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 --filtrad=filter_radius --apix=pixel_size --shrink=shrink_factor --align_isac_dir=isac_directory --format=stack_format --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 --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_factors

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

input_class_avgs

Set of 2D class averages, with particle-membership information in header. (default required string)

Filtered particles of TcdA1 corresponding to class #9 below

input_image_stack

Particle image stack. (default required string)

output_directory

Directory where outputs will be written. (default required string)

--filtrad

Gaussian low-pass filter radius, Angstroms if apix specified below, else pixels^-1. (default None)

--apix

Angstroms per pixel, might be downsampled already by ISAC2. (default None)

--shrink

Downsampling factor, e.g., 6 → 1/6 original size. (default None)

--align_isac_dir

If applying alignments, directory for ISAC output (default None)

--verbose

Writes additional messages to the terminal during execution. (default False)

--format

Format of optional output aligned-imaged stacks. (default .mrcs)

classmap.txt

Class-to-particle lookup table, one file for all classes

For 10 classes (from left to right): average, variance, and 5 eigenimages

docclass???.txt

List of particles for each class, one file per class

params_combined.txt

(Optional) Combined particle alignment parameters

stack_all.bdb

Virtual stack with all particles

stkclass_???.bdb

Virtual stacks of particles for each class

stkclass_???.bdb

Virtual stacks of unaligned particles for each class

stkalign_???.bdb

(Optional) Virtual stacks of aligned and optionally filtered particles for each class

: Should allow filter types other than Gaussian low-pass

Tapu Shaikh

Category 1:: APPLICATIONS

sphire/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.