diff --git a/fsl/data/melodicresults.py b/fsl/data/melodicresults.py
index c3a1987da2daeb16f40104a9edff7bc182e3ca70..3b8d8dc33be34509741543a5957e873935898fc2 100644
--- a/fsl/data/melodicresults.py
+++ b/fsl/data/melodicresults.py
@@ -212,7 +212,9 @@ class MelodicClassification(props.HasProperties):
clearComponents
- .. note:: All component labels are converted to lower case.
+ .. note:: All component labels are internally stored as lower case;
+ their cased version (whatever is initially used) is accssible
+ via the :meth:`getDisplayLabel` method.
.. warning:: Do not modify the :attr:`labels` list directly - use the
@@ -235,12 +237,18 @@ class MelodicClassification(props.HasProperties):
"""Create a ``MelodicClassification`` instance.
"""
- self.__melimage = melimage
- self.__ncomps = melimage.numComponents()
+ self.__melimage = melimage
+ self.__ncomps = melimage.numComponents()
+ self.__displayLabels = {}
self.clear()
+ def getDisplayLabel(self, label):
+ """Returns the display name for the given label. """
+ return self.__displayLabels.get(label.lower(), label)
+
+
def clear(self):
"""Removes all labels from all components. """
@@ -376,7 +384,13 @@ class MelodicClassification(props.HasProperties):
noise = not (self.hasLabel(comp, 'signal') or
self.hasLabel(comp, 'unknown'))
- tokens = [str(comp + 1)] + self.getLabels(comp) + [str(noise)]
+
+ # Make sure there are no
+ # commas in any label names
+ labels = [self.getDisplayLabel(l) for l in self.getLabels(comp)]
+ labels = [l.replace(',', '_') for l in labels]
+
+ tokens = [str(comp + 1)] + labels + [str(noise)]
lines.append(', '.join(tokens))
@@ -406,9 +420,10 @@ class MelodicClassification(props.HasProperties):
def addLabel(self, component, label):
"""Adds the given label to the given component. """
- label = label.lower()
- labels = list(self.labels[component])
- comps = list(self.__components.get(label, []))
+ display = label
+ label = label.lower()
+ labels = list(self.labels[component])
+ comps = list(self.__components.get(label, []))
if label in labels:
return
@@ -416,6 +431,8 @@ class MelodicClassification(props.HasProperties):
labels.append(label)
comps .append(component)
+ self.__displayLabels[label] = display
+
# Change __components first, so
# any listeners on labels are
# not notified before our intenral
diff --git a/fsl/fsleyes/controls/atlasinfopanel.py b/fsl/fsleyes/controls/atlasinfopanel.py
index 367e43d5b4e95f1e9ed464777a5e88e68679001a..6ceea0e159cff72e07000d20b81f2f5653c30af2 100644
--- a/fsl/fsleyes/controls/atlasinfopanel.py
+++ b/fsl/fsleyes/controls/atlasinfopanel.py
@@ -170,14 +170,19 @@ class AtlasInfoPanel(fslpanel.FSLEyesPanel):
text.SetPage(strings.messages['AtlasInfoPanel.chooseAnAtlas'])
return
- opts = self._displayCtx.getOpts(overlay)
- loc = self._displayCtx.location
- loc = opts.transformCoords([loc], 'display', 'world')[0]
-
lines = []
if topText is not None:
lines.append(topText)
+
+ if overlay is None:
+ text.SetPage('<br>'.join(lines))
+ text.Refresh()
+ return
+
+ opts = self._displayCtx.getOpts(overlay)
+ loc = self._displayCtx.location
+ loc = opts.transformCoords([loc], 'display', 'world')[0]
# Three types of hyperlink:
# - one for complete (summary) label atlases,
diff --git a/fsl/fsleyes/controls/melodicclassificationgrid.py b/fsl/fsleyes/controls/melodicclassificationgrid.py
index e521f641a1da32ba47b2357a2112280daa1a378d..892dcbda910faf9059933541cfd3fc057522d8b3 100644
--- a/fsl/fsleyes/controls/melodicclassificationgrid.py
+++ b/fsl/fsleyes/controls/melodicclassificationgrid.py
@@ -17,7 +17,6 @@ import pwidgets.widgetgrid as widgetgrid
import pwidgets.texttag as texttag
import fsl.fsleyes.panel as fslpanel
-import fsl.fsleyes.colourmaps as fslcm
import fsl.fsleyes.displaycontext as fsldisplay
import fsl.data.melodicimage as fslmelimage
import fsl.data.strings as strings
@@ -169,7 +168,6 @@ class ComponentGrid(fslpanel.FSLEyesPanel):
tags = texttag.TextTagPanel(self.__grid,
style=(texttag.TTP_ALLOW_NEW_TAGS |
- texttag.TTP_ADD_NEW_TAGS |
texttag.TTP_NO_DUPLICATES |
texttag.TTP_KEYBOARD_NAV))
@@ -185,11 +183,32 @@ class ComponentGrid(fslpanel.FSLEyesPanel):
tags.Bind(texttag.EVT_TTP_TAG_ADDED, self.__onTagAdded)
tags.Bind(texttag.EVT_TTP_TAG_REMOVED, self.__onTagRemoved)
+ self.__refreshTagOptions()
self.__refreshTags()
self.Layout()
+
+ def __refreshTagOptions(self):
+ """Updates the options available on each :class:`.TextTagPanel`, from
+ the entries in the melodic classification :class:`.LookupTable`.
+ """
+
+ overlay = self.__overlay
+ numComps = overlay.numComponents()
+ lut = self.__lut
+ displayLabels = [l.displayName() for l in lut.labels]
+ colours = [l.colour() for l in lut.labels]
+
+ for i in range(len(colours)):
+ colours[i] = [int(round(c * 255)) for c in colours[i]]
+
+ for comp in range(numComps):
+ tags = self.__grid.GetWidget(comp, 1)
+ tags.SetOptions(displayLabels, colours)
+
+
def __refreshTags(self):
"""Re-generates the tags on every :class:`.TextTagPanel` in the grid.
"""
@@ -197,33 +216,17 @@ class ComponentGrid(fslpanel.FSLEyesPanel):
overlay = self.__overlay
melclass = overlay.getICClassification()
numComps = overlay.numComponents()
- lut = self.__lut
-
- labels = [l.name() for l in lut.labels]
- colours = [l.colour() for l in lut.labels]
-
- # Compile lists of all the existing
- # labels, and the colours for each one
- for i in range(numComps):
-
- for label in melclass.getLabels(i):
- if label in labels:
- continue
-
- labels .append(label)
- colours.append(fslcm.randomBrightColour())
-
- for i in range(len(colours)):
- colours[i] = [int(round(c * 255)) for c in colours[i]]
for row in range(numComps):
+
tags = self.__grid.GetWidget(row, 1)
tags.ClearTags()
- tags.SetOptions(labels, colours)
for label in melclass.getLabels(row):
- tags.AddTag(label)
+ tags.AddTag(melclass.getDisplayLabel(label))
+
+ self.__grid.FitInside()
def __onTagAdded(self, ev):
@@ -232,22 +235,26 @@ class ComponentGrid(fslpanel.FSLEyesPanel):
:class:`.MelodicClassification` instance.
"""
- tags = ev.GetEventObject()
- label = ev.tag
- component = tags._melodicComponent
- overlay = self.__overlay
- lut = self.__lut
- melclass = overlay.getICClassification()
+ tags = ev.GetEventObject()
+ label = ev.tag
+ comp = tags._melodicComponent
+ overlay = self.__overlay
+ lut = self.__lut
+ melclass = overlay.getICClassification()
+
+ log.debug('Label added to component {} ("{}")'.format(comp, label))
# Add the new label to the melodic component
melclass.disableListener('labels', self._name)
- melclass.addLabel(component, label)
+ melclass.addLabel(comp, label)
# If the tag panel previously just contained
# the 'Unknown' tag, remove that tag
- if tags.TagCount() == 2 and tags.HasTag('unknown'):
- melclass.removeLabel(component, 'unknown')
- tags.RemoveTag('unknown')
+ if tags.TagCount() == 2 and \
+ tags.HasTag('Unknown') and \
+ label.lower() != 'unknown':
+ melclass.removeLabel(comp, 'Unknown')
+ tags.RemoveTag('Unknown')
melclass.enableListener('labels', self._name)
@@ -257,10 +264,14 @@ class ComponentGrid(fslpanel.FSLEyesPanel):
colour = tags.GetTagColour(label)
colour = [c / 255.0 for c in colour]
+ log.debug('Adding new lookup table '
+ 'entry for label {}'.format(label))
+
lut.disableListener('labels', self._name)
lut.new(name=label, colour=colour)
lut.enableListener('labels', self._name)
+ self.__refreshTagOptions()
self.__grid.FitInside()
@@ -270,16 +281,18 @@ class ComponentGrid(fslpanel.FSLEyesPanel):
:class:`.MelodicClassification` instance.
"""
- tags = ev.GetEventObject()
- label = ev.tag
- component = tags._melodicComponent
- overlay = self.__overlay
- melclass = overlay.getICClassification()
+ tags = ev.GetEventObject()
+ label = ev.tag
+ comp = tags._melodicComponent
+ overlay = self.__overlay
+ melclass = overlay.getICClassification()
+
+ log.debug('Label removed from component {} ("{}")'.format(comp, label))
# Remove the label from
# the melodic component
melclass.disableListener('labels', self._name)
- melclass.removeLabel(component, label)
+ melclass.removeLabel(comp, label)
melclass.enableListener('labels', self._name)
# If the tag panel now has no tags,
@@ -299,6 +312,8 @@ class ComponentGrid(fslpanel.FSLEyesPanel):
component = ev.row
opts = self._displayCtx.getOpts(self.__overlay)
+ log.debug('Grid row selected (component {})'.format(component))
+
opts.disableListener('volume', self._name)
opts.volume = component
opts.enableListener('volume', self._name)
@@ -321,6 +336,8 @@ class ComponentGrid(fslpanel.FSLEyesPanel):
grid = self.__grid
opts = self._displayCtx.getOpts(self.__overlay)
tags = grid.GetWidget(opts.volume, 1)
+
+ log.debug('Overlay volume changed ({})'.format(opts.volume))
grid.SetSelection(opts.volume, -1)
tags.FocusNewTagCtrl()
@@ -330,14 +347,18 @@ class ComponentGrid(fslpanel.FSLEyesPanel):
"""Called when the :attr:`.MelodicClassification.labels` change.
Re-generates the tags shown on every :class:`.TextTagPanel`.
"""
+ log.debug('Melodic classification changed - '
+ 'refreshing component grid tags')
self.__refreshTags()
def __lutChanged(self, *a):
"""Called when the :attr:`.LookupTable.labels` change.
- Re-generates the tags shown on every :class:`.TextTagPanel`.
- """
- self.__refreshTags()
+ Updates the options on every :class:`.TextTagPanel`.
+ """
+ log.debug('Lookup table changed - refreshing '
+ 'component grid tag options')
+ self.__refreshTagOptions()
class LabelGrid(fslpanel.FSLEyesPanel):
@@ -391,7 +412,7 @@ class LabelGrid(fslpanel.FSLEyesPanel):
self._name,
self.__selectedOverlayChanged)
- self.__overlay = None
+ self.__overlay = None
self.__recreateGrid()
self.__selectedOverlayChanged()
@@ -474,7 +495,7 @@ class LabelGrid(fslpanel.FSLEyesPanel):
tags._label = label.name()
- self.__grid.SetText( i, 0, label.name())
+ self.__grid.SetText( i, 0, label.displayName())
self.__grid.SetWidget(i, 1, tags)
tags.Bind(texttag.EVT_TTP_TAG_ADDED, self.__onTagAdded)
@@ -521,6 +542,9 @@ class LabelGrid(fslpanel.FSLEyesPanel):
overlay = self.__overlay
melclass = overlay.getICClassification()
comp = int(ev.tag)
+ label = tags._label
+
+ log.debug('Component added to label {} ({})'.format(label, comp))
melclass.disableListener('labels', self._name)
@@ -528,10 +552,11 @@ class LabelGrid(fslpanel.FSLEyesPanel):
# the other label is 'Unknown', remove the
# 'Unknown' label.
if len(melclass.getLabels(comp)) == 1 and \
- melclass.hasLabel(comp, 'Unknown'):
- melclass.removeLabel(comp, 'Unknown')
+ label != 'unknown' and \
+ melclass.hasLabel(comp, 'unknown'):
+ melclass.removeLabel(comp, 'unknown')
- melclass.addComponent(tags._label, comp)
+ melclass.addComponent(label, comp)
melclass.enableListener('labels', self._name)
self.__refreshTags()
@@ -547,10 +572,13 @@ class LabelGrid(fslpanel.FSLEyesPanel):
overlay = self.__overlay
melclass = overlay.getICClassification()
comp = int(ev.tag)
+ label = tags._label
+
+ log.debug('Component removed from label {} ({})'.format(label, comp))
melclass.disableListener('labels', self._name)
- melclass.removeComponent(tags._label, comp)
+ melclass.removeComponent(label, comp)
# If the component has no more labels,
# give it an 'Unknown' label
@@ -567,6 +595,9 @@ class LabelGrid(fslpanel.FSLEyesPanel):
"""
tags = self.__grid.GetWidget(ev.row, 1)
+
+ log.debug('Grid row selected (label "{}")'.format(tags._label))
+
tags.FocusNewTagCtrl()
@@ -575,10 +606,13 @@ class LabelGrid(fslpanel.FSLEyesPanel):
Changes the current :attr:`.ImageOpts.volume` to the component
corresponding to the selected tag.
"""
-
+
tag = int(ev.tag)
overlay = self.__overlay
opts = self._displayCtx.getOpts(overlay)
+
+ log.debug('Tag selected on label grid: component {}'.format(tag))
+
opts.volume = tag
@@ -595,5 +629,6 @@ class LabelGrid(fslpanel.FSLEyesPanel):
"""Called when the :attr:`.MelodicClassification.labels` change.
Re-populates the :class:`.WidgetGrid`.
"""
- log.debug('Melodic classification changed - refreshing tags')
+ log.debug('Melodic classification changed - '
+ 'refreshing label grid tags')
self.__refreshTags()
diff --git a/fsl/fsleyes/controls/melodicclassificationpanel.py b/fsl/fsleyes/controls/melodicclassificationpanel.py
index 77d49920d790a5ad066306633d03388efba5bcdd..9e788a7444757523b51f43240023ff8c7298b6e4 100644
--- a/fsl/fsleyes/controls/melodicclassificationpanel.py
+++ b/fsl/fsleyes/controls/melodicclassificationpanel.py
@@ -74,12 +74,11 @@ class MelodicClassificationPanel(fslpanel.FSLEyesPanel):
self._displayCtx,
self.__lut)
- # self.__labelGrid = melodicgrid.LabelGrid(
- # self.__notebook,
- # self._overlayList,
- # self._displayCtx,
- # self.__lut)
- self.__labelGrid = wx.Panel(self.__notebook)
+ self.__labelGrid = melodicgrid.LabelGrid(
+ self.__notebook,
+ self._overlayList,
+ self._displayCtx,
+ self.__lut)
self.__loadButton = wx.Button(self)
self.__saveButton = wx.Button(self)
@@ -211,15 +210,14 @@ class MelodicClassificationPanel(fslpanel.FSLEyesPanel):
# lookup table exists for all labels
for comp, labels in enumerate(melclass.labels):
for label in labels:
-
- lutLabel = lut.getByName(label)
- if lutLabel is not None:
- print 'Label {} is already in lookup table'.format(label)
- continue
- print 'New melodic classification label: {}'.format(label)
- log.debug('New melodic classification label: {}'.format(label))
- lut.new(label)
+ label = melclass.getDisplayLabel(label)
+ lutLabel = lut.getByName(label)
+
+ if lutLabel is None:
+ log.debug('New melodic classification '
+ 'label: {}'.format(label))
+ lut.new(label)
melclass.enableNotification('labels')
lut .enableNotification('labels')
@@ -264,3 +262,11 @@ class MelodicClassificationPanel(fslpanel.FSLEyesPanel):
melclass = overlay.getICClassification()
melclass.clear()
+
+ melclass.disableNotification('labels')
+
+ for c in range(overlay.numComponents()):
+ melclass.addLabel(c, 'Unknown')
+
+ melclass.enableNotification('labels')
+ melclass.notify('labels')