This version (2020/01/31 11:38) is a draft.
Approvals: 0/1
The Previously approved version (2019/12/11 18:58) is available.Diff

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 --align_isac_dir=isac_dir --filtrad=filter_radius --apix=pixel_size --shrink=shrink_factor --nvec=number_of_eigenimages --ctf --verbose

The purpose of sp_separate_class.py is to:

: write particle-membership lists for each class
: write separate stacks for each class, 
: optionally low-pass filter and/or downsample the images, and
: optionally compute eigenimages (basis images) for each class

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 --apix=pixel_size

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:

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, the alignments applied to the ordered class averages will be applied to the particles.

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_eigenimages

The additional output, stkeigen.hdf, will contain the average, variance, and the requested number of eigenimages.

Main Parameters

Set of 2D class averages, with particle-membership information in header. (default required string)
Filtered, aligned particles of TcdA1 corresponding to class #9 below
Particle image stack. (default required string)
Directory where outputs will be written. (default required string)
Gaussian low-pass filter radius, Angstroms if apix specified below, else pixels^-1. (default None)
Angstroms per pixel, might be downsampled already by ISAC2. (default None)
Downsampling factor, e.g., 6 → 1/6 original size. (default None)
If applying alignments, directory for ISAC output (default None)
Number of eigenimages to compute. (default None)
Applies CTF correction. (default False)
Writes additional messages to the terminal during execution. (default False)

Advanced Parameters

Format of optional output aligned-imaged stacks. (default .mrcs)
Writes additional diagnostics for debugging. (default False)

Class-to-particle lookup table, one file for all classes
For each class (from left to right): average, variance, and first 5 eigenimages
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
(Optional) Particle alignment parameters, one file per class
(Optional) Montage of class averages and variances
(Optional) Montage of class averages, variances, and eigenimages

: Should allow filter types other than Gaussian low-pass

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.txt
  • Last modified: 2020/01/31 11:38
  • by shaikh