Diff for "EMAN2/Programs/e2simmx2stage"

Differences between revisions 1 and 3 (spanning 2 versions)

| Command line arguments | Check functionality | e2simmx2stage FAQ |

e2simmx2stage

Contents

e2simmx2stage
1. Command Line Arguments

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.

Command Line Arguments

e2simmx2stage.py [options] <c input> <r input> <output> <ref simmx> <stg1 refs> <stg1 simmx>

For command line options, see 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:

-  ⇤ ← Revision 1 as of 2010-01-06 21:09:10 → 
  Size: 727
  Editor: SteveLudtke
  Comment:
+   ← Revision 3 as of 2010-01-06 21:13:50 → ⇥
  Size: 1060
  Editor: SteveLudtke
  Comment:
-Deletions are marked like this.
+Additions are marked like this.
 Line 4:
+||<35%><<TableOfContents>> ||
-Line 6:
+Line 7:
-||<35%><<TableOfContents>>||

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.    '''Fig. 1. Overview of data inputs and outputs in the EMAN2 refinement pipeline. Pink objects are data supplied by the user, blue objects are programs, and green objects are data output by EMAN2 programs.'''
+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.
-Line 19:
+Line 12:
+e2simmx2stage.py [options] <c input> <r input> <output> <ref simmx> <stg1 refs> <stg1 simmx>
-Line 20:
+Line 15:
+<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:

{{attachment:speedup.jpg}}