diff --git a/fsl/data/strings.py b/fsl/data/strings.py
index e44661918c450926956342bcbd3bc4576d7f0ce6..a21dd084bb615466f83c8080e4cee459a616ea9f 100644
--- a/fsl/data/strings.py
+++ b/fsl/data/strings.py
@@ -527,16 +527,16 @@ properties = TypeDict({
'ImageOpts.transform' : 'Image transform',
'ImageOpts.volume' : 'Volume',
- 'VolumeOpts.displayRange' : 'Display range',
- 'VolumeOpts.clippingRange' : 'Clipping range',
- 'VolumeOpts.linkLowRanges' : 'Link low display/clipping ranges',
- 'VolumeOpts.linkHighRanges' : 'Link high display/clipping ranges',
- 'VolumeOpts.cmap' : 'Colour map',
- 'VolumeOpts.negativeCmap' : '-ve colour map',
- 'VolumeOpts.enableNegativeCmap' : '-ve colour map',
- 'VolumeOpts.invert' : 'Invert colour map',
- 'VolumeOpts.invertClipping' : 'Invert clipping range',
- 'VolumeOpts.interpolation' : 'Interpolation',
+ 'VolumeOpts.displayRange' : 'Display range',
+ 'VolumeOpts.clippingRange' : 'Clipping range',
+ 'VolumeOpts.linkLowRanges' : 'Link low display/clipping ranges',
+ 'VolumeOpts.linkHighRanges' : 'Link high display/clipping ranges',
+ 'VolumeOpts.cmap' : 'Colour map',
+ 'VolumeOpts.negativeCmap' : '-ve colour map',
+ 'VolumeOpts.useNegativeCmap' : '-ve colour map',
+ 'VolumeOpts.invert' : 'Invert colour map',
+ 'VolumeOpts.invertClipping' : 'Invert clipping range',
+ 'VolumeOpts.interpolation' : 'Interpolation',
'MaskOpts.colour' : 'Colour',
'MaskOpts.invert' : 'Invert',
diff --git a/fsl/fsleyes/autodisplay.py b/fsl/fsleyes/autodisplay.py
index 98ee4a67014cc5ca36e518e424cf4e0202fdd606..fa9e0a1a6324659f3e0115438838a326ccfc8fbe 100644
--- a/fsl/fsleyes/autodisplay.py
+++ b/fsl/fsleyes/autodisplay.py
@@ -64,7 +64,7 @@ def _isStatImage(overlay):
basename = op.basename(overlay.dataSource)
basename = fslimage.removeExt(basename)
tokens = ['zstat', 'tstat', 'fstat', 'zfstat']
- pattern = '_({})\d+'.format('|'.join(tokens))
+ pattern = '({})\d+'.format('|'.join(tokens))
return re.search(pattern, basename) is not None
@@ -90,7 +90,6 @@ def _statImageDisplay(overlay, overlayList, displayCtx):
basename = op.basename(overlay.dataSource)
basename = fslimage.removeExt(basename)
- nameTokens = basename.split('_')
pTokens = ['p', 'corrp']
statTokens = ['zstat', 'tstat', 'zfstat']
fStatTokens = ['fstat']
@@ -100,7 +99,7 @@ def _statImageDisplay(overlay, overlayList, displayCtx):
# generated specifically for
# use with the Render1 colour
# map.
- if 'rendered' in nameTokens:
+ if 'rendered' in basename:
opts.cmap = 'Render1'
# Give each normal stat image
@@ -111,25 +110,28 @@ def _statImageDisplay(overlay, overlayList, displayCtx):
_statImageDisplay.currentCmap += 1
_statImageDisplay.currentCmap %= len(_statImageDisplay.cmaps)
opts.cmap = cmap
+ opts.negativeCmap = cmap
# The order of these tests is
# important, due to name overlap
+ print 'which one', basename
+
# P-value image ?
- if any([token in nameTokens for token in pTokens]):
+ if any([token in basename for token in pTokens]):
opts.displayRange = [0.95, 1.0]
opts.clippingRange = [0.95, 1.0]
# T or Z stat image?
- elif any([token in nameTokens for token in statTokens]):
-
- opts.clippingRange = [-0.1, 0.1]
- opts.displayRange = [-7.5, 7.5]
- opts.centreRanges = True
- opts.invertClipping = True
+ elif any([token in basename for token in statTokens]) and \
+ 'rendered' not in basename:
+
+ opts.clippingRange = [2.3, opts.dataMax]
+ opts.displayRange = [2.3, 7.5]
+ opts.useNegativeCmap = True
# F stat image?
- elif any([token in nameTokens for token in fStatTokens]):
+ elif any([token in basename for token in fStatTokens]):
opts.displayRange = [0, 10]
@@ -157,11 +159,11 @@ def _peImageDisplay(overlay, overlayList, displayCtx):
"""
opts = displayCtx.getOpts(overlay)
- opts.cmap = 'Render3'
- opts.clippingRange = [-1, 1]
- opts.displayRange = [-100, 100]
- opts.centreRanges = True
- opts.invertClipping = True
+ opts.cmap = 'Red-Yellow'
+ opts.negativeCmap = 'Blue-LightBlue'
+ opts.displayRange = [1.0, 100.0]
+ opts.clippingRange = [1.0, opts.dataMax]
+ opts.useNegativeCmap = True
def _FEATImageDisplay(overlay, overlayList, displayCtx):
@@ -178,12 +180,11 @@ def _MelodicImageDisplay(overlay, overlayList, displayCtx):
opts = displayCtx.getOpts(overlay)
- opts.cmap = 'Render3'
- opts.displayRange = [-5.0, 5.0]
- opts.clippingRange = [-1.5, 1.5]
-
- opts.centreRanges = True
- opts.invertClipping = True
+ opts.cmap = 'Red-Yellow'
+ opts.negativeCmap = 'Blue-LightBlue'
+ opts.displayRange = [1.5, 5.0]
+ opts.clippingRange = [1.5, opts.dataMax]
+ opts.useNegativeCmap = True
def _ModelDisplay(overlay, display, overlayList, displayCtx):
diff --git a/fsl/fsleyes/controls/overlaydisplaypanel.py b/fsl/fsleyes/controls/overlaydisplaypanel.py
index 0c9fe561fbbfe8d04d06c7ad2be85a62f8f1b6af..c69721c3a4f62b230673ee3acd0b08bb5c5e1d44 100644
--- a/fsl/fsleyes/controls/overlaydisplaypanel.py
+++ b/fsl/fsleyes/controls/overlaydisplaypanel.py
@@ -237,7 +237,7 @@ class OverlayDisplayPanel(fslpanel.FSLEyesPanel):
def __buildColourMapWidget(self, target, cmapWidget):
"""Builds a panel which contains widgets for controlling the
:attr:`.VolumeOpts.cmap`, :attr:`.VolumeOpts.negativeCmap`, and
- :attr:`.VolumeOpts.enableNegativeCmap`.
+ :attr:`.VolumeOpts.useNegativeCmap`.
"""
widgets = self.__widgets
@@ -253,24 +253,23 @@ class OverlayDisplayPanel(fslpanel.FSLEyesPanel):
loadAction.bindToWidget(self, wx.EVT_BUTTON, loadButton)
# Negative colour map widget
- negCmap = props.Widget('negativeCmap',
- enabledWhen=lambda i, enc: enc,
- dependencies=['enableNegativeCmap'])
- enableNegCmap = props.Widget('enableNegativeCmap')
+ negCmap = props.Widget('negativeCmap',
+ enabledWhen=lambda i, enc: enc,
+ dependencies=['useNegativeCmap'])
+ useNegCmap = props.Widget('useNegativeCmap')
- negCmap = props.buildGUI(widgets, target, negCmap)
- enableNegCmap = props.buildGUI(widgets, target, enableNegCmap)
+ negCmap = props.buildGUI(widgets, target, negCmap)
+ useNegCmap = props.buildGUI(widgets, target, useNegCmap)
- enableNegCmap.SetLabel(
- strings.properties[target, 'enableNegativeCmap'])
+ useNegCmap.SetLabel(strings.properties[target, 'useNegativeCmap'])
sizer = wx.FlexGridSizer(2, 2)
sizer.AddGrowableCol(0)
- sizer.Add(cmapWidget, flag=wx.EXPAND)
- sizer.Add(loadButton, flag=wx.EXPAND)
- sizer.Add(negCmap, flag=wx.EXPAND)
- sizer.Add(enableNegCmap, flag=wx.EXPAND)
+ sizer.Add(cmapWidget, flag=wx.EXPAND)
+ sizer.Add(loadButton, flag=wx.EXPAND)
+ sizer.Add(negCmap, flag=wx.EXPAND)
+ sizer.Add(useNegCmap, flag=wx.EXPAND)
return sizer
diff --git a/fsl/fsleyes/displaycontext/volumeopts.py b/fsl/fsleyes/displaycontext/volumeopts.py
index 4e303f0ec971d8566d2ba5167f443db9f3e67ced..599bce8b9bc4ab89c32a9bc660eb2441e6dbc6a4 100644
--- a/fsl/fsleyes/displaycontext/volumeopts.py
+++ b/fsl/fsleyes/displaycontext/volumeopts.py
@@ -494,13 +494,13 @@ class VolumeOpts(ImageOpts):
negativeCmap = props.ColourMap()
- """A second colour map, used if :attr:`enableNegativeCmap` is ``True``.
+ """A second colour map, used if :attr:`useNegativeCmap` is ``True``.
When active, the :attr:`cmap` is used to colour positive values, and
the :attr:`negativeCmap` is used to colour negative values.
"""
- enableNegativeCmap = props.Boolean(default=False)
+ useNegativeCmap = props.Boolean(default=False)
"""When ``True``, the :attr:`cmap` is used to colour positive values,
and the :attr:`negativeCmap` is used to colour negative values.
When this property is enabled, the minimum value for both the
@@ -607,9 +607,9 @@ class VolumeOpts(ImageOpts):
self .addListener('displayRange',
self.name,
self.__displayRangeChanged)
- self .addListener('enableNegativeCmap',
+ self .addListener('useNegativeCmap',
self.name,
- self.__enableNegativeCmapChanged)
+ self.__useNegativeCmapChanged)
self .addListener('linkLowRanges',
self.name,
self.__linkLowRangesChanged)
@@ -630,13 +630,13 @@ class VolumeOpts(ImageOpts):
display,
display.getSyncPropertyName('contrast'))
- # If enableNegativeCmap, linkLowRanges or linkHighRanges
+ # If useNegativeCmap, linkLowRanges or linkHighRanges
# have been set to True (this will happen if they
# are true on the parent VolumeOpts instance), make
# sure the property / listener states are up to date.
- if self.enableNegativeCmap: self.__enableNegativeCmapChanged()
- if self.linkLowRanges: self.__linkLowRangesChanged()
- if self.linkHighRanges: self.__linkHighRangesChanged()
+ if self.useNegativeCmap: self.__useNegativeCmapChanged()
+ if self.linkLowRanges: self.__linkLowRangesChanged()
+ if self.linkHighRanges: self.__linkHighRangesChanged()
@actions.action
@@ -741,7 +741,7 @@ class VolumeOpts(ImageOpts):
See :func:`.colourmaps.displayRangeToBricon`.
"""
- if self.enableNegativeCmap:
+ if self.useNegativeCmap:
return
brightness, contrast = fslcm.displayRangeToBricon(
@@ -757,14 +757,14 @@ class VolumeOpts(ImageOpts):
self.__toggleListeners(True)
- def __enableNegativeCmapChanged(self, *a):
- """Called when the :attr:`enableNegativeCmap` property changes.
+ def __useNegativeCmapChanged(self, *a):
+ """Called when the :attr:`useNegativeCmap` property changes.
Enables/disables the :attr:`.Display.brightness` and
:attr:`.Display.contrast` properties, and configures limits
on the :attr:`clippingRange` and :attr:`displayRange` properties.
"""
- if self.enableNegativeCmap:
+ if self.useNegativeCmap:
self.display.disableProperty('brightness')
self.display.disableProperty('contrast')
self.displayRange .xmin = 0.0
diff --git a/fsl/fsleyes/gl/gl14/glvolume_funcs.py b/fsl/fsleyes/gl/gl14/glvolume_funcs.py
index 9fa8aa1b5455cac044074d087f08cd12c5edbf2a..41a1bdbc5ee35561b3d5f2ea5d43f5968119004e 100644
--- a/fsl/fsleyes/gl/gl14/glvolume_funcs.py
+++ b/fsl/fsleyes/gl/gl14/glvolume_funcs.py
@@ -93,8 +93,8 @@ def updateShaderState(self):
# And the clipping range, normalised
# to the image texture value range
- invClip = 1 if opts.invertClipping else -1
- useNegCmap = 1 if opts.enableNegativeCmap else 0
+ invClip = 1 if opts.invertClipping else -1
+ useNegCmap = 1 if opts.useNegativeCmap else 0
xform = self.imageTexture.invVoxValXform
clipLo = opts.clippingRange[0] * xform[0, 0] + xform[3, 0]
diff --git a/fsl/fsleyes/gl/gl21/glvolume_frag.glsl b/fsl/fsleyes/gl/gl21/glvolume_frag.glsl
index 5b56722b1689e91bf76b86e20b90c7d2b0aad90d..12e0684fe3e55e8f5823ad1473ec5777ba46e43b 100644
--- a/fsl/fsleyes/gl/gl21/glvolume_frag.glsl
+++ b/fsl/fsleyes/gl/gl21/glvolume_frag.glsl
@@ -27,7 +27,7 @@ uniform sampler1D negColourTexture;
* Flag which determines whether to
* use the negative colour map.
*/
-uniform bool enableNegCmap;
+uniform bool useNegCmap;
/*
* Shape of the imageTexture.
@@ -61,7 +61,7 @@ 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
+ * regular, or the negative colour texture (if useNegCmap
* is true).
*/
uniform float texZero;
@@ -87,8 +87,8 @@ void main(void) {
float voxValue;
vec4 normVoxValue;
- bool useNegCmap = false;
- vec3 voxCoord = fragVoxCoord;
+ bool negCmap = false;
+ vec3 voxCoord = fragVoxCoord;
/*
* Skip voxels that are out of the image bounds
@@ -116,10 +116,10 @@ void main(void) {
* value, and set a flag telling the code
* below to use the neagtive colour map.
*/
- if (enableNegCmap && voxValue <= texZero) {
+ if (useNegCmap && voxValue <= texZero) {
- useNegCmap = true;
- voxValue = texZero + (texZero - voxValue);
+ negCmap = true;
+ voxValue = texZero + (texZero - voxValue);
}
/*
@@ -138,6 +138,6 @@ void main(void) {
*/
normVoxValue = voxValXform * vec4(voxValue, 0, 0, 1);
- if (useNegCmap) gl_FragColor = texture1D(negColourTexture, normVoxValue.x);
- else gl_FragColor = texture1D(colourTexture, normVoxValue.x);
+ if (negCmap) 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 a0e87d615f59d0043b3f2c0993e19d1f88860a9d..ce9fffc1557c3b42d494473dd1c36b9c8f422921 100644
--- a/fsl/fsleyes/gl/gl21/glvolume_funcs.py
+++ b/fsl/fsleyes/gl/gl21/glvolume_funcs.py
@@ -70,8 +70,8 @@ def compileShaders(self):
'colourTexture')
self.negColourTexturePos = gl.glGetUniformLocation(self.shaders,
'negColourTexture')
- self.enableNegCmapPos = gl.glGetUniformLocation(self.shaders,
- 'enableNegCmap')
+ self.useNegCmapPos = gl.glGetUniformLocation(self.shaders,
+ 'useNegCmap')
self.texZeroPos = gl.glGetUniformLocation(self.shaders,
'texZero')
self.imageShapePos = gl.glGetUniformLocation(self.shaders,
@@ -113,11 +113,11 @@ def updateShaderState(self):
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.texZeroPos, texZero)
- gl.glUniform1f(self.invertClipPos, opts.invertClipping)
- gl.glUniform1f(self.enableNegCmapPos, opts.enableNegativeCmap)
+ gl.glUniform1f(self.clipLowPos, clipLow)
+ gl.glUniform1f(self.clipHighPos, clipHigh)
+ gl.glUniform1f(self.texZeroPos, texZero)
+ gl.glUniform1f(self.invertClipPos, opts.invertClipping)
+ gl.glUniform1f(self.useNegCmapPos, opts.useNegativeCmap)
# Bind transformation matrix to transform
# from image texture values to voxel values,
diff --git a/fsl/fsleyes/gl/glvolume.py b/fsl/fsleyes/gl/glvolume.py
index 9c19c478467afd626255286d892341aa603c1e96..227a2042945ecf92e28cdf9c5228ca38a333bf82 100644
--- a/fsl/fsleyes/gl/glvolume.py
+++ b/fsl/fsleyes/gl/glvolume.py
@@ -227,7 +227,7 @@ class GLVolume(globject.GLImageObject):
opts .addListener('invertClipping', lName, shaderUpdate, weak=False)
opts .addListener('cmap', lName, colourUpdate, weak=False)
opts .addListener('negativeCmap', lName, colourUpdate, weak=False)
- opts .addListener('enableNegativeCmap',
+ opts .addListener('useNegativeCmap',
lName, colourUpdate, weak=False)
opts .addListener('invert', lName, colourUpdate, weak=False)
opts .addListener('volume', lName, imageUpdate, weak=False)
@@ -263,19 +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( '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)
+ 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( 'useNegativeCmap', 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)
diff --git a/fsl/fsleyes/tooltips.py b/fsl/fsleyes/tooltips.py
index f5c62a995f1a2249c63b3d2579ef56415a14c8e2..674becd8e8ee22494da8b8d7529b0b6cdb317ca8 100644
--- a/fsl/fsleyes/tooltips.py
+++ b/fsl/fsleyes/tooltips.py
@@ -80,12 +80,12 @@ properties = TypeDict({
'voxels outside of the range are displayed.'
'This option is useful for displaying '
'statistic images.',
- 'VolumeOpts.cmap' : 'The colour map to use.',
- 'VolumeOpts.negativeCmap' : 'The colour map to use for negative '
- 'values.',
- 'VolumeOpts.enableNegativeCmap' : 'Enable the negative colour map - '
- 'this allows positive and negative '
- 'values to be coloured independently.',
+ 'VolumeOpts.cmap' : 'The colour map to use.',
+ 'VolumeOpts.negativeCmap' : 'The colour map to use for negative '
+ 'values.',
+ 'VolumeOpts.useNegativeCmap' : 'Enable the negative colour map - '
+ 'this allows positive and negative '
+ 'values to be coloured independently.',
'VolumeOpts.interpolation' : 'Interpolate the image data for display '
'purposes. You can choose no '
'interpolation (equivalent to nearest '