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== EMAN2 Concepts and Conventions == = EMAN2 Concepts and Conventions =
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 * [[EMAN2/ProjectDatabase|Projects, e2desktop.py and the database]] === 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]]

=== Mathematical Conventions ===
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 * [[EMAN2/Symmetry|EMAN2 and the asymmetric unit]]
 * [[Eman2DataStorage|File Formats, Data storage conventions, and the internal database (what is BDB: ?)]]
 * [[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]]
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 * [[Eman2TransformInPython|Transformations in the context of projections, reconstructions, and in general]]
 * [[EMAN2/AlignersDescription|More information regarding the aligners]]
 * [[EMAN2/SimmxFiles|Similarity matrix image files (simmx_*)]]
 * [[EMAN2/ClassmxFiles|Classification matrix image files (classify_*)]]
 * [[EMAN2/ClsResultFiles|Class-Averaging Results matrix image files (cls_result_*)]]
 * [[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]]

=== 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

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

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EMAN2/Concepts (last edited 2024-02-03 17:16:45 by SteveLudtke)