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| == EMAN2 Concepts and Conventions == | = EMAN2 Concepts and Conventions = |
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| This page describes some important concepts in EMAN2 | === Data Storage === * [[Eman2DataStorage|File Formats, Data storage conventions]] * [[Eman2NFS|Using EMAN2 in environments with NFS or other network-shared directories]] * [[Eman2HDF|How EMAN2 stores data in HDF5 files]] * [[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]] * [[Eman2InfoMetadata|Parameters/Metadata associated with projects stored in the ''info'' folder]] |
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| * [:EMAN2/Symmetry:EMAN2 and the asymmetric unit] * [:Eman2DataStorage:Data storage conventions, and the internal database (what is BDB: ?)] * [:EMAN2/CtfModel:CTF model used in EMAN2] * [: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] |
=== 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
Using EMAN2 in environments with NFS or other network-shared directories
Parameters/Metadata for applications, not associated with a specific image, stored in bdb:project
Parameters/Metadata associated with projects stored in the ''info'' folder
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.
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
