diff --git a/fsl/fslview/gl/gl14/glcircle_funcs.py b/fsl/fslview/gl/gl14/glcircle_funcs.py
index 0ffc8d483e5cfb0a4a40761604d0097f90a11777..25e2de8afa40b381ed7cb459f344ac7009c3c470 100644
--- a/fsl/fslview/gl/gl14/glcircle_funcs.py
+++ b/fsl/fslview/gl/gl14/glcircle_funcs.py
@@ -8,15 +8,16 @@
import logging
log = logging.getLogger(__name__)
-import scipy.ndimage as ndi
-import OpenGL.GL as gl
+import scipy.ndimage as ndi
+import OpenGL.GL as gl
+
+import fsl.utils.transform as transform
def draw(glimg, zpos, xform=None):
"""Draws a slice of the image at the given Z location using immediate
mode rendering.
"""
- image = glimg.image
display = glimg.display
# Don't draw the slice if this
@@ -31,7 +32,7 @@ def draw(glimg, zpos, xform=None):
# Transform world texture coordinates
# to (floating point) voxel coordinates
- voxCoords = image.worldToVox(texCoords)
+ voxCoords = transform.transform(texCoords, display.displayToVoxMat)
imageData = glimg.imageData
texCoordXform = glimg.texCoordXform
colourTexture = glimg.colourTexture
diff --git a/fsl/fslview/gl/gl14/glimage_funcs.py b/fsl/fslview/gl/gl14/glimage_funcs.py
index 8fec7cfec923e3a45e0b3de483d940b3b7a8aa4e..837aa687a13c87a54729ffbbb9f20df2629f0a37 100644
--- a/fsl/fslview/gl/gl14/glimage_funcs.py
+++ b/fsl/fslview/gl/gl14/glimage_funcs.py
@@ -34,9 +34,11 @@ This module provides the following functions:
import logging
log = logging.getLogger(__name__)
-import numpy as np
-import scipy.ndimage as ndi
-import OpenGL.GL as gl
+import numpy as np
+import scipy.ndimage as ndi
+import OpenGL.GL as gl
+
+import fsl.utils.transform as transform
def init(glimg, xax, yax):
@@ -86,7 +88,6 @@ def draw(glimg, zpos, xform=None):
mode rendering.
"""
- image = glimg.image
display = glimg.display
# Don't draw the slice if this
@@ -101,7 +102,7 @@ def draw(glimg, zpos, xform=None):
# Transform world texture coordinates
# to (floating point) voxel coordinates
- voxCoords = image.worldToVox(texCoords)
+ voxCoords = transform.transform(texCoords, display.displayToVoxMat)
imageData = glimg.imageData
texCoordXform = glimg.texCoordXform
colourTexture = glimg.colourTexture
diff --git a/fsl/fslview/gl/gl21/glcircle_funcs.py b/fsl/fslview/gl/gl21/glcircle_funcs.py
index 36e68f70709f425532ea01b0137a0732a75cb483..f2d3f258b6872a95b7985d7d5ead2f54bb761319 100644
--- a/fsl/fslview/gl/gl21/glcircle_funcs.py
+++ b/fsl/fslview/gl/gl21/glcircle_funcs.py
@@ -39,9 +39,9 @@ def draw(glimg, zpos, xform=None):
# to the shader variable
if xform is None: xform = np.identity(4)
- w2w = np.array(xform, dtype=np.float32).ravel('C')
- w2v = np.array(image.worldToVoxMat, dtype=np.float32).ravel('C')
- tcx = np.array(glimg.texCoordXform, dtype=np.float32).ravel('C')
+ w2w = np.array(xform, dtype=np.float32).ravel('C')
+ w2v = np.array(display.displayToVoxMat, dtype=np.float32).ravel('C')
+ tcx = np.array(glimg.texCoordXform, dtype=np.float32).ravel('C')
gl.glUniformMatrix4fv(glimg.worldToVoxMatPos, 1, False, w2v)
gl.glUniformMatrix4fv(glimg.worldToWorldMatPos, 1, False, w2w)
diff --git a/fsl/fslview/gl/gl21/glimage_funcs.py b/fsl/fslview/gl/gl21/glimage_funcs.py
index 58c9f84b94f1fac5f0e86d0083f96652b36a0c9d..9d6e3af221bc64f6d685e7fc855a99d5ff38092d 100644
--- a/fsl/fslview/gl/gl21/glimage_funcs.py
+++ b/fsl/fslview/gl/gl21/glimage_funcs.py
@@ -47,8 +47,6 @@ This module provides the following functions:
import logging
log = logging.getLogger(__name__)
-import os.path as op
-
import numpy as np
import OpenGL.GL as gl
import OpenGL.arrays.vbo as vbo
@@ -397,9 +395,9 @@ def draw(glimg, zpos, xform=None):
# to the shader variable
if xform is None: xform = np.identity(4)
- w2w = np.array(xform, dtype=np.float32).ravel('C')
- w2v = np.array(image.worldToVoxMat, dtype=np.float32).ravel('C')
- tcx = np.array(glimg.texCoordXform, dtype=np.float32).ravel('C')
+ w2w = np.array(xform, dtype=np.float32).ravel('C')
+ w2v = np.array(display.displayToVoxMat, dtype=np.float32).ravel('C')
+ tcx = np.array(glimg.texCoordXform, dtype=np.float32).ravel('C')
gl.glUniformMatrix4fv(glimg.worldToVoxMatPos, 1, False, w2v)
gl.glUniformMatrix4fv(glimg.worldToWorldMatPos, 1, False, w2w)
diff --git a/fsl/fslview/gl/glcircle.py b/fsl/fslview/gl/glcircle.py
index 4be7ff3c3393c2fd9bd7c8dab43141646770991f..16f8d030d47fe757cf98927e1edeb8825e6a74c9 100644
--- a/fsl/fslview/gl/glcircle.py
+++ b/fsl/fslview/gl/glcircle.py
@@ -10,6 +10,8 @@ import logging
log = logging.getLogger(__name__)
import numpy as np
+
+import fsl.utils.transform as transform
import fsl.fslview.gl as fslgl
import fsl.fslview.gl.glimage as glimage
@@ -27,21 +29,22 @@ class GLCircle(glimage.GLImage):
def genVertexData(image, display, xax, yax):
- zax = 3 - xax - yax
- worldRes = display.worldResolution
- voxelRes = display.voxelResolution
- transform = display.transform
+ zax = 3 - xax - yax
+ worldRes = display.worldResolution
+ voxelRes = display.voxelResolution
+ transformCode = display.transform
+ transformMat = display.voxToDisplayMat
# These values give the min/max x/y values
# of a bounding box which encapsulates
# the entire image
- xmin, xmax = image.imageBounds(xax)
- ymin, ymax = image.imageBounds(yax)
+ xmin, xmax = transform.axisBounds(image.shape, transformMat, xax)
+ ymin, ymax = transform.axisBounds(image.shape, transformMat, yax)
# The width/height of a displayed voxel.
# If we are displaying in real world space,
# we use the world display resolution
- if transform in ('affine'):
+ if transformCode in ('affine'):
xpixdim = worldRes
ypixdim = worldRes
@@ -64,7 +67,7 @@ def genVertexData(image, display, xax, yax):
log.debug('Generating coordinate buffers for {} '
'({} resolution {}/{}, num samples {})'.format(
- image.name, transform, worldRes, voxelRes,
+ image.name, transformCode, worldRes, voxelRes,
xNumSamples * yNumSamples))
# The location of every displayed
diff --git a/fsl/fslview/gl/globject.py b/fsl/fslview/gl/globject.py
index 43022578080a49174e97d08c56f62928d66a7c7b..ada9fcb28ee032eabc5a799e612b348240554d40 100644
--- a/fsl/fslview/gl/globject.py
+++ b/fsl/fslview/gl/globject.py
@@ -18,7 +18,8 @@ GL Objects must have the following methods:
import logging
log = logging.getLogger(__name__)
-import numpy as np
+import numpy as np
+import fsl.utils.transform as transform
def createGLObject(image, display):
@@ -68,20 +69,21 @@ def calculateSamplePoints(image, display, xax, yax):
"""
- worldRes = display.worldResolution
- voxelRes = display.voxelResolution
- transform = display.transform
+ worldRes = display.worldResolution
+ voxelRes = display.voxelResolution
+ transformCode = display.transform
+ transformMat = display.voxToDisplayMat
# These values give the min/max x/y values
# of a bounding box which encapsulates
# the entire image
- xmin, xmax = image.imageBounds(xax)
- ymin, ymax = image.imageBounds(yax)
+ xmin, xmax = transform.axisBounds(image.shape, transformMat, xax)
+ ymin, ymax = transform.axisBounds(image.shape, transformMat, yax)
# The width/height of a displayed voxel.
# If we are displaying in real world space,
# we use the world display resolution
- if transform in ('affine'):
+ if transformCode in ('affine'):
xpixdim = worldRes
ypixdim = worldRes
@@ -104,7 +106,7 @@ def calculateSamplePoints(image, display, xax, yax):
log.debug('Generating coordinate buffers for {} '
'({} resolution {}/{}, num samples {})'.format(
- image.name, transform, worldRes, voxelRes,
+ image.name, transformCode, worldRes, voxelRes,
xNumSamples * yNumSamples))
# The location of every displayed
diff --git a/fsl/fslview/gl/gltensorline.py b/fsl/fslview/gl/gltensorline.py
index 0f9653b82b8277e6182f7cf7022ca55c4f3869bd..007ec2d23b22735c0d6d3ebf5874f94c8bc5ec50 100644
--- a/fsl/fslview/gl/gltensorline.py
+++ b/fsl/fslview/gl/gltensorline.py
@@ -18,6 +18,8 @@ import scipy.ndimage as ndi
import globject
+import fsl.utils.transform as transform
+
class GLTensorLine(object):
"""The :class:`GLTensorLine` class encapsulates the data and logic required to
render 2D slices of a X*Y*Z*3 image as tensor lines.
@@ -104,7 +106,9 @@ class GLTensorLine(object):
# Transform the world coordinates to
# floating point voxel coordinates
- voxCoords = image.worldToVox(worldCoords).transpose()
+ dToVMat = display.displayToVoxMat
+
+ voxCoords = transform.transform(worldCoords, dToVMat).transpose()
imageData = image.data
nVoxels = worldCoords.shape[0]
diff --git a/fsl/utils/transform.py b/fsl/utils/transform.py
index b564ce0e290cc2d221deab3c55c2a905cd6b208b..9cf3b688e201b3e6de8b0f844e48af0a84d9aee4 100644
--- a/fsl/utils/transform.py
+++ b/fsl/utils/transform.py
@@ -60,7 +60,7 @@ def axisLength(shape, x, axis):
return sum((tx[0, :] - tx[1, :]) ** 2) ** 0.5
-def transform(p, x, axes):
+def transform(p, x, axes=None):
"""Transforms the given set of points ``p`` according to the given affine
transformation ``x``. The transformed points are returned as a
:class:``numpy.float64`` array.