Package mvpa :: Package atlases :: Module base :: Class XMLBasedAtlas

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# Class XMLBasedAtlas

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Instance Methods | [hide private]

__init__(self, filename=None, resolution=None, image_file=None, query_voxel=False, coordT=None, levels=None) Create an atlas object based on the... XXX | source code

_checkRange(self, c) check and adjust the voxel coordinates | source code

_loadImages(self) To be overriden in the derived classes. By default does nothing | source code

_loadData(self) To be overriden in the derived classes. By default does nothing | source code

loadAtlas(self, filename) | source code

version(self) | source code

__getattr__(self, attr) Lazy way to provide access to the definitions in the atlas | source code

setCoordT(self, coordT) Set coordT transformation. | source code

labelPoint(self, coord, levels=None) Return labels for the given spatial point at specified levels | source code

levelsListing(self) | source code

_getLevels(self, levels=None) Helper to provide list of levels to operate on | source code

__getitem__(self, index) Accessing the elements via simple indexing. Examples: print atlas[ 0, -7, 20, [1,2,3] ] print atlas[ (0, -7, 20), 1:2 ] print atlas[ (0, -7, 20) ] print atlas[ (0, -7, 20), : ] | source code

_getLevelsDict(self) | source code

_getLevelsDict_virtual(self) | source code

Inherited from `object`: `__delattr__`, `__format__`, `__getattribute__`, `__hash__`, `__new__`, `__reduce__`, `__reduce_ex__`, `__repr__`, `__setattr__`, `__sizeof__`, `__str__`, `__subclasshook__`

Static Methods | [hide private]

_checkVersion(version) To be overriden in the derived classes. By default anything is good | source code

_compare_lists(checkitems, neededitems) | source code

_children_tags(root) | source code

Class Variables | [hide private]

| levels_dict = `property(fget= _getLevelsDict)`
| origin = `property(fget= lambda self: self._origin)`
| extent = `property(fget= lambda self: self._extent)`
| voxdim = `property(fget= lambda self: self._voxdim)`
| spaceT = `property(fget= lambda self: self._spaceT)`
| coordT = `property(fget= lambda self: self._spaceT, fset= setCo`...``

Properties | [hide private]

Inherited from `object`: `__class__`

Method Details | [hide private]

### __init__(self, filename=None, resolution=None, image_file=None, query_voxel=False, coordT=None, levels=None)
(Constructor)

source code

Create an atlas object based on the... XXX

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
Overrides: object.__init__

### version(self)

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Decorators:
  - `@property`

### setCoordT(self, coordT)

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Set coordT transformation.

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

### labelPoint(self, coord, levels=None)

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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

### _getLevels(self, levels=None)

source code

Helper to provide list of levels to operate on

Depends on given `levels` as well as self.levels

Class Variable Details | [hide private]

### coordT

Value:

      property(fget= lambda self: self._spaceT, fset= setCoordT)