Wiki Page Content

Differences between revisions 33 and 34
Revision 33 as of 2011-10-10 15:45:38
Size: 4164
Editor: SteveLudtke
Comment:
Revision 34 as of 2011-10-12 14:58:00
Size: 2321
Editor: SteveLudtke
Comment:
Deletions are marked like this. Additions are marked like this.
Line 1: Line 1:
== EMAN2 Concepts and Conventions == = EMAN2 Concepts and Conventions =
Line 3: Line 3:
=== Data Storage ===
 * [[Eman2DataStorage|File Formats, Data storage conventions, and the internal database (what is BDB: ?)]]
 * [[Eman2NFS|Using EMAN2 in environments with NFS or other network-shared directories]]
 * [[Eman2Metadata|Parameters/Metadata appearing in EMData attributes (and stored on disk with the image), accessed with get_attr and set_attr]]
 * [[Eman2AppMetadata|Parameters/Metadata for applications, not associated with a specific image, stored in bdb:project]]

=== Mathematical Conventions ===
Line 6: Line 13:
 * [[Eman2DataStorage|File Formats, Data storage conventions, and the internal database (what is BDB: ?)]]
 * [[Eman2NFS|Using EMAN2 in environments with NFS or other network-shared directories]]
Line 9: Line 14:
 * [[Eman2Metadata|Parameters/Metadata appearing in EMData attributes (and stored on disk with the image), accessed with get_attr and set_attr]]
 * [[Eman2AppMetadata|Parameters/Metadata for applications, not associated with a specific image, stored in bdb:project]]
Line 28: Line 31:
=== Information on specific files used in 3-D single particle refinement ===
This section documents the contents of all of the files produced by running e2refine.py in one of the refine_xx directories.
 * [[EMAN2/ProjectionFiles|Map projection files (projections_xx, proj_stg1_xx)]]
 * [[EMAN2/SimmxFiles|Similarity matrix image files (simmx_xx, simmx_stg1_xx, proj_simmx_xx)]]
 * [[EMAN2/ClassmxFiles|Classification matrix image files (classify_xx)]]
 * [[EMAN2/ClsResultFiles|Class-Averaging Results matrix image files (cls_result_xx)]]
 * [[EMAN2/ClassesFiles|Class-averages (classes_xx)]]
 * [[EMAN2/ThreedFiles|3-D reconstructions (threed_xx, threed_filt_xx, threed_mask_xx)]]

=== Information on specific files used in 2-D reference-free class-averaging ===
You may also wish to look at: [[EMAN2/Programs/e2refine2d|e2refine2d]]

 * '''input_fp''' - rotational/translational invariants for each particle
 * '''input_fp_basis''' - MSA basis vectors (images) from input_fp
 * '''input_fp_basis_proj''' - MSA subspace projections of the input_fp invariants
 * '''classmx_00''' - Initial classification of particles, same format as [[EMAN2/ClassmxFiles|classmx]] above
 * '''classes_init''' - Initial set of class-averages from invariant method (not very good usually)
 * '''allrefs_XX''' - All of the references (sorted) to be used for the current iteration
 * '''basis_XX''' - MSA basis from allrefs_xx
 * '''aliref_XX''' - Subset of allrefs used for alignment of raw particles
 * '''simmx_XX''' - Similarity matrix in same format as [[EMAN2/SimmxFiles|simmx]] above
 * '''input_XX_proj''' - Aligned particles projected into '''basis_XX''' subspace
 * '''classmx_XX''' - Classification matrix for the current iteration (as above)
 * '''classes_XX''' - Class averages at the end of the iteration. The highest numbered classes_XX file is the final output of the program

EMAN2 Concepts and Conventions

Data Storage

Mathematical 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 e2proc2d.py and e2proc3d.py uses 'processors' as defined below.

  • Overview of how to use modular functions

  • 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

single_image_iso_c.png

EMAN2/Concepts (last edited 2018-10-08 13:00:17 by SteveLudtke)