Alternative to e2spt_align.py, but uses 2D subtilt images instead of 3D particle volume for alignment. Also a modified scipy minimizer is used in place of EMAN2 aligners. 
	e2spt_align_subtlt.py sets/ptcls.lst reference.hdf --path spt_xx --iter x

Option Type Description
--version None show program's version number and exit
--path str Path to a folder where results should be stored, following standard naming conventions (default = spt_XX)
--iter int Iteration number within path. Default = 0
--goldcontinue None Will use even/odd refs corresponding to specified reference to continue refining without phase randomizing again
--sym str Symmetry of the input. Must be aligned in standard orientation to work properly.
--maxres float Maximum resolution to consider in alignment (in A, not 1/A)
--minres float Minimum resolution to consider in alignment (in A, not 1/A)
--parallel str Thread/mpi parallelism to use
--fromscratch None Start from exhaustive coarse alignment. Otherwise will use alignment from the previous rounds and do local search only.
--use3d None use projection of 3d particles instead of 2d sub tilt series
--preprocess str Preprocess each 2-D subtilt while loading (alignment only)
--debug None Debug mode. Will run a small number of particles directly without parallelism with lots of print out.
--plst str list of 2d particle with alignment parameters. The program will reconstruct before alignment so it can be slower.
--maxshift int Maximum shift from the center of the box or the previous alignment. default box size//6
--maxang int Maximum angle difference from starting point. Ignored when --fromscratch is on.
--curve None Mode for filament structure refinement. Still under testing. Ignored when --fromscratch is on.
--skipali None Skip alignment and only calculate the score. Incompatible with --fromscratch, but --breaksym will still be considered.
--breaksym str Specify symmetry to break. Ignored when --fromscratch is on.
--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