Wiki Page Content

Similarity Matrix Image Files

Generated by: e2simmx.py or e2simmx2stage.py

These files, normally named bdb:refine_XX#simmx_YY are produced during e2refine.py runs. One such file should appear in each iteration. If the --twostage option is being used, then two additional files simmx_stg1_YY and proj_simmx_YY will also be produced with the same general format, though some of these files will not be completely filled in (not exhaustive).

Similarity matrices are normally produced by the e2simmx.py program. They contain the results of exhaustive comparisons between two sets of images. In this format a standard image object is used to store the contents of what would normally be a matrix. The x-axis of the image represents the first (reference) image set and the y-axis represents the second image set. In the context of single particle reconstruction, the Y axis of the matrix represents the different particles to be classified and the X-axis represents the different reference projection images. Each pixel in the matrix contains the similarity value produced when comparing two images. For example, the similarity of particle 0 (the first one) compared to reference projection 0 would be found in the pixel at (0,0). The similarity of particle 9234 with projection 23 would be found at (23,9234).

These files conventionally contain 5 images. The first image contains the actual similarity values. The other images contain supplementary information about the alignment performed before comparison. In some cases, if no alignment is required before the images are compared, the other images may be absent:

For 2-D files

  • Image 0 - similarity matrix
  • Image 1 - dx alignment value
  • Image 2 - dy alignment value
  • Image 3 - dalpha (in-plane rotation) alignment value
  • Image 4 - 0 or 1 indicating whether the image must be mirrored for alignment
  • Image 5 - scale factor (1.0 is no scaling), NEW 1/2011

For 3-D files

  • Image 0 - similarity matrix
  • Image 1 - dx, translation to bring particle in alignment with this reference
  • Image 2 - dy, same
  • Image 3 - dz, same
  • Image 4 - az, rotation in EMAN convention
  • Image 5 - alt, same
  • Image 6 - phi, same
  • Image 7 - scale factor (1.0 no scaling)

EMAN2/SimmxFiles (last edited 2012-01-27 21:02:59 by SteveLudtke)