mvpa2.atlases.base¶
Base classes for Anatomy atlases support
TODOs:¶
- major optimization. Now code is sloppy and slow – plenty of checks etc
Module Organization¶
mvpa2.atlases.base module contains support for various atlases
| group Base: | BaseAtlas XMLBasedAtlas Label Level LabelsLevel |
|---|---|
| group Talairach: | |
| PyMVPAAtlas LabelsAtlas ReferencesAtlas | |
| group Exceptions: | |
| XMLAtlasException | |
Functions
| check_range(coord, range) | Check if coordinates are within range (0,0,0) - (range) |
| enhanced_doc_string(item, *args, **kwargs) | Generate enhanced doc strings for various items. |
| norm(x[, ord, axis]) | Matrix or vector norm. |
| reuse_absolute_path(file1, file2[, force]) | Use path to file1 as the path to file2 is no absolute |
Classes
| BaseAtlas | Base class for the atlases. |
| Label(text[, abbr, coord, count, index]) | Represents a label. |
| LabelsAtlas(*args, **kwargs) | Atlas which provides labels for the given coordinate |
| LabelsLevel(description[, index, labels]) | Level of labels. |
| Level(description) | Represents a level. |
| Linear((transf=array([[ 1., 0., 0., ...) | Simple linear transformation defined by a matrix |
| PyMVPAAtlas(*args, **kwargs) | Base class for PyMVPA atlases, such as LabelsAtlas and ReferenceAtlas |
| ReferencesAtlas([distance, reference_level]) | Atlas which provides references to the other atlases. |
| ReferencesLevel(description[, indexes]) | Level which carries reference points |
| SpaceTransformation([voxelSize, origin, ...]) | To perform transformation from Voxel into Real Space. |
| XMLBasedAtlas([filename, resolution, ...]) | Base class for atlases using XML as the definition backend |
Exceptions
| BaseAtlas | Base class for the atlases. |
| Label(text[, abbr, coord, count, index]) | Represents a label. |
| LabelsAtlas(*args, **kwargs) | Atlas which provides labels for the given coordinate |
| LabelsLevel(description[, index, labels]) | Level of labels. |
| Level(description) | Represents a level. |
| Linear((transf=array([[ 1., 0., 0., ...) | Simple linear transformation defined by a matrix |
| PyMVPAAtlas(*args, **kwargs) | Base class for PyMVPA atlases, such as LabelsAtlas and ReferenceAtlas |
| ReferencesAtlas([distance, reference_level]) | Atlas which provides references to the other atlases. |
| ReferencesLevel(description[, indexes]) | Level which carries reference points |
| SpaceTransformation([voxelSize, origin, ...]) | To perform transformation from Voxel into Real Space. |
| XMLBasedAtlas([filename, resolution, ...]) | Base class for atlases using XML as the definition backend |
