def on_activation(self): overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr) overlayWidget.setVisible(False) self.ilastik.labelWidget.setOverlayWidget(overlayWidget) self.ilastik.labelWidget.setLabelWidget(ve.DummyLabelWidget())
def on_activation(self): ovs = self.ilastik._activeImage.module[self.__class__.moduleName].getOverlayRefs() if len(ovs) == 0: raw = self.ilastik._activeImage.overlayMgr["Raw Data"] if raw is not None: ovs.append(raw.getRef()) overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr) overlayWidget.setVisible(False) self.ilastik.labelWidget.setOverlayWidget(overlayWidget) self.ilastik.labelWidget.setLabelWidget(ve.DummyLabelWidget())
def on_activation(self): ovs = self.ilastik._activeImage.module[ self.__class__.moduleName].getOverlayRefs() if len(ovs) == 0: raw = self.ilastik._activeImage.overlayMgr["Raw Data"] if raw is not None: ovs.append(raw.getRef()) overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr) overlayWidget.setVisible(False) self.ilastik.labelWidget.setOverlayWidget(overlayWidget) self.ilastik.labelWidget.setLabelWidget(ve.DummyLabelWidget())
def on_activation(self): if self.ilastik.project is None: return ovs = self.ilastik._activeImage.module[ self.__class__.moduleName].getOverlayRefs() if len(ovs) == 0: raw = self.ilastik._activeImage.overlayMgr["Raw Data"] if raw is not None: ovs.append(raw.getRef()) self.ilastik.labelWidget._history.volumeEditor = self.ilastik.labelWidget overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr) self.ilastik.labelWidget.setOverlayWidget(overlayWidget) self.objectLabels = ObjectListWidget( self.ilastik._activeImage.Object_Picking, self.ilastik._activeImage.Object_Picking.objects, self.ilastik.labelWidget) self.ilastik.labelWidget.setLabelWidget(self.objectLabels) #create ObjectsOverlay ov = ObjectOverlayItem( self.objectLabels, self.ilastik._activeImage.Object_Picking.objects._data, color=0, alpha=1.0, autoAdd=True, autoVisible=True, linkColorTable=True) self.ilastik._activeImage.overlayMgr["Objects/Selection"] = ov ov = self.ilastik._activeImage.overlayMgr["Objects/Selection"] self.ilastik.labelWidget.setLabelWidget(self.objectLabels)
def on_activation(self): if self.ilastik.project is None: self.ilastik.setTabBusy(True) return ovs = self.ilastik._activeImage.module[ self.__class__.moduleName].getOverlayRefs() if len(ovs) == 0: raw = self.ilastik._activeImage.overlayMgr["Raw Data"] if raw is not None: ovs.append(raw.getRef()) self.ilastik.labelWidget._history.volumeEditor = self.ilastik.labelWidget overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr) overlayWidget.setVisible(False) self.ilastik.labelWidget.setOverlayWidget(overlayWidget) self.ilastik.labelWidget.setLabelWidget(ve.DummyLabelWidget())
def on_activation(self): if self.ilastik.project is None: return if self.ilastik._activeImage.module[self.name] is None: self.ilastik._activeImage.module[self.name] = PropertyMgr( self.ilastik._activeImage) ovs = self.ilastik._activeImage.module[self.name].getOverlayRefs() raw = self.ilastik._activeImage.overlayMgr["Raw Data"] self.ilastik.labelWidget._history.volumeEditor = self.ilastik.labelWidget overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr) self.ilastik.labelWidget.setOverlayWidget(overlayWidget) ov = self.ilastik._activeImage.overlayMgr["Classification/Labels"] overlayWidget.addOverlayRef(ov.getRef()) overlayWidget.addOverlayRef(raw.getRef()) self.ilastik.labelWidget.setLabelWidget( LabelListWidget( self.ilastik.project.dataMgr.module["Classification"].labelMgr, self.ilastik.project.dataMgr.module["Classification"] ["labelDescriptions"], self.ilastik.labelWidget, ov))
def on_activation(self): if self.ilastik.project is None: return if self.ilastik._activeImage.module[self.name] is None: self.ilastik._activeImage.module[self.name] = PropertyMgr(self.ilastik._activeImage) ovs = self.ilastik._activeImage.module[self.name].getOverlayRefs() raw = self.ilastik._activeImage.overlayMgr["Raw Data"] self.ilastik.labelWidget._history.volumeEditor = self.ilastik.labelWidget overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr) self.ilastik.labelWidget.setOverlayWidget(overlayWidget) ov = self.ilastik._activeImage.overlayMgr["Classification/Labels"] overlayWidget.addOverlayRef(ov.getRef()) overlayWidget.addOverlayRef(raw.getRef()) self.ilastik.labelWidget.setLabelWidget(LabelListWidget(self.ilastik.project.dataMgr.module["Classification"].labelMgr, self.ilastik.project.dataMgr.module["Classification"]["labelDescriptions"], self.ilastik.labelWidget, ov))
def on_activation(self): if self.ilastik.project is None: return self._initContent() self._initConnects() self.interactionLog = [] self.defaultSegmentor = False #initially add 'Raw Data' overlay ovs = self.ilastik._activeImage.module[self.__class__.moduleName].getOverlayRefs() if "Raw Data" in self.ilastik._activeImage.overlayMgr.keys(): raw = self.ilastik._activeImage.overlayMgr["Raw Data"] if raw is not None: ovs.append(raw.getRef()) self.ilastik.labelWidget.interactionLog = self.interactionLog self.ilastik.labelWidget._history.volumeEditor = self.ilastik.labelWidget self.overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr) self.ilastik.labelWidget.setOverlayWidget(self.overlayWidget) if self.parent.project.dataMgr.Interactive_Segmentation.segmentor is None: segmentors = self.parent.project.dataMgr.Interactive_Segmentation.segmentorClasses for i, seg in enumerate(segmentors): if seg.name == "Supervoxel Segmentation": self.parent.project.dataMgr.Interactive_Segmentation.segmentor = seg() ui = self.parent.project.dataMgr.Interactive_Segmentation.segmentor.getInlineSettingsWidget(self.inlineSettings.childWidget, view='default') self.inlineSettings.changeWidget(ui) self.defaultSegmentor = True break #Finally, initialize the core module s = self.ilastik._activeImage.Interactive_Segmentation self.connect(s, QtCore.SIGNAL('overlaysChanged()'), self.on_overlaysChanged) self.connect(s, QtCore.SIGNAL('doneOverlaysAvailable()'), self.on_doneOverlaysAvailable) self.connect(s, QtCore.SIGNAL('weightsSetup()'), self.on_setupWeights) self.connect(s, QtCore.SIGNAL('newSegmentation()'), self.on_newSegmentation) self.connect(s, QtCore.SIGNAL('numColorsNeeded(int)'), self.on_numColorsNeeded) self.connect(s, QtCore.SIGNAL('saveAsPossible(bool)'), lambda b: self.btnSaveAs.setEnabled(b)) self.connect(s, QtCore.SIGNAL('savePossible(bool)'), lambda b: self.btnSave.setEnabled(b)) self.connect(s, QtCore.SIGNAL('seedsAvailable(bool)'), lambda b: self.btnSegment.setEnabled(b)) s.init() #add 'Seeds' overlay self.seedOverlay = OverlayItem(s.seedLabelsVolume._data, color = 0, alpha = 1.0, colorTable = s.seedLabelsVolume.getColorTab(), autoAdd = True, autoVisible = True, linkColorTable = True) self.ilastik._activeImage.overlayMgr["Segmentation/Seeds"] = self.seedOverlay self.seedWidget = SeedListWidget(self.ilastik.project.dataMgr.Interactive_Segmentation.seedMgr, s.seedLabelsVolume, self.ilastik.labelWidget, self.seedOverlay) self.ilastik.labelWidget.setLabelWidget(self.seedWidget) self.seedOverlay.displayable3D = True self.seedOverlay.backgroundClasses = set([0]) self.seedOverlay.smooth3D = False
def on_activation(self): if self.ilastik.project is None: return ovs = self.ilastik._activeImage.module[self.__class__.moduleName].getOverlayRefs() if len(ovs) == 0: raw = self.ilastik._activeImage.overlayMgr["Raw Data"] if raw is not None: ovs.append(raw.getRef()) self.ilastik.labelWidget._history.volumeEditor = self.ilastik.labelWidget overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr) self.ilastik.labelWidget.setOverlayWidget(overlayWidget) self.ilastik.labelWidget.setLabelWidget(ve.DummyLabelWidget()) self.btnUnsupervisedOptions.setEnabled(True)
def on_activation(self): if self.ilastik.project is None: return ovs = self.ilastik._activeImage.module[ self.__class__.moduleName].getOverlayRefs() if len(ovs) == 0: raw = self.ilastik._activeImage.overlayMgr["Raw Data"] if raw is not None: ovs.append(raw.getRef()) self.ilastik.labelWidget._history.volumeEditor = self.ilastik.labelWidget overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr) self.ilastik.labelWidget.setOverlayWidget(overlayWidget) self.ilastik.labelWidget.setLabelWidget(DummyLabelWidget()) self.volumeEditorVisible = self.ilastik.volumeEditorDock.isVisible( ) self.ilastik.volumeEditorDock.setVisible(False) if self.consoleWidget is None: locals = {} locals["activeImage"] = self.ilastik._activeImage locals["dataMgr"] = self.ilastik.project.dataMgr self.interpreter = code.InteractiveInterpreter(locals) self.consoleWidget = SciShell(self.interpreter) dock = QtGui.QDockWidget("ilastik interactive console", self.ilastik) dock.setAllowedAreas(QtCore.Qt.BottomDockWidgetArea | QtCore.Qt.RightDockWidgetArea | QtCore.Qt.TopDockWidgetArea | QtCore.Qt.LeftDockWidgetArea) dock.setWidget(self.consoleWidget) self.consoleDock = dock area = QtCore.Qt.BottomDockWidgetArea self.ilastik.addDockWidget(area, dock) self.consoleDock.setVisible(True) self.consoleDock.setFocus() self.consoleWidget.multipleRedirection(True)
def on_activation(self): if self.ilastik.project is None: return ovs = self.ilastik._activeImage._dataVol.backgroundOverlays if len(ovs) == 0: raw = self.ilastik._activeImage.overlayMgr["Raw Data"] if raw is not None: ovs.append(raw.getRef()) overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr) self.ilastik.labelWidget.setOverlayWidget(overlayWidget) #create background overlay ov = OverlayItem(self.ilastik._activeImage._dataVol.background._data, color=0, alpha=1.0, colorTable = self.ilastik._activeImage._dataVol.background.getColorTab(), autoAdd = True, autoVisible = True, linkColorTable = True) self.ilastik._activeImage.overlayMgr["Connected Components/Background"] = ov ov = self.ilastik._activeImage.overlayMgr["Connected Components/Background"] self.ilastik.labelWidget.setLabelWidget(BackgroundWidget(self.ilastik.project.backgroundMgr, self.ilastik._activeImage._dataVol.background, self.ilastik.labelWidget, ov))
def on_activation(self): if self.ilastik.project is None: return ovs = self.ilastik._activeImage.module[ self.__class__.moduleName].getOverlayRefs() if len(ovs) == 0: raw = self.ilastik._activeImage.overlayMgr["Raw Data"] if raw is not None: ovs.append(raw.getRef()) self.ilastik.labelWidget._history.volumeEditor = self.ilastik.labelWidget overlayWidget = OverlayWidget(self.ilastik.labelWidget, self.ilastik.project.dataMgr) self.ilastik.labelWidget.setOverlayWidget(overlayWidget) self.backgroundLabels = BackgroundWidget( self.ilastik._activeImage.Connected_Components, self.ilastik._activeImage.Connected_Components.background, self.ilastik.labelWidget) self.ilastik.labelWidget.setLabelWidget(self.backgroundLabels) #create ObjectsOverlay ov = BackgroundOverlayItem( self.backgroundLabels, self.ilastik._activeImage.Connected_Components.background._data, color=0, alpha=1.0, autoAdd=True, autoVisible=True, linkColorTable=True) self.ilastik._activeImage.overlayMgr[ "Connected Components/Background"] = ov ov = self.ilastik._activeImage.overlayMgr[ "Connected Components/Background"] self.ilastik.labelWidget.setLabelWidget(self.backgroundLabels)