Base

Common interface for transforms.

classnitransforms.base.ImageGrid(image)[source]

Class to represent spaces of gridded data (images).

propertyaffine

Access the indexes-to-RAS affine.

propertyheader

Access the original reference’s header.

index(x)[source]

Get the image array’s indexes corresponding to coordinates.

propertyinverse

Access the RAS-to-indexes affine.

propertyndcoords

List the physical coordinates of this gridded space samples.

propertyndindex

List the indexes corresponding to the space grid.

ras(ijk)[source]

Get RAS+ coordinates from input indexes.

classnitransforms.base.SampledSpatialData(dataset)[source]

Represent sampled spatial data: regularly gridded (images) and surfaces.

propertyndcoords

List the physical coordinates of this sample.

propertyndim

Access the number of dimensions.

propertynpoints

Access the total number of voxels.

propertyshape

Access the space’s size of each dimension.

classnitransforms.base.SpatialReference[source]

Factory to create spatial references.

staticfactory(dataset)[source]

Create a reference for spatial transforms.

classnitransforms.base.SurfaceMesh(dataset)[source]

Class to represent surface meshes.

check_sphere(tolerance=1.001)[source]

Check sphericity of surface.Based onhttps://github.com/Washington-University/workbench/blob/7ba3345d161d567a4b628ceb02ab4471fc96cb20/src/Files/SurfaceResamplingHelper.cxx#L503

classnitransforms.base.TransformBase(reference=None)[source]

Abstract image class to represent transforms.

apply(*args,**kwargs)[source]

Apply the transform to a dataset.

Deprecated. Please usenitransforms.resampling.apply instead.

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) – IfTrue, 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

propertyndim

Access the dimensions of the reference space.

propertyreference

Access a reference space where data will be resampled onto.

to_filename(filename,fmt='X5',moving=None,x5_inverse=False)[source]

Store the transform in BIDS-Transforms HDF5 file format (.x5).

exceptionnitransforms.base.TransformError[source]

A custom exception for transforms.