usage: Usage: e2spt_average.py [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.

Option Type Description
--version None show program's version number and exit
--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.
--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
--keep float fraction of particles to keep. will overwrite simthr if set.
--replace str Replace the input subtomograms used for alignment with the specified file (used when the aligned particles were masked or filtered)
--outfile str Normally even/odd and overall outputs automatically generated. If specified, only overall file written with this specified filename. Suppresses postprocessing.
--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).
--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.
--automaskexpand int Default=boxsize/20. Specify number of voxels to expand mask before soft edge. Use this if low density peripheral features are cut off by the mask.
--symalimasked str This will translationally realign each asymmetric unit to the specified (usually masked) reference
--sym str Symmetry of the input. Must be aligned in standard orientation to work properly.
--path str Path to a folder containing current results (default = highest spt_XX)
--skippostp None Skip post process steps (fsc, mask and filters)
--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
--parallel str Thread/mpi parallelism to use