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| == EMAN2 Concepts and Conventions == | = EMAN2 Concepts and Conventions = |
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| * [[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|Using EMAN2 in environments with NFS or other network-shared directories]] * [[EMAN2/CtfModel|CTF model used in EMAN2]] * [[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 === * [[Eman2DataStorage|Supported '''image file formats''' and usage]] * [[Eman2HDF|How EMAN2 stores data in '''HDF5 files''']] * [[Eman2Metadata|'''Header information''' stored within image files]] * [[Eman2InfoMetadata|Information stored in '''JSON files''' in the ''info/'' folder and elsewhere]] === 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]] |
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| * [[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)]] === Information on specific files used in 2-D reference-free class-averaging === You may also wish to look at: [[EMAN2/Programs/e2refine2d|e2refine2d]] * '''input_fp''' - rotational/translational invariants for each particle * '''input_fp_basis''' - MSA basis vectors (images) from input_fp * '''input_fp_basis_proj''' - MSA subspace projections of the input_fp invariants * '''classmx_00''' - Initial classification of particles, same format as [[EMAN2/ClassmxFiles|classmx]] above * '''classes_init''' - Initial set of class-averages from invariant method (not very good usually) * '''allrefs_XX''' - All of the references (sorted) to be used for the current iteration * '''basis_XX''' - MSA basis from allrefs_xx * '''aliref_XX''' - Subset of allrefs used for alignment of raw particles * '''simmx_XX''' - Similarity matrix in same format as [[EMAN2/SimmxFiles|simmx]] above * '''input_XX_proj''' - Aligned particles projected into '''basis_XX''' subspace * '''classmx_XX''' - Classification matrix for the current iteration (as above) * '''classes_XX''' - Class averages at the end of the iteration. The highest numbered classes_XX file is the final output of the program |
EMAN2 Concepts and Conventions
Data Storage
Mathematical Conventions
Particle '''box-size''' and refinement speed, what size to use
3D and 2D '''Transformations''' (rotation, translation, etc.)
'''Symmetry''' in EMAN2, and generating projections in an asymmetric unit
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
