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| == EMAN2 Concepts and Conventions == | = EMAN2 Concepts and Conventions = |
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| === Data Storage === * [[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]] * [[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]] === Mathematical Conventions === |
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| * [[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]] |
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| * [[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]] |
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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
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
