Commit 0e5e0aa7 authored by Paul McCarthy's avatar Paul McCarthy 🚵
Browse files

Merge branch 'enh/nonlinear' into 'master'

Enh/nonlinear

See merge request fsl/fslpy!211
parents d5039cf7 1b997118
Pipeline #5126 passed with stages
in 14 minutes and 29 seconds
......@@ -15,6 +15,8 @@ Added
* New ``firstDot`` option to the :func:`.path.getExt`,
:func:`.path.removeExt`, and :func:`.path.splitExt`, functions, offering
rudimentary support for double-barrelled filenames.
* The :func:`.nonlinear.applyDeformation` function now accepts a ``premat``
affine, which is applied to the input image before the deformation field.
Changed
......
......@@ -679,7 +679,13 @@ def convertDeformationSpace(field, from_, to):
defType=field.deformationType)
def applyDeformation(image, field, ref=None, order=1, mode=None, cval=None):
def applyDeformation(image,
field,
ref=None,
order=1,
mode=None,
cval=None,
premat=None):
"""Applies a :class:`DeformationField` to an :class:`.Image`.
The image is transformed into the space of the field's reference image
......@@ -691,25 +697,30 @@ def applyDeformation(image, field, ref=None, order=1, mode=None, cval=None):
the input image. It is therefore assumed that an alternate ``ref`` is
aligned in world coordinates with the field's actual reference image.
:arg image: :class:`.Image` to be transformed
:arg image: :class:`.Image` to be transformed
:arg field: :class:`DeformationField` to use
:arg field: :class:`DeformationField` to use
:arg ref: Alternate reference image - if not provided, ``field.ref``
is used
:arg ref: Alternate reference image - if not provided, ``field.ref``
is used
:arg order: Spline interpolation order, passed through to the
``scipy.ndimage.affine_transform`` function - ``0``
corresponds to nearest neighbour interpolation, ``1``
(the default) to linear interpolation, and ``3`` to
cubic interpolation.
:arg order: Spline interpolation order, passed through to the
``scipy.ndimage.affine_transform`` function - ``0``
corresponds to nearest neighbour interpolation, ``1``
(the default) to linear interpolation, and ``3`` to
cubic interpolation.
:arg mode: How to handle regions which are outside of the image FOV.
Defaults to `''nearest'``.
:arg mode: How to handle regions which are outside of the image FOV.
Defaults to `''nearest'``.
:arg cval: Constant value to use when ``mode='constant'``.
:arg cval: Constant value to use when ``mode='constant'``.
:return: ``numpy.array`` containing the transformed image data.
:arg premat: Optional affine transform which can be used if ``image`` is
not in the same space as ``field.src``. Assumed to transform
from ``image`` **voxel** coordinates into ``field.src``
**voxel** coordinates.
:return: ``numpy.array`` containing the transformed image data.
"""
if order is None: order = 1
......@@ -763,12 +774,15 @@ def applyDeformation(image, field, ref=None, order=1, mode=None, cval=None):
# We assume world-world alignment
# between the original source
# and the image to be resampled
if not image.sameSpace(src):
post = affine.concat(image.getAffine('world', 'voxel'),
src .getAffine('voxel', 'world'))
if (premat is not None) or (not image.sameSpace(src)):
if premat is None:
premat = affine.concat(image.getAffine('world', 'voxel'),
src .getAffine('voxel', 'world'))
else:
premat = affine.invert(premat)
shape = field.shape
field = field.reshape((-1, 3))
field = affine.transform(field, post)
field = affine.transform(field, premat)
field = field.reshape(shape)
field = field.transpose((3, 0, 1, 2))
......
......@@ -411,6 +411,60 @@ def test_applyDeformation_altsrc():
assert np.all(np.isclose(expect, result))
def test_applyDeformation_premat():
src2ref = affine.compose(
np.random.randint(2, 5, 3),
np.random.randint(1, 10, 3),
[0, 0, 0])
ref2src = affine.invert(src2ref)
srcdata = np.random.randint(1, 65536, (10, 10, 10))
refdata = np.random.randint(1, 65536, (10, 10, 10))
src = fslimage.Image(srcdata)
ref = fslimage.Image(refdata, xform=src2ref)
field = _affine_field(src, ref, ref2src, 'world', 'world')
# First try a down-sampled version
# of the original source image
altsrc, xf = resample.resample(src, (5, 5, 5), origin='corner')
altsrc = fslimage.Image(altsrc, xform=xf, header=src.header)
expect, xf = resample.resampleToReference(
altsrc, ref, matrix=src2ref, order=1, mode='nearest')
premat = affine.concat(src .getAffine('world', 'voxel'),
altsrc.getAffine('voxel', 'world'))
result = nonlinear.applyDeformation(
altsrc, field, order=1, mode='nearest', premat=premat)
assert np.all(np.isclose(expect, result))
# Now try a down-sampled ROI
# of the original source image
altsrc = roi.roi(src, [(2, 9), (2, 9), (2, 9)])
altsrc, xf = resample.resample(altsrc, (4, 4, 4))
altsrc = fslimage.Image(altsrc, xform=xf, header=src.header)
expect, xf = resample.resampleToReference(
altsrc, ref, matrix=src2ref, order=1, mode='nearest')
premat = affine.concat(src .getAffine('world', 'voxel'),
altsrc.getAffine('voxel', 'world'))
result = nonlinear.applyDeformation(
altsrc, field, order=1, mode='nearest', premat=premat)
assert np.all(np.isclose(expect, result))
# down-sampled and offset ROI
# of the original source image
altsrc = roi.roi(src, [(-5, 8), (-5, 8), (-5, 8)])
altsrc, xf = resample.resample(altsrc, (6, 6, 6))
altsrc = fslimage.Image(altsrc, xform=xf, header=src.header)
expect, xf = resample.resampleToReference(
altsrc, ref, matrix=src2ref, order=1, mode='nearest')
premat = affine.concat(src .getAffine('world', 'voxel'),
altsrc.getAffine('voxel', 'world'))
result = nonlinear.applyDeformation(
altsrc, field, order=1, mode='nearest', premat=premat)
assert np.all(np.isclose(expect, result))
def test_applyDeformation_altref():
src2ref = affine.compose(
np.random.randint(2, 5, 3),
......
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