Base
Common interface for transforms.
- class nitransforms.base.ImageGrid(image)[source]
Class to represent spaces of gridded data (images).
- property affine
Access the indexes-to-RAS affine.
- property header
Access the original reference’s header.
- property inverse
Access the RAS-to-indexes affine.
- property ndcoords
List the physical coordinates of this gridded space samples.
- property ndindex
List the indexes corresponding to the space grid.
- class nitransforms.base.SampledSpatialData(dataset)[source]
Represent sampled spatial data: regularly gridded (images) and surfaces.
- property ndcoords
List the physical coordinates of this sample.
- property ndim
Access the number of dimensions.
- property npoints
Access the total number of voxels.
- property shape
Access the space’s size of each dimension.
- class nitransforms.base.TransformBase(reference=None)[source]
Abstract image class to represent transforms.
- apply(spatialimage, reference=None, order=3, mode='constant', cval=0.0, prefilter=True, output_dtype=None)[source]
Apply a transformation to an image, resampling on the reference spatial object.
- Parameters
spatialimage (spatialimage) – The image object containing the data to be resampled in reference space
reference (spatial object, optional) – The image, surface, or combination thereof containing the coordinates of samples that will be sampled.
order (int, optional) – The order of the spline interpolation, default is 3. The order has to be in the range 0-5.
mode ({'constant', 'reflect', 'nearest', 'mirror', 'wrap'}, optional) – Determines how the input image is extended when the resamplings overflows a border. Default is ‘constant’.
cval (float, optional) – Constant value for
mode='constant'
. Default is 0.0.prefilter (bool, optional) – Determines if the image’s data array is prefiltered with a spline filter before interpolation. The default is
True
, which will create a temporary float64 array of filtered values if order > 1. If setting this toFalse
, the output will be slightly blurred if order > 1, unless the input is prefiltered, i.e. it is the result of calling the spline filter on the original input.output_dtype (dtype specifier, optional) – The dtype of the returned array or image, if specified. If
None
, the default behavior is to use the effective dtype of the input image. If slope and/or intercept are defined, the effective dtype is float64, otherwise it is equivalent to the input image’sget_data_dtype()
(on-disk type). Ifreference
is defined, then the return value is an image, with a data array of the effective dtype but with the on-disk dtype set to the input image’s on-disk dtype.
- Returns
resampled – The data imaged after resampling to reference space.
- Return type
spatialimage or ndarray
- map(x, inverse=False)[source]
Apply \(y = f(x)\).
TransformBase implements the identity transform.
- Parameters
x (N x D numpy.ndarray) – Input RAS+ coordinates (i.e., physical coordinates).
inverse (bool) – If
True
, apply the inverse transform \(x = f^{-1}(y)\).
- Returns
y – Transformed (mapped) RAS+ coordinates (i.e., physical coordinates).
- Return type
N x D numpy.ndarray
- property ndim
Access the dimensions of the reference space.
- property reference
Access a reference space where data will be resampled onto.