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--- eman2:programs:e2simmx [2025/07/06 16:05] – created steveludtke
+++ eman2:programs:e2simmx [2025/07/06 16:24] (current) – created steveludtke
@@ Line 1: / Line 1: @@
-| [[#args|Command line arguments]] |  [[#checkfunc|Check functionality]] | [[EMAN2:e2simmx2stagefaq|e2simmx2stage FAQ]] |
+<code>
+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.
-===== e2simmx2stage =====
+positional arguments:
-||<35%><<TableOfContents>> ||
+  positionalargs
-This program computes a similarity matrix similar to e2simmx, but in this case, the matrix is sparse to make the computation faster. The populated regions will correspond to the best similarity values.
-<<Anchor(args)>>
-==== Command Line Arguments ====
-e2simmx2stage.py [options] <c input> <r input> <output> <ref simmx> <stg1 refs> <stg1 simmx>
-For command line options, see [[EMAN2:Programs/e2simmx|e2simmx.py]]
-<c input> <r input> <output> are the same as in e2simmx.py <ref simmx> - Similarity between the various reference images used to generate the stage 1 references and classification tree <stg1 refs> - References used for the coarse stage 1 similarity search <stg1 simmx> - Similarity matrix for all particles vs the stage 1 references
-Anticipated speedups for this prorgram vs. e2simmx.py when no stage1 shrinking is used:
-{{http://blake.bcm.edu/dl/EMAN2/speedup.jpg}}
+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
+</code>