diff --git a/fsl/fslview/slicecanvas.py b/fsl/fslview/slicecanvas.py
index 46e6fad4b940a9c82299a69cae812d898be7e6da..e31a4d6ad0ae14e66326214a0aacbd912b3ab709 100644
--- a/fsl/fslview/slicecanvas.py
+++ b/fsl/fslview/slicecanvas.py
@@ -60,7 +60,9 @@ class GLImageData(object):
self.image = image
self.canvas = canvas
- # Maximum number of colours used to draw image data
+ # Maximum number of colours used to draw image data.
+ # Keep this to a power of two, as some GL implementations
+ # will complain/misbehave if it isn't.
self.colourResolution = 256
self.initGLImageData()
@@ -75,16 +77,16 @@ class GLImageData(object):
image = self.image
canvas = self.canvas
- # Data stored in the geometry buffer. Defines
- # the geometry of a single voxel, rendered as
- # a triangle strip.
+ # The geometry buffer defines the geometry of
+ # a single voxel, rendered as a triangle strip.
geomData = np.zeros((4, 3), dtype=np.float32)
geomData[:, [canvas.xax, canvas.yax]] = [[-0.5, -0.5],
[ 0.5, -0.5],
[-0.5, 0.5],
[ 0.5, 0.5]]
- geomData = geomData.ravel('C')
+ geomData = geomData.ravel('C')
+ geomBuffer = vbo.VBO(geomData, gl.GL_STATIC_DRAW)
# x/y/z coordinates are stored as VBO arrays
voxData = []
@@ -101,20 +103,28 @@ class GLImageData(object):
xBuffer = vbo.VBO(voxData[0], gl.GL_STATIC_DRAW)
yBuffer = vbo.VBO(voxData[1], gl.GL_STATIC_DRAW)
- zBuffer = vbo.VBO(voxData[2], gl.GL_STATIC_DRAW)
-
- geomBuffer = vbo.VBO(geomData, gl.GL_STATIC_DRAW)
+ zBuffer = vbo.VBO(voxData[2], gl.GL_STATIC_DRAW)
- self.dataBuffer = self.initImageBuffer()
- self.voxXBuffer = xBuffer
- self.voxYBuffer = yBuffer
- self.voxZBuffer = zBuffer
- self.geomBuffer = geomBuffer
+ # The colour buffer, containing a map of
+ # colours (stored on the GPU as a 1D texture)
+ # This is initialised in the updateColourBuffer
+ # method
+ colourBuffer = gl.glGenTextures(1)
+
+ self.dataBuffer = self.initImageBuffer()
+ self.voxXBuffer = xBuffer
+ self.voxYBuffer = yBuffer
+ self.voxZBuffer = zBuffer
+ self.geomBuffer = geomBuffer
+ self.colourBuffer = colourBuffer
# Add listeners to this image so the view can be
# updated when its display properties are changed
self.configDisplayListeners()
+ # Create the colour buffer for the given image
+ self.updateColourBuffer()
+
def initImageBuffer(self):
"""
@@ -193,6 +203,66 @@ class GLImageData(object):
return imageBuffer
+ def updateColourBuffer(self):
+ """
+ Regenerates the colour buffer used to colour image voxels.
+ """
+
+ display = self.image.display
+ colourBuffer = self.colourBuffer
+
+ # Here we are creating a range of values to be passed
+ # to the matplotlib.colors.Colormap instance of the
+ # image display. We scale this range such that data
+ # values which lie outside the configured display range
+ # will map to values below 0.0 or above 1.0. It is
+ # assumed that the Colormap instance is configured to
+ # generate appropriate colours for these out-of-range
+ # values.
+
+ normalRange = np.linspace(0.0, 1.0, self.colourResolution)
+ normalStep = 1.0 / (self.colourResolution - 1)
+
+ normMin = (display.displayMin - display.dataMin) / \
+ (display.dataMax - display.dataMin)
+ normMax = (display.displayMax - display.dataMin) / \
+ (display.dataMax - display.dataMin)
+
+ newStep = normalStep / (normMax - normMin)
+ newRange = (normalRange - normMin) * (newStep / normalStep)
+
+ # Create [self.colourResolution] rgb values,
+ # spanning the entire range of the image
+ # colour map
+ colourmap = display.cmap(newRange)
+
+ # The colour data is stored on
+ # the GPU as 8 bit rgb triplets
+ colourmap = np.floor(colourmap * 255)
+ colourmap = np.array(colourmap, dtype=np.uint8)
+ colourmap = colourmap.ravel(order='C')
+
+ # GL texture creation stuff
+ gl.glBindTexture(gl.GL_TEXTURE_1D, colourBuffer)
+ gl.glTexParameteri(gl.GL_TEXTURE_1D,
+ gl.GL_TEXTURE_MAG_FILTER,
+ gl.GL_NEAREST)
+ gl.glTexParameteri(gl.GL_TEXTURE_1D,
+ gl.GL_TEXTURE_MIN_FILTER,
+ gl.GL_NEAREST)
+ gl.glTexParameteri(gl.GL_TEXTURE_1D,
+ gl.GL_TEXTURE_WRAP_S,
+ gl.GL_CLAMP_TO_EDGE)
+
+ gl.glTexImage1D(gl.GL_TEXTURE_1D,
+ 0,
+ gl.GL_RGBA8,
+ self.colourResolution,
+ 0,
+ gl.GL_RGBA,
+ gl.GL_UNSIGNED_BYTE,
+ colourmap)
+
def configDisplayListeners(self):
"""
@@ -286,12 +356,15 @@ void main(void) {
fragment_shader = """
#version 120
-uniform float alpha;
+uniform float alpha;
+uniform sampler1D colourMap;
varying float fragVoxValue;
void main(void) {
- vec3 voxColour = vec3(fragVoxValue, fragVoxValue, fragVoxValue);
+ vec4 voxTexture = texture1D(colourMap, fragVoxValue);
+ vec3 voxColour = voxTexture.rgb;
+ //vec3 voxColour = vec3(fragVoxValue, fragVoxValue, fragVoxValue);
float voxAlpha = alpha;
gl_FragColor = vec4(voxColour, voxAlpha);
@@ -494,6 +567,55 @@ class SliceCanvas(wxgl.GLCanvas):
self.Refresh()
+ def _compileShaders(self):
+ """
+ Compiles and links the vertex and fragment shader programs,
+ and returns a reference to the resulting program. Raises
+ an error if compilation/linking fails.
+
+ I'm explicitly not using the PyOpenGL
+ OpenGL.GL.shaders.compileProgram function, because it
+ attempts to validate the program after compilation, which
+ fails due to texture data not being bound at the time of
+ validation.
+ """
+
+ # vertex shader
+ vertShader = gl.glCreateShader(gl.GL_VERTEX_SHADER)
+ gl.glShaderSource(vertShader, vertex_shader)
+ gl.glCompileShader(vertShader)
+ vertResult = gl.glGetShaderiv(vertShader, gl.GL_COMPILE_STATUS)
+
+ if vertResult != gl.GL_TRUE:
+ raise '{}'.format(gl.glGetShaderInfoLog(vertShader))
+
+ # fragment shader
+ fragShader = gl.glCreateShader(gl.GL_FRAGMENT_SHADER)
+ gl.glShaderSource(fragShader, fragment_shader)
+ gl.glCompileShader(fragShader)
+ fragResult = gl.glGetShaderiv(fragShader, gl.GL_COMPILE_STATUS)
+
+ if fragResult != gl.GL_TRUE:
+ raise '{}'.format(gl.glGetShaderInfoLog(fragShader))
+
+ # link all of the shaders!
+ program = gl.glCreateProgram()
+ gl.glAttachShader(program, vertShader)
+ gl.glAttachShader(program, fragShader)
+
+ gl.glLinkProgram(program)
+
+ gl.glDeleteShader(vertShader)
+ gl.glDeleteShader(fragShader)
+
+ linkResult = gl.glGetProgramiv(program, gl.GL_LINK_STATUS)
+
+ if linkResult != gl.GL_TRUE:
+ raise '{}'.format(gl.glGetProgramInfoLog(program))
+
+ return program
+
+
def _initGLData(self):
"""
Compiles the vertex and fragment shader programs, and
@@ -504,9 +626,7 @@ class SliceCanvas(wxgl.GLCanvas):
self.context.SetCurrent(self)
- self.shaders = shaders.compileProgram(
- shaders.compileShader(vertex_shader, gl.GL_VERTEX_SHADER),
- shaders.compileShader(fragment_shader, gl.GL_FRAGMENT_SHADER))
+ self.shaders = self._compileShaders()
# Indices of all vertex/fragment shader parameters
self.alphaPos = gl.glGetUniformLocation(self.shaders, 'alpha')
@@ -514,6 +634,8 @@ class SliceCanvas(wxgl.GLCanvas):
'dataBuffer')
self.voxToWorldMatPos = gl.glGetUniformLocation(self.shaders,
'voxToWorldMat')
+ self.colourMapPos = gl.glGetUniformLocation(self.shaders,
+ 'colourMap')
self.xdimPos = gl.glGetUniformLocation(self.shaders, 'xdim')
self.ydimPos = gl.glGetUniformLocation(self.shaders, 'ydim')
self.zdimPos = gl.glGetUniformLocation(self.shaders, 'zdim')
@@ -523,12 +645,10 @@ class SliceCanvas(wxgl.GLCanvas):
self.voxYPos = gl.glGetAttribLocation( self.shaders, 'voxY')
self.voxZPos = gl.glGetAttribLocation( self.shaders, 'voxZ')
-
# initialise data for the images that
# are already in the image list
self._imageListChanged()
-
# A bit hacky. We can only set the GL context (and create
# the GL data) once something is actually displayed on the
# screen. The _initGLData method is called (asynchronously)
@@ -610,13 +730,13 @@ class SliceCanvas(wxgl.GLCanvas):
try: glImageData = image.getAttribute(self.name)
except: continue
- imageDisplay = image.display
-
- dataBuffer = glImageData.dataBuffer
- voxXBuffer = glImageData.voxXBuffer
- voxYBuffer = glImageData.voxYBuffer
- voxZBuffer = glImageData.voxZBuffer
- geomBuffer = glImageData.geomBuffer
+ imageDisplay = image.display
+ dataBuffer = glImageData.dataBuffer
+ voxXBuffer = glImageData.voxXBuffer
+ voxYBuffer = glImageData.voxYBuffer
+ voxZBuffer = glImageData.voxZBuffer
+ geomBuffer = glImageData.geomBuffer
+ colourBuffer = glImageData.colourBuffer
xdim = image.shape[self.xax]
ydim = image.shape[self.yax]
@@ -632,11 +752,11 @@ class SliceCanvas(wxgl.GLCanvas):
if zi < 0 or zi >= zdim:
continue
- # bind the current alpha value to the
- # shader alpha variable
+ # bind the current alpha value
+ # to the shader alpha variable
gl.glUniform1f(self.alphaPos, imageDisplay.alpha)
- #
+ # Bind the voxel coordinate buffers
gl.glUniform1f(self.xdimPos, glImageData.imageTexShape[0])
gl.glUniform1f(self.ydimPos, glImageData.imageTexShape[1])
gl.glUniform1f(self.zdimPos, glImageData.imageTexShape[2])
@@ -647,17 +767,16 @@ class SliceCanvas(wxgl.GLCanvas):
gl.glUniformMatrix4fv(self.voxToWorldMatPos, 1, True, xmat)
# Set up the colour buffer
- # gl.glEnable(gl.GL_TEXTURE_1D)
- # gl.glActiveTexture(gl.GL_TEXTURE0)
- # gl.glBindTexture(gl.GL_TEXTURE_1D, colourBuffer)
- # gl.glUniform1i(self.colourMapPos, 0)
+ gl.glEnable(gl.GL_TEXTURE_1D)
+ gl.glActiveTexture(gl.GL_TEXTURE0)
+ gl.glBindTexture(gl.GL_TEXTURE_1D, colourBuffer)
+ gl.glUniform1i(self.colourMapPos, 0)
# Set up the image data buffer
gl.glEnable(gl.GL_TEXTURE_3D)
- # change to texxture 1 when you get working
- gl.glActiveTexture(gl.GL_TEXTURE0)
+ gl.glActiveTexture(gl.GL_TEXTURE1)
gl.glBindTexture(gl.GL_TEXTURE_3D, dataBuffer)
- gl.glUniform1i(self.dataBufferPos, 0)
+ gl.glUniform1i(self.dataBufferPos, 1)
# voxel coordinates
voxOffs = [0, 0, 0]
@@ -705,7 +824,7 @@ class SliceCanvas(wxgl.GLCanvas):
gl.glDisableVertexAttribArray(self.voxXPos)
gl.glDisableVertexAttribArray(self.voxYPos)
gl.glDisableVertexAttribArray(self.voxZPos)
-# gl.glDisable(gl.GL_TEXTURE_1D)
+ gl.glDisable(gl.GL_TEXTURE_1D)
gl.glDisable(gl.GL_TEXTURE_3D)
gl.glUseProgram(0)