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Revision 29 as of 2011-08-26 20:31:07

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EMAN2 Concepts and Conventions

Modular functions in EMAN2

Many aspects of EMAN2 are modular, meaning new functions can be easily added for a variety of tasks. These categories are used in the GUI and from the command-line, and are not just useful for programmers. For example, the '--process' option in and uses 'processors' as defined below.

  • Processors - Filters, masks and other basic image processing operations

  • Comparators (cmp) - Similarity metrics (cmp) for comparing two images/volumes

  • Aligners - Algorithms for aligning one image/volume to another

  • Averagers - Methods for averaging many images/volumes together

  • Projectors - Generate 2-D projections of 3-D volumes (or 1-D projections of 2-D images)

  • Reconstructors - Generate 3-D volumetric reconstructions from sets of 2-D images and orientation paramters

  • Analyzers - Perform various analyses on sets of images/volumes

  • Symmetries - Permissible symmetries to use in EMAN2

  • Orientation Generators (orientgen) - Methods for generating sets of orientations filling an asymmetric unit

Information on specific files used in 3-D single particle refinement

This section documents the contents of all of the files produced by running in one of the refine_xx directories.

Information on specific files used in 2-D reference-free class-averaging

You may also wish to look at /EMAN2/programs/e2refine2d

  • input_fp
  • input_fp_basis
  • input_fp_basis_proj
  • classmx_00
  • classes_init
  • allrefs_XX
  • basis_XX
  • aliref_XX
  • simmx_XX
  • input_XX_proj
  • classmx_XX
  • classes_XX