From f162bb5b987537acdf75997c65fcf2129052c4ae Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Thu, 5 Oct 2017 18:18:30 +0100
Subject: [PATCH] Image.resample uses scipy.ndimage.affine_transform instead of
zoom, because the former aligns on the centre of voxel (0, 0, 0), whereas the
latter aligns on the corner.
---
fsl/data/image.py | 20 ++++++++++++++------
1 file changed, 14 insertions(+), 6 deletions(-)
diff --git a/fsl/data/image.py b/fsl/data/image.py
index 0f8a9995d..c85d3ab61 100644
--- a/fsl/data/image.py
+++ b/fsl/data/image.py
@@ -1137,7 +1137,7 @@ class Image(Nifti):
- A ``numpy`` array of shape ``shape``, containing an
interpolated copy of the data in this ``Image``.
- - A ``numpy`` array of shape ``(4, 4``), containing the
+ - A ``numpy`` array of shape ``(4, 4)``, containing the
adjusted voxel-to-world transformation for the resampled
data.
"""
@@ -1152,13 +1152,21 @@ class Image(Nifti):
if tuple(data.shape) != tuple(shape):
oldShape = data.shape
- zooms = [float(shape[i]) / data.shape[i] for i in range(ndims)]
- data = ndimage.zoom(data, zooms, **kwargs)
-
+ zooms = [float(data.shape[i]) / shape[i] for i in range(ndims)]
+ zooms = np.diag(zooms)
+
+ data = ndimage.affine_transform(data,
+ zooms,
+ output_shape=shape,
+ **kwargs)
+
+ # Construct an affine transform which
+ # puts the resampled image into the
+ # same world coordinate system as this
+ # image.
newShape = data.shape
scale = [os / float(ns) for os, ns in zip(oldShape, newShape)]
- offset = [(s - 1) / 2.0 for s in scale]
- scale = transform.scaleOffsetXform(scale, offset)
+ scale = transform.scaleOffsetXform(scale, 0)
xform = transform.concat(self.voxToWorldMat, scale)
else:
xform = self.voxToWorldMat
--
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