e2simmx

usage: prog [options] <c input> <r input> <output>
	Computes a similarity matrix between c-input (col - projections) and r-input (row - particles) stacks of 2-D images. Images may
	optionally be aligned before comparison. Output is a matrix stored as an image with similarity value
	pairs. When used for classification, c input is the references and r input are the particles. More information on
	the output file can be found in the Wiki.

Option	Type	Description
--version	None	show program's version number and exit
--align	str	The name of an 'aligner' to use prior to comparing the images
--aligncmp	str	Name of the aligner along with its construction arguments
--ralign	str	The name and parameters of the second stage aligner which refines the results of the first alignment
--raligncmp	str	The name and parameters of the comparitor used by the second stage aligner. Default is dot.
--cmp	str	The name of a 'cmp' to be used in comparing the aligned images
--prefilt	None	Filter each reference (c) to match the power spectrum of each particle (r) before alignment and comparison
--prectf	None	Apply CTF to each projection before comparison
--mask	str	File containing a single mask image to apply after alignment, but before similarity comparison
--colmasks	str	File containing one mask for each column (projection) image, to be used when refining row (particle) image alignments.
--range	str	Range of images to process (c0,r0,c1,r1) c0,r0 inclusive c1,r1 exclusive
--saveali	None	Save alignment values, output is 5, c x r images instead of 1. Images are (score,dx,dy,da,flip).
--verbose, -v	int	verbose level [0-9], higher number means higher level of verboseness
--init	None	Initialize the output matrix file before performing 'range' calculations
--fillzero	None	Checks the existing output file, and fills only matrix elements which are exactly zero.
--exclude	str	The named file should contain a set of integers, each representing an image from the input file to exclude. Matrix elements will still be created, but will be zeroed.
--shrink	float	Optionally shrink the input particles by an integer amount prior to computing similarity scores. This will speed the process up.
--nofilecheck	None	Turns file checking off in the check functionality - used by e2refine.py.
--check, -c	None	Performs a command line argument check only.
--ppid	int	Set the PID of the parent process, used for cross platform PPID
--parallel	str	Parallelism string