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Describe EMAN2/Concepts here. = EMAN2 Concepts and Conventions =

=== Box Size (Important) ===
 * Particle [[EMAN2/BoxSize|box-size]] - Impacts quality and speed of reconstructions!

=== Data Storage ===
 * Supported [[Eman2DataStorage|image file formats]] and usage
 * How EMAN2 stores data in [[Eman2HDF|HDF5 files]]
 * [[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 [[Eman2TransformInPython|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''Note: These pages are often out of date.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 2019-07-19 15:35:37 by SteveLudtke)