Differences between revisions 7 and 40 (spanning 33 versions)
Revision 7 as of 2008-09-18 16:58:05
Size: 334
Comment:
Revision 40 as of 2013-08-11 18:12:07
Size: 2211
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:
This page describes some important concepts in EMAN2 === Data Storage ===
 * [[Eman2DataStorage|Supported image file formats and usage]]
 * [[Eman2HDF|How EMAN2 stores data in HDF5 files]]
 * [[Eman2Metadata|Header information stored within image files]]
 * [[Eman2InfoMetadata|Information stored in JSON files in the ''info/'' folder and elsewhere]]
Line 5: Line 9:
 * [:EMAN2/Symmetry:EMAN2 and the asymmetric unit]
 * [:EMAN2/TransformConventions:Transformations in the context of Projections, Reconstructions, and in General]
 * [:EMAN2/AlignersDescription:More information regarding the aligners]
=== Mathematical Conventions ===
 * [[EMAN2/BoxSize|Particle box-size and refinement speed, what size to use]]
 * [[EMAN2/AngStep|Angular sampling, number of projection and resolution]]
 * [[Eman2TransformInPython|3D and 2D Transformations (rotation, translation, etc.)]]
 * [[EMAN2/Symmetry|Symmetry in EMAN2, and generating projections in an asymmetric unit]]
 * [[EMAN2/CtfModel|CTF model used in EMAN2]]

=== 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.

 * [[EMAN2/Modular/Overview|Overview of how to use modular functions]]
 * [[EMAN2/Modular/Processors|Processors]] - Filters, masks and other basic image processing operations
 * [[EMAN2/Modular/Cmps|Comparators]] (cmp) - Similarity metrics (cmp) for comparing two images/volumes
 * [[EMAN2/Modular/Aligners|Aligners]] - Algorithms for aligning one image/volume to another
 * [[EMAN2/Modular/Averagers|Averagers]] - Methods for averaging many images/volumes together
 * [[EMAN2/Modular/Projectors|Projectors]] - Generate 2-D projections of 3-D volumes (or 1-D projections of 2-D images)
 * [[EMAN2/Modular/Reconstructors|Reconstructors]] - Generate 3-D volumetric reconstructions from sets of 2-D images and orientation paramters
 * [[EMAN2/Modular/Analyzers|Analyzers]] - Perform various analyses on sets of images/volumes
 * [[EMAN2/Modular/Symmetries|Symmetries]] - Permissible symmetries to use in EMAN2
 * [[EMAN2/Modular/OrientGens|Orientation Generators]] (orientgen) - Methods for generating sets of orientations filling an asymmetric unit



{{attachment:single_image_iso_c.png}}

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 2024-02-03 17:16:45 by SteveLudtke)