usage: prog [options] <command> <file A> ...
Performs various options with basis sets, such as the orthogonal
basis produced by e2msa.py. 

project <basis input> <image input> <projection output>
	Projects a set of images into the input basis subspace. The default
	is to normalize the individual basis vectors, but not the final resulting
	projection. The projections are stored as a 1-D image stack.
projectrot <basis input> <image input> <simmx input> <projection output>
	Same as project, except it will rotate/translate the particles based on the
	best match found in simmx before projection.

Option Type Description
--version None show program's version number and exit
--normproj None Normalize the projections resulting from 'project', such that the length of each vector is 1
--normcomponent None Normalize the dot product for each component of the output vector. If the basis spans the input vector, then the projected vector length will be 1, otherwise it will be less than 1.
--normalize str Normalize the input images using the named processor. Specify 'tomean' for mean-based scaling. Specify None to disable.
--mask int Mask radius
--maskfile, -M str File containing a mask to apply to the particles before normalization
--mean1 None Indicates that the first image in the basis set is actually the mean image, which should be subtracted prior to projection. Output from e2msa requires this flag.
--recalcmean None This will recompute the mean from the input set and subtract before projection. Useful if a different normalization is used than in the original basis file.
--txtout None Output will be a multicolumn text file suitable for plotting
--oneout None Output is a single 2-D image rather than a set of 1-D images
--nbasis, -n int Will use the first n basis images from the input, excluding the mean if present
--basislist, -z str List of basis vectors to use, comma delimited.
--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