def updateSelection(self, row): self.targetTable.clearSelection() first = self.targetTable.model().index(row, 0) second = self.targetTable.model().index(row, 1) selection = qt.QItemSelection(first, second) self.targetTable.selectionModel().select(selection, qt.QItemSelectionModel.Select)
def selectStructure(self, idx): """programmatically select the specified structure""" selectionModel = self.structuresView.selectionModel() selectionModel.select(qt.QItemSelection(self.structures.index(idx,0), self.structures.index(idx,4)), selectionModel.ClearAndSelect) selectionModel.setCurrentIndex(self.structures.index(idx,0), selectionModel.NoUpdate) self.structuresView.activated(self.structures.index(idx,0))
def _selectAllSeries(self, selected): if selected: m = self._seriesTableModel itemSelection = \ qt.QItemSelection(m.index(0, 0), m.index(m.rowCount()-1, m.columnCount()-1)) self._seriesTable.selectionModel().select( itemSelection, qt.QItemSelectionModel.Select | qt.QItemSelectionModel.Rows) else: self._seriesTable.selectionModel().clearSelection()
def run(self, enableScreenshots=0, screenshotScaleFactor=1): """ Run the actual algorithm """ self.delayDisplay( 'Running test of the Neurosurgical Planning tutorial') self.enableScreenshots = enableScreenshots self.screenshotScaleFactor = screenshotScaleFactor # conventional layout lm = slicer.app.layoutManager() lm.setLayout(2) moduleSelector = slicer.util.mainWindow().moduleSelector() # # first load the data # if self.enableScreenshots == 1: # for the tutorial, do it through the welcome module moduleSelector.selectModule('Welcome') self.delayDisplay("Screenshot") self.takeScreenshot('NeurosurgicalPlanning-Welcome', 'Welcome module', -1) else: # otherwise show the sample data module moduleSelector.selectModule('SampleData') # use the sample data module logic to load data for the self test import SampleData sampleDataLogic = SampleData.SampleDataLogic() self.delayDisplay("Getting Baseline volume") baselineVolume = sampleDataLogic.downloadWhiteMatterExplorationBaselineVolume( ) self.takeScreenshot('NeurosurgicalPlanning-Loaded', 'Data loaded', -1) # # link the viewers # if self.enableScreenshots == 1: # for the tutorial, pop up the linking control sliceController = slicer.app.layoutManager().sliceWidget( "Red").sliceController() popupWidget = sliceController.findChild("ctkPopupWidget") if popupWidget is not None: popupWidget.pinPopup(1) self.takeScreenshot('NeurosurgicalPlanning-Link', 'Link slice viewers', -1) popupWidget.pinPopup(0) sliceLogic = slicer.app.layoutManager().sliceWidget('Red').sliceLogic() compositeNode = sliceLogic.GetSliceCompositeNode() compositeNode.SetLinkedControl(1) # # baseline in the background # sliceLogic.StartSliceCompositeNodeInteraction(1) compositeNode.SetBackgroundVolumeID(baselineVolume.GetID()) sliceLogic.EndSliceCompositeNodeInteraction() self.takeScreenshot('NeurosurgicalPlanning-Baseline', 'Baseline in background', -1) # # adjust window level on baseline # moduleSelector.selectModule('Volumes') baselineDisplay = baselineVolume.GetDisplayNode() baselineDisplay.SetAutoWindowLevel(0) baselineDisplay.SetWindow(2600) baselineDisplay.SetLevel(1206) self.takeScreenshot('NeurosurgicalPlanning-WindowLevel', 'Set W/L on baseline', -1) # # switch to red slice only # lm.setLayout(6) self.takeScreenshot('NeurosurgicalPlanning-RedSliceOnly', 'Set layout to Red Slice only', -1) # # segmentation of tumour # # # create a label map and set it for editing # volumesLogic = slicer.modules.volumes.logic() baselineVolumeLabel = volumesLogic.CreateAndAddLabelVolume( slicer.mrmlScene, baselineVolume, baselineVolume.GetName() + '-label') baselineDisplayNode = baselineVolumeLabel.GetDisplayNode() baselineDisplayNode.SetAndObserveColorNodeID( 'vtkMRMLColorTableNodeFileGenericAnatomyColors.txt') selectionNode = slicer.app.applicationLogic().GetSelectionNode() selectionNode.SetReferenceActiveVolumeID(baselineVolume.GetID()) selectionNode.SetReferenceActiveLabelVolumeID( baselineVolumeLabel.GetID()) slicer.app.applicationLogic().PropagateVolumeSelection(0) # # editor module # moduleSelector.selectModule('Editor') self.takeScreenshot('NeurosurgicalPlanning-Editor', 'Showing Editor Module', -1) # set the slice offset so drawing is right sliceNode = sliceLogic.GetSliceNode() sliceOffset = 58.7 sliceNode.SetSliceOffset(sliceOffset) # # paint # parameterNode = EditUtil.getParameterNode() paintEffect = EditorLib.PaintEffectOptions() paintEffect.setMRMLDefaults() paintEffect.__del__() sliceWidget = lm.sliceWidget('Red') paintTool = EditorLib.PaintEffectTool(sliceWidget) self.takeScreenshot('NeurosurgicalPlanning-Paint', 'Paint tool in Editor Module', -1) # # paint in cystic part of tumor, using converstion from RAS coords to # avoid slice widget size differences # EditUtil.setLabel(293) displayCoords = self.rasToDisplay(-7.4, 71, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) displayCoords = self.rasToDisplay(-11, 73, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) displayCoords = self.rasToDisplay(-12, 85, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) displayCoords = self.rasToDisplay(-13, 91, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) displayCoords = self.rasToDisplay(-15, 78, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) paintTool.paintApply() self.takeScreenshot('NeurosurgicalPlanning-PaintCystic', 'Paint cystic part of tumor', -1) # # paint in solid part of tumor # EditUtil.setLabel(7) displayCoords = self.rasToDisplay(-0.5, 118.5, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) displayCoords = self.rasToDisplay(-7.4, 116, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) paintTool.paintApply() self.takeScreenshot('NeurosurgicalPlanning-PaintSolid', 'Paint solid part of tumor', -1) # # paint around the tumor # EditUtil.setLabel(295) rMax = 25 rMin = -50 aMax = 145 aMin = 50 rasStep = 5 # draw the top and bottom for r in range(rMin, rMax, rasStep): displayCoords = self.rasToDisplay(r, aMin, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) displayCoords = self.rasToDisplay(r, aMax, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) # draw the left and right for a in range(aMin, aMax, rasStep): displayCoords = self.rasToDisplay(rMin, a, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) displayCoords = self.rasToDisplay(rMax, a, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) paintTool.paintApply() self.takeScreenshot('NeurosurgicalPlanning-PaintAround', 'Paint around tumor', -1) # # clean up after painting # paintTool.cleanup() paintTool = None # # Grow cut # growCutLogic = EditorLib.GrowCutEffectLogic(sliceWidget.sliceLogic()) growCutLogic.growCut() self.takeScreenshot('NeurosurgicalPlanning-Growcut', 'Growcut', -1) # # Merge split volume # slicer.util.selectModule('Editor') slicer.util.findChildren(text='Split Merge Volume')[0].clicked() self.takeScreenshot('NeurosurgicalPlanning-SplitMerge', 'SplitMerge', -1) # # go to the data module # moduleSelector.selectModule('Data') self.takeScreenshot('NeurosurgicalPlanning-SplitMergeData', 'SplitMerge results in Data', -1) # # Ventricles Segmentation # moduleSelector.selectModule('Editor') # # select the label volume with the area around the tumor slicer.util.findChildren( name='PerStructureVolumesFrame')[0].collapsed = False treeView = slicer.util.findChildren(name='StructuresView')[0] selection = qt.QItemSelection() # selecting the last split volume in the third row row = 2 rowStart = treeView.model().index(row, 0) rowEnd = treeView.model().index(row, treeView.model().columnCount() - 1) # rowSel = qt.QItemSelection(rowStart, rowEnd) selection.select(rowStart, rowEnd) # backup: select the label map in the slice logic too baselinelabel295 = slicer.mrmlScene.GetFirstNodeByName( "BaselineVolume-region 3-label") sliceLogic.StartSliceCompositeNodeInteraction(1) compositeNode.SetLabelVolumeID(baselinelabel295.GetID()) sliceLogic.EndSliceCompositeNodeInteraction() self.takeScreenshot('NeurosurgicalPlanning-SelOutside', 'Select outside region', -1) # # Threshold tool # slicer.modules.EditorWidget.toolsBox.selectEffect('ThresholdEffect') parameterNode = EditUtil.getParameterNode() parameterNode.SetParameter('ThresholdEffect,min', str(1700)) slicer.modules.EditorWidget.toolsBox.currentTools[0].apply() self.takeScreenshot('NeurosurgicalPlanning-Ventricles', 'Ventricles segmentation', -1) # # Save Islands # slicer.modules.EditorWidget.toolsBox.selectEffect('SaveIslandEffect') saveIslandLogic = EditorLib.SaveIslandEffectLogic( sliceWidget.sliceLogic()) displayCoords = self.rasToDisplay(25.3, 5.8, sliceOffset) xy = (displayCoords[0], displayCoords[1]) saveIslandLogic.saveIsland(xy) self.takeScreenshot('NeurosurgicalPlanning-SaveIsland', 'Ventricles save island', -1) # # Merge and build # slicer.util.findChildren(text='Merge And Build')[0].clicked() # # switch to conventional layout # lm.setLayout(2) self.takeScreenshot('NeurosurgicalPlanning-MergeAndBuild', 'Merged and built models', -1) # # select label volume with label 293, in the second row # row = 1 rowStart = treeView.model().index(row, 0) rowEnd = treeView.model().index(row, treeView.model().columnCount() - 1) # rowSel = qt.QItemSelection(rowStart, rowEnd) selection.select(rowStart, rowEnd) # backup: select the label map in the slice logic too baselinelabel293 = slicer.mrmlScene.GetFirstNodeByName( "BaselineVolume-region 1-label") sliceLogic.StartSliceCompositeNodeInteraction(1) compositeNode.SetLabelVolumeID(baselinelabel293.GetID()) sliceLogic.EndSliceCompositeNodeInteraction() self.takeScreenshot('NeurosurgicalPlanning-SelCystic', 'Select cystic region', -1) # # Dilate # slicer.modules.EditorWidget.toolsBox.selectEffect('DilateEffect') EditUtil.setLabel(293) self.takeScreenshot('NeurosurgicalPlanning-Dilate', 'Dilate tool', -1) # tutorial says to click apply three times for d in range(1, 3): print d # slicer.util.findChildren(name='DilateEffectOptionsApply')[0].clicked() # slicer.modules.EditorWidget.toolsBox.currentTools[0].apply() slicer.modules.EditorWidget.toolsBox.currentOption.onApply() self.takeScreenshot('NeurosurgicalPlanning-Dilated', 'Dilated tumor', -1) return True
def run(self, enableScreenshots=0, screenshotScaleFactor=1): """ Run the actual algorithm """ self.delayDisplay( 'Running test of the Neurosurgical Planning tutorial') self.enableScreenshots = enableScreenshots self.screenshotScaleFactor = screenshotScaleFactor # conventional layout lm = slicer.app.layoutManager() lm.setLayout(2) moduleSelector = slicer.util.mainWindow().moduleSelector() # # first load the data # if self.enableScreenshots == 1: # for the tutorial, do it through the welcome module moduleSelector.selectModule('Welcome') self.delayDisplay("Screenshot") self.takeScreenshot('NeurosurgicalPlanning-Welcome', 'Welcome module', -1) else: # otherwise show the sample data module moduleSelector.selectModule('SampleData') # use the sample data module logic to load data for the self test import SampleData sampleDataLogic = SampleData.SampleDataLogic() self.delayDisplay("Getting Baseline volume") baselineVolume = sampleDataLogic.downloadWhiteMatterExplorationBaselineVolume( ) self.delayDisplay("Getting DTI volume") dtiVolume = sampleDataLogic.downloadWhiteMatterExplorationDTIVolume() self.takeScreenshot('NeurosurgicalPlanning-Loaded', 'Data loaded', -1) # # link the viewers # if self.enableScreenshots == 1: # for the tutorial, pop up the linking control sliceController = slicer.app.layoutManager().sliceWidget( "Red").sliceController() popupWidget = sliceController.findChild("ctkPopupWidget") if popupWidget != None: popupWidget.pinPopup(1) self.takeScreenshot('NeurosurgicalPlanning-Link', 'Link slice viewers', -1) popupWidget.pinPopup(0) sliceLogic = slicer.app.layoutManager().sliceWidget('Red').sliceLogic() compositeNode = sliceLogic.GetSliceCompositeNode() compositeNode.SetLinkedControl(1) # # baseline in the background # sliceLogic.StartSliceCompositeNodeInteraction(1) compositeNode.SetBackgroundVolumeID(baselineVolume.GetID()) sliceLogic.EndSliceCompositeNodeInteraction() self.takeScreenshot('NeurosurgicalPlanning-Baseline', 'Baseline in background', -1) # # adjust window level on baseline # moduleSelector.selectModule('Volumes') baselineDisplay = baselineVolume.GetDisplayNode() baselineDisplay.SetAutoWindowLevel(0) baselineDisplay.SetWindow(2600) baselineDisplay.SetLevel(1206) self.takeScreenshot('NeurosurgicalPlanning-WindowLevel', 'Set W/L on baseline', -1) # # switch to red slice only # lm.setLayout(6) self.takeScreenshot('NeurosurgicalPlanning-RedSliceOnly', 'Set layout to Red Slice only', -1) # # segmentation of tumour # # # create a label map and set it for editing # volumesLogic = slicer.modules.volumes.logic() baselineVolumeLabel = volumesLogic.CreateAndAddLabelVolume( slicer.mrmlScene, baselineVolume, baselineVolume.GetName() + '-label') baselineDisplayNode = baselineVolumeLabel.GetDisplayNode() baselineDisplayNode.SetAndObserveColorNodeID( 'vtkMRMLColorTableNodeFileGenericAnatomyColors.txt') selectionNode = slicer.app.applicationLogic().GetSelectionNode() selectionNode.SetReferenceActiveVolumeID(baselineVolume.GetID()) selectionNode.SetReferenceActiveLabelVolumeID( baselineVolumeLabel.GetID()) slicer.app.applicationLogic().PropagateVolumeSelection(0) # # editor module # moduleSelector.selectModule('Editor') self.takeScreenshot('NeurosurgicalPlanning-Editor', 'Showing Editor Module', -1) # set the slice offset so drawing is right sliceNode = sliceLogic.GetSliceNode() sliceOffset = 58.7 sliceNode.SetSliceOffset(sliceOffset) # # paint # parameterNode = EditUtil.getParameterNode() paintEffect = EditorLib.PaintEffectOptions() paintEffect.setMRMLDefaults() paintEffect.__del__() sliceWidget = lm.sliceWidget('Red') paintTool = EditorLib.PaintEffectTool(sliceWidget) self.takeScreenshot('NeurosurgicalPlanning-Paint', 'Paint tool in Editor Module', -1) # # paint in cystic part of tumor, using converstion from RAS coords to # avoid slice widget size differences # EditUtil.setLabel(293) displayCoords = self.rasToDisplay(-7.4, 71, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) displayCoords = self.rasToDisplay(-11, 73, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) displayCoords = self.rasToDisplay(-12, 85, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) displayCoords = self.rasToDisplay(-13, 91, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) displayCoords = self.rasToDisplay(-15, 78, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) paintTool.paintApply() self.takeScreenshot('NeurosurgicalPlanning-PaintCystic', 'Paint cystic part of tumor', -1) # # paint in solid part of tumor # EditUtil.setLabel(7) displayCoords = self.rasToDisplay(-0.5, 118.5, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) displayCoords = self.rasToDisplay(-7.4, 116, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) paintTool.paintApply() self.takeScreenshot('NeurosurgicalPlanning-PaintSolid', 'Paint solid part of tumor', -1) # # paint around the tumor # EditUtil.setLabel(295) rMax = 25 rMin = -50 aMax = 145 aMin = 50 rasStep = 5 # draw the top and bottom for r in range(rMin, rMax, rasStep): displayCoords = self.rasToDisplay(r, aMin, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) displayCoords = self.rasToDisplay(r, aMax, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) # draw the left and right for a in range(aMin, aMax, rasStep): displayCoords = self.rasToDisplay(rMin, a, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) displayCoords = self.rasToDisplay(rMax, a, sliceOffset) paintTool.paintAddPoint(displayCoords[0], displayCoords[1]) paintTool.paintApply() self.takeScreenshot('NeurosurgicalPlanning-PaintAround', 'Paint around tumor', -1) # # clean up after painting # paintTool.cleanup() paintTool = None # # Grow cut # growCutLogic = EditorLib.GrowCutEffectLogic(sliceWidget.sliceLogic()) growCutLogic.growCut() self.takeScreenshot('NeurosurgicalPlanning-Growcut', 'Growcut', -1) # # Merge split volume # slicer.util.selectModule('Editor') slicer.util.findChildren(text='Split Merge Volume')[0].clicked() self.takeScreenshot('NeurosurgicalPlanning-SplitMerge', 'SplitMerge', -1) # # go to the data module # moduleSelector.selectModule('Data') self.takeScreenshot('NeurosurgicalPlanning-SplitMergeData', 'SplitMerge results in Data', -1) # # Ventricles Segmentation # moduleSelector.selectModule('Editor') # # select the label volume with the area around the tumor slicer.util.findChildren( name='PerStructureVolumesFrame')[0].collapsed = False treeView = slicer.util.findChildren(name='StructuresView')[0] selection = qt.QItemSelection() # selecting the last split volume in the third row row = 2 rowStart = treeView.model().index(row, 0) rowEnd = treeView.model().index(row, treeView.model().columnCount() - 1) # rowSel = qt.QItemSelection(rowStart, rowEnd) selection.select(rowStart, rowEnd) # backup: select the label map in the slice logic too baselinelabel295 = slicer.mrmlScene.GetFirstNodeByName( "BaselineVolume-region 3-label") sliceLogic.StartSliceCompositeNodeInteraction(1) compositeNode.SetLabelVolumeID(baselinelabel295.GetID()) sliceLogic.EndSliceCompositeNodeInteraction() self.takeScreenshot('NeurosurgicalPlanning-SelOutside', 'Select outside region', -1) # # Threshold tool # slicer.modules.EditorWidget.toolsBox.selectEffect('ThresholdEffect') parameterNode = EditUtil.getParameterNode() parameterNode.SetParameter('ThresholdEffect,min', str(1700)) slicer.modules.EditorWidget.toolsBox.currentTools[0].apply() self.takeScreenshot('NeurosurgicalPlanning-Ventricles', 'Ventricles segmentation', -1) # # Save Islands # slicer.modules.EditorWidget.toolsBox.selectEffect('SaveIslandEffect') saveIslandLogic = EditorLib.SaveIslandEffectLogic( sliceWidget.sliceLogic()) displayCoords = self.rasToDisplay(25.3, 5.8, sliceOffset) xy = (displayCoords[0], displayCoords[1]) saveIslandLogic.saveIsland(xy) self.takeScreenshot('NeurosurgicalPlanning-SaveIsland', 'Ventricles save island', -1) # # Merge and build # slicer.util.findChildren(text='Merge And Build')[0].clicked() # # switch to conventional layout # lm.setLayout(2) self.takeScreenshot('NeurosurgicalPlanning-MergeAndBuild', 'Merged and built models', -1) # # Tractography label map seeding # # # select label volume with label 293, in the second row # row = 1 rowStart = treeView.model().index(row, 0) rowEnd = treeView.model().index(row, treeView.model().columnCount() - 1) # rowSel = qt.QItemSelection(rowStart, rowEnd) selection.select(rowStart, rowEnd) # backup: select the label map in the slice logic too baselinelabel293 = slicer.mrmlScene.GetFirstNodeByName( "BaselineVolume-region 1-label") sliceLogic.StartSliceCompositeNodeInteraction(1) compositeNode.SetLabelVolumeID(baselinelabel293.GetID()) sliceLogic.EndSliceCompositeNodeInteraction() self.takeScreenshot('NeurosurgicalPlanning-SelCystic', 'Select cystic region', -1) # # Dilate # slicer.modules.EditorWidget.toolsBox.selectEffect('DilateEffect') EditUtil.setLabel(293) self.takeScreenshot('NeurosurgicalPlanning-Dilate', 'Dilate tool', -1) # tutorial says to click apply three times for d in range(1, 3): print d # slicer.util.findChildren(name='DilateEffectOptionsApply')[0].clicked() # slicer.modules.EditorWidget.toolsBox.currentTools[0].apply() slicer.modules.EditorWidget.toolsBox.currentOption.onApply() self.takeScreenshot('NeurosurgicalPlanning-Dilated', 'Dilated tumor', -1) # # Tractography Label Map Seeding module # moduleSelector.selectModule('TractographyLabelMapSeeding') self.takeScreenshot('NeurosurgicalPlanning-LabelMapSeedingModule', 'Showing Tractography Label Seeding Module', -1) tractographyLabelSeeding = slicer.modules.tractographylabelmapseeding parameters = {} parameters['InputVolume'] = dtiVolume.GetID() baselinelabel293 = slicer.mrmlScene.GetFirstNodeByName( "BaselineVolume-region 1-label") # VTK6 TODO - set 'InputROIPipelineInfo' parameters['InputROI'] = baselinelabel293.GetID() fibers = slicer.vtkMRMLFiberBundleNode() slicer.mrmlScene.AddNode(fibers) parameters['OutputFibers'] = fibers.GetID() parameters['UseIndexSpace'] = 1 parameters['StoppingValue'] = 0.15 parameters['ROIlabel'] = 293 parameters['StoppingMode'] = 'FractionalAnisotropy' # defaults # parameters['ClTh'] = 0.3 # parameters['MinimumLength'] = 20 # parameters['MaximumLength'] = 800 # parameters['StoppingCurvature'] = 0.7 # parameters['IntegrationStepLength'] = 0.5 # parameters['SeedSpacing'] = 2 # and run it slicer.cli.run(tractographyLabelSeeding, None, parameters) self.takeScreenshot('NeurosurgicalPlanning-LabelMapSeeding', 'Showing Tractography Label Seeding Results', -1) # # tractography fiducial seeding # moduleSelector.selectModule('TractographyInteractiveSeeding') self.takeScreenshot('NeurosurgicalPlanning-TIS', 'Showing Tractography Interactive Seeding Module', -1) # DTI in background sliceLogic.StartSliceCompositeNodeInteraction(1) compositeNode.SetBackgroundVolumeID(dtiVolume.GetID()) sliceLogic.EndSliceCompositeNodeInteraction() # DTI visible in 3D sliceNode = sliceLogic.GetSliceNode() sliceLogic.StartSliceNodeInteraction(128) sliceNode.SetSliceVisible(1) sliceLogic.EndSliceNodeInteraction() self.takeScreenshot( 'NeurosurgicalPlanning-TIS-DTI', 'DTI volume with Tractography Interactive Seeding Module', -1) # place a fiducial displayNode = slicer.vtkMRMLMarkupsDisplayNode() slicer.mrmlScene.AddNode(displayNode) fidNode = slicer.vtkMRMLMarkupsFiducialNode() fidNode.SetName('F') slicer.mrmlScene.AddNode(fidNode) fidNode.SetAndObserveDisplayNodeID(displayNode.GetID()) r = 28.338526 a = 34.064367 s = sliceOffset fidNode.AddFiducial(r, a, s) # make it active selectionNode = slicer.mrmlScene.GetNodeByID( "vtkMRMLSelectionNodeSingleton") if (selectionNode != None): selectionNode.SetReferenceActivePlaceNodeID(fidNode.GetID()) self.takeScreenshot( 'NeurosurgicalPlanning-TIS-Fid1', 'Fiducial in Tractography Interactive Seeding Module', -1) # set up the arguments wr = slicer.modules.tractographyinteractiveseeding.widgetRepresentation( ) wr.setDiffusionTensorVolumeNode(dtiVolume) # create a fiber bundle fiducialFibers = slicer.vtkMRMLFiberBundleNode() slicer.mrmlScene.AddNode(fiducialFibers) wr.setFiberBundleNode(fiducialFibers) wr.setSeedingNode(fidNode) wr.setMinimumPath(10) wr.setStoppingValue(0.15) self.takeScreenshot('NeurosurgicalPlanning-TIS-Args', 'Tractography Interactive Seeding arguments', -1) self.delayDisplay("Moving the fiducial") for y in range(-20, 100, 5): msg = "Moving the fiducial to y = " + str(y) self.delayDisplay(msg, 250) fidNode.SetNthFiducialPosition(0, r, y, s) self.takeScreenshot( 'NeurosurgicalPlanning-TIS-Moved', 'Moved fiducial and did Tractography Interactive Seeding', -1) return True
def setup(self): """ Called when the user opens the module the first time and the widget is initialized. """ ScriptedLoadableModuleWidget.setup(self) # Load widget from .ui file (created by Qt Designer). # Additional widgets can be instantiated manually and added to self.layout. uiWidget = slicer.util.loadUI( self.resourcePath('UI/antsRegistration.ui')) self.layout.addWidget(uiWidget) self.ui = slicer.util.childWidgetVariables(uiWidget) # Set custom UI components self.ui.stagesTableWidget = StagesTable() stagesTableLayout = qt.QVBoxLayout(self.ui.stagesFrame) stagesTableLayout.addWidget(self.ui.stagesTableWidget) self.ui.metricsTableWidget = MetricsTable() metricsTableLayout = qt.QVBoxLayout(self.ui.metricsFrame) metricsTableLayout.addWidget(self.ui.metricsTableWidget) self.ui.levelsTableWidget = LevelsTable() levelsTableLayout = qt.QVBoxLayout(self.ui.levelsFrame) levelsTableLayout.addWidget(self.ui.levelsTableWidget) self.ui.cliWidget = slicer.modules.antsregistrationcli.createNewWidgetRepresentation( ) self.layout.addWidget(self.ui.cliWidget.children()[3]) # progress bar self._cliObserver = None # Set scene in MRML widgets. Make sure that in Qt designer the top-level qMRMLWidget's # "mrmlSceneChanged(vtkMRMLScene*)" signal in is connected to each MRML widget's. # "setMRMLScene(vtkMRMLScene*)" slot. uiWidget.setMRMLScene(slicer.mrmlScene) # Create logic class. Logic implements all computations that should be possible to run # in batch mode, without a graphical user interface. self.logic = antsRegistrationLogic() self.ui.stagesPresetsComboBox.addItems( ['Select...'] + PresetManager().getPresetNames()) # Connections # These connections ensure that we update parameter node when scene is closed self.addObserver(slicer.mrmlScene, slicer.mrmlScene.StartCloseEvent, self.onSceneStartClose) self.addObserver(slicer.mrmlScene, slicer.mrmlScene.EndCloseEvent, self.onSceneEndClose) # These connections ensure that whenever user changes some settings on the GUI, that is saved in the MRML scene # (in the selected parameter node). self.ui.stagesTableWidget.view.selectionModel( ).selectionChanged.connect(self.updateParameterNodeFromGUI) self.ui.outputInterpolationComboBox.connect( "currentIndexChanged(int)", self.updateParameterNodeFromGUI) self.ui.outputTransformComboBox.connect( "currentNodeChanged(vtkMRMLNode*)", self.updateParameterNodeFromGUI) self.ui.outputVolumeComboBox.connect( "currentNodeChanged(vtkMRMLNode*)", self.updateParameterNodeFromGUI) self.ui.initialTransformTypeComboBox.connect( "currentIndexChanged(int)", self.updateParameterNodeFromGUI) self.ui.initialTransformNodeComboBox.connect( "currentNodeChanged(vtkMRMLNode*)", self.updateParameterNodeFromGUI) self.ui.dimensionalitySpinBox.connect("valueChanged(int)", self.updateParameterNodeFromGUI) self.ui.histogramMatchingCheckBox.connect( "toggled(bool)", self.updateParameterNodeFromGUI) self.ui.outputDisplacementFieldCheckBox.connect( "toggled(bool)", self.updateParameterNodeFromGUI) self.ui.winsorizeRangeWidget.connect("rangeChanged(double,double)", self.updateParameterNodeFromGUI) self.ui.computationPrecisionComboBox.connect( "currentIndexChanged(int)", self.updateParameterNodeFromGUI) self.ui.fixedImageNodeComboBox.connect( "currentNodeChanged(vtkMRMLNode*)", self.updateStagesFromFixedMovingNodes) self.ui.movingImageNodeComboBox.connect( "currentNodeChanged(vtkMRMLNode*)", self.updateStagesFromFixedMovingNodes) # Stages Parameter self.ui.stagesTableWidget.removeButton.clicked.connect( self.onRemoveStageButtonClicked) self.ui.metricsTableWidget.removeButton.clicked.connect( self.updateStagesParameterFromGUI) self.ui.levelsTableWidget.removeButton.clicked.connect( self.updateStagesParameterFromGUI) self.ui.stagesTableWidget.model.itemChanged.connect( self.updateStagesParameterFromGUI) self.ui.metricsTableWidget.model.itemChanged.connect( self.updateStagesParameterFromGUI) self.ui.levelsTableWidget.model.itemChanged.connect( self.updateStagesParameterFromGUI) self.ui.fixedMaskComboBox.connect("currentNodeChanged(vtkMRMLNode*)", self.updateStagesParameterFromGUI) self.ui.movingMaskComboBox.connect("currentNodeChanged(vtkMRMLNode*)", self.updateStagesParameterFromGUI) self.ui.levelsTableWidget.smoothingSigmasUnitComboBox.currentTextChanged.connect( self.updateStagesParameterFromGUI) self.ui.levelsTableWidget.convergenceThresholdSpinBox.valueChanged.connect( self.updateStagesParameterFromGUI) self.ui.levelsTableWidget.convergenceWindowSizeSpinBox.valueChanged.connect( self.updateStagesParameterFromGUI) self.ui.metricsTableWidget.linkStagesPushButton.toggled.connect( self.updateStagesParameterFromGUI) self.ui.levelsTableWidget.linkStagesPushButton.toggled.connect( self.updateStagesParameterFromGUI) self.ui.linkMaskingStagesPushButton.toggled.connect( self.updateStagesParameterFromGUI) # Preset Stages self.ui.stagesPresetsComboBox.currentTextChanged.connect( self.onPresetSelected) # Buttons self.ui.stagesTableWidget.savePresetPushButton.connect( 'clicked(bool)', self.onSavePresetPushButton) self.ui.runRegistrationButton.connect('clicked(bool)', self.onRunRegistrationButton) # Make sure parameter node is initialized (needed for module reload) self.initializeParameterNode() # Init tables self.ui.stagesTableWidget.view.selectionModel().emitSelectionChanged( self.ui.stagesTableWidget.view.selectionModel().selection, qt.QItemSelection()) self.ui.metricsTableWidget.view.selectionModel().emitSelectionChanged( self.ui.metricsTableWidget.view.selectionModel().selection, qt.QItemSelection())