e2tomopreproc

usage: e2tomopreproc.py <imgs> <options> . 
	This program takes a tiltseries ('.st' or '.ali' file from IMOD) and applies preprocessing operations to them, such as lowpass, highpass, masking, etc.
	The options should be supplied in "--option=value" format, replacing "option" for a valid option name, and "value" for an acceptable value for that option.

Option	Type	Description
--version	None	show program's version number and exit
--path	str	Directory to store results in. \n\t\tThe default is a numbered series of directories containing the prefix 'tomopreproc';\n\t\tfor example, tomopreproc_02 will be the directory by default if 'tomopreproc_01' \n\t\talready exists.
--input	str	"tiltseries to process. redundant with --tiltseries, or with providing images as arguments (separated by a space: e2tomopreproc.py stack1.hdf stack2.hdf), but --input takes precedence.
--tiltseries	str	"tiltseries to process. redundant with --input
--tltfile	str	".tlt file containing the tilt angles for --tiltseries
--outmode	str	All EMAN2 programs write images with 4-byte floating point values when possible by default. This allows specifying an alternate format when supported: float, int8, int16, int32, uint8, uint16, uint32. Values are rescaled to fill MIN-MAX range.
--dontcleanup	None	If specified, intermediate files will be kept.
--clip	str	Default=None. This resizes the 2-D images in the tilt series. If one number is provided, then x and y dimensions will be made the same. To specify both dimensions, supply two numbers, --clip=x,y. Clipping will be about the center of the image.
--shrink	float	Default=0.0 (no shrinking). Can use decimal numbers, larger than 1.0. Optionally shrink the images by this factor. Uses processor math.fft.resample.
--threshold	str	Default=None. A threshold processor applied to each image.
--erasegold	None	Default=False. Runs erase_gold.py on the stack.
--mask	str	Default=None. Masking processor applied to each image.
--maskbyangle	None	Default=False. Requires --tltfile. This will mask out from tilted images the info that isn't present at the 0 tilt angle. It uses the tomo.tiltedgemask processor (type 'e2help.py processors' at the commandline to read a description of the processor and its parameters). Provide --maskbyanglefalloff and --maskbyanglesigma to modify the default parameters.
--maskbyanglefalloff	int	Default=4. Number of pixels over which --maskbyangle will fall off to zero.
--maskbyanglesigma	float	Default=2.0. Number of sigmas for the width of the gaussian fall off in --maskbyangle and --maskbyanglefalloff
--normproc	str	Default=None (see 'e2help.py processors -v 10' at the command line). Normalization processor applied to each image.
--normalizeimod	None	Default=False. This will apply 'newstack -float 2' to the input stack. Requires IMOD.
--preprocess	str	Any processor (see 'e2help.py processors -v 10' at the command line) to be applied to each image.
--lowpassfrac	float	Default=0.0 (not used). Fraction of Nyquist to lowpass at. The processor used is filter.lowpass.tanh
--highpasspix	int	Default=0 (not used). Number of Fourier pixels to apply highpass filter at. The processor used is filter.highpass.gauss.
--parallel	str	default=thread:1. Parallelism. See http://blake.bcm.edu/emanwiki/EMAN2/Parallel
--prenadminite	int	Default=0. Requires IMOD to be installed. Used to apply prenad filtering to a tiltseries. This is the --minite parameter in IMOD's preNAD program (minimum number of iterations).
--prenadmaxite	int	Default=0. Requires IMOD to be installed. Used to apply prenad filtering to a tiltseries. This is the --maxite parameter in IMOD's preNAD program (maximum number of iterations).
--prenadsigma	int	Default=0. Requires IMOD to be installed. Used to apply prenad filtering to a tiltseries. This is the --sigma parameter in IMOD's preNAD program (initial sigma for 'smoothing structure tensor').
--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