mvpa2.atlases.warehouse.XMLBasedAtlas

class mvpa2.atlases.warehouse.XMLBasedAtlas(filename=None, resolution=None, image_file=None, coordT=None, default_levels=None, load_maps=True)

Base class for atlases using XML as the definition backend

Methods

Parameters:

filename : str

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

coordT :

Optional transformation to apply first

default_levels : None or slice or list of int

What levels by default to operate on

load_maps : bool

Load spatial maps for the atlas.

Methods

coordT

extent

label_point(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

levels

levels_listing()

load_atlas(filename)

Load atlas from a file

origin

query(index, query_voxel=False)

Generic query method.

Use shortcuts __getitem__ for querying by voxel indices and __call__ for querying by space coordinates.

Parameters:

index : tuple or list

Arguments of the query, such as coordinates and optionally levels

query_voxel : bool

Either at the end query a voxel indexes or point coordinates

Allows to access 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), : ]

resolution

set_coordT(coordT)

Set coordT transformation.

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

spaceT

version

voxdim