e2spt_preproc

usage: prog <output> [options]

	This program is used to preprocess subtomograms before aligning them. The same can be accomplished with 
	e2proc3d, except that this program is parallelized and thus should be substantially faster for large subtomograms.

Option	Type	Description
--version	None	show program's version number and exit
--apix	float	Default=0.0 (not used). Use this apix value where relevant instead of whatever is in the header of the reference and the particles. Will overwrite particle header as well.
--clip	int	Default=0 (which means it's not used). Boxsize to clip particles. For example, the boxsize of the particles might be 100 pixels, but the particles are only 50 pixels in diameter. Aliasing effects are not always as deleterious for all specimens, and sometimes 2x padding isn't necessary.
--highpass	str	Default=None. A highpass filtering processor (see 'e2help.py processors -v 10' at the command line) to be applied to each volume prior to COARSE alignment. Not applied to aligned particles before averaging.
--input	str	Default=None. The name of the input volume stack. MUST be HDF since volume stack support is required.
--lowpass	str	Default=None. A lowpass filtering processor (see 'e2help.py processors -v 10' at the command line) to be applied to each volume prior to COARSE alignment. Not applied to aligned particles before averaging.
--mask	str	Default=None. Masking processor applied to particles before alignment. IF using --clip, make sure to express outer mask radii as negative pixels from the edge.
--maskfile	str	Default=None. Mask file (3D IMAGE) applied to particles before alignment. Must be in HDF format. Default is None.
--nopath	None	If supplied, this option will save results in the directory where the command is run. A directory to store the results will not be made.
--normproc	str	Default=None (see 'e2help.py processors -v 10' at the command line). Normalization processor applied to particles before alignment. If normalize.mask is used, results of the mask option will be passed in automatically. If you want to turn this option off specify 'None'
--output	str	Default=None. Specific name of HDF file to write processed particles to.
--path	str	Default=spt. Directory to store results in. The default is a numbered series of directories containing the prefix 'sptpreproc'; for example, sptpreproc_02 will be the directory by default if 'sptpreproc_01' already exists.
--parallel	str	default=None. Parallelism. See http://blake.bcm.edu/emanwiki/EMAN2/Parallel
--ppid	int	Default=-1. Set the PID of the parent process, used for cross platform PPID
--preprocess	str	Any processor (see 'e2help.py processors -v 10' at the command line) to be applied to each volume prior to COARSE alignment. Not applied to aligned particles before averaging.
--shrink	int	Default=0 (no shrinking). Optionally shrink the input volumes by an integer amount for coarse alignment.
--subset	int	Default=0 (not used). Refine only this substet of particles from the stack provided through --input
--threshold	str	Default=None. A threshold applied to the subvolumes after normalization. For example, --threshold=threshold.belowtozero:minval=0 makes all negative pixels equal 0, so that they do not contribute to the correlation score.
--verbose, -v	int	Default=0. Verbose level [0-9], higher number means higher level of verboseness; 10-11 will trigger many messages that might make little sense since this level of verboseness corresponds to 'debugging mode'