From 0f391b2e0b0e17d851342b0aa2078b0102f85d27 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Tue, 24 Mar 2020 16:03:36 +0000
Subject: [PATCH] ENH: applyDeformation accepts a premat option
---
fsl/transform/nonlinear.py | 50 ++++++++++++++++++++++++--------------
1 file changed, 32 insertions(+), 18 deletions(-)
diff --git a/fsl/transform/nonlinear.py b/fsl/transform/nonlinear.py
index 3010cda86..daf13adcf 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))
--
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