|
Size: 2321
Comment:
|
Size: 2544
Comment:
|
| Deletions are marked like this. | Additions are marked like this. |
| Line 3: | Line 3: |
| === Box Size (Important) === * Particle [[EMAN2/BoxSize|box-size]] - Impacts quality and speed of reconstructions! |
|
| Line 4: | Line 7: |
| * [[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]] |
* Supported [[Eman2DataStorage|image file formats]] and usage * How EMAN2 stores data in [[Eman2HDF|HDF5 files]] * [[Eman2Metadata|Header information]] (key/value pairs) associated with a specific image * Information stored in [[Eman2InfoMetadata|JSON files]] in the ''info/'' folder and elsewhere * Setting local and global [[EMAN2/ApplicationPreferences|application preferences]] * [[Eman2OtherFiles|Other misc. files]] such as .box and .lst |
| Line 10: | Line 15: |
| * [[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]] * [[EMAN2/CtfModel|CTF model used in EMAN2]] |
* [[EMAN2/Symmetry|Symmetry]] in EMAN2, and generating projections in an asymmetric unit * [[EMAN2/AngStep|Angular sampling]], number of projection and resolution * 3D and 2D [[Eman2TransformInPython|Transformations]] (rotation, translation, etc.) * [[EMAN2/CtfModel|CTF]] model used in EMAN2 |
| Line 19: | Line 24: |
''Note: These pages are often out of date. For up to date details please run'' {{{e2help.py <object type> -v 2}}} |
EMAN2 Concepts and Conventions
Box Size (Important)
Particle box-size - Impacts quality and speed of reconstructions!
Data Storage
Supported image file formats and usage
How EMAN2 stores data in HDF5 files
Header information (key/value pairs) associated with a specific image
Information stored in JSON files in the info/ folder and elsewhere
Setting local and global application preferences
Other misc. files such as .box and .lst
Mathematical Conventions
Symmetry in EMAN2, and generating projections in an asymmetric unit
Angular sampling, number of projection and resolution
3D and 2D Transformations (rotation, translation, etc.)
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.
Note: These pages are often out of date. For up to date details please run e2help.py <object type> -v 2
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
