From d503ec725076add96d5236b2e9600e2e1b74fe99 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Wed, 1 May 2019 15:26:09 +0100
Subject: [PATCH] ENH: Image.resample now accepts 'offset' and 'origin'
arguments, allowing the alignemnt of the input and resampled images to be
adjusted.
---
fsl/data/image.py | 55 ++++++++++++++++++++++++++++++++++++++++++-----
1 file changed, 50 insertions(+), 5 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 24e129c8b..f0a4ae974 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -34,6 +34,7 @@ and file names:
import os
import os.path as op
+import collections.abc as abc
import string
import logging
import tempfile
@@ -1171,10 +1172,15 @@ class Image(Nifti):
sliceobj=None,
dtype=None,
order=1,
- smooth=True):
+ smooth=True,
+ offset=None,
+ origin='centre'):
"""Returns a copy of the data in this ``Image``, resampled to the
specified ``newShape``.
+ See the ``scipy.ndimage.affine_transform`` function for more details,
+ particularly on the ``order`` and ``offset`` arguments.
+
: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
@@ -1199,6 +1205,19 @@ class Image(Nifti):
down-sampled (i.e. where
``newShape[i] < self.shape[i]``).
+ :arg offset: Offset (in voxel coordinates) into this image to
+ apply when retrieving values during the resampling. May
+ be a scalar value, or a sequence of three values.
+ Default value is determined by the ``origin`` argument.
+
+ :arg origin: ``'centre'`` (the default) or ``'corner'``. ``'centre'``
+ resamples the image such that the centre of the corner
+ voxels of this image and the resampled data are
+ aligned. ``'corner'`` resamples the image such that
+ the corner of the corner voxels are aligned (and
+ therefore the voxel grids are aligned).
+ Ignored if ``offset`` is specified.
+
:returns: A tuple containing:
- A ``numpy`` array of shape ``newShape``, containing
@@ -1209,8 +1228,12 @@ class Image(Nifti):
dimensions of the resampled data.
"""
- if sliceobj is None: sliceobj = slice(None)
- if dtype is None: dtype = self.dtype
+ if sliceobj is None: sliceobj = slice(None)
+ if dtype is None: dtype = self.dtype
+ if origin == 'center': origin = 'centre'
+
+ if origin not in ('centre', 'corner'):
+ raise ValueError('Invalid value for origin: {}'.format(origin))
data = self[sliceobj]
data = np.array(data, dtype=dtype, copy=False)
@@ -1227,6 +1250,26 @@ class Image(Nifti):
newShape = np.array(np.round(newShape), dtype=np.int)
scale = np.diag(ratio)
+ # If an offest hasn't been provided,
+ # calculate it from the origin -
+ # the default behaviour (centre)
+ # causes the corner voxel of the
+ # output to have the same centre
+ # as the corner voxel of the input.
+ # If the origin is 'corner', we
+ # apply an offset which effectively
+ # causes the voxel grids of the
+ # input and output to be aligned.
+ if offset is None:
+ if origin == 'centre': offset = 0
+ elif origin == 'corner': offset = list((ratio - 1) / 2)
+
+ if not isinstance(offset, abc.Sequence):
+ offset = [offset] * 3
+
+ if len(offset) < len(newShape):
+ offset = list(offset) + [0] * (len(newShape) - len(offset))
+
# If interpolating and smoothing, we apply a
# gaussian filter along axes with a resampling
# ratio greater than 1.1. We do this so that
@@ -1244,13 +1287,15 @@ class Image(Nifti):
data = ndimage.affine_transform(data,
scale,
output_shape=newShape,
- order=order)
+ offset=offset,
+ order=order,
+ mode='nearest')
# Construct an affine transform which
# puts the resampled image into the
# same world coordinate system as this
# image.
- scale = transform.scaleOffsetXform(ratio[:3], 0)
+ scale = transform.scaleOffsetXform(ratio[:3], offset)
xform = transform.concat(self.voxToWorldMat, scale)
else:
xform = self.voxToWorldMat
--
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