e2tiltvalidate

usage: prog [options]
	Tiltvalidation using Richard Henderson's technique. To use a stack of untilted and tiltimages whose set relationship is one-to-one is required along with a
	volume to validate. This can be generated using e2RCTboxer.py. After running this program two bits of data are products. A contour plot similar to Figure 5 in the Henderson paper(see below), and a list of
	titlangles and tiltaxes between particle paris, which can be used to makes plot similar to Figure 6 in Hendersons paper. The contour plot is stored as contour.hdf and the tiltpairs data is
	stored as bdb:perparticletilts.
	For more information see:
	Optimal determination of particle orientation, absolute hand, and contrast loss in 
	single-particle electron cryomicroscopy.
	Rosenthal PB, Henderson R.
	J Mol Biol. 2003 Oct 31;333(4):721-45

Option	Type	Description
--version	None	show program's version number and exit
--untiltdata	str	Stack of untilted images
--tiltdata	str	Stack of tilted images
--volume	str	3D volume to validate
--maxtiltangle	float	Maximum tiltangle permitted when finding tilt distances
--quaternion	None	Use Quaterions for tilt distance computation
--sym	str	The recon symmetry
--docontourplot	None	Compute a contour plot
--tiltrange	int	The angular tiltrange to search
--align	str	The name of a aligner to be used in comparing the aligned images
--cmp	str	The name of a 'cmp' to be used in comparing the aligned images
--delta	float	The angular step size for alingment
--shrink	int	Optionally shrink the input particles by an integer amount prior to computing similarity scores. For speed purposes. Defulat = 0, no shrinking
--simcmp	str	The name of a 'cmp' to be used in comparing the aligned images (default=ccc)
--simalign	str	The name of an 'aligner' to use prior to comparing the images (default=rotate_translate)
--simaligncmp	str	Name of the aligner along with its construction arguments (default=ccc)
--simralign	str	The name and parameters of the second stage aligner which refines the results of the first alignment
--simraligncmp	str	The name and parameters of the comparitor used by the second stage aligner. (default=dot).
--parallel	str	Parallelism string
--verbose	int	verbose level [0-9], higher number means higher level of verboseness
--path	str	The folder the results are placed
--radcut	float	For use in the GUI, truncate the polar plot after R. -1 = no truncation
--gui	None	Start the GUI for viewing the tiltvalidate plots
--planethres	float	Maximum out of plane threshold for the tiltaxis. 0 = perfectly in plane, 1 = normal to plane
--datalabelscolor	str	Set the color of the data labels. Any vaild matplotlib color is ok
--datalabels	None	Add data labels to the plot
--colorzaxis	None	Color scatter dots by Z axis
--eulerfile	str	Euler angles file, to create tiltdistance from pre-aligned particles. Format is: imgnum, name, az, alt, phi
--ppid	int	Set the PID of the parent process, used for cross platform PPID

For more information go to emanwiki/EMAN2/Programs/e2tiltvalidate.