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