EMAN Wiki

usage: prog [options] <c input> <r input> <output>
	Computes a similarity matrix between c-input (col - projections) and r-input (row - particles) stacks of 2-D images. Images may
	optionally be aligned before comparison. Output is a matrix stored as an image with similarity value
	pairs. When used for classification, c input is the references and r input are the particles. More information on
	the output file can be found in the Wiki.

positional arguments:
  positionalargs

options:
  -h, --help            show this help message and exit
  --version             show program's version number and exit
  --help-to-html        print this help message in html format
  --align ALIGN         The name of an 'aligner' to use prior to comparing the images
  --aligncmp ALIGNCMP   Name of the aligner along with its construction arguments
  --ralign RALIGN       The name and parameters of the second stage aligner which refines the results of the first alignment
  --raligncmp RALIGNCMP
                        The name and parameters of the comparitor used by the second stage aligner. Default is dot.
  --cmp CMP             The name of a 'cmp' to be used in comparing the aligned images
  --prefilt             Filter each reference (c) to match the power spectrum of each particle (r) before alignment and comparison
  --prectf              Apply CTF to each projection before comparison
  --mask MASK           File containing a single mask image to apply after alignment, but before similarity comparison
  --colmasks COLMASKS   File containing one mask for each column (projection) image, to be used when refining row (particle) image
                        alignments.
  --range RANGE         Range of images to process (c0,r0,c1,r1) c0,r0 inclusive c1,r1 exclusive
  --saveali             Save alignment values, output is 5, c x r images instead of 1. Images are (score,dx,dy,da,flip).
  --verbose n, -v n     verbose level [0-9], higher number means higher level of verboseness
  --init                Initialize the output matrix file before performing 'range' calculations
  --fillzero            Checks the existing output file, and fills only matrix elements which are exactly zero.
  --exclude EXCLUDE     The named file should contain a set of integers, each representing an image from the input file to exclude. Matrix
                        elements will still be created, but will be zeroed.
  --shrink SHRINK       Optionally shrink the input particles by an integer amount prior to computing similarity scores. This will speed
                        the process up.
  --nofilecheck         Turns file checking off in the check functionality - used by e2refine.py.
  --check, -c           Performs a command line argument check only.
  --ppid PPID           Set the PID of the parent process, used for cross platform PPID
  --parallel PARALLEL   Parallelism string