From 95adaa452ee82d8eb9f46afcb782ac851887bd10 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Thu, 12 Oct 2017 09:56:03 +0100
Subject: [PATCH] Atlas mask query methods raise an error if the provided mask
is not in the same space as the atlas. This might change in the future.
---
fsl/data/atlases.py | 14 +++++++++++---
1 file changed, 11 insertions(+), 3 deletions(-)
diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py
index 51f2adcb2..22ddbb7e7 100644
--- a/fsl/data/atlases.py
+++ b/fsl/data/atlases.py
@@ -711,12 +711,16 @@ class LabelAtlas(Atlas):
# Use nearest neighbour interpolation
# for resampling, as it is most likely
# that the mask is binary.
- mask = mask.resample(self.shape[:3], dtype=np.float32, order=0)[0]
- boolmask = mask > 0
+ mask, xform = mask.resample(self.shape[:3], dtype=np.float32, order=0)
+
+ if not fslimage.Image(mask, xform=xform).sameSpace(self):
+ raise ValueError('Mask is not in the same space as atlas')
+
# Extract the labels that are in
# the mask, and their corresponding
# mask weights
+ boolmask = mask > 0
vals = self[boolmask]
weights = mask[boolmask]
weightsum = weights.sum()
@@ -851,7 +855,11 @@ class ProbabilisticAtlas(Atlas):
# Make sure that the mask has the same
# number of voxels as the atlas image
- mask = mask.resample(self.shape[:3], dtype=np.float32, order=0)[0]
+ mask, xform = mask.resample(self.shape[:3], dtype=np.float32, order=0)
+
+ if not fslimage.Image(mask, xform=xform).sameSpace(self):
+ raise ValueError('Mask is not in the same space as atlas')
+
boolmask = mask > 0
weights = mask[boolmask]
weightsum = weights.sum()
--
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