diff --git a/fsl/fslview/displaycontext/display.py b/fsl/fslview/displaycontext/display.py
index 15781f8730aff23d98462d5872c063da3a22eef5..9616e3cbe87fa93efbe3ce2d9853c3d0b4672f82 100644
--- a/fsl/fslview/displaycontext/display.py
+++ b/fsl/fslview/displaycontext/display.py
@@ -4,7 +4,15 @@
#
# Author: Paul McCarthy <pauldmccarthy@gmail.com>
#
-"""
+"""This module provides definitions of an important class - the
+:class:`Display` class.
+
+A ``Display`` contains a specification for the way in which an
+:class:`~fsl.data.image.Image` instance is to be displayed.
+
+
+..note:: Put a description of the three coordinate systems which
+ exist in the system.
"""
import logging
@@ -295,12 +303,6 @@ class Display(props.SyncableHasProperties):
elif self.transform == 'affine':
voxToDisplayMat = self.voxToWorldMat
- # for pixdim/identity transformations, we want the world
- # location (0, 0, 0) to map to voxel location (0, 0, 0)
- if self.transform in ('id', 'pixdim'):
- for i in range(3):
- voxToDisplayMat[3, i] = pixdim[i] * 0.5
-
# Transformation matrices for moving between the voxel
# coordinate system and the display coordinate system
self.voxToDisplayMat = np.array(voxToDisplayMat, dtype=np.float32)
diff --git a/fsl/fslview/gl/gl21/generic_vert.glsl b/fsl/fslview/gl/gl21/generic_vert.glsl
index 719683b2c0c5b22b685e21bdf6491f71a7f95742..abef9271bbcd979692143e8ce21706b683c88221 100644
--- a/fsl/fslview/gl/gl21/generic_vert.glsl
+++ b/fsl/fslview/gl/gl21/generic_vert.glsl
@@ -8,6 +8,9 @@
*/
#version 120
+
+uniform mat4 displayToVoxMat;
+
/*
* Optional transformation matrix which is applied to all
* vertex coordinates (used by the e.g. lightbox canvas to
@@ -38,6 +41,12 @@ uniform float zCoord;
varying vec3 fragTexCoords;
+/*
+ * Image voxel coordinates corresponding to this vertex.
+ */
+varying vec3 fragVoxCoords;
+
+
void main(void) {
vec4 worldLoc = vec4(0, 0, 0, 1);
@@ -45,6 +54,26 @@ void main(void) {
worldLoc[yax] = worldCoords.y;
worldLoc[zax] = zCoord;
+ /*
+ * Transform the texture coordinates into voxel coordinates
+ */
+ fragVoxCoords = (displayToVoxMat * worldLoc).xyz;
+
+ /*
+ * Centre voxel coordinates - the display space of a voxel
+ * at a particular location (x, y, z) extends from
+ *
+ * (x-0.5, y-0.5, z-0.5)
+ *
+ * to
+ *
+ * (x+0.5, y+0.5, z+0.5),
+ *
+ * so we need to offset the coordinates by 0.5 to
+ * make the coordinates usable as voxel indices
+ */
+ fragVoxCoords.xyz = fragVoxCoords.xyz + 0.5;
+
/*
* Pass the vertex coordinates as texture
* coordinates to the fragment shader
diff --git a/fsl/fslview/gl/gl21/gltensor_rgb_frag.glsl b/fsl/fslview/gl/gl21/gltensor_rgb_frag.glsl
index 76b28d8243a52bad5e95de4756be44b435606e0f..0cd2cdfe070b3e273b423daade81a18280691818 100644
--- a/fsl/fslview/gl/gl21/gltensor_rgb_frag.glsl
+++ b/fsl/fslview/gl/gl21/gltensor_rgb_frag.glsl
@@ -7,6 +7,8 @@
#pragma include spline_interp.glsl
+#pragma include test_in_bounds.glsl
+
/*
* image data texture
*/
@@ -29,50 +31,26 @@ uniform vec3 imageShape;
*/
uniform bool useSpline;
-/*
- * Transformation from display space to voxel coordinates.
- */
-uniform mat4 displayToVoxMat;
-
/*
* Image texture coordinates.
*/
varying vec3 fragTexCoords;
+/*
+ * Image voxel coordinates
+ */
+varying vec3 fragVoxCoords;
void main(void) {
- /*
- * Transform the texture coordinates into voxel coordinates
- */
- vec4 voxCoords = displayToVoxMat * vec4(fragTexCoords, 1);
+ vec3 voxCoords = fragVoxCoords;
- /*
- * Centre voxel coordinates
- */
- voxCoords.xyz = voxCoords.xyz + 0.5;
+ if (!test_in_bounds(voxCoords, imageShape)) {
- /*
- * Don't render the fragment if it's outside the image space
- */
- if (voxCoords.x < -0.01 || voxCoords.x >= imageShape.x + 0.01 ||
- voxCoords.y < -0.01 || voxCoords.y >= imageShape.y + 0.01 ||
- voxCoords.z < -0.01 || voxCoords.z >= imageShape.z + 0.01) {
-
gl_FragColor = vec4(0.0, 0.0, 0.0, 0.0);
return;
}
- /*
- * Be lenient at voxel boundaries
- */
- if (voxCoords.x < 0.0) voxCoords.x = 0.01;
- if (voxCoords.y < 0.0) voxCoords.y = 0.01;
- if (voxCoords.z < 0.0) voxCoords.z = 0.01;
- if (voxCoords.x >= imageShape.x) voxCoords.x = imageShape.x - 0.01;
- if (voxCoords.y >= imageShape.y) voxCoords.y = imageShape.y - 0.01;
- if (voxCoords.z >= imageShape.z) voxCoords.z = imageShape.z - 0.01;
-
/*
* Normalise voxel coordinates to (0.0, 1.0)
*/
diff --git a/fsl/fslview/gl/gl21/glvolume_frag.glsl b/fsl/fslview/gl/gl21/glvolume_frag.glsl
index e850a297a4c45bce0bbebc6f1bc0e22d22e015d2..15a508dd10a92fd0f2324fca9b0ce13983a81ac4 100644
--- a/fsl/fslview/gl/gl21/glvolume_frag.glsl
+++ b/fsl/fslview/gl/gl21/glvolume_frag.glsl
@@ -6,6 +6,7 @@
#version 120
#pragma include spline_interp.glsl
+#pragma include test_in_bounds.glsl
/*
* image data texture
@@ -27,11 +28,6 @@ uniform sampler1D colourTexture;
*/
uniform bool useSpline;
-/*
- * Transformation from display space to voxel coordinates.
- */
-uniform mat4 displayToVoxMat;
-
/*
* Transformation matrix to apply to the 1D texture coordinate.
*/
@@ -43,39 +39,22 @@ uniform mat4 voxValXform;
varying vec3 fragTexCoords;
-void main(void) {
+/*
+ * Image voxel coordinates
+ */
+varying vec3 fragVoxCoords;
- /*
- * Transform the texture coordinates into voxel coordinates
- */
- vec4 voxCoords = displayToVoxMat * vec4(fragTexCoords, 1);
- /*
- * Centre voxel coordinates
- */
- voxCoords.xyz = voxCoords.xyz + 0.5;
+void main(void) {
- /*
- * Don't render the fragment if it's outside the image space
- */
- if (voxCoords.x < -0.01 || voxCoords.x >= imageShape.x + 0.01 ||
- voxCoords.y < -0.01 || voxCoords.y >= imageShape.y + 0.01 ||
- voxCoords.z < -0.01 || voxCoords.z >= imageShape.z + 0.01) {
+ vec3 voxCoords = fragVoxCoords;
+
+ if (!test_in_bounds(voxCoords, imageShape)) {
gl_FragColor = vec4(0.0, 0.0, 0.0, 0.0);
return;
}
- /*
- * Be lenient at voxel boundaries
- */
- if (voxCoords.x < 0.0) voxCoords.x = 0.01;
- if (voxCoords.y < 0.0) voxCoords.y = 0.01;
- if (voxCoords.z < 0.0) voxCoords.z = 0.01;
- if (voxCoords.x >= imageShape.x) voxCoords.x = imageShape.x - 0.01;
- if (voxCoords.y >= imageShape.y) voxCoords.y = imageShape.y - 0.01;
- if (voxCoords.z >= imageShape.z) voxCoords.z = imageShape.z - 0.01;
-
/*
* Normalise voxel coordinates to (0.0, 1.0)
*/
diff --git a/fsl/fslview/gl/gl21/test_in_bounds.glsl b/fsl/fslview/gl/gl21/test_in_bounds.glsl
new file mode 100644
index 0000000000000000000000000000000000000000..d01b2dd56e853a5e7c7fec4591b78ae66fcb7626
--- /dev/null
+++ b/fsl/fslview/gl/gl21/test_in_bounds.glsl
@@ -0,0 +1,29 @@
+/**
+ * Simple bounds test to determine whether the given voxel coordinates
+ * are within the bounds specified by the given array/image shape.
+ */
+bool test_in_bounds(inout vec3 coords, vec3 shape) {
+
+ /*
+ * Don't render the fragment if it's outside the image space
+ */
+ if (coords.x < -0.01 || coords.x >= shape.x + 0.01 ||
+ coords.y < -0.01 || coords.y >= shape.y + 0.01 ||
+ coords.z < -0.01 || coords.z >= shape.z + 0.01) {
+
+ return false;
+ }
+
+ /*
+ * Be lenient at voxel boundaries
+ */
+ if (coords.x < 0.0) coords.x = 0.01;
+ if (coords.y < 0.0) coords.y = 0.01;
+ if (coords.z < 0.0) coords.z = 0.01;
+ if (coords.x >= shape.x) coords.x = shape.x - 0.01;
+ if (coords.y >= shape.y) coords.y = shape.y - 0.01;
+ if (coords.z >= shape.z) coords.z = shape.z - 0.01;
+
+
+ return true;
+}
\ No newline at end of file
diff --git a/fsl/utils/transform.py b/fsl/utils/transform.py
index 1ffea567dda9e29ae8efd9df46219a4135db71f6..f8d427ca3bc09276442ded2312020db754b64969 100644
--- a/fsl/utils/transform.py
+++ b/fsl/utils/transform.py
@@ -51,7 +51,21 @@ def scaleOffsetXform(scales, offsets):
def axisBounds(shape, xform, axes=None):
- """Returns the (lo, hi) bounds of the specified axis/axes."""
+ """Returns the (lo, hi) bounds of the specified axis/axes.
+
+ This function assumes that voxel indices correspond to the voxel
+ centre. For example, the voxel at ``(4, 5, 6)`` covers the space:
+
+ ``[3.5 - 4.5, 4.5 - 5.5, 5.5 - 6.5]``
+
+ So the bounds of the specified shape extends from the corner at
+
+ ``(-0.5, -0.5, -0.5)``
+
+ to the corner at
+
+ ``(shape[0] - 0.5, shape[1] - 0.5, shape[1] - 0.5)``
+ """
scalar = False
@@ -64,12 +78,12 @@ def axisBounds(shape, xform, axes=None):
x, y, z = shape[:3]
+ points = np.zeros((8, 3), dtype=np.float32)
+
x -= 0.5
y -= 0.5
z -= 0.5
- points = np.zeros((8, 3), dtype=np.float32)
-
points[0, :] = [-0.5, -0.5, -0.5]
points[1, :] = [-0.5, -0.5, z]
points[2, :] = [-0.5, y, -0.5]