usage: prog <simMatrixIn> <classMatrixOut> [options]

	This program analyzes a similarity matrix as produced by e2simmx.py and produces a classification matrix mapping class
	membership for each particle, which can in-turn be used with e2classaverage.py.

	Takes a similarity matrix that has been created between reprojections-input (col) and particles-input (row) stacks of 2-D images.
	Typically these have been created via e2simmx such as

	e2simmx.py proj.hed part.hed simMatrix.hed --saveali --align=rotate_translate:maxshift=5

	The similarity matrix is a stack of 1 or 5 images: similarity, dx,dy,dalpha,mirror.
	The output is 6 images: class, weight, dx, dy, dalpha, mirror).
	See the wiki for more complete documentation of the files.

Option Type Description
--version None show program's version number and exit
--sep int The number of classes a particle can contribute towards (default is 1)
--simvec None Instead of using the class for the peak value, uses the pattern of similarities for each orientation for assignment.
--verbose, -v int verbose level [0-9], higher number means higher level of verboseness
--nofilecheck None Turns file checking off in the check functionality - used by e2refine.py.
--check, -c None Performs a command line argument check only.
--noalign None Ignore the alignments
--ppid int Set the PID of the parent process, used for cross platform PPID