usage: Usage: e22da_align.py [options] <sets/file.lst> <reference>[,nref]
	This program will align a stack of 2-D particle images to a single 2-D reference image, recording all of the alignment parameters in a
	JSON file. This is designed as the first step in a longer 2-D processing sequence. 
	This could, for example, be used to align a full particle set against a 2-D reference, then select a subset which matches well, as opposed 
	to the normal 3-D refinement process where particles are competed against many references.

Option Type Description
--version None show program's version number and exit
--threads int Number of alignment threads to run in parallel on a single computer
--iter int Iteration number within path. Default = start a new iteration
--saveali None Save a stack file (aliptcls_XX.hdf) containing the aligned particles.
--path str Path to a folder where results should be stored. Creates a new folder if none specified (default = m2d_XX)
--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.
--verbose, -v int verbose level [0-9], higher number means higher level of verboseness
--ppid int Set the PID of the parent process, used for cross platform PPID