e2tomo_tiltstacker

usage: e2tomo_tiltstacker.py <imgs> <options> . 
	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. 
	
	The program stacks individual .dm3, .tiff, .mrc, or .hdf images into an .mrc (or .st) stack,
	by supplying a common string to all the images to stack.
	
	For example:
	e2tomo_tiltstacker.py --input=my_imgs --anglesindxinfilename=6

	It also generates a .rawtlt file with tilt angle values if --lowerend, --upperend and --tiltstep are provided.

Option	Type	Description
--version	None	show program's version number and exit
--anglesindxinfilename	int	Default=None. The filename of the images will be split at any occurence of the following delimiters: '_', '-', '+', '[' , ']' , ',' , ' ' (the two last ones are a comma and a blank space). Provide the index (position) of the angle in the split filename. For example, if the filename of an image is "my_specimen-oct-10-2015_-50_deg-from_k2 camera.mrc", it will be split into ['my','specimen','oct','10','2015','','50','deg','from','k2','camera','mrc']. The angle '-50', is at position 6 (starting from 0). Therefore, you would provide --anglesindxinfilename=6, assuming all images to be stacked/processed are similarly named. No worries about the minus sign disappearing. The program will look at whether there's a minus sign immediately preceeding the position where the angle info is.
--apix	float	True apix of images to be written on final stack.
--exclude_extremes	None	Default=False. Will exclude images with a mean value 3 standard deviations away from the "mean of means" of all images.
--highesttilt	float	Highest tilt angle. If not supplied, it will be assumed to be 1* --tiltrange.
--input	str	String common all files to process. For example, to process all .mrc files in a directory, you would run e2tomo_tiltstacker.py --input=.mrc <parameters>.
--lowesttilt	float	Lowest tilt angle. If not supplied, it will be assumed to be -1* --tiltrange.
--path	str	Directory to store results in. The default is a numbered series of directories containing the prefix 'sptstacker'; for example, sptstacker_02 will be the directory by default if 'sptstacker_01' already exists.
--ppid	int	Set the PID of the parent process, used for cross platform PPID
--precheckfiles	None	"Make sure that only valid images found by --input=* are processed -if unreadable or bad images are fed to the program, it might crash.
--stackregardless	None	"Stack images found with the common string provided through --stem2stack, even if the number of images does not match the predicted number of tilt angles.
--tag	str	"String to append to the beginning of the tiltseries output filename. The default is filename is 'stack.st'; if tag=xxx, the output will be 'xxx_stack.st'
--tiltrange	float	If provided, this will make --lowesttilt=-1*tiltrange and --highesttilt=tiltrange. If the range is asymmetric, supply --lowesttilt and --highesttilt directly.
--tiltstep	float	Step between tilts. Required if using --stem2stack.
--verbose, -v	int	verbose level [0-9], higher number means higher level of verboseness.