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| * [[EMAN2/ProjectDatabase|Projects, e2desktop.py and the database]] | |
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| * [[EMAN2/Symmetry|EMAN2 and the asymmetric unit]] | * [[Eman2TransformInPython|3D and 2D Transformations (rotation, translation, etc.)]] * [[EMAN2/Symmetry|Symmetry in EMAN2, and generating projections in an asymmetric unit]] |
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| * [[Eman2NFS|Practical Advice on EMAN2 in environments with network-shared directories (like NFS)]] | * [[Eman2NFS|Using EMAN2 in environments with NFS or other network-shared directories]] |
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| * [[Eman2TransformInPython|Transformations in the context of projections, reconstructions, and in general]] * [[EMAN2/AlignersDescription|More information regarding the aligners]] |
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| === Modular classes 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. |
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| === 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
Symmetry in EMAN2, and generating projections in an asymmetric unit
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
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.
Similarity matrix image files (simmx_xx, simmx_stg1_xx, proj_simmx_xx)
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: 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
