From 7a7d289541eb976591e45cede4abcf96c787b3dd Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Mon, 23 Jun 2014 12:03:37 +0100
Subject: [PATCH] Fixed image bounds calculation for pixdim/identity
transformations - they were not being calculated correctly.
---
fsl/data/fslimage.py | 26 +++++++++++++++++++++-----
fsl/fslview/orthopanel.py | 6 +++---
2 files changed, 24 insertions(+), 8 deletions(-)
diff --git a/fsl/data/fslimage.py b/fsl/data/fslimage.py
index a8cd635a6..2ea2b34db 100644
--- a/fsl/data/fslimage.py
+++ b/fsl/data/fslimage.py
@@ -176,15 +176,27 @@ class Image(props.HasProperties):
if self.transform == 'affine':
voxToWorldMat = self.nibImage.get_affine().transpose()
+ pixdims = self.nibImage.get_header().get_zooms()
+
elif self.transform == 'pixdim':
- pixdims = [self.pixdim[0], self.pixdim[1], self.pixdim[2], 1]
- voxToWorldMat = np.diag(pixdims)
+ pixdims = self.nibImage.get_header().get_zooms()
+ voxToWorldMat = np.diag([pixdims[0], pixdims[1], pixdims[2], 1.0])
+
elif self.transform == 'id':
voxToWorldMat = np.identity(4)
+ pixdims = [1.0, 1.0, 1.0]
self.voxToWorldMat = np.array(voxToWorldMat, dtype=np.float32)
self.worldToVoxMat = linalg.inv(self.voxToWorldMat)
-
+ self.pixdims = pixdims
+
+ # for pixdim/identity transformations, we want the world
+ # location (0, 0) to map to voxel location (0, 0)
+ if self.transform in ['pixdim', 'id']:
+ for i in range(3):
+ self.voxToWorldMat[3, i] = self.pixdims[i] * 0.5
+ self.worldToVoxMat[3, i] = -self.pixdims[i] * 0.5
+
log.debug('Image {} transformation matrix changed: {}'.format(
self.name, self.voxToWorldMat))
@@ -197,6 +209,10 @@ class Image(props.HasProperties):
x, y, z = self.shape[:3]
+ x = x - 1
+ y = y - 1
+ z = z - 1
+
points = np.zeros((8, 3), dtype=np.float32)
points[0, :] = [0, 0, 0]
@@ -210,8 +226,8 @@ class Image(props.HasProperties):
tx = self.voxToWorld(points)
- lo = tx[:, axis].min()
- hi = tx[:, axis].max()
+ lo = tx[:, axis].min() - self.pixdims[axis] * 0.5
+ hi = tx[:, axis].max() + self.pixdims[axis] * 0.5
return (lo, hi)
diff --git a/fsl/fslview/orthopanel.py b/fsl/fslview/orthopanel.py
index 34f0aa614..62b0dc734 100644
--- a/fsl/fslview/orthopanel.py
+++ b/fsl/fslview/orthopanel.py
@@ -264,14 +264,14 @@ class OrthoPanel(wx.Panel, props.HasProperties):
source = ev.GetEventObject()
w, h = source.GetClientSize()
- log.debug('Mouse click on canvas {}: ({}, {})'.format(
- source.name, mx, my))
-
my = h - my
xpos = source.canvasToWorldX(mx)
ypos = source.canvasToWorldY(my)
+ log.debug('Mouse click on canvas {}: ({}, {} -> {}, {})'.format(
+ source.name, mx, my, xpos, ypos))
+
if source == self.xcanvas: self.imageList.location.yz = [xpos, ypos]
elif source == self.ycanvas: self.imageList.location.xz = [xpos, ypos]
elif source == self.zcanvas: self.imageList.location.xy = [xpos, ypos]
--
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