usage: prog [options] <c input> <r input> <output> <ref simmx> <stg1 refs> <stg1 simmx>
	Computes a similarity matrix between c-input (col - projections) and r-input (row - particles) stacks of 2-D images. Unlike
	e2simmx.py, this will perform classification in two stages, first a coarse classification, then a local classification. Particle
	association for coarse classification, however, is not assigned based on Euler angle, but rather on mutual similarity in a subsampled
	reference-image self-classification. Output is the same as e2simmx, with coarsely sampled results inserted in unsampled local regions.
	When used for classification, c input is the references and r input are the particles.

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
--mask str File containing a single mask image to apply before similarity comparison
--colmasks str File containing one mask for each column (projection) image, to be used when refining row (particle) image alignments.
--saveali None Save alignment values, output is c x r x 4 instead of c x r x 1
--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
--verbose, -v int verbose level [0-9], higher number means higher level of verboseness
--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 but may change classifications.
--shrinks1 float Shrinking performed for first stage classification, default=2
--finalstage None Assume that existing preliminary particle classifications are correct, and only recompute final local orientations
--ppid int Set the PID of the parent process, used for cross platform PPID
--parallel str Parallelism string

For more information go to emanwiki/EMAN2/Programs/e2simmx2stage.