def genMeshColour(overlay):
"""Called by :meth:`MeshOpts.__init__`. Generates an initial colour for
the given :class:`.Mesh` overlay.
If the overlay file name looks like it was generated by the FSL FIRST
segmentation tool, returns a colour from the ``freesurfercolorlut`` colour
map. Otherwise returns a random colour.
"""
filename = str(overlay.dataSource)
subcorticalCmap = colourmaps.getLookupTable('freesurfercolorlut')
if 'L_Thal' in filename: return subcorticalCmap.get(10).colour
elif 'L_Caud' in filename: return subcorticalCmap.get(11).colour
elif 'L_Puta' in filename: return subcorticalCmap.get(12).colour
elif 'L_Pall' in filename: return subcorticalCmap.get(13).colour
elif 'BrStem' in filename: return subcorticalCmap.get(16).colour
elif 'L_Hipp' in filename: return subcorticalCmap.get(17).colour
elif 'L_Amyg' in filename: return subcorticalCmap.get(18).colour
elif 'L_Accu' in filename: return subcorticalCmap.get(26).colour
elif 'R_Thal' in filename: return subcorticalCmap.get(49).colour
elif 'R_Caud' in filename: return subcorticalCmap.get(50).colour
elif 'R_Puta' in filename: return subcorticalCmap.get(51).colour
elif 'R_Pall' in filename: return subcorticalCmap.get(52).colour
elif 'R_Hipp' in filename: return subcorticalCmap.get(53).colour
elif 'R_Amyg' in filename: return subcorticalCmap.get(54).colour
elif 'R_Accu' in filename: return subcorticalCmap.get(58).colour
return colourmaps.randomBrightColour()
def test_randomX():
c1 = fslcm.randomColour()
c2 = fslcm.randomBrightColour()
c3 = fslcm.randomDarkColour()
for c in [c1, c2, c3]:
assert c.shape == (3,)
assert np.all((c >= 0) & (c <= 1))
def drawClipPlanes(self, xform=None, bbox=None):
"""A convenience method for use with overlays being displayed
in terms of a :class:`.Volume3DOpts` instance.
Draws the active clipping planes, as specified by the
:class:`.Volume3DOpts` clipping properties.
:arg xform: A transformation matrix to apply to the clip plane
vertices before drawing them.
:arg bbox: A bounding box by which the clip planes can be limited
(not currently honoured).
"""
if not self.opts.showClipPlanes:
return
for i in range(self.opts.numClipPlanes):
verts, idxs = self.clipPlaneVertices(i, bbox)
if len(idxs) == 0:
continue
if xform is not None:
verts = transform.transform(verts, xform)
verts = np.array(verts.ravel('C'), dtype=np.float32, copy=False)
# A consistent colour for
# each clipping plane
rgb = self.__clipPlaneColours.get(i, None)
if rgb is None:
rgb = fslcmaps.randomBrightColour()[:3]
self.__clipPlaneColours[i] = rgb
r, g, b = rgb
with glroutines.enabled(gl.GL_VERTEX_ARRAY):
gl.glColor4f(r, g, b, 0.3)
gl.glVertexPointer(3, gl.GL_FLOAT, 0, verts)
gl.glDrawElements(gl.GL_TRIANGLES,
len(idxs),
gl.GL_UNSIGNED_INT,
idxs)
def __onLabelAdd(self, ev):
"""Called when the user pushes the *add* button on the lookup table
label list. Displays a :class:`LutLabelDialog`, prompting the user
to select a name, value and colour, and then adds a new label to the
current :class:`.LookupTable` instance.
"""
lut = self.__selectedLut
value = lut.max() + 1
name = strings.labels['LutLabelDialog.newLabel']
colour = fslcmaps.randomBrightColour()
colour = [int(round(c * 255.0)) for c in colour]
dlg = LutLabelDialog(self.GetTopLevelParent(), value, name, colour)
if dlg.ShowModal() != wx.ID_OK:
return
lut = self.__selectedLut
value = dlg.GetValue()
name = dlg.GetName()
colour = dlg.GetColour()[:3]
colour = [c / 255.0 for c in colour]
if lut.get(value) is not None:
wx.MessageBox(
strings.messages[self, 'labelExists'].format(lut.name, value),
strings.titles[self,
'labelExists'], (wx.ICON_INFORMATION | wx.OK))
return
log.debug('New lut label for {}: {}, {}, {}'.format(
lut.name, value, name, colour))
with lut.skip(self.name, 'added'):
label = lut.insert(value, name=name, colour=colour)
widget = LabelWidget(self, lut, label)
idx = lut.index(label)
self.__labelList.Insert(str(label.value),
idx,
clientData=label.value,
extraWidget=widget)
def applyLabels(labelFile, overlay, allLabels, newOverlay):
# labelFile: Path to the loaded label file
# overlay: Overlay to apply them to
# allLabels: Loaded labels (list of (component, [label]) tuples)
# newOverlay: True if the selected overlay has changed, False
# otherwise
lut = self.__lut
volLabels = self.overlayList.getData(overlay, 'VolumeLabels')
ncomps = volLabels.numComponents()
nlabels = len(allLabels)
# Error: number of labels in the
# file is greater than the number
# of components in the overlay.
if ncomps < nlabels:
msg = strings.messages[self, 'wrongNComps'].format(
labelFile, overlay.dataSource)
title = strings.titles[ self, 'loadError']
wx.MessageBox(msg, title, wx.ICON_ERROR | wx.OK)
return
# Number of labels in the file is
# less than number of components
# in the overlay - we pad the
# labels with 'Unknown'
elif ncomps > nlabels:
for i in range(nlabels, ncomps):
allLabels.append(['Unknown'])
# Disable notification while applying
# labels so the component/label grids
# don't confuse themselves.
with volLabels.skip(self.__componentGrid.name), \
volLabels.skip(self.__labelGrid .name):
volLabels.clear()
for comp, lbls in enumerate(allLabels):
for lbl in lbls:
volLabels.addLabel(comp, lbl)
# Make sure a colour in the melodic
# lookup table exists for all labels
for label in volLabels.getAllLabels():
label = volLabels.getDisplayLabel(label)
lutLabel = lut.getByName(label)
if lutLabel is None:
log.debug('New melodic classification '
'label: {}'.format(label))
lut.new(label, colour=fslcm.randomBrightColour())
# New overlay was loaded
if newOverlay:
# Make sure the new image is selected.
with props.skip(self.displayCtx,
'selectedOverlay',
self.name):
self.displayCtx.selectOverlay(overlay)
self.__componentGrid.setOverlay(overlay)
self.__labelGrid .setOverlay(overlay)
# Labels were applied to
# already selected overlay.
else:
self.__componentGrid.refreshTags()
self.__labelGrid .refreshTags()