Inheritance diagram for nipy.neurospin.datasets.volumes.volume_grid:
The volume grid class.
This class represents data lying on a (non rigid, non regular) grid embedded in a 3D world represented as a 3+D array.
Bases: nipy.neurospin.datasets.volumes.volume_data.VolumeData
A class representing data stored in a 3+D array embedded in a 3D world.
This object has data stored in an array-like multidimensional indexable objects, with the 3 first dimensions corresponding to spatial axis and defining a 3D grid that may be non-regular or non-rigid.
The object knows how the data is mapped to a 3D “real-world space”, and how it can change real-world coordinate system. The transform mapping it to world is arbitrary, and thus the grid can be warped: in the world space, the grid may not be regular or orthogonal.
Notes
The data is stored in an undefined way: prescalings might need to be applied to it before using it, or the data might be loaded on demand. The best practice to access the data is not to access the _data attribute, but to use the get_data method.
If the transform associated with the image has no inverse mapping, data corresponding to a given world space position cannot be calulated. If it has no forward mapping, it is impossible to resample another dataset on the same support.
Attributes
world_space: string | World space the data is embedded in. For instance mni152. |
metadata: dictionnary | Optional, user-defined, dictionnary used to carry around extra information about the data as it goes through transformations. The consistency of this information is not maintained as the data is modified. |
_data: | Private pointer to the data. |
Methods
as_volume_img | |
composed_with_transform | |
get_data | |
get_transform | |
get_world_coords | |
like_from_data | |
resampled_to_img | |
values_in_world |
The base image containing data.
Parameters : | data: ndarray :
transform: nipy transform object :
metadata : dictionnary, optional
interpolation : ‘continuous’ or ‘nearest’, optional
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Resample the image to be an image with the data points lying on a regular grid with an affine mapping to the word space (a nipy VolumeImg).
Parameters : | affine: 4x4 or 3x3 ndarray, optional :
shape: (n_x, n_y, n_z), tuple of integers, optional :
interpolation : None, ‘continuous’ or ‘nearest’, optional
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Returns : | resampled_image : nipy VolumeImg
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Notes
The coordinate system of the image is not changed: the returned image points to the same world space.
Return a new image embedding the same data in a different word space using the given world to world transform.
Parameters : | w2w_transform : transform object
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Returns : | remapped_image : nipy image
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Return data as a numpy array.
Returns the transform object associated with the volumetric structure which is a general description of the mapping from the values to the world space.
Returns : | transform : nipy.datasets.Transform object |
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Return the data points coordinates in the world space.
Returns : | x: ndarray :
y: ndarray :
z: ndarray :
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Returns an volumetric data structure with the same relationship between data and world space, and same metadata, but different data.
Parameters : | data: ndarray : |
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Resample the data to be on the same voxel grid than the target volume structure.
Parameters : | target_image : nipy image
interpolation : None, ‘continuous’ or ‘nearest’, optional
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Returns : | resampled_image : nipy_image
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Notes
Both the target image and the original image should be embedded in the same world space.
Return the values of the data at the world-space positions given by x, y, z
Parameters : | x : number or ndarray
y : number or ndarray
z : number or ndarray
interpolation : None, ‘continuous’ or ‘nearest’, optional
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Returns : | values : number or ndarray
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