usage: prog [options] 
	This program takes aligned stacks produced by e2spt_classaverage.py and raw tomograms
	to recompute averages with different options (such as extracting recentered particles,
	and possibly with a larger or smaller boxisze).
	All the necessary files (aligned stacks in HDF format and raw tomograms in MRC format 
	ending in .rec, as produced by IMOD) should be in the running directory.

Option Type Description
--version None show program's version number and exit
--stacks str Comma separated list of HDF image stacks to process.
--tomograms str Comma separated list of tomograms with REC extension from which all particles in --stacks came from.
--sym str Symmetry to impose - choices are: c<n>, d<n>, h<n>, tet, oct, icos
--path str Name of directory where to save the output file.
--boxsize, -B int Default=0 (option not used). Provide a value for the boxsize of the output average in pixels. If not provided, the boxsize of --stacks will be used.
--normproc str Normalization processor applied to particles before extraction. Default=normalize.edgemean. If using the latter, you must provide --masknorm, otherwise, a default --masknorm=mask.sharp:outer_radius=-2 will be used.
--threshold str Threshold processor to apply to particles before writing them out to get rid of too high and/or too low pixel values.
--usetomograms None "Re-extract particles from the original tomogram.
--useinverseali None "Use the inverse of the value stored in xform.align3d in the header of each particle.
--shrink int Shrink factor to shrink particles before averaging. Default=1, which means no shrinking.
--lowpass str Lowpass filtering processor to apply to particles before averaging. Default=None.
--preprocess str A processor (as in e2proc3d.py) to be applied to the tomogram before opening it. \nFor example, a specific filter with specific parameters you might like. \nType 'e2proc3d.py --processors' at the commandline to see a list of the available processors and their usage
--invert None Default=False. This parameer indicates you want the contrast to me inverted while boxing, AND for the extracted sub-volumes. Remember that EMAN2 **MUST** work with "white" protein. You can very easily figure out what the original color\nof the protein is in your data by looking at the gold fiducials or the edge of the carbon hole in your tomogram. If they look black you MUST specify this option
--averager str The type of averager used to produce the class average. Default=mean.tomo
--keep float The fraction of particles to keep in each class. Default=1.0
--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.