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

Advanced Parameters

Class-to-particle lookup table, one file for all classes
List of particles for each class, one file per class
Virtual stacks of particles for each class
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



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