From b48ecb3dc9677eb4fd71a6e66db3004a8b41de18 Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauld.mccarthy@gmail.com>
Date: Mon, 1 Jun 2015 17:30:11 +0100
Subject: [PATCH] Initial implementation of Label images. Very rough right now.
---
fsl/data/strings.py | 1 +
fsl/fslview/displaycontext/__init__.py | 1 +
fsl/fslview/displaycontext/display.py | 6 +-
fsl/fslview/displaycontext/labelopts.py | 32 +++++
fsl/fslview/displaycontext/modelopts.py | 3 +
fsl/fslview/gl/__init__.py | 1 +
fsl/fslview/gl/gl21/__init__.py | 1 +
fsl/fslview/gl/gl21/gllabel_frag.glsl | 83 +++++++++++
fsl/fslview/gl/gl21/gllabel_funcs.py | 71 ++++++++++
fsl/fslview/gl/gllabel.py | 133 ++++++++++++++++++
fsl/fslview/gl/globject.py | 4 +-
fsl/fslview/gl/shaders.py | 7 +-
fsl/fslview/gl/textures/__init__.py | 1 +
fsl/fslview/gl/textures/lookuptabletexture.py | 103 ++++++++++++++
fsl/fslview/layouts.py | 8 +-
fsl/fslview/lookuptables.py | 86 +++++++++++
fsl/fslview/luts/harvard-oxford-cortical.txt | 48 +++++++
17 files changed, 584 insertions(+), 5 deletions(-)
create mode 100644 fsl/fslview/displaycontext/labelopts.py
create mode 100644 fsl/fslview/gl/gl21/gllabel_frag.glsl
create mode 100644 fsl/fslview/gl/gl21/gllabel_funcs.py
create mode 100644 fsl/fslview/gl/gllabel.py
create mode 100644 fsl/fslview/gl/textures/lookuptabletexture.py
create mode 100644 fsl/fslview/lookuptables.py
create mode 100644 fsl/fslview/luts/harvard-oxford-cortical.txt
diff --git a/fsl/data/strings.py b/fsl/data/strings.py
index 047a8c0b4..aa6b48b08 100644
--- a/fsl/data/strings.py
+++ b/fsl/data/strings.py
@@ -316,6 +316,7 @@ choices = TypeDict({
'Display.overlayType.volume' : '3D/4D volume',
'Display.overlayType.mask' : '3D/4D mask image',
+ 'Display.overlayType.label' : 'Label image',
'Display.overlayType.rgbvector' : '3-direction vector image (RGB)',
'Display.overlayType.linevector' : '3-direction vector image (Line)',
'Display.overlayType.model' : '3D model'
diff --git a/fsl/fslview/displaycontext/__init__.py b/fsl/fslview/displaycontext/__init__.py
index 0cad30f68..a70f549b0 100644
--- a/fsl/fslview/displaycontext/__init__.py
+++ b/fsl/fslview/displaycontext/__init__.py
@@ -20,6 +20,7 @@ from maskopts import MaskOpts
from vectoropts import VectorOpts
from vectoropts import LineVectorOpts
from modelopts import ModelOpts
+from labelopts import LabelOpts
ALL_OVERLAY_TYPES = list(set(
diff --git a/fsl/fslview/displaycontext/display.py b/fsl/fslview/displaycontext/display.py
index 534ac88e2..5fd7329a4 100644
--- a/fsl/fslview/displaycontext/display.py
+++ b/fsl/fslview/displaycontext/display.py
@@ -244,12 +244,13 @@ class Display(props.SyncableHasProperties):
import volumeopts
import vectoropts
import maskopts
+import labelopts
import modelopts
OVERLAY_TYPES = td.TypeDict({
- 'Image' : ['volume', 'mask', 'rgbvector', 'linevector'],
+ 'Image' : ['volume', 'mask', 'rgbvector', 'linevector', 'label'],
'Model' : ['model']
})
"""This dictionary provides a mapping between the overlay classes, and
@@ -265,7 +266,8 @@ DISPLAY_OPTS_MAP = {
'rgbvector' : vectoropts.VectorOpts,
'linevector' : vectoropts.LineVectorOpts,
'mask' : maskopts. MaskOpts,
- 'model' : modelopts. ModelOpts
+ 'model' : modelopts. ModelOpts,
+ 'label' : labelopts. LabelOpts,
}
"""This dictionary provides a mapping between each overlay type, and
the :class:`DisplayOpts` subclass which contains overlay type-specific
diff --git a/fsl/fslview/displaycontext/labelopts.py b/fsl/fslview/displaycontext/labelopts.py
new file mode 100644
index 000000000..f644d1587
--- /dev/null
+++ b/fsl/fslview/displaycontext/labelopts.py
@@ -0,0 +1,32 @@
+#!/usr/bin/env python
+#
+# labelopts.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import props
+
+import volumeopts
+
+import fsl.fslview.lookuptables as lookuptables
+
+
+class LabelOpts(volumeopts.ImageOpts):
+
+
+ lut = props.Choice()
+ outline = props.Boolean(default=False)
+ showNames = props.Boolean(default=False)
+
+
+ def __init__(self, overlay, *args, **kwargs):
+
+ luts = lookuptables.all_luts
+ names = [lut.lutName() for lut in luts]
+
+ self.getProp('lut').setChoices(luts, names, self)
+
+ self.lut = luts[0]
+
+ volumeopts.ImageOpts.__init__(self, overlay, *args, **kwargs)
diff --git a/fsl/fslview/displaycontext/modelopts.py b/fsl/fslview/displaycontext/modelopts.py
index 530d4c94e..254bf1b2a 100644
--- a/fsl/fslview/displaycontext/modelopts.py
+++ b/fsl/fslview/displaycontext/modelopts.py
@@ -28,6 +28,9 @@ class ModelOpts(fsldisplay.DisplayOpts):
outline = props.Boolean(default=False)
+
+ showName = props.Boolean(default=False)
+
refImage = props.Choice()
diff --git a/fsl/fslview/gl/__init__.py b/fsl/fslview/gl/__init__.py
index d0f7e3b21..a35cbbbe1 100644
--- a/fsl/fslview/gl/__init__.py
+++ b/fsl/fslview/gl/__init__.py
@@ -212,6 +212,7 @@ def bootstrap(glVersion=None):
thismod.glrgbvector_funcs = glpkg.glrgbvector_funcs
thismod.gllinevector_funcs = glpkg.gllinevector_funcs
thismod.glmodel_funcs = glpkg.glmodel_funcs
+ thismod.gllabel_funcs = glpkg.gllabel_funcs
thismod._bootstrapped = True
diff --git a/fsl/fslview/gl/gl21/__init__.py b/fsl/fslview/gl/gl21/__init__.py
index 5e1427459..2c0843a8b 100644
--- a/fsl/fslview/gl/gl21/__init__.py
+++ b/fsl/fslview/gl/gl21/__init__.py
@@ -9,3 +9,4 @@ import glvolume_funcs
import glrgbvector_funcs
import gllinevector_funcs
import glmodel_funcs
+import gllabel_funcs
diff --git a/fsl/fslview/gl/gl21/gllabel_frag.glsl b/fsl/fslview/gl/gl21/gllabel_frag.glsl
new file mode 100644
index 000000000..d5eb3a682
--- /dev/null
+++ b/fsl/fslview/gl/gl21/gllabel_frag.glsl
@@ -0,0 +1,83 @@
+#version 120
+
+#pragma include spline_interp.glsl
+#pragma include test_in_bounds.glsl
+
+uniform sampler3D imageTexture;
+
+uniform sampler1D lutTexture;
+
+uniform mat4 voxValXform;
+
+uniform vec3 imageShape;
+
+uniform float numLabels;
+
+uniform bool useSpline;
+
+uniform bool outline;
+
+varying vec3 fragVoxCoord;
+
+varying vec3 fragTexCoord;
+
+
+void main(void) {
+
+ vec3 voxCoord = fragVoxCoord;
+
+ if (!test_in_bounds(voxCoord, imageShape)) {
+
+ gl_FragColor = vec4(0, 0, 0, 0);
+ return;
+ }
+
+ float voxValue;
+ if (useSpline) voxValue = spline_interp(imageTexture,
+ fragTexCoord,
+ imageShape,
+ 0);
+ else voxValue = texture3D( imageTexture,
+ fragTexCoord).r;
+
+ float lutCoord = (voxValXform * vec4(voxValue, 0, 0, 1)).x / numLabels;
+ vec4 colour = texture1D(lutTexture, lutCoord);
+
+ if (outline) {
+
+ // TODO take into account resolution
+ vec3 off = 0.1 / imageShape;
+
+ float left = texture3D(imageTexture,
+ fragTexCoord + vec3(-off.x, 0, 0)) .r;
+ float right = texture3D(imageTexture,
+ fragTexCoord + vec3( off.x, 0, 0)) .r;
+ float top = texture3D(imageTexture,
+ fragTexCoord + vec3( 0, off.y, 0)) .r;
+ float bottom = texture3D(imageTexture,
+ fragTexCoord + vec3( 0, -off.y, 0)) .r;
+ float back = texture3D(imageTexture,
+ fragTexCoord + vec3( 0, 0, -off.z)).r;
+ float front = texture3D(imageTexture,
+ fragTexCoord + vec3( 0, 0, off.z)).r;
+
+
+ voxValue = (voxValXform * vec4(voxValue, 0, 0, 1)).x;
+ left = (voxValXform * vec4(left, 0, 0, 1)).x;
+ right = (voxValXform * vec4(right, 0, 0, 1)).x;
+ top = (voxValXform * vec4(top, 0, 0, 1)).x;
+ bottom = (voxValXform * vec4(bottom, 0, 0, 1)).x;
+ back = (voxValXform * vec4(back, 0, 0, 1)).x;
+ front = (voxValXform * vec4(front, 0, 0, 1)).x;
+
+ if (abs(voxValue - top) < 0.001 &&
+ abs(voxValue - bottom) < 0.001 &&
+ abs(voxValue - left) < 0.001 &&
+ abs(voxValue - right) < 0.001 &&
+ abs(voxValue - back) < 0.001 &&
+ abs(voxValue - front) < 0.001)
+ colour.a = 0.0;
+ }
+
+ gl_FragColor = colour;
+}
diff --git a/fsl/fslview/gl/gl21/gllabel_funcs.py b/fsl/fslview/gl/gl21/gllabel_funcs.py
new file mode 100644
index 000000000..8a7e4dbf9
--- /dev/null
+++ b/fsl/fslview/gl/gl21/gllabel_funcs.py
@@ -0,0 +1,71 @@
+#!/usr/bin/env python
+#
+# gllabel_funcs.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import OpenGL.GL as gl
+import numpy as np
+
+import fsl.fslview.gl.shaders as shaders
+import glvolume_funcs
+
+
+def compileShaders(self):
+
+ vertShaderSrc = shaders.getVertexShader( self,
+ sw=self.display.softwareMode)
+ fragShaderSrc = shaders.getFragmentShader(self,
+ sw=self.display.softwareMode)
+ self.shaders = shaders.compileShaders(vertShaderSrc, fragShaderSrc)
+
+ 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.lutTexturePos = gl.glGetUniformLocation(self.shaders,
+ 'lutTexture')
+ self.voxValXformPos = gl.glGetUniformLocation(self.shaders,
+ 'voxValXform')
+ self.imageShapePos = gl.glGetUniformLocation(self.shaders,
+ 'imageShape')
+ self.useSplinePos = gl.glGetUniformLocation(self.shaders,
+ 'useSpline')
+ self.numLabelsPos = gl.glGetUniformLocation(self.shaders,
+ 'numLabels')
+ self.outlinePos = gl.glGetUniformLocation(self.shaders,
+ 'outline')
+
+
+def updateShaderState(self):
+
+ display = self.display
+ opts = self.displayOpts
+
+ gl.glUseProgram(self.shaders)
+
+
+ gl.glUniform1f( self.outlinePos, opts.outline)
+ gl.glUniform1f( self.numLabelsPos, 64)
+ gl.glUniform1f( self.useSplinePos, display.interpolation == 'spline')
+ gl.glUniform3fv(self.imageShapePos, 1, np.array(self.image.shape[:3],
+ dtype=np.float32))
+
+ vvx = self.imageTexture.voxValXform.ravel('C')
+ gl.glUniformMatrix4fv(self.voxValXformPos, 1, False, vvx)
+
+ gl.glUniform1i(self.imageTexturePos, 0)
+ gl.glUniform1i(self.lutTexturePos, 1)
+
+ gl.glUseProgram(0)
+
+
+preDraw = glvolume_funcs.preDraw
+draw = glvolume_funcs.draw
+drawAll = glvolume_funcs.drawAll
+postDraw = glvolume_funcs.postDraw
diff --git a/fsl/fslview/gl/gllabel.py b/fsl/fslview/gl/gllabel.py
new file mode 100644
index 000000000..f50fa5bed
--- /dev/null
+++ b/fsl/fslview/gl/gllabel.py
@@ -0,0 +1,133 @@
+#!/usr/bin/env python
+#
+# gllabel.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import OpenGL.GL as gl
+
+import fsl.utils.transform as transform
+import fsl.fslview.gl as fslgl
+import resources as glresources
+import routines as glroutines
+import globject
+import textures
+
+
+class GLLabel(globject.GLImageObject):
+
+
+ def __init__(self, image, display):
+
+ globject.GLImageObject.__init__(self, image, display)
+
+
+ imageTexName = '{}_{}' .format(type(self).__name__, id(image))
+ lutTexName = '{}_lut'.format(self.name)
+
+ self.lutTexture = textures.LookupTableTexture(lutTexName)
+ self.imageTexture = glresources.get(
+ imageTexName,
+ textures.ImageTexture,
+ imageTexName,
+ image,
+ display)
+
+ self.vertexAttrBuffer = gl.glGenBuffers(1)
+
+ fslgl.gllabel_funcs.compileShaders( self)
+ fslgl.gllabel_funcs.updateShaderState(self)
+
+ self.refreshLutTexture()
+
+ self.addListeners()
+
+
+ def addListeners(self):
+
+ display = self.display
+ opts = self.displayOpts
+
+ def shaderUpdate(*a):
+ fslgl.gllabel_funcs.updateShaderState(self)
+ self.onUpdate()
+
+ def lutUpdate(*a):
+ self.refreshLutTexture()
+ self.onUpdate()
+
+ opts .addListener('outline', self.name, shaderUpdate)
+ opts .addListener('lut', self.name, lutUpdate)
+ display.addListener('alpha', self.name, lutUpdate)
+ display.addListener('brightness', self.name, lutUpdate)
+ display.addListener('contrast', self.name, lutUpdate)
+
+
+ def removeListeners(self):
+ display = self.display
+ opts = self.displayOpts
+
+ opts .removeListener('outline', self.name)
+ opts .removeListener('lut', self.name)
+ display.removeListener('alpha', self.name)
+ display.removeListener('brightness', self.name)
+ display.removeListener('contrast', self.name)
+
+
+ def destroy(self):
+
+ glresources.delete(self.imageTexture.getTextureName())
+ self.lutTexture.destroy()
+
+ self.removeListeners()
+ fslgl.gllabel_funcs.destroy(self)
+
+
+ def setAxes(self, xax, yax):
+ """This method should be called when the image display axes change."""
+
+ self.xax = xax
+ self.yax = yax
+ self.zax = 3 - xax - yax
+
+
+ def generateVertices(self, zpos, xform):
+ vertices, voxCoords, texCoords = glroutines.slice2D(
+ self.image.shape[:3],
+ self.xax,
+ self.yax,
+ zpos,
+ self.displayOpts.getTransform('voxel', 'display'),
+ self.displayOpts.getTransform('display', 'voxel'))
+
+ if xform is not None:
+ vertices = transform.transform(vertices, xform)
+
+ return vertices, voxCoords, texCoords
+
+
+ def refreshLutTexture(self, *a):
+
+ display = self.display
+ opts = self.displayOpts
+
+ self.lutTexture.set(alpha=display.alpha / 100.0,
+ lut=opts.lut)
+
+
+ def preDraw(self):
+
+ self.imageTexture.bindTexture(gl.GL_TEXTURE0)
+ self.lutTexture .bindTexture(gl.GL_TEXTURE1)
+ fslgl.gllabel_funcs.preDraw(self)
+
+
+ def draw(self, zpos, xform=None):
+ fslgl.gllabel_funcs.draw(self, zpos, xform)
+
+
+ def postDraw(self):
+ self.imageTexture.unbindTexture()
+ self.lutTexture .unbindTexture()
+ fslgl.gllabel_funcs.postDraw(self)
diff --git a/fsl/fslview/gl/globject.py b/fsl/fslview/gl/globject.py
index 8466cd6c0..41dea3119 100644
--- a/fsl/fslview/gl/globject.py
+++ b/fsl/fslview/gl/globject.py
@@ -240,6 +240,7 @@ import glmask
import glrgbvector
import gllinevector
import glmodel
+import gllabel
GLOBJECT_OVERLAY_TYPE_MAP = {
@@ -247,7 +248,8 @@ GLOBJECT_OVERLAY_TYPE_MAP = {
'mask' : glmask .GLMask,
'rgbvector' : glrgbvector .GLRGBVector,
'linevector' : gllinevector.GLLineVector,
- 'model' : glmodel .GLModel
+ 'model' : glmodel .GLModel,
+ 'label' : gllabel .GLLabel
}
"""This dictionary provides a mapping between all available overlay types (see
the :attr:`.Display.overlayType` property), and the :class:`GLObject` subclass
diff --git a/fsl/fslview/gl/shaders.py b/fsl/fslview/gl/shaders.py
index fc4d01e14..7b966a37c 100644
--- a/fsl/fslview/gl/shaders.py
+++ b/fsl/fslview/gl/shaders.py
@@ -37,6 +37,11 @@ _shaderTypePrefixMap = td.TypeDict({
('GLVolume', 'vert', True) : 'glvolume_sw',
('GLVolume', 'frag', False) : 'glvolume',
('GLVolume', 'frag', True) : 'glvolume_sw',
+
+ ('GLLabel', 'vert', False) : 'glvolume',
+ ('GLLabel', 'vert', True) : 'glvolume_sw',
+ ('GLLabel', 'frag', False) : 'gllabel',
+ ('GLLabel', 'frag', True) : 'gllabel_sw',
('GLRGBVector', 'vert', False) : 'glvolume',
('GLRGBVector', 'vert', True) : 'glvolume_sw',
@@ -53,7 +58,7 @@ _shaderTypePrefixMap = td.TypeDict({
('GLModel', 'vert', False) : 'glmodel',
('GLModel', 'vert', True) : 'glmodel',
('GLModel', 'frag', False) : 'glmodel',
- ('GLModel', 'frag', True) : 'glmodel',
+ ('GLModel', 'frag', True) : 'glmodel',
})
"""This dictionary provides a mapping between :class:`.GLObject` types,
and file name prefixes, identifying the shader programs to use.
diff --git a/fsl/fslview/gl/textures/__init__.py b/fsl/fslview/gl/textures/__init__.py
index a10bec9ac..8ddaf9bc7 100644
--- a/fsl/fslview/gl/textures/__init__.py
+++ b/fsl/fslview/gl/textures/__init__.py
@@ -19,6 +19,7 @@ from texture import Texture
from texture import Texture2D
from imagetexture import ImageTexture
from colourmaptexture import ColourMapTexture
+from lookuptabletexture import LookupTableTexture
from selectiontexture import SelectionTexture
from rendertexture import RenderTexture
from rendertexture import GLObjectRenderTexture
diff --git a/fsl/fslview/gl/textures/lookuptabletexture.py b/fsl/fslview/gl/textures/lookuptabletexture.py
new file mode 100644
index 000000000..8cb2ec93f
--- /dev/null
+++ b/fsl/fslview/gl/textures/lookuptabletexture.py
@@ -0,0 +1,103 @@
+#!/usr/bin/env python
+#
+# lookuptabletexture.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+import logging
+
+import OpenGL.GL as gl
+import numpy as np
+
+import texture
+
+
+log = logging.getLogger(__name__)
+
+
+class LookupTableTexture(texture.Texture):
+
+ def __init__(self, name):
+
+ texture.Texture.__init__(self, name, 1)
+
+ self.__lut = None
+ self.__alpha = None
+ self.__border = None
+
+
+ def set(self, **kwargs):
+
+ lut = kwargs.get('lut', self)
+ alpha = kwargs.get('alpha', self)
+ border = kwargs.get('border', self)
+
+ if lut is not self: self.__lut = lut
+ if alpha is not self: self.__alpha = alpha
+ if border is not self: self.__border = border
+
+ self.__refresh()
+
+
+ def refresh(self):
+ self.__refresh()
+
+
+ def __refresh(self):
+
+ alpha = self.__alpha
+ border = self.__border
+
+ # TODO check maximum lut label value,
+ # and use corresponding number
+ # of slots in colour map
+ data = np.zeros((64, 4), dtype=np.uint8)
+
+ if self.__lut is not None:
+ values = self.__lut.values()
+ colours = self.__lut.colours()
+
+ for value, colour in zip(values, colours):
+
+ data[value, :3] = [np.floor(c * 255) for c in colour]
+
+ if alpha is not None: data[value, 3] = alpha * 255
+ else: data[value, 3] = 255
+
+
+ data = data.ravel('C')
+
+ self.bindTexture()
+
+ if border is not None:
+ if alpha is not None:
+ border[3] = alpha * 255
+
+ gl.glTexParameterfv(gl.GL_TEXTURE_1D,
+ gl.GL_TEXTURE_BORDER_COLOR,
+ border)
+ gl.glTexParameteri( gl.GL_TEXTURE_1D,
+ gl.GL_TEXTURE_WRAP_S,
+ gl.GL_CLAMP_TO_BORDER)
+ else:
+ gl.glTexParameteri(gl.GL_TEXTURE_1D,
+ gl.GL_TEXTURE_WRAP_S,
+ gl.GL_CLAMP_TO_EDGE)
+
+ 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.glTexImage1D(gl.GL_TEXTURE_1D,
+ 0,
+ gl.GL_RGBA8,
+ 64,
+ 0,
+ gl.GL_RGBA,
+ gl.GL_UNSIGNED_BYTE,
+ data)
+ self.unbindTexture()
diff --git a/fsl/fslview/layouts.py b/fsl/fslview/layouts.py
index 325bbf729..6e2242bba 100644
--- a/fsl/fslview/layouts.py
+++ b/fsl/fslview/layouts.py
@@ -32,6 +32,7 @@ from fsl.fslview.displaycontext import MaskOpts
from fsl.fslview.displaycontext import VectorOpts
from fsl.fslview.displaycontext import LineVectorOpts
from fsl.fslview.displaycontext import ModelOpts
+from fsl.fslview.displaycontext import LabelOpts
from fsl.fslview.displaycontext import SceneOpts
from fsl.fslview.displaycontext import OrthoOpts
@@ -171,7 +172,11 @@ ModelOptsToolBarLayout = [
widget(ModelOpts, 'colour'),
widget(ModelOpts, 'outline'),
widget(ModelOpts, 'refImage'),
- actions.ActionButton(OverlayDisplayToolBar, 'more')]
+ actions.ActionButton(OverlayDisplayToolBar, 'more')]
+
+LabelOptsToolBarLayout = [
+ widget(LabelOpts, 'lut'),
+ widget(LabelOpts, 'outline')]
DisplayLayout = props.VGroup(
@@ -277,6 +282,7 @@ layouts = td.TypeDict({
('OverlayDisplayToolBar', 'MaskOpts') : MaskOptsToolBarLayout,
('OverlayDisplayToolBar', 'VectorOpts') : VectorOptsToolBarLayout,
('OverlayDisplayToolBar', 'ModelOpts') : ModelOptsToolBarLayout,
+ ('OverlayDisplayToolBar', 'LabelOpts') : LabelOptsToolBarLayout,
('OverlayDisplayPanel', 'Display') : DisplayLayout,
('OverlayDisplayPanel', 'VolumeOpts') : VolumeOptsLayout,
diff --git a/fsl/fslview/lookuptables.py b/fsl/fslview/lookuptables.py
new file mode 100644
index 000000000..e433efff6
--- /dev/null
+++ b/fsl/fslview/lookuptables.py
@@ -0,0 +1,86 @@
+#!/usr/bin/env python
+#
+# lookuptables.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+
+class LookupTable(object):
+
+
+ def __init__(self, lutName):
+ self.__lutName = lutName
+ self.__names = {}
+ self.__colours = {}
+
+
+ def __len__(self):
+ return len(self.__names.keys())
+
+
+ def lutName(self):
+ return self.__lutName
+
+
+ def values(self):
+ return sorted(self.__names.keys())
+
+
+ def names(self):
+ return [self.__names[v] for v in self.values()]
+
+
+ def colours(self):
+ return [self.__colours[v] for v in self.values()]
+
+
+ def name(self, value):
+ return self.__names[value]
+
+
+ def colour(self, value):
+ return self.__colours[value]
+
+
+ def set(self, value, name, colour):
+
+ # At the moment, we are restricting
+ # lookup tables to be unsigned 16 bit.
+ # See gl/textures/lookuptabletexture.py
+ if not isinstance(value, (int, long)) or \
+ value < 0 or value > 65535:
+ raise ValueError('Lookup table values must be '
+ '16 bit unsigned integers.')
+
+ self.__names[ value] = name
+ self.__colours[value] = colour
+
+
+ def load(self, lutFile):
+
+ with open(lutFile, 'rt') as f:
+ lines = f.readlines()
+
+ for line in lines:
+ tkns = line.split()
+
+ label = int( tkns[0])
+ r = float( tkns[1])
+ g = float( tkns[2])
+ b = float( tkns[3])
+ lName = ' '.join(tkns[4:])
+
+ self.set(label, lName, (r, g, b))
+
+ return self
+
+
+import os.path as op
+
+all_luts = []
+dirname = op.join(op.dirname(__file__), 'luts')
+
+all_luts.append(
+ LookupTable('Harvard-Oxford').load(
+ op.join(dirname, 'harvard-oxford-cortical.txt')))
diff --git a/fsl/fslview/luts/harvard-oxford-cortical.txt b/fsl/fslview/luts/harvard-oxford-cortical.txt
new file mode 100644
index 000000000..8863dc889
--- /dev/null
+++ b/fsl/fslview/luts/harvard-oxford-cortical.txt
@@ -0,0 +1,48 @@
+1 0.00000 0.93333 0.00000 Frontal Pole
+2 0.62745 0.32157 0.17647 Insular Cortex
+3 1.00000 0.85490 0.72549 Superior Frontal Gyrus
+4 0.00000 0.80784 0.81961 Middle Frontal Gyrus
+5 0.49804 1.00000 0.83137 Inferior Frontal Gyrus, pars triangularis
+6 0.69804 0.13333 0.13333 Inferior Frontal Gyrus, pars opercularis
+7 0.93333 0.00000 0.00000 Precentral Gyrus
+8 0.13333 0.54510 0.13333 Temporal Pole
+9 0.81569 0.12549 0.56471 Superior Temporal Gyrus, anterior division
+10 0.67843 1.00000 0.18431 Superior Temporal Gyrus, posterior division
+11 0.94118 0.90196 0.54902 Middle Temporal Gyrus, anterior division
+12 0.67843 0.84706 0.90196 Middle Temporal Gyrus, posterior division
+13 0.93333 0.93333 0.00000 Middle Temporal Gyrus, temporooccipital part
+14 0.19608 0.80392 0.19608 Inferior Temporal Gyrus, anterior division
+15 1.00000 0.00000 1.00000 Inferior Temporal Gyrus, posterior division
+16 0.69020 0.18824 0.37647 Inferior Temporal Gyrus, temporooccipital part
+17 0.00000 1.00000 0.49804 Postcentral Gyrus
+18 0.96078 0.87059 0.70196 Superior Parietal Lobule
+19 1.00000 0.64706 0.00000 Supramarginal Gyrus, anterior division
+20 1.00000 0.27059 0.00000 Supramarginal Gyrus, posterior division
+21 0.80392 0.35686 0.27059 Angular Gyrus
+22 1.00000 0.75294 0.79608 Lateral Occipital Cortex, superior division
+23 0.59608 0.98431 0.59608 Lateral Occipital Cortex, inferior division
+24 0.39216 0.58431 0.92941 Intracalcarine Cortex
+25 0.62745 0.12549 0.94118 Frontal Medial Cortex
+26 0.93333 0.50980 0.93333 Juxtapositional Lobule Cortex (formerly Supplementary Motor Cortex)
+27 0.93333 0.78824 0.00000 Subcallosal Cortex
+28 0.85490 0.43922 0.83922 Paracingulate Gyrus
+29 1.00000 0.24314 0.58824 Cingulate Gyrus, anterior division
+30 0.00000 0.00000 1.00000 Cingulate Gyrus, posterior division
+31 0.15294 0.25098 0.54510 Precuneous Cortex
+32 0.98039 0.50196 0.44706 Cuneal Cortex
+33 1.00000 0.43137 0.70588 Frontal Orbital Cortex
+34 1.00000 0.38824 0.27843 Parahippocampal Gyrus, anterior division
+35 1.00000 1.00000 0.00000 Parahippocampal Gyrus, posterior division
+36 0.00000 0.39216 0.00000 Lingual Gyrus
+37 0.80392 0.36078 0.36078 Temporal Fusiform Cortex, anterior division
+38 0.64706 0.16471 0.16471 Temporal Fusiform Cortex, posterior division
+39 0.60000 0.19608 0.80000 Temporal Occipital Fusiform Cortex
+40 0.00000 1.00000 1.00000 Occipital Fusiform Gyrus
+41 0.86667 0.62745 0.86667 Frontal Operculum Cortex
+42 0.52941 0.80784 0.92157 Central Opercular Cortex
+43 0.82353 0.70588 0.54902 Parietal Operculum Cortex
+44 1.00000 0.84314 0.00000 Planum Polare
+45 0.00000 0.00000 0.50196 Heschl's Gyrus (includes H1 and H2)
+46 0.18039 0.54510 0.34118 Planum Temporale
+47 0.40000 0.80392 0.66667 Supracalcarine Cortex
+48 0.00000 1.00000 0.00000 Occipital Pole
--
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