usage: prog [options] <refine_xx folder>

	WARNING: this program is still considered experimental!

	Based on a completed refinement, this will perform per-particle alignment using reference projections from the reconstruction.
	It will only perform alignments on particles used in the specified refinement run. 
	This will make an attempt to rename the original particles as *__orig before writing the new particles with the original particle
	names. It will do this only the first time. If __orig files already exist, it will not replace them. This way if you run this
	program multiple times, you can produce new versions of the aligned particles without destroying the true originals.

Option Type Description
--version None show program's version number and exit
--noalign None Regenerates unaligned particle averages into __orig
--invert None Invert the contrast of the particles in output files (default false)
--filefilt str Only processes image stacks where the filename contains the specified string. Mostly used for debugging.
--frac str Processes a fraction of the data, used automatically by --threads. <n>,<ntot>
--step str Specify <first>,<last>,<step>. Processes only a subset of the input frames. For example, 0,6,2 would process only frames 0,2,4. 1,5,1 would process frames 1,2,3 and 4, skipping frame 0. First is inclusive, last exclusive
--parallel None parallelism argument. This program supports only thread:<n>
--threads int Number of threads to run in parallel on a single computer when multi-computer parallelism isn't useful
--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