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== EMAN2 concepts == == EMAN2 Concepts and Conventions ==
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This page describes some important concepts in EMAN2  * [[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|Using EMAN2 in environments with NFS or other network-shared directories]]
 * [[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]]
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 * [:EMAN2/Symmetry:EMAN2 and the 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.

 * [[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

=== 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



{{attachment:single_image_iso_c.png}}

EMAN2 Concepts and 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

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.

Information on specific files used in 2-D reference-free class-averaging

You may also wish to look at: 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 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 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

single_image_iso_c.png

EMAN2/Concepts (last edited 2024-02-03 17:16:45 by SteveLudtke)