From 252cd24cbae0a35e3cde305d9367c3563fcc6d50 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Fri, 13 Jan 2017 13:53:15 +0000
Subject: [PATCH] Dangerous change - scaleOffsetXform and transform.transform
were returning/assuming transposed affines (column-major). This is because
that's what OpenGL uses.
---
fsl/data/atlases.py | 6 +++---
fsl/data/featanalysis.py | 2 +-
fsl/utils/transform.py | 10 +++++-----
3 files changed, 9 insertions(+), 9 deletions(-)
diff --git a/fsl/data/atlases.py b/fsl/data/atlases.py
index daa62700e..36b0d48f9 100644
--- a/fsl/data/atlases.py
+++ b/fsl/data/atlases.py
@@ -495,7 +495,7 @@ class AtlasDescription(object):
# Load the appropriate transformation matrix
# and transform all those voxel coordinates
# into world coordinates
- coords = transform.transform(coords, self.xforms[0].T)
+ coords = transform.transform(coords, self.xforms[0])
# Update the coordinates
# in our label objects
@@ -594,7 +594,7 @@ class LabelAtlas(Atlas):
location, or ``None`` if the location is out of bounds.
"""
- voxelLoc = transform.transform([worldLoc], self.worldToVoxMat.T)[0]
+ voxelLoc = transform.transform([worldLoc], self.worldToVoxMat)[0]
voxelLoc = [int(v) for v in voxelLoc.round()]
if voxelLoc[0] < 0 or \
@@ -642,7 +642,7 @@ class ProbabilisticAtlas(Atlas):
location. Returns an empty list if the given
location is out of bounds.
"""
- voxelLoc = transform.transform([worldLoc], self.worldToVoxMat.T)[0]
+ voxelLoc = transform.transform([worldLoc], self.worldToVoxMat)[0]
voxelLoc = [int(v) for v in voxelLoc.round()]
if voxelLoc[0] < 0 or \
diff --git a/fsl/data/featanalysis.py b/fsl/data/featanalysis.py
index 1860a5e8d..5d527863d 100644
--- a/fsl/data/featanalysis.py
+++ b/fsl/data/featanalysis.py
@@ -355,7 +355,7 @@ def loadClusterResults(featdir, settings, contrast):
# later on.
coordXform = fslimage.Image(
getDataFile(featdir),
- loadData=False).worldToVoxMat.T
+ loadData=False).worldToVoxMat
if not op.exists(clusterFile):
return None
diff --git a/fsl/utils/transform.py b/fsl/utils/transform.py
index ed90bf35e..df82ddc55 100644
--- a/fsl/utils/transform.py
+++ b/fsl/utils/transform.py
@@ -73,9 +73,9 @@ def scaleOffsetXform(scales, offsets):
xform[1, 1] = scales[1]
xform[2, 2] = scales[2]
- xform[3, 0] = offsets[0]
- xform[3, 1] = offsets[1]
- xform[3, 2] = offsets[2]
+ xform[0, 3] = offsets[0]
+ xform[1, 3] = offsets[1]
+ xform[2, 3] = offsets[2]
return xform
@@ -337,8 +337,8 @@ def transform(p, xform, axes=None):
scalings.
"""
- p = _fillPoints(p, axes)
- t = np.dot(xform[:3, :3].T, p.T).T + xform[3, :3]
+ p = _fillPoints(p, axes)
+ t = np.dot(xform[:3, :3], p.T).T + xform[:3, 3]
if axes is not None:
t = t[:, axes]
--
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