usage: Usage: e2spt_average.py <ref1> <ref2> ... [options] 
Note that this program is not part of the original e2spt hierarchy, but is part of an experimental refactoring.

Will read metadata from the specified spt_XX directory, as produced by e2spt_align.py, and average a selected subset of subtomograms in the predetermined orientation.
This version of the program competes each particle against N reference volumes, and only averages it with the best match. Alignment parameters from a previous
e2spt_align run are used to define the coarse orientation, so the references must be similar and in the same orientation. Alignments are translationally adjusted only.
If --sym is specified, each possible symmetric orientation is tested starting with the exisiting alignment parameters, and only the best is kept.

Option Type Description
--version None show program's version number and exit
--iter int Iteration number within path. Default = start a new iteration
--simthr float Similarity is smaller for better 'quality' particles. Specify the highest value to include from e2spt_hist.py. Default -0.1
--simthr2 float Simlarity score for the best matching final alignment. Scaling may be different due to resolution limit. Default 0
--replace str Replace the input subtomograms used for alignment with the specified file (used when the aligned particles were masked or filtered)
--wedgesigma float Threshold for identifying missing data in Fourier space in terms of standard deviation of each Fourier shell. Default 3.0
--minalt float Minimum alignment altitude to include. Default=0
--maxalt float Maximum alignment altitude to include. Deafult=180
--maxtilt float Explicitly zeroes data beyond specified tilt angle. Assumes tilt axis exactly on Y and zero tilt in X-Y plane. Default 90 (no limit).
--maxres float Lowpass filter applied to particles prior to alignment/averaging, resolution in A. Default disabled
--listfile str Specify a filename containing a list of integer particle numbers to include in the average, one per line, first is 0. Additional exclusions may apply.
--shrinkcompare int Shrink factor for classification only (for speed)
--sym str Symmetry of the input. Must be aligned in standard orientation to work properly. The structure will be expanded from this symmetry to c1.
--applysym str Symmetry to apply to the structure after classification.
--path str Path to a folder containing current results (default = highest spt_XX)
--parallel str parallel mode. Not all functions are implemented yet..
--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.
--maskclass str Mask each reference before classification
--mask str Mask applied to final averages
--verbose, -v int verbose level [0-9], higher number means higher level of verboseness
--noali None Skip translational alignment.
--symcopy None Copy each particle for each asymetrical unit. need a maskclass to focus on one unit. do not work with applysym
--nolstout None Skip writting lst output.
--sample int use only N samples.
--randnclass int split into N random classes. ignore refs
--ppid int Set the PID of the parent process, used for cross platform PPID