diff --git a/fsl/fsleyes/gl/gl21/glvolume_frag.glsl b/fsl/fsleyes/gl/gl21/glvolume_frag.glsl
index 006509b51051ee001a4e2a870901d3dca23c6066..5b56722b1689e91bf76b86e20b90c7d2b0aad90d 100644
--- a/fsl/fsleyes/gl/gl21/glvolume_frag.glsl
+++ b/fsl/fsleyes/gl/gl21/glvolume_frag.glsl
@@ -18,6 +18,16 @@ uniform sampler3D imageTexture;
*/
uniform sampler1D colourTexture;
+/*
+ * Texture containing the negative colour map.
+ */
+uniform sampler1D negColourTexture;
+
+/*
+ * Flag which determines whether to
+ * use the negative colour map.
+ */
+uniform bool enableNegCmap;
/*
* Shape of the imageTexture.
@@ -37,15 +47,25 @@ uniform bool useSpline;
uniform mat4 voxValXform;
/*
- * Clip voxels below this value.
+ * Clip voxels below this value. This must be specified
+ * in the image texture data range.
*/
uniform float clipLow;
/*
- * Clip voxels above this value.
+ * Clip voxels above this value. This must be specified
+ * in the image texture data range.
*/
uniform float clipHigh;
+/*
+ * Value in the image texture data range which corresponds
+ * to zero - this is used to determine whether to use the
+ * regular, or the negative colour texture (if enableNegCmap
+ * is true).
+ */
+uniform float texZero;
+
/*
* Invert clipping behaviour - clip voxels
* that are inside the clipLow/High bounds.
@@ -65,7 +85,10 @@ varying vec3 fragTexCoord;
void main(void) {
- vec3 voxCoord = fragVoxCoord;
+ float voxValue;
+ vec4 normVoxValue;
+ bool useNegCmap = false;
+ vec3 voxCoord = fragVoxCoord;
/*
* Skip voxels that are out of the image bounds
@@ -79,7 +102,6 @@ void main(void) {
/*
* Look up the voxel value
*/
- float voxValue;
if (useSpline) voxValue = spline_interp(imageTexture,
fragTexCoord,
imageShape,
@@ -87,20 +109,35 @@ void main(void) {
else voxValue = texture3D( imageTexture,
fragTexCoord).r;
+ /*
+ * If we are using a negative colour map,
+ * and the voxel value is below the negative
+ * threshold (texZero) invert the voxel
+ * value, and set a flag telling the code
+ * below to use the neagtive colour map.
+ */
+ if (enableNegCmap && voxValue <= texZero) {
+
+ useNegCmap = true;
+ voxValue = texZero + (texZero - voxValue);
+ }
+
/*
* Clip out of range voxel values
*/
-
if ((!invertClip && (voxValue < clipLow || voxValue > clipHigh)) ||
- (invertClip && (voxValue >= clipLow && voxValue <= clipHigh))) {
- gl_FragColor = vec4(0.0, 0.0, 0.0, 0.0);
- return;
+ ( invertClip && (voxValue >= clipLow && voxValue <= clipHigh))) {
+
+ gl_FragColor = vec4(0.0, 0.0, 0.0, 0.0);
+ return;
}
/*
* Transform the voxel value to a colour map texture
* coordinate, and look up the colour for the voxel value
- */
- vec4 normVoxValue = voxValXform * vec4(voxValue, 0, 0, 1);
- gl_FragColor = texture1D(colourTexture, normVoxValue.x);
+ */
+ normVoxValue = voxValXform * vec4(voxValue, 0, 0, 1);
+
+ if (useNegCmap) gl_FragColor = texture1D(negColourTexture, normVoxValue.x);
+ else gl_FragColor = texture1D(colourTexture, normVoxValue.x);
}
diff --git a/fsl/fsleyes/gl/gl21/glvolume_funcs.py b/fsl/fsleyes/gl/gl21/glvolume_funcs.py
index 009ad30bcee83fafb86dfbe7b8f3e0983d3d7210..a0e87d615f59d0043b3f2c0993e19d1f88860a9d 100644
--- a/fsl/fsleyes/gl/gl21/glvolume_funcs.py
+++ b/fsl/fsleyes/gl/gl21/glvolume_funcs.py
@@ -58,28 +58,34 @@ def compileShaders(self):
self.shaders = shaders.compileShaders(vertShaderSrc, fragShaderSrc)
# indices of all vertex/fragment shader parameters
- self.vertexPos = gl.glGetAttribLocation( self.shaders,
- 'vertex')
- self.voxCoordPos = gl.glGetAttribLocation( self.shaders,
- 'voxCoord')
- self.texCoordPos = gl.glGetAttribLocation( self.shaders,
- 'texCoord')
- self.imageTexturePos = gl.glGetUniformLocation(self.shaders,
- 'imageTexture')
- self.colourTexturePos = gl.glGetUniformLocation(self.shaders,
- 'colourTexture')
- self.imageShapePos = gl.glGetUniformLocation(self.shaders,
- 'imageShape')
- self.useSplinePos = gl.glGetUniformLocation(self.shaders,
- 'useSpline')
- self.voxValXformPos = gl.glGetUniformLocation(self.shaders,
- 'voxValXform')
- self.clipLowPos = gl.glGetUniformLocation(self.shaders,
- 'clipLow')
- self.clipHighPos = gl.glGetUniformLocation(self.shaders,
- 'clipHigh')
- self.invertClipPos = gl.glGetUniformLocation(self.shaders,
- 'invertClip')
+ self.vertexPos = gl.glGetAttribLocation( self.shaders,
+ 'vertex')
+ self.voxCoordPos = gl.glGetAttribLocation( self.shaders,
+ 'voxCoord')
+ self.texCoordPos = gl.glGetAttribLocation( self.shaders,
+ 'texCoord')
+ self.imageTexturePos = gl.glGetUniformLocation(self.shaders,
+ 'imageTexture')
+ self.colourTexturePos = gl.glGetUniformLocation(self.shaders,
+ 'colourTexture')
+ self.negColourTexturePos = gl.glGetUniformLocation(self.shaders,
+ 'negColourTexture')
+ self.enableNegCmapPos = gl.glGetUniformLocation(self.shaders,
+ 'enableNegCmap')
+ self.texZeroPos = gl.glGetUniformLocation(self.shaders,
+ 'texZero')
+ self.imageShapePos = gl.glGetUniformLocation(self.shaders,
+ 'imageShape')
+ self.useSplinePos = gl.glGetUniformLocation(self.shaders,
+ 'useSpline')
+ self.voxValXformPos = gl.glGetUniformLocation(self.shaders,
+ 'voxValXform')
+ self.clipLowPos = gl.glGetUniformLocation(self.shaders,
+ 'clipLow')
+ self.clipHighPos = gl.glGetUniformLocation(self.shaders,
+ 'clipHigh')
+ self.invertClipPos = gl.glGetUniformLocation(self.shaders,
+ 'invertClip')
def updateShaderState(self):
@@ -105,10 +111,13 @@ def updateShaderState(self):
xform = self.imageTexture.invVoxValXform
clipLow = opts.clippingRange[0] * xform[0, 0] + xform[3, 0]
clipHigh = opts.clippingRange[1] * xform[0, 0] + xform[3, 0]
+ texZero = 0.0 * xform[0, 0] + xform[3, 0]
- gl.glUniform1f(self.clipLowPos, clipLow)
- gl.glUniform1f(self.clipHighPos, clipHigh)
- gl.glUniform1f(self.invertClipPos, opts.invertClipping)
+ gl.glUniform1f(self.clipLowPos, clipLow)
+ gl.glUniform1f(self.clipHighPos, clipHigh)
+ gl.glUniform1f(self.texZeroPos, texZero)
+ gl.glUniform1f(self.invertClipPos, opts.invertClipping)
+ gl.glUniform1f(self.enableNegCmapPos, opts.enableNegativeCmap)
# Bind transformation matrix to transform
# from image texture values to voxel values,
@@ -121,8 +130,9 @@ def updateShaderState(self):
gl.glUniformMatrix4fv(self.voxValXformPos, 1, False, vvx)
# Set up the colour and image textures
- gl.glUniform1i(self.imageTexturePos, 0)
- gl.glUniform1i(self.colourTexturePos, 1)
+ gl.glUniform1i(self.imageTexturePos, 0)
+ gl.glUniform1i(self.colourTexturePos, 1)
+ gl.glUniform1i(self.negColourTexturePos, 2)
gl.glUseProgram(0)
diff --git a/fsl/fsleyes/gl/glvolume.py b/fsl/fsleyes/gl/glvolume.py
index 2a9317a704350097e26566df7df5349f1ec6c167..9c19c478467afd626255286d892341aa603c1e96 100644
--- a/fsl/fsleyes/gl/glvolume.py
+++ b/fsl/fsleyes/gl/glvolume.py
@@ -81,10 +81,28 @@ class GLVolume(globject.GLImageObject):
OpenGL version-specific module is used. The image data itself is stored
as an :class:`.ImageTexture`. This ``ImageTexture`` is managed by the
:mod:`.resources` module, so may be shared by many ``GLVolume`` instances.
- The current colour map (defined by the :class:`.VolumeOpts.cmap` property)
- is stored as a :class:`.ColourMapTexture`. A slice through the texture is
+ The current colour maps (defined by the :attr:`.VolumeOpts.cmap` and
+ :attr:`.VolumeOpts.negativeCmap` properties) are stored as
+ :class:`.ColourMapTexture` instances. A slice through the texture is
rendered using six vertices, located at the respective corners of the
- image bounds.
+ image bounds.
+
+
+ **Textures**
+
+
+ The ``GLVolume`` class uses three textures:
+
+ - An :class:`.ImageTexture`, a 3D texture which contains image data.
+ This is bound to texture unit 0.
+
+ - A :class:`.ColourMapTexture`, a 1D texture which contains the
+ colour map defined by the :attr:`.VolumeOpts.cmap` property.
+ This is bound to texture unit 1.
+
+ - A :class:`.ColourMapTexture`, a 1D texture which contains the
+ colour map defined by the :attr:`.VolumeOpts.negativeCmap` property.
+ This is bound to texture unit 2.
**Attributes**
@@ -92,13 +110,17 @@ class GLVolume(globject.GLImageObject):
The following attributes are available on a ``GLVolume`` instance:
- ================= =======================================================
- ``imageTexture`` The :class:`.ImageTexture` which stores the image data.
- ``colourTexture`` The :class:`.ColourMapTexture` used to store the
- colour map.
- ``texName`` A name used for the ``imageTexture`` and
- ``colourTexture``.
- ================= =======================================================
+ ==================== =================================================
+ ``imageTexture`` The :class:`.ImageTexture` which stores the image
+ data.
+ ``colourTexture`` The :class:`.ColourMapTexture` used to store the
+ colour map.
+ ``negColourTexture`` The :class:`.ColourMapTexture` used to store the
+ negative colour map.
+ ``texName`` A name used for the ``imageTexture``,
+ ``colourTexture``, and ``negColourTexture`. The
+ name for the latter is suffixed with ``'_neg'``.
+ ==================== =================================================
"""
@@ -120,11 +142,13 @@ class GLVolume(globject.GLImageObject):
# Create an image texture and a colour map texture
self.texName = '{}_{}'.format(type(self).__name__, id(self.image))
- self.colourTexture = textures.ColourMapTexture(self.texName)
- self.imageTexture = None
-
+ self.imageTexture = None
+ self.colourTexture = textures.ColourMapTexture(self.texName)
+ self.negColourTexture = textures.ColourMapTexture(
+ '{}_neg'.format(self.texName))
+
self.refreshImageTexture()
- self.refreshColourTexture()
+ self.refreshColourTextures()
fslgl.glvolume_funcs.init(self)
@@ -138,14 +162,16 @@ class GLVolume(globject.GLImageObject):
glresources.delete(self.imageTexture.getTextureName())
- self.colourTexture.destroy()
+ self.colourTexture .destroy()
+ self.negColourTexture.destroy()
- self.imageTexture = None
- self.colourTexture = None
+ self.imageTexture = None
+ self.colourTexture = None
+ self.negColourTexture = None
self.removeDisplayListeners()
- fslgl.glvolume_funcs.destroy(self)
+ fslgl.glvolume_funcs .destroy(self)
globject.GLImageObject.destroy(self)
@@ -168,7 +194,7 @@ class GLVolume(globject.GLImageObject):
self.onUpdate()
def colourUpdate(*a):
- self.refreshColourTexture()
+ self.refreshColourTextures()
fslgl.glvolume_funcs.updateShaderState(self)
self.onUpdate()
@@ -176,11 +202,6 @@ class GLVolume(globject.GLImageObject):
fslgl.glvolume_funcs.updateShaderState(self)
self.onUpdate()
- def shaderCompile(*a):
- fslgl.glvolume_funcs.compileShaders( self)
- fslgl.glvolume_funcs.updateShaderState(self)
- self.onUpdate()
-
def imageRefresh(*a):
self.refreshImageTexture()
fslgl.glvolume_funcs.updateShaderState(self)
@@ -205,6 +226,9 @@ class GLVolume(globject.GLImageObject):
opts .addListener('clippingRange', lName, shaderUpdate, weak=False)
opts .addListener('invertClipping', lName, shaderUpdate, weak=False)
opts .addListener('cmap', lName, colourUpdate, weak=False)
+ opts .addListener('negativeCmap', lName, colourUpdate, weak=False)
+ opts .addListener('enableNegativeCmap',
+ lName, colourUpdate, weak=False)
opts .addListener('invert', lName, colourUpdate, weak=False)
opts .addListener('volume', lName, imageUpdate, weak=False)
opts .addListener('resolution', lName, imageUpdate, weak=False)
@@ -239,16 +263,19 @@ class GLVolume(globject.GLImageObject):
lName = self.name
- display.removeListener( 'alpha', lName)
- opts .removeListener( 'displayRange', lName)
- opts .removeListener( 'clippingRange', lName)
- opts .removeListener( 'invertClipping', lName)
- opts .removeListener( 'cmap', lName)
- opts .removeListener( 'invert', lName)
- opts .removeListener( 'volume', lName)
- opts .removeListener( 'resolution', lName)
- opts .removeListener( 'interpolation', lName)
- opts .removeListener( 'transform', lName)
+ display.removeListener( 'alpha', lName)
+ opts .removeListener( 'displayRange', lName)
+ opts .removeListener( 'clippingRange', lName)
+ opts .removeListener( 'invertClipping', lName)
+ opts .removeListener( 'cmap', lName)
+ opts .removeListener( 'negativeCmap', lName)
+ opts .removeListener( 'enableNegativeCmap', lName)
+ opts .removeListener( 'cmap', lName)
+ opts .removeListener( 'invert', lName)
+ opts .removeListener( 'volume', lName)
+ opts .removeListener( 'resolution', lName)
+ opts .removeListener( 'interpolation', lName)
+ opts .removeListener( 'transform', lName)
if self.__syncListenersRegistered:
opts.removeSyncChangeListener('volume', lName)
@@ -298,15 +325,16 @@ class GLVolume(globject.GLImageObject):
interp=interp)
- def refreshColourTexture(self):
- """Refreshes the :class:`.ColourMapTexture` used to colour image
- voxels.
+ def refreshColourTextures(self):
+ """Refreshes the :class:`.ColourMapTexture` instances used to colour
+ image voxels.
"""
display = self.display
opts = self.displayOpts
alpha = display.alpha / 100.0
cmap = opts.cmap
+ negCmap = opts.negativeCmap
invert = opts.invert
dmin = opts.displayRange[0]
dmax = opts.displayRange[1]
@@ -316,6 +344,11 @@ class GLVolume(globject.GLImageObject):
alpha=alpha,
displayRange=(dmin, dmax))
+ self.negColourTexture.set(cmap=negCmap,
+ invert=invert,
+ alpha=alpha,
+ displayRange=(dmin, dmax))
+
def preDraw(self):
"""Binds the :class:`.ImageTexture` to ``GL_TEXTURE0`` and the
@@ -324,8 +357,9 @@ class GLVolume(globject.GLImageObject):
"""
# Set up the image and colour textures
- self.imageTexture .bindTexture(gl.GL_TEXTURE0)
- self.colourTexture.bindTexture(gl.GL_TEXTURE1)
+ self.imageTexture .bindTexture(gl.GL_TEXTURE0)
+ self.colourTexture .bindTexture(gl.GL_TEXTURE1)
+ self.negColourTexture.bindTexture(gl.GL_TEXTURE2)
fslgl.glvolume_funcs.preDraw(self)
@@ -359,7 +393,8 @@ class GLVolume(globject.GLImageObject):
version-dependent ``postDraw`` function.
"""
- self.imageTexture .unbindTexture()
- self.colourTexture.unbindTexture()
+ self.imageTexture .unbindTexture()
+ self.colourTexture .unbindTexture()
+ self.negColourTexture.unbindTexture()
fslgl.glvolume_funcs.postDraw(self)