| Multivariate Pattern Analysis in Python

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This content refers to the previous stable release of PyMVPA. Please visit www.pymvpa.org for the most recent version of PyMVPA and its documentation.

# atlases.base

## Module: `atlases.base`

Inheritance diagram for `mvpa.atlases.base`:

Base classes for Anatomy atlases support

### TODOs:

> - major optimization. Now code is sloppy and slow – plenty of checks etc

### Module Organization

mvpa.atlases.base module contains support for various atlases

group Base: | BaseAtlas XMLBasedAtlas Label Level LabelsLevel
group Talairach:
| PyMVPAAtlas LabelsAtlas ReferencesAtlas
group Exceptions:
| XMLAtlasException

## Classes

### `BaseAtlas`

class `mvpa.atlases.base.``BaseAtlas`

  Bases: `object`

  Base class for the atlases.

  Create an atlas object based on the... XXX

### `Label`

class `mvpa.atlases.base.``Label`(text, abbr=None, coord=(None, None, None), count=0, index=0)

  Bases: `object`

  Represents a label. Just to bring all relevant information together

  Parameters:

  - text (basestring) – fullname of the label
  - abbr (basestring) – abbreviated name (optional)
  - coord (tuple of float) – coordinates (optional)
  - count (int) – count of those labels in the atlas (optional)

  `abbr`

    Returns abbreviated version if such is available

  `coord`
  `count`
  static `generateFromXML`(Elabel)
  `index`
  `text`

### `LabelsAtlas`

class `mvpa.atlases.base.``LabelsAtlas`(*args, **kwargs)

  Bases: `mvpa.atlases.base.PyMVPAAtlas`

  Atlas which provides labels for the given coordinate

  See also

  Please refer to the documentation of the base class for more information:

  `PyMVPAAtlas`

  Initialize instance of PyMVPAAtlas

  Parameters:

  - filename (string) – Filename for the xml definition of the atlas
  - resolution (None or float) – Some atlases link to multiple images at different resolutions. if None – best resolution is selected using 0th dimension resolution
  - image_file (None or str) – If None, overrides filename for the used imagefile, so it could load a custom (re-registered) atlas maps
  - query_voxel (bool) – By default [x,y,z] assumes coordinates in space, but if query_voxel is True, they are assumed to be voxel coordinates
  - coordT – Optional transformation to apply first
  - levels (None or slice or list of int) – What levels by default to operate on

  `labelVoxel`(c, levels=None)

    Return labels for the given voxel at specified levels specified by index

### `LabelsLevel`

class `mvpa.atlases.base.``LabelsLevel`(description, index=None, labels=[])

  Bases: `mvpa.atlases.base.Level`

  Level of labels.

  XXX extend

  `find`(target, unique=True)

    Return labels descr of which matches the string

    Parameters:

    - target (str or re._pattern_type) – Substring in abbreviation to be searched for, or compiled regular expression to be searched or matched if anchored.
    - unique (bool) – If True, raise exception if none or more than 1 was found. Return just a single item if found (not list).

  static `generateFromXML`(Elevel, levelIndex=[0])
  `index`
  `labels`

### `Level`

class `mvpa.atlases.base.``Level`(description)

  Bases: `object`

  Represents a level. Just to bring all relevant information together

  static `generateFromXML`(Elevel, levelType=None)

    Simple factory of levels

  `levelType`

### `PyMVPAAtlas`

class `mvpa.atlases.base.``PyMVPAAtlas`(*args, **kwargs)

  Bases: `mvpa.atlases.base.XMLBasedAtlas`

  Base class for PyMVPA atlases, such as LabelsAtlas and ReferenceAtlas

  See also

  Please refer to the documentation of the base class for more information:

  `XMLBasedAtlas`

  Initialize instance of PyMVPAAtlas

  Parameters:

  - filename (string) – Filename for the xml definition of the atlas
  - resolution (None or float) – Some atlases link to multiple images at different resolutions. if None – best resolution is selected using 0th dimension resolution
  - image_file (None or str) – If None, overrides filename for the used imagefile, so it could load a custom (re-registered) atlas maps
  - query_voxel (bool) – By default [x,y,z] assumes coordinates in space, but if query_voxel is True, they are assumed to be voxel coordinates
  - coordT – Optional transformation to apply first
  - levels (None or slice or list of int) – What levels by default to operate on

  `Nlevels`
  `source` = 'PyMVPA'
  `space`
  `spaceFlavor`

### `ReferencesAtlas`

class `mvpa.atlases.base.``ReferencesAtlas`(distance=0, *args, **kwargs)

  Bases: `mvpa.atlases.base.PyMVPAAtlas`

  Atlas which provides references to the other atlases.

  Example: the atlas which has references to the closest points (closest Gray, etc) in another atlas.

  See also

  Please refer to the documentation of the base class for more information:

  `PyMVPAAtlas`

  Initialize ReferencesAtlas

  Parameters:

  - filename (string) – Filename for the xml definition of the atlas
  - resolution (None or float) – Some atlases link to multiple images at different resolutions. if None – best resolution is selected using 0th dimension resolution
  - image_file (None or str) – If None, overrides filename for the used imagefile, so it could load a custom (re-registered) atlas maps
  - query_voxel (bool) – By default [x,y,z] assumes coordinates in space, but if query_voxel is True, they are assumed to be voxel coordinates
  - coordT – Optional transformation to apply first
  - levels (None or slice or list of int) – What levels by default to operate on

  `distance`
  `labelVoxel`(c, levels=None)
  `levelsListing`()
  `setDistance`(distance)

    Set desired maximal distance for the reference

  `setReferenceLevel`(level)

    Set the level which will be queried

### `ReferencesLevel`

class `mvpa.atlases.base.``ReferencesLevel`(description, indexes=[])

  Bases: `mvpa.atlases.base.Level`

  Level which carries reference points

  static `generateFromXML`(Elevel)
  `indexes`

### `XMLAtlasException`

class `mvpa.atlases.base.``XMLAtlasException`(msg='')

  Bases: `exceptions.Exception`

  Exception to be thrown if smth goes wrong dealing with XML based atlas

### `XMLBasedAtlas`

class `mvpa.atlases.base.``XMLBasedAtlas`(filename=None, resolution=None, image_file=None, query_voxel=False, coordT=None, levels=None)

  Bases: `mvpa.atlases.base.BaseAtlas`

  Parameters:

  - filename (string) – Filename for the xml definition of the atlas
  - resolution (None or float) – Some atlases link to multiple images at different resolutions. if None – best resolution is selected using 0th dimension resolution
  - image_file (None or str) – If None, overrides filename for the used imagefile, so it could load a custom (re-registered) atlas maps
  - query_voxel (bool) – By default [x,y,z] assumes coordinates in space, but if query_voxel is True, they are assumed to be voxel coordinates
  - coordT – Optional transformation to apply first
  - levels (None or slice or list of int) – What levels by default to operate on

  `coordT`
  `extent`
  `labelPoint`(coord, levels=None)

    Return labels for the given spatial point at specified levels

    Function takes care about first transforming the point into the voxel space

    Parameters:

    - coord (tuple) – Coordinates of the point (xyz)
    - levels (None or list of int) – At what levels to return the results

  `levelsListing`()
  `levels_dict`
  `loadAtlas`(filename)
  `origin`
  `setCoordT`(coordT)

    Set coordT transformation.

    spaceT needs to be adjusted since we glob those two transformations together

  `spaceT`
  `version`
  `voxdim`

## Function

`mvpa.atlases.base.``checkRange`(coord, range)

  Check if coordinates are within range (0,0,0) - (range) Return True on success

### Navigation

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- next |
- previous |
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- NeuroDebian Project |
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