From 07fc4c17e05732b2b6915f5a793da30b5070a7f7 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Sun, 21 Jul 2019 13:43:35 +0100
Subject: [PATCH] ENH: resampleToReference now accepts a custom matrix,
allowing us to apply a transformation (e.g. FLIRT registration) during the
resampling. Missed imports in deprecated fsl.utils.transform
---
fsl/utils/image/resample.py | 38 ++++++++++++++++++++++++++++++++-----
fsl/utils/transform.py | 4 +++-
2 files changed, 36 insertions(+), 6 deletions(-)
diff --git a/fsl/utils/image/resample.py b/fsl/utils/image/resample.py
index bf11d7a4e..1aa52b9d2 100644
--- a/fsl/utils/image/resample.py
+++ b/fsl/utils/image/resample.py
@@ -39,7 +39,7 @@ def resampleToPixdims(image, newPixdims, **kwargs):
return resample(image, newShape, **kwargs)
-def resampleToReference(image, reference, **kwargs):
+def resampleToReference(image, reference, matrix=None, **kwargs):
"""Resample ``image`` into the space of the ``reference``.
This is a wrapper around :func:`resample` - refer to its documenttion
@@ -49,6 +49,7 @@ def resampleToReference(image, reference, **kwargs):
along the spatial (first three) dimensions.
:arg image: :class:`.Image` to resample
+ :arg matrix: Optional world-to-world affine alignment matrix
:arg reference: :class:`.Nifti` defining the space to resample ``image``
into
"""
@@ -56,6 +57,9 @@ def resampleToReference(image, reference, **kwargs):
oldShape = list(image.shape)
newShape = list(reference.shape[:3])
+ if matrix is None:
+ matrix = np.eye(4)
+
# If the input image is >3D, pad the
# new shape so that we only resample
# along the first 3 dimensions.
@@ -64,7 +68,9 @@ def resampleToReference(image, reference, **kwargs):
# Align the two images together
# via their vox-to-world affines.
- matrix = affine.concat(image.worldToVoxMat, reference.voxToWorldMat)
+ matrix = affine.concat(image.worldToVoxMat,
+ affine.invert(matrix),
+ reference.voxToWorldMat)
# If the input image is >3D, we
# have to adjust the resampling
@@ -82,7 +88,12 @@ def resampleToReference(image, reference, **kwargs):
kwargs['newShape'] = newShape
kwargs['matrix'] = matrix
- return resample(image, **kwargs)
+ data = resample(image, **kwargs)[0]
+
+ # The image is now in the same space
+ # as the reference, so it inherits
+ # ref's voxel-to-world affine
+ return data, reference.voxToWorldMat
def resample(image,
@@ -113,6 +124,12 @@ def resample(image,
particularly on the ``order``, ``matrix``, ``mode`` and
``cval`` arguments.
+ .. note:: If a custom resampling ``matrix`` is specified, the adjusted
+ voxel-to-world afffine cannot be calculated by this function,
+ so ``None`` will be returned instead.
+
+ :arg image: :class:`.Image` object to resample
+
:arg newShape: Desired shape. May containg floating point values, in which
case the resampled image will have shape
``round(newShape)``, but the voxel sizes will have scales
@@ -159,7 +176,8 @@ def resample(image,
- A ``numpy`` array of shape ``(4, 4)``, containing the
adjusted voxel-to-world transformation for the spatial
- dimensions of the resampled data.
+ dimensions of the resampled data, or ``None`` if a ``matrix``
+ was provided.
"""
if sliceobj is None: sliceobj = slice(None)
@@ -168,6 +186,8 @@ def resample(image,
if mode is None: mode = 'nearest'
if origin == 'center': origin = 'centre'
+ ownMatrix = matrix is None
+
if origin not in ('centre', 'corner'):
raise ValueError('Invalid value for origin: {}'.format(origin))
@@ -218,7 +238,15 @@ def resample(image,
matrix[:3, :3] = rotmat
matrix[:3, -1] = offsets
- matrix = affine.concat(image.voxToWorldMat, matrix)
+ # We can only adjust the v2w affine if
+ # the input space and resampling space
+ # are aligned (e.g. if we're just
+ # resampling to different dimensions).
+ # We can't assume this when a custom
+ # matrix is specified, so we just give
+ # up and return None.
+ if ownMatrix: matrix = affine.concat(image.voxToWorldMat, matrix)
+ else: matrix = None
return data, matrix
diff --git a/fsl/utils/transform.py b/fsl/utils/transform.py
index b8c003968..e682cc1be 100644
--- a/fsl/utils/transform.py
+++ b/fsl/utils/transform.py
@@ -10,7 +10,9 @@
import fsl.utils.deprecated as deprecated
-from fsl.transform.affine import * # noqa
+from fsl.transform.affine import * # noqa
+from fsl.transform.flirt import (flirtMatrixToSform, # noqa
+ sformToFlirtMatrix)
deprecated.warn('fsl.utils.transform',
--
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