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== EMAN2 Concepts and Conventions == = EMAN2 Concepts and Conventions =
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 * [[EMAN2/ProjectDatabase|Projects, e2desktop.py and the database]]
 * [[EMAN2/BoxSize|Particle box-size and refinement speed, what size to use]]
 * [[Eman2TransformInPython|3D and 2D Transformations (rotation, translation, etc.)]]
 * [[EMAN2/Symmetry|Symmetry in EMAN2, and generating projections in an asymmetric unit]]
 * [[Eman2DataStorage|File Formats, Data storage conventions, and the internal database (what is BDB: ?)]]
 * [[Eman2NFS|Practical Advice on EMAN2 in environments with network-shared directories (like NFS)]]
 * [[EMAN2/CtfModel|CTF model used in EMAN2]]
 * [[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]]
=== Box Size (Important) ===
 * Particle [[EMAN2/BoxSize|box-size]] - Impacts quality and speed of reconstructions!
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=== Modular classes in EMAN2 === === 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''Note: These pages are often out of date.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]]
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=== 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)]]

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 2018-10-08 13:00:17 by SteveLudtke)