e2ddd_movie

usage: prog [options] <ddd_movie_stack>

	This program will do various processing operations on "movies" recorded on direct detection cameras. It
	is primarily used to do whole-frame alignment of movies using all-vs-all CCFs with a global optimization
	strategy. Several outputs including different frame subsets are produced, as well as a text file with the
	translation vector map.

	See e2ddd_particles for per-particle alignment.

	Note: We have found the following to work on DE64 images:
	e2ddd_movie.py <movies> --de64 --dark <dark_frames> --gain <gain_frames> --gain_darkcorrected --reverse_gain --invert_gain

	Note: For multi-image files in MRC format, use the .mrcs extension. Do not use .mrc, as it will handle input stack as a 3D volume.

Option	Type	Description
--version	None	show program's version number and exit
--tiltseries_name	None	Specify a name for the tilt series to be generated from the input movies.
--tomo	None	Process input movies as tilts from a tomogram.
--dark	str	Perform dark image correction using the specified image file
--gain	str	Perform gain image correction using the specified image file
--ref_label	str	Optional: Specify a label for the averaged dark and gain references when using multiple, individual frames.\nA labeled will be written as movierefs/dark_<label>.hdf and movierefs/gain_<label>.hdf.\nNote: This option is ignored when using a single reference image/stack.
--rotate_dark	str	Rotate dark reference by 0, 90, 180, or 270 degrees. Default is 0. Transformation order is rotate then reverse.
--reverse_dark	None	Flip dark reference along y axis. Default is False. Transformation order is rotate then reverse.
--k2	None	Perform gain image correction on gain images from a Gatan K2. Note, these are the reciprocal of typical DDD gain images.
--de64	None	Perform gain image correction on DE64 data. Note, these should not be normalized.
--rotate_gain	str	Rotate gain reference by 0, 90, 180, or 270 degrees. Default is 0. Transformation order is rotate then reverse.
--reverse_gain	None	Flip gain reference along y axis (about x axis). Default is False. Transformation order is rotate then reverse.
--gain_darkcorrected	None	Do not dark correct gain image. False by default.
--invert_gain	None	Use reciprocal of input gain image
--bad_columns	str	Comma separated list of camera defect columns
--bad_rows	str	Comma separated list of camera defect rows
--align_frames	None	Perform whole-frame alignment of the input stacks
--realign	None	Align frames using previous alignment parameters.
--round	None	If float (default), apply subpixel frame shifts. If integer, use integer shifts.
--noali	None	Average of non-aligned frames.
--allali	None	Average of all aligned frames.
--rangeali	str	Average frames 'n1-n2'
--goodali	None	Average of good aligned frames.
--bestali	None	Average of best aligned frames.
--groupby	int	Combine every N frames using a moving window approach.
--optbox	int	Box size to use during alignment optimization. Default is 512.
--optstep	int	Step size to use during alignment optimization. Default is 448.
--optalpha	float	Penalization to apply during robust regression. Default is 0.1. If 0.0, unpenalized least squares will be performed (i.e., no trajectory smoothing).
--optccf	str	Use this approach to determine relative frame translations.\nNote: 'robust' utilizes a bimodal Gaussian to robustly determine CCF peaks between pairs of frames in the presence of a fixed background.
--step	str	Specify <first>,<step>,[last]. Processes only a subset of the input data. ie- 0,2 would process all even particles. Same step used for all input files. [last] is exclusive. Default= 0,1
--frames	None	Write corrected stack of frames.
--ext	str	Save frames with this extension. Default is 'hdf'.
--threads	int	Number of threads to run in parallel. The default is 4, and our alignment routine requires 2+ threads. Using more threads will result in faster processing times.
--verbose, -v	int	verbose level [0-9], higher number means higher level of verboseness
--debug	None	run with debugging output
--ppid	int	Set the PID of the parent process, used for cross platform PPID
--fixbadpixels	None	Tries to identify bad pixels in the dark/gain reference, and fills images in with sane values instead
--suffix	str	Specify a unique suffix for output frames. Default is 'proc'. Note that the output of --frames will be overwritten if identical suffix is already present.
--phaseplate	None	Use this flag when aligning phase plate frames.