e2stacksort

usage: prog [options] <input_stack> <output_stack> <input #2> <output #2>

	This program will sort a stack of images based on some similarity criterion. Note that byptcl, iterative and reverse are mutually exclusive.

	It can handle file sequences rather than a single stack file as well, in a limited form. If you have files named var3d_000.mrc, var3d_001.mrc, ...
	you can specify input (and output) files as (for example) var3d_03d.mrc. The '3' indicates the number of digits in the value, the '0'
	means there should be leading zeroes in the name, and the 'd' means it is a decimal number.

	If specified input#2 and output#2 will be sorted in the same order as input_stack. Input #2 must have the same number of images as input_stack.

	Note that there is no low-memory option for this command, and all images in the sequence are read in, so make sure you have enough RAM.

Option	Type	Description
--version	None	show program's version number and exit
--simcmp	str	The name of a 'cmp' to be used in comparing the after optional alignment (default=optvariance:keepzero=1:matchfilt=1)
--simalign	str	The name of an 'aligner' to use prior to comparing the images (default=no alignment)
--simmask	str	A file containing a mask to apply prior to comparisons, to focus the sort on one particular region
--reverse	None	Sort in order of least mutual similarity
--byptcl	None	Sort in order of number of particles represented in each class-average. No alignment, shrinking, etc. is performed
--bykurtosis	None	Sort by image Kurtosis. No alignment, shrinking, etc. is performed
--byheader	str	Uses the named header parameter to sort the images
--iterative	None	Iterative approach for achieving a good 'consensus alignment' among the set of particles
--invar	None	Sorting and alignment using invariants.
--useali	None	Save aligned particles to the output file, note that if used with shrink= this will store the reduced aligned particles
--seqali	None	Align each particle to the previous particle before saving with rotate_translate_tree. No flip in alignment. Aligns stack #2 instead if provided.
--seqalicen	None	Align each particle to the previous particle before saving, with a postalignment recentering. No flip in alignment. Aligns stack #2 instead if provided.
--center	None	After alignment, particles are centered via center of mass before comparison
--nsort	int	Number of output particles to generate (mainly for reverse mode)
--ninput	int	Number of input particles to read (first n in the file)
--shrink	int	Reduce the particles for comparisons
--ppid	int	Set the PID of the parent process, used for cross platform PPID
--verbose, -v	int	verbose level [0-9], higher number means higher level of verboseness