usage: Usage: e2spt_classify_byproj.py --ncls <n> --path <spt_XX> --iter <N> 
This program is part of the 'new' hierarchy of e2spt_ programs.

This program will generate a set of 3 orthogonal projections of the central slices of each aligned particle from an existing spt_XX result, 
then use this triplet of projections to perform a k-means classification on the particles. In addition to the class-averages, will also 
produce new sets/ for each class, which could be further-refined.

Option Type Description
--version None show program's version number and exit
--path str Path to an existing spt_XX folder with the alignment results to use, defualt = highest spt_XX
--iter int Iteration number within path, default = last iteration
--ncls int Number of classes to generate
--nbasis int Number of basis vectors for the MSA phase, default=4
--layers int number of 1 pixel layers about the center to use for the projection in each direction (size in reduced image if --shrink used), ie 0->1, 1->3, 2->5. Default=2
--sym str Symmetry of the input. Must be aligned in standard orientation to work properly.
--shrink int shrink the particles before processing
--mask str A 3D mask file or a single mask processor specification to apply prior to local projection generation
--threads int Number of alignment threads to run in parallel on a single computer. This is the only parallelism supported by e2spt_align at present.
--hp float Apply a high-pass filter at the specified resolution when generating projections. Specify as resolution in A, eg - 100
--lp float Apply a low-pass filter at the specified resolution when generating projections. Specify the resolution in A, eg - 25
--saveali None In addition to the unaligned sets/ for each class, generate aligned particle stacks per class
--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