usage: prog <input> [options]

	Aligns a stack of particle images to a reference. If output is not specified, input file
	is overwritten with the aligned particles.

Option Type Description
--version None show program's version number and exit
--output str The name of the output class stack
--ref str Reference image to use for alignment. Required
--refn int Number of the reference image in 'ref'. Default=0
--align str This is the aligner used to align particles to the previous class average. Default is None.
--aligncmp str The comparitor used for the --align aligner. Default is dot.
--ralign str This is the second stage aligner used to refine the first alignment. This is usually the 'refine' aligner.
--raligncmp str The comparitor used by the second stage aligner.
--cmp str The comparitor used to generate quality scores for the purpose of particle exclusion in classes, strongly linked to the keep argument.
--ppid int Set the PID of the parent process, used for cross platform PPID
--verbose, -v int verbose level [0-9], higher number means higher level of verboseness