def onCalculateButton(self):
"""
Run processing when user clicks "Apply" button.
"""
# cursor
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
qt.QApplication.processEvents()
# create nodes
sourceFiducial = self._parameterNode.GetNodeReference("SourceFiducial")
targetFiducial = self._parameterNode.GetNodeReference("TargetFiducial")
# reference
size, origin, spacing = GridNodeHelper.getGridDefinition(
self._parameterNode.GetNodeReference("InputNode"))
userSpacing = [float(self._parameterNode.GetParameter("Spacing"))] * 3
size = np.array(size) * (np.array(spacing) / np.array(userSpacing))
auxVolumeNode = GridNodeHelper.emptyVolume([int(s) for s in size],
origin, userSpacing)
# output
outputNode = self._parameterNode.GetNodeReference(
"OutputGridTransform")
# params
RBFRadius = []
for i in range(targetFiducial.GetNumberOfControlPoints()):
if targetFiducial.GetNthControlPointSelected(i):
RBFRadius.append(
targetFiducial.GetNthControlPointDescription(i))
RBFRadius = ",".join(RBFRadius)
stiffness = float(self._parameterNode.GetParameter("Stiffness"))
# save current state if leadDBS call in case of error
if self._parameterNode.GetParameter("subjectPath") != '':
LeadDBSCall.saveSourceTarget(
self._parameterNode.GetParameter("subjectPath"),
sourceFiducial, targetFiducial)
# preview
visualizationNodes = self.logic.previewWarp(sourceFiducial,
targetFiducial)
qt.QApplication.processEvents()
self._parameterNode.SetParameter("Running", "true")
cliNode = self.logic.run(auxVolumeNode, outputNode, sourceFiducial,
targetFiducial, RBFRadius, stiffness)
if cliNode is not None:
# set up for UI
self.ui.landwarpWidget.setCurrentCommandLineModuleNode(cliNode)
# add observer
cliNode.AddObserver(slicer.vtkMRMLCommandLineModuleNode.StatusModifiedEvent, \
lambda c,e,o=outputNode,v=visualizationNodes,a=auxVolumeNode: self.onStatusModifiedEvent(c,o,v,a))
else:
self.onStatusModifiedEvent(None, outputNode, visualizationNodes,
auxVolumeNode)
def enter(self):
"""
Called each time the user opens this module.
"""
# Make sure parameter node exists and observed
self.initializeParameterNode()
# Lead-DBS call
if LeadDBSCall.updateParameterNodeFromArgs(
self._parameterNode): # was called from command line
self.showSingleModule()
slicer.util.mainWindow().addToolBar(Toolbar.reducedToolbar())
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)
uiWidget = slicer.util.loadUI(self.resourcePath('UI/WarpDrive.ui'))
self.layout.addWidget(uiWidget)
self.ui = slicer.util.childWidgetVariables(uiWidget)
# Add tools buttons
toolsLayout = qt.QHBoxLayout(self.ui.toolsFrame)
toolWidgets = [
NoneTool.NoneToolWidget(),
SmudgeTool.SmudgeToolWidget(),
DrawTool.DrawToolWidget(),
PointToPointTool.PointToPointToolWidget()
]
for toolWidget in toolWidgets:
toolsLayout.addWidget(toolWidget.effectButton)
self.ui.drawModeMenu = toolWidgets[2].effectButton.menu()
# Add Tree View
dataControlTree = TreeView.WarpDriveTreeView()
dataControlLayout = qt.QVBoxLayout(self.ui.dataControlFrame)
dataControlLayout.addWidget(dataControlTree)
# add plastimatch progress bar
self.ui.landwarpWidget = slicer.modules.plastimatch_slicer_landwarp.createNewWidgetRepresentation(
)
self.ui.calculateFrame.layout().addWidget(
self.ui.landwarpWidget.children()[3], 2, 0, 1, 2) # progress bar
# Set scene in MRML widgets. Make sure that in Qt designer
# "mrmlSceneChanged(vtkMRMLScene*)" signal in is connected to each MRML widget's.
# "setMRMLScene(vtkMRMLScene*)" slot.
uiWidget.setMRMLScene(slicer.mrmlScene)
# Create a new parameterNode
# This parameterNode stores all user choices in parameter values, node selections, etc.
# so that when the scene is saved and reloaded, these settings are restored.
self.logic = WarpDriveLogic()
# Connections
self.ui.calculateButton.connect('clicked(bool)',
self.onCalculateButton)
self.ui.spacingSameAsInputCheckBox.toggled.connect(
lambda b: self.ui.spacingSpinBox.setEnabled(not b))
self.ui.autoRBFRadiusCheckBox.toggled.connect(
lambda b: self.ui.RBFRadiusSpinBox.setEnabled(not b))
# 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.inputSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.updateParameterNodeFromGUI)
self.ui.outputSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.onOutputNodeChanged)
self.ui.outputSelector.connect("currentNodeChanged(vtkMRMLNode*)",
self.updateParameterNodeFromGUI)
self.ui.spreadSlider.connect("valueChanged(double)",
self.updateParameterNodeFromGUI)
self.ui.spacingSameAsInputCheckBox.connect(
"toggled(bool)", self.updateParameterNodeFromGUI)
self.ui.spacingSpinBox.connect("valueChanged(double)",
self.updateParameterNodeFromGUI)
self.ui.autoRBFRadiusCheckBox.connect("toggled(bool)",
self.updateParameterNodeFromGUI)
self.ui.RBFRadiusSpinBox.connect("valueChanged(double)",
self.updateParameterNodeFromGUI)
self.ui.stiffnessSpinBox.connect("valueChanged(double)",
self.updateParameterNodeFromGUI)
self.ui.drawModeMenu.triggered.connect(self.updateParameterNodeFromGUI)
# MRML Scene
self.addObserver(slicer.mrmlScene, slicer.mrmlScene.StartCloseEvent,
self.onSceneStartClose)
self.addObserver(slicer.mrmlScene, slicer.mrmlScene.EndCloseEvent,
self.onSceneEndClose)
self.addObserver(slicer.mrmlScene, slicer.mrmlScene.NodeAddedEvent,
dataControlTree.updateTree)
# check dependencies
if slicer.app.mainApplicationName != 'SlicerCustom':
if LeadDBSCall.checkExtensionInstall(extensionName='SlicerRT'):
return
if LeadDBSCall.checkExtensionInstall(
extensionName='MarkupsToModel'):
return
# Initial GUI update
self.updateGUIFromParameterNode()
def onCalculateButton(self):
"""
Run processing when user clicks "Apply" button.
"""
# cursor
qt.QApplication.setOverrideCursor(qt.Qt.WaitCursor)
qt.QApplication.processEvents()
# update (sets the RBF value)
self.updateParameterNodeFromGUI()
# get source and target from points
sourcePoints = WarpDriveUtil.getPointsFromAttribute('source')
targetPoints = WarpDriveUtil.getPointsFromAttribute('target')
fixedPoints = WarpDriveUtil.getPointsFromAttribute('fixed')
# add fixed to source and target
sourcePoints.InsertPoints(sourcePoints.GetNumberOfPoints(),
fixedPoints.GetNumberOfPoints(), 0,
fixedPoints)
targetPoints.InsertPoints(targetPoints.GetNumberOfPoints(),
fixedPoints.GetNumberOfPoints(), 0,
fixedPoints)
# create nodes
sourceFiducial = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLMarkupsFiducialNode')
sourceFiducial.SetControlPointPositionsWorld(sourcePoints)
sourceFiducial.GetDisplayNode().SetTextScale(0)
targetFiducial = slicer.mrmlScene.AddNewNodeByClass(
'vtkMRMLMarkupsFiducialNode')
targetFiducial.SetControlPointPositionsWorld(targetPoints)
targetFiducial.GetDisplayNode().SetVisibility(0)
# reference
size, origin, spacing = GridNodeHelper.getGridDefinition(
self._parameterNode.GetNodeReference("InputNode"))
userSpacing = [float(self._parameterNode.GetParameter("Spacing"))] * 3
size = np.array(size) * (np.array(spacing) / np.array(userSpacing))
auxVolumeNode = GridNodeHelper.emptyVolume([int(s) for s in size],
origin, userSpacing)
# output
outputNode = self._parameterNode.GetNodeReference(
"OutputGridTransform")
# params
RBFRadius = float(self._parameterNode.GetParameter("Spread"))
stiffness = float(self._parameterNode.GetParameter("Stiffness"))
# mask
maskVolume = WarpDriveUtil.getMaskVolume(auxVolumeNode)
# save current state if leadDBS call in case of error
if self._parameterNode.GetParameter("subjectPath") != '':
LeadDBSCall.saveCurrentScene(
self._parameterNode.GetParameter("subjectPath"))
# unset current warp
self._parameterNode.GetNodeReference(
"InputNode").SetAndObserveTransformNodeID(None)
# preview
visualizationNode = WarpDriveUtil.previewWarp(sourceFiducial,
targetFiducial,
outputNode)
# run
self._parameterNode.SetParameter("Running", "true")
cliNode = self.logic.run(auxVolumeNode, outputNode, sourceFiducial,
targetFiducial, RBFRadius, stiffness,
maskVolume)
if cliNode is not None:
# set up for UI
self.ui.landwarpWidget.setCurrentCommandLineModuleNode(cliNode)
# add observer
cliNode.AddObserver(slicer.vtkMRMLCommandLineModuleNode.StatusModifiedEvent, \
lambda c,e,o=outputNode,m=maskVolume,v=visualizationNode,s=sourceFiducial,t=targetFiducial,a=auxVolumeNode: self.onStatusModifiedEvent(c,o,m,v,s,t,a))
else:
self.onStatusModifiedEvent(None, outputNode, maskVolume,
visualizationNode, sourceFiducial,
targetFiducial, auxVolumeNode)
# cursor
qt.QApplication.setOverrideCursor(qt.Qt.ArrowCursor)