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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]] * [[EMAN2/Symmetry|EMAN2 and the asymmetric unit]] |
=== Data Storage === |
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| * [[Eman2NFS|Practical Advice on EMAN2 in environments with network-shared directories (like NFS)]] * [[EMAN2/CtfModel|CTF model used in EMAN2]] * [[Eman2TransformInPython|Transformations in the context of projections, reconstructions, and in general]] * [[EMAN2/AlignersDescription|More information regarding the aligners]] |
* [[Eman2NFS|Using EMAN2 in environments with NFS or other network-shared directories]] * [[Eman2HDF|How EMAN2 stores data in HDF5 files]] |
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| * [[Eman2InfoMetadata|Parameters/Metadata associated with projects stored in the ''info'' folder]] | |
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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)]] |
=== 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 |
EMAN2 Concepts and Conventions
Data Storage
File Formats, Data storage conventions, and the internal database (what is BDB: ?)
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
