diff --git a/fsl/fsleyes/gl/gl14/gllinevector_funcs.py b/fsl/fsleyes/gl/gl14/gllinevector_funcs.py
index d786be442e8c82fa95e2f0f142a320b59ff54e9e..da3229af77d836f97098abf3dc36fc50b01012db 100644
--- a/fsl/fsleyes/gl/gl14/gllinevector_funcs.py
+++ b/fsl/fsleyes/gl/gl14/gllinevector_funcs.py
@@ -40,6 +40,7 @@ def init(self):
def vertexUpdate(*a):
updateVertices(self)
+ updateShaderState(self)
self.onUpdate()
name = '{}_vertices'.format(self.name)
@@ -122,8 +123,12 @@ def updateShaderState(self):
invShape = 1.0 / shape
modThreshold = [opts.modThreshold / 100.0, 0.0, 0.0, 0.0]
+ if opts.transform in ('id', 'pixdim'): offset = [0.0, 0.0, 0.0, 0.0]
+ else: offset = [0.5, 0.5, 0.5, 0.0]
+
# Vertex program inputs
shaders.setVertexProgramVector( 0, invShape)
+ shaders.setVertexProgramVector( 1, offset)
# Fragment program inputs
shaders.setFragmentProgramMatrix(0, voxValXform)
diff --git a/fsl/fsleyes/gl/gl14/gllinevector_vert.prog b/fsl/fsleyes/gl/gl14/gllinevector_vert.prog
index 88cf875568b08046ba203c74695a3b73f63ea86d..bbcb7e5c1c73b654f095048929b8dc456b5c4582 100644
--- a/fsl/fsleyes/gl/gl14/gllinevector_vert.prog
+++ b/fsl/fsleyes/gl/gl14/gllinevector_vert.prog
@@ -7,6 +7,10 @@
# vertex.position - Vertex position in the voxel coordinate system.
#
# program.local[0] - (first three components) inverse of image shape
+# program.local[1] - (first three components) Offset to apply to transformed
+# voxel coordinates before flooring to integers (this
+# should be 0 in id/pixdim display mode, and 0.5 in
+# affine display mode).
#
# Outputs:
# result.position - the vertex position
@@ -17,6 +21,7 @@
TEMP texCoord;
PARAM invImageShape = program.local[0];
+PARAM voxelOffsets = program.local[1];
# Transform the vertex position (which is in voxel
# coordinates) into display coordinates. It is
@@ -30,7 +35,7 @@ DP4 result.position.w, state.matrix.mvp.row[3], vertex.position;
# Transform the vertex coordinates
# into integer voxel coordinates
MOV texCoord, vertex.position;
-ADD texCoord, texCoord, { 0.5, 0.5, 0.5, 0.0 };
+ADD texCoord, texCoord, voxelOffsets;
FLR texCoord, texCoord;
MOV result.texcoord[1], texCoord;
diff --git a/fsl/fsleyes/gl/gl21/gllinevector_funcs.py b/fsl/fsleyes/gl/gl21/gllinevector_funcs.py
index 14734bb8a7918410580597aec392ab3ed057aa61..76094c499a907e12d83b639e52c59cae217d581c 100644
--- a/fsl/fsleyes/gl/gl21/gllinevector_funcs.py
+++ b/fsl/fsleyes/gl/gl21/gllinevector_funcs.py
@@ -114,7 +114,9 @@ def compileShaders(self):
self.voxToDisplayMatPos = gl.glGetUniformLocation(self.shaders,
'voxToDisplayMat')
self.displayToVoxMatPos = gl.glGetUniformLocation(self.shaders,
- 'displayToVoxMat')
+ 'displayToVoxMat')
+ self.voxelOffsetPos = gl.glGetUniformLocation(self.shaders,
+ 'voxelOffset')
self.cmapXformPos = gl.glGetUniformLocation(self.shaders,
'cmapXform')
@@ -160,13 +162,18 @@ def updateShaderState(self):
d2vMat = opts.getTransform('display', 'voxel')
v2dMat = opts.getTransform('voxel', 'display')
+ if opts.transform in ('id', 'pixdim'): offset = [0, 0, 0]
+ else: offset = [0.5, 0.5, 0.5]
+
+ offset = np.array(offset, dtype=np.float32)
imageDims = np.array(imageDims, dtype=np.float32)
d2vMat = np.array(d2vMat, dtype=np.float32).ravel('C')
v2dMat = np.array(v2dMat, dtype=np.float32).ravel('C')
- gl.glUniform1f( self.directedPos, directed)
- gl.glUniform3fv(self.imageDimsPos, 1, imageDims)
-
+ gl.glUniform1f( self.directedPos, directed)
+ gl.glUniform3fv(self.imageDimsPos, 1, imageDims)
+ gl.glUniform3fv(self.voxelOffsetPos, 1, offset)
+
gl.glUniformMatrix4fv(self.displayToVoxMatPos, 1, False, d2vMat)
gl.glUniformMatrix4fv(self.voxToDisplayMatPos, 1, False, v2dMat)
@@ -277,12 +284,16 @@ def hardwareDraw(self, zpos, xform=None):
elif opts.transform == 'pixdim':
resolution = map(lambda r, p: max(r, p), resolution, image.pixdim[:3])
+ if opts.transform == 'affine': origin = 'centre'
+ else: origin = 'corner'
+
vertices = glroutines.calculateSamplePoints(
image.shape,
resolution,
v2dMat,
self.xax,
- self.yax)[0]
+ self.yax,
+ origin)[0]
vertices[:, self.zax] = zpos
diff --git a/fsl/fsleyes/gl/gl21/gllinevector_vert.glsl b/fsl/fsleyes/gl/gl21/gllinevector_vert.glsl
index ad5865da1719f205352cf6d884c35cf530550543..c3217b5e44aa21751b3a026759f6dcfd23d0e89e 100644
--- a/fsl/fsleyes/gl/gl21/gllinevector_vert.glsl
+++ b/fsl/fsleyes/gl/gl21/gllinevector_vert.glsl
@@ -17,6 +17,8 @@ uniform sampler3D imageTexture;
uniform mat4 displayToVoxMat;
uniform mat4 voxToDisplayMat;
+uniform vec3 voxelOffset;
+
/*
* Transformation matrix which transforms the
@@ -74,7 +76,7 @@ void main(void) {
* There is no round function in GLSL 1.2, so we use
* floor(x + 0.5).
*/
- voxCoord = floor(vertVoxCoord + 0.5);
+ voxCoord = floor(vertVoxCoord + voxelOffset);
/*
* Normalise the voxel coordinates to [0.0, 1.0],
diff --git a/fsl/fsleyes/gl/gllinevector.py b/fsl/fsleyes/gl/gllinevector.py
index 817b6add0eb255b6c3ff64a09185db45cb06e6f8..e9557197e9573b25512714785f96c247b3e69148 100644
--- a/fsl/fsleyes/gl/gllinevector.py
+++ b/fsl/fsleyes/gl/gllinevector.py
@@ -100,6 +100,9 @@ class GLLineVertices(object):
texCoords = (texCoords + 0.5) / np.array(image.shape[:3],
dtype=np.float32)
+ if opts.transform in ('id', 'pixdim'):
+ vertices += 0.5
+
self.vertices = vertices
self.texCoords = texCoords
self.starts = starts
diff --git a/fsl/fsleyes/gl/routines.py b/fsl/fsleyes/gl/routines.py
index 6e70da4e63cd03a50f4cb7b1ae3a786b4f6f066b..a9430e02b887d2b830ce89f26e76a1470146af9e 100644
--- a/fsl/fsleyes/gl/routines.py
+++ b/fsl/fsleyes/gl/routines.py
@@ -53,7 +53,7 @@ def show2D(xax, yax, width, height, lo, hi):
gl.glRotatef(270, 1, 0, 0)
-def calculateSamplePoints(shape, resolution, xform, xax, yax):
+def calculateSamplePoints(shape, resolution, xform, xax, yax, origin='centre'):
"""Calculates a uniform grid of points, in the display coordinate system
(as specified by the given :class:`.Display` object properties) along the
x-y plane (as specified by the xax/yax indices), at which the given image
@@ -93,8 +93,8 @@ def calculateSamplePoints(shape, resolution, xform, xax, yax):
# values of a bounding box which
# encapsulates the entire image,
# in the display coordinate system
- xmin, xmax = transform.axisBounds(shape, xform, xax)
- ymin, ymax = transform.axisBounds(shape, xform, yax)
+ xmin, xmax = transform.axisBounds(shape, xform, xax, origin)
+ ymin, ymax = transform.axisBounds(shape, xform, yax, origin)
# Number of samples along each display
# axis, given the requested resolution