From 1abeddcc0b33fad4f91f620e70cba8915c24d662 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Thu, 2 May 2019 23:09:37 +0100
Subject: [PATCH] ENH,RF: Deprecated Image.resample. New convenience wrappers -
resampleToPixdims and resampleToReference
---
fsl/data/image.py | 8 +++-----
fsl/utils/image/resample.py | 37 +++++++++++++++++++++++++++++++++++++
2 files changed, 40 insertions(+), 5 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index b39e66e6f..651992c4d 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -1165,12 +1165,10 @@ class Image(Nifti):
self.notify(topic='saveState')
+ @deprecated.deprecated('2.2.0', '3.0.0',
+ 'Use fsl.utils.image.resample instead.')
def resample(self, *args, **kwargs):
- """Returns a copy of the data in this ``Image``, resampled to the
- specified ``newShape``.
-
- See the :mod:`.image.resample` module for more details.
- """
+ """Deprecated - use :func:`.image.resample` instead. """
from fsl.utils.image.resample import resample
return resample(self, *args, **kwargs)
diff --git a/fsl/utils/image/resample.py b/fsl/utils/image/resample.py
index 377ddffac..0b4c4c00c 100644
--- a/fsl/utils/image/resample.py
+++ b/fsl/utils/image/resample.py
@@ -7,6 +7,9 @@
"""This module defines the :func:`resample` function, which can be used
to resample an :class:`.Image` object to a different resolution.
+The :func:`resampleToPixdims` and :func:`resampleToReference` functions
+are convenience wrappers around :func:`resample`.
+
The :func:`applySmoothing` and :func:`calculateMatrix` functions are
sub-functions of :func:`resample`.
"""
@@ -20,6 +23,40 @@ import scipy.ndimage as ndimage
import fsl.utils.transform as transform
+def resampleToPixdims(image, newPixdims, **kwargs):
+ """Resample ``image`` so that it has the specified voxel dimensions.
+
+ This is a wrapper around :func:`resample` - refer to its documenttion
+ for details on the other arguments and the return values.
+
+ :arg image: :class:`.Image` to resample
+ :arg pixdims: New voxel dimensions to resample ``image`` to.
+ """
+ oldShape = image.shape
+ oldPixdims = image.pixdim
+ fac = [o / float(n) for o, n in zip(oldPixdims, newPixdims)]
+ newShape = [p * f for p, f in zip(oldShape, fac)]
+ return resample(image, newShape, **kwargs)
+
+
+def resampleToReference(image, reference, **kwargs):
+ """Resample ``image`` into the space of the ``reference``.
+
+ This is a wrapper around :func:`resample` - refer to its documenttion
+ for details on the other arguments and the return values.
+
+ :arg image: :class:`.Image` to resample
+ :arg reference: :class:`.Nifti` defining the space to resample ``image``
+ into
+ """
+
+ kwargs['mode'] = kwargs.get('mode', 'constant')
+ kwargs['newShape'] = reference.shape
+ kwargs['matrix'] = transform.concat(image.worldToVoxMat,
+ reference.voxToWorldMat)
+ return resample(image, **kwargs)
+
+
def resample(image,
newShape,
sliceobj=None,
--
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