labs.viz_tools.coord_tools¶
Module: labs.viz_tools.coord_tools
¶
Misc tools to find activations and cut on maps
Functions¶
-
nipy.labs.viz_tools.coord_tools.
coord_transform
(x, y, z, affine)¶ Convert the x, y, z coordinates from one image space to another space.
Parameters: x : number or ndarray
The x coordinates in the input space
y : number or ndarray
The y coordinates in the input space
z : number or ndarray
The z coordinates in the input space
affine : 2D 4x4 ndarray
affine that maps from input to output space.
Returns: x : number or ndarray
The x coordinates in the output space
y : number or ndarray
The y coordinates in the output space
z : number or ndarray
The z coordinates in the output space
Warning: The x, y and z have their Talairach ordering, not 3D :
numy image ordering. :
-
nipy.labs.viz_tools.coord_tools.
find_cut_coords
(map, mask=None, activation_threshold=None)¶ Find the center of the largest activation connect component.
Parameters: map : 3D ndarray
The activation map, as a 3D image.
mask : 3D ndarray, boolean, optional
An optional brain mask.
activation_threshold : float, optional
The lower threshold to the positive activation. If None, the activation threshold is computed using find_activation.
Returns: x: float :
the x coordinate in voxels.
y: float :
the y coordinate in voxels.
z: float :
the z coordinate in voxels.
-
nipy.labs.viz_tools.coord_tools.
find_maxsep_cut_coords
(map3d, affine, slicer='z', n_cuts=None, threshold=None)¶ Heuristic function to find n_cuts along a given axis, which are maximally separated in space.
- map3d: 3D array
- the data under consideration
- slicer: string, optional (default “z”)
- sectional slicer; possible values are “x”, “y”, or “z”
- n_cuts: int > 1, optional (default None)
- number of cuts in the plot; if no value is specified, then a default value of 5 is forced
- threshold: float, optional (default None)
- thresholding to be applied to the map
Returns: n_cuts: 1D array of length n_cuts :
the computed n_cuts
Raises: ValueError :
-
nipy.labs.viz_tools.coord_tools.
get_mask_bounds
(mask, affine)¶ Return the world-space bounds occupied by a mask given an affine.
Notes
The mask should have only one connect component.
The affine should be diagonal or diagonal-permuted.