usage: prog [options]

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