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== EMAN2 Concepts and Conventions == = EMAN2 Concepts and Conventions =
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This page describes some important concepts in EMAN2 === Box Size (Important) ===
 * Particle [[EMAN2/BoxSize|box-size]] - Impacts quality and speed of reconstructions!
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 * [: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]
 * [: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]		 === Data Storage ===
 * Supported [[Eman2DataStorage|image file formats]] and usage
 * How EMAN2 stores data in [[EMAN2/Hdf5Format|HDF5 files]]
 * [[EMAN2/Eman2Metadata|Header information]] (key/value pairs) associated with a specific image
 * Information stored in [[Eman2InfoMetadata|JSON files]] in the ''info/'' folder and elsewhere
 * Setting local and global [[EMAN2/ApplicationPreferences|application preferences]]
 * [[Eman2OtherFiles|Other misc. files]] such as .box and .lst

=== Mathematical Conventions ===
 * [[EMAN2/Symmetry|Symmetry]] in EMAN2, and generating projections in an asymmetric unit
 * [[EMAN2/AngStep|Angular sampling]], number of projection and resolution
 * 3D and 2D [[EMAN2/TransformInPython|Transformations]] (rotation, translation, etc.)
 * [[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.

''Note: These pages are often out of date. For up to date details please run'' {{{e2help.py <object type> -v 2}}}

 * [[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

Box Size (Important)

  • Particle box-size - Impacts quality and speed of reconstructions!

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.

Note: These pages are often out of date. For up to date details please run e2help.py <object type> -v 2

  • 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)