Extract 2D subtilt particles from the tilt series, and reconstruct 3D subvolumes.
	There are a number of modes for the program and it is probably easier to get the right commands from the GUI.
	To extract particles of a certain label from one tomogram
	e2spt_extract.py tomograms/tomox__bin4.hdf --boxsz_unbin 128 --label <label from particle picking> 
	To extract the particles of the same label from all tomograms
	e2spt_extract.py --alltomograms --boxsz_unbin 128 --label <label from particle picking> 
	To extract particles along curves drawn using e2tomo_drawcurve.py. The direction of particles along the curve will be written to the header of particles which can be used in downstream refinement. The spacing of particles along the curve is controlled by the box size and the overlap between adjacent boxes. 
	e2spt_extract.py --curves <curve ID> --curves_overlap 0.75 --alltomograms --boxsz_unbin 128 --newlabel <new particle label> 
	To extract particls from an existing refinement (either the particle_param_xx.json from e2spt_refine, or aliptcls3d_xx.lst from e2spt_refine_new)
	e2spt_extract.py --jsonali <json/lst from existing alignment> --boxsz_unbin 128 --newlabel <new particle label> 

Option Type Description
--version None show program's version number and exit
--boxsz_unbin int box size in unbinned tomogram
--label str Only extract particle with this name. Leave blank to extract all particles.
--newlabel str Label of output particles. Same as original particle label by default.
--threads int threads
--maxtilt int max tilt
--padtwod float padding factor
--noctf None skip ctf correction.
--wiener None wiener filter the particles using ctf information. Not very useful...
--alltomograms None use all tomograms.
--dotest None only make 1 batch of subtomograms for testing
--shrink float Shrinking factor for output particles. 1.5 or integers allowed. Default is 1 (no shrink).
--tltkeep float keep a fraction of tilt images with good score determined from tomogram reconstruction
--rmbeadthr float remove 2d particles with high contrast object beyond N sigma at 100A. Note that this may result in generating fewer particles than selected. Default is -1 (include all particles). 0.5 might be a good choice for removing gold beads but may need some testing...
--curves int specify curve id to extract particles from saved curves.
--curves_overlap float fraction of overlap when generating particle along curves. default is 0.5
--jsonali str re-extract particles using a particle_param_xx json file from a spt alignment
--mindist float minimum distance between particles in A. for reextraction only
--keep float fraction of particles to keep fron previous alignment. for reextraction only.
--postproc str processor after 3d particle reconstruction
--postmask str masking after 3d particle reconstruction. The mask is transformed if json
--compressbits int Bits to keep for compression. default is -1 meaning uncompressed floating point. 8 bit seems fine...
--norewrite None skip existing files. do not rewrite.
--append None append to existing files.
--parallel str parallel
--postxf str a file listing post transforms (see http://eman2.org/e2tomo_more), or for simple symmetry, <sym>,<cx>,<cy>,<cz> where the coordinates specify the center of a single subunit
--ppid int Set the PID of the parent process, used for cross platform PPID
--skip3d None do not make 3d particles. only generate 2d particles and 3d header.
--verbose int verbose