usage: Usage: e2maskbyclass.py [options]
This program will generate a masked stack of particles for each micrograph based on the class-average each particle belongs to. While this will run with any EMAN2.2 generated class-average stack, it is designed to work on averages produced from __ctf_flip_fullres particles.

In short:
- read a class-average stack
- convert each class-average into a 2-D mask
- find the original phase-flipped particle for each particle in the class-average
- mask each particle on a per-micrograph basis

once complete, bispectra can be recomputed based on the masked particles, or the masked particles can be used directly, potentially producing better alignments and averages.

Option Type Description
--version None show program's version number and exit
--classes str Path to a class-average file (must be EMAN2 HDF averages)
--threads int Number of alignment threads to run in parallel on a single computer.
--nofullresok None Overrides the requirement that the class-averages be made from _fullres particle images.
--redobispec None Recomputes bispectra from masked particles
--redoharmonic None Recomputes harmonic power from masked particles
--gui None Permits interactive adjustment of mask parameters
--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