diff --git a/CHANGELOG.rst b/CHANGELOG.rst
index a9102c536d131052e048e8ca04a498659cfcdcbb..4ad29971d0ad8acdce7eb7975cdac8e1479860ff 100644
--- a/CHANGELOG.rst
+++ b/CHANGELOG.rst
@@ -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
diff --git a/fsl/transform/nonlinear.py b/fsl/transform/nonlinear.py
index 3010cda86f246e1e8697a4cfaee412a000fc91b5..daf13adcf35f85995f1b309acf38dc2d6c145d37 100644
--- a/fsl/transform/nonlinear.py
+++ b/fsl/transform/nonlinear.py
@@ -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))
diff --git a/tests/test_transform/test_nonlinear.py b/tests/test_transform/test_nonlinear.py
index b161f4f23748eba7f25766dc96edccdadae1bbd9..aaf4e07fec41df2428a7863bae6e8a229a34659a 100644
--- a/tests/test_transform/test_nonlinear.py
+++ b/tests/test_transform/test_nonlinear.py
@@ -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),