig