usage: prog [options] <c input> <r input> <output> <ref simmx> <stg1 refs> <stg1 simmx> Computes a similarity matrix between c-input (col - projections) and r-input (row - particles) stacks of 2-D images. Unlike e2simmx.py, this will perform classification in two stages, first a coarse classification, then a local classification. Particle association for coarse classification, however, is not assigned based on Euler angle, but rather on mutual similarity in a subsampled reference-image self-classification. Output is the same as e2simmx, with coarsely sampled results inserted in unsampled local regions. When used for classification, c input is the references and r input are the particles.
| Option | Type | Description |
|---|---|---|
| --version | None | show program's version number and exit |
| --align | str | The name of an 'aligner' to use prior to comparing the images |
| --aligncmp | str | Name of the aligner along with its construction arguments |
| --ralign | str | The name and parameters of the second stage aligner which refines the results of the first alignment |
| --raligncmp | str | The name and parameters of the comparitor used by the second stage aligner. Default is dot. |
| --cmp | str | The name of a 'cmp' to be used in comparing the aligned images |
| --mask | str | File containing a single mask image to apply before similarity comparison |
| --colmasks | str | File containing one mask for each column (projection) image, to be used when refining row (particle) image alignments. |
| --saveali | None | Save alignment values, output is c x r x 4 instead of c x r x 1 |
| --prefilt | None | Filter each reference (c) to match the power spectrum of each particle (r) before alignment and comparison |
| --prectf | None | Apply CTF to each projection before comparison |
| --verbose, -v | int | verbose level [0-9], higher number means higher level of verboseness |
| --exclude | str | 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 | float | Optionally shrink the input particles by an integer amount prior to computing similarity scores. This will speed the process up but may change classifications. |
| --shrinks1 | float | Shrinking performed for first stage classification, default=2 |
| --finalstage | None | Assume that existing preliminary particle classifications are correct, and only recompute final local orientations |
| --ppid | int | Set the PID of the parent process, used for cross platform PPID |
| --parallel | str | Parallelism string |
For more information go to emanwiki/EMAN2/Programs/e2simmx2stage.