e2spt_extract

usage: 
	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