e2ddd_external

usage: prog [options] <ddd_movie_stacks>
	This program is a wrapper for various DDD alignment routines including:
		alignframes (IMOD)
		motioncor2 (UCSF)

	Note, this is a simple script that mainly uses default alignment parameters for each
	external program. It is mainly intended to make some external ddd alignment routines
	available from the EMAN2 GUI for streamlined processing. In order for this program to
	run, the alignment routine you wish to use must be installed and accessible via the PATH 
	environment variable. To customize alignment, you will need to run these programs 
	from the command line independently and import the aligned averages/tiltseries into 
	your EMAN2 project.

Option	Type	Description
--version	None	show program's version number and exit
--program	str	Use this external program to align frames. Choose between imod_alignframes and ucsf_motioncor2. Note, programs must be accessible from your PATH environment variable.
--device	str	When possible, use this device to process movie frames. Default is gpu.
--mdoc	str	When an mdoc or idoc is provided, the raw files are automatically found within the input directory
--apix	float	Specify the Apix of the movies to be processed.
--dark	str	Use this dark reference.
--gain	str	Use this gain reference.
--defect_file	str	Specify the camera defects file.
--mc2_rotgain	int	Rotates the gain 90 degress counter clockwise X times. Rotation is applied before flipping.
--mc2_flipgain	int	A value of 1 flips gain image vertically, 2 flips gain image horizontally. Default is 0.
--imod_rotflipgain	int	Rotates the gain 90 degress counter clockwise X times. If value is greater than 3, gain image is flipped about the y axis before rotation.
--device_num	str	When possible, use this device to process movie frames. Default is GPU.
--binby	int	The degree of binning for final image. Default is 1, i.e. no binning. Note that this option takes only integer values.
--groupby	int	Before alignment, sum raw frames in groups of X to increase signal to noise ratio.
--first	int	The index of the leading frame to include in alignment.
--last	int	The index of the last frame to include in alignment.
--mc2_patchX	int	Use this many patches along X with MotionCor2. Default is 1, i.e. whole-frame alignment.
--mc2_patchY	int	Use this many patches along Y with MotionCor2. Default is 1, i.e. whole-frame alignment.
--tomo	None	If checked, aligned frames will be placed in a tiltseries located in the 'tiltseries' directory. Otherwise, aligned sums will populate the 'micrographs_mrc' directory.
--tiltseries_name	str	Specify the name of the output tiltseries. A .mrc extension will be appended to the filename provided.
--verbose, -v	int	verbose level [0-9], higner number means higher level of verboseness
--ppid	int	Set the PID of the parent process, used for cross platform PPID