algorithms.registration.resample

Module: algorithms.registration.resample

Functions

nipy.algorithms.registration.resample.cast_array(arr, dtype)

arrarray

Input array

dtypedtype

Desired dtype

nipy.algorithms.registration.resample.resample(moving, transform=None, reference=None, mov_voxel_coords=False, ref_voxel_coords=False, dtype=None, interp_order=3, mode='constant', cval=0.0)

Resample movimg into voxel space of reference using transform

Apply a transformation to the image considered as ‘moving’ to bring it into the same grid as a given reference image. The transformation usually maps world space in reference to world space in movimg, but can also be a voxel to voxel mapping (see parameters below).

This function uses scipy.ndimage except for the case interp_order==3, where a fast cubic spline implementation is used.

Parameters:

moving: nipy-like image

Image to be resampled.

transform: transform object or None

Represents a transform that goes from the reference image to the moving image. None means an identity transform. Otherwise, it should have either an apply method, or an as_affine method or be a shape (4, 4) array. By default, transform maps between the output (world) space of reference and the output (world) space of moving. If mov_voxel_coords is True, maps to the voxel space of moving and if ref_vox_coords is True, maps from the voxel space of reference.

referenceNone or nipy-like image or tuple, optional

The reference image defines the image dimensions and xyz affine to which to resample. It can be input as a nipy-like image or as a tuple (shape, affine). If None, use movimg to define these.

mov_voxel_coordsboolean, optional

True if the transform maps to voxel coordinates, False if it maps to world coordinates.

ref_voxel_coordsboolean, optional

True if the transform maps from voxel coordinates, False if it maps from world coordinates.

interp_order: int, optional

Spline interpolation order, defaults to 3.

modestr, optional

Points outside the boundaries of the input are filled according to the given mode (‘constant’, ‘nearest’, ‘reflect’ or ‘wrap’). Default is ‘constant’.

cvalscalar, optional

Value used for points outside the boundaries of the input if mode=’constant’. Default is 0.0.

Returns:

aligned_imgImage

Image resliced to reference with reference-to-movimg transform transform