def __init__(self):
ScriptedModuleGUI.__init__(self)
self.SetCategory("Vascular Modeling Toolkit")
self.SetGUIName("Branch Splitting using VMTK")
self._moduleFrame = slicer.vtkSlicerModuleCollapsibleFrame()
self._inCenterLineSelector = slicer.vtkSlicerNodeSelectorWidget()
self._inModelSelector = slicer.vtkSlicerNodeSelectorWidget()
self._outModelSelector = slicer.vtkSlicerNodeSelectorWidget()
self._topFrame = slicer.vtkSlicerModuleCollapsibleFrame()
self._startButton = slicer.vtkKWPushButton()
self._checkButton = slicer.vtkKWCheckButton()
self._helper = VMTKBranchSplittingHelper(self)
self._logic = VMTKBranchSplittingLogic(self)
self._updating = 0
def __init__(self):
ScriptedModuleGUI.__init__(self)
self.SetCategory("Vascular Modeling Toolkit")
self.SetGUIName("Branch Splitting using VMTK")
self._moduleFrame = slicer.vtkSlicerModuleCollapsibleFrame()
self._inCenterLineSelector = slicer.vtkSlicerNodeSelectorWidget()
self._inModelSelector = slicer.vtkSlicerNodeSelectorWidget()
self._outModelSelector = slicer.vtkSlicerNodeSelectorWidget()
self._topFrame = slicer.vtkSlicerModuleCollapsibleFrame()
self._startButton = slicer.vtkKWPushButton()
self._checkButton = slicer.vtkKWCheckButton()
self._helper = VMTKBranchSplittingHelper(self)
self._logic = VMTKBranchSplittingLogic(self)
self._updating = 0
class VMTKBranchSplittingGUI(ScriptedModuleGUI):
def __init__(self):
ScriptedModuleGUI.__init__(self)
self.SetCategory("Vascular Modeling Toolkit")
self.SetGUIName("Branch Splitting using VMTK")
self._moduleFrame = slicer.vtkSlicerModuleCollapsibleFrame()
self._inCenterLineSelector = slicer.vtkSlicerNodeSelectorWidget()
self._inModelSelector = slicer.vtkSlicerNodeSelectorWidget()
self._outModelSelector = slicer.vtkSlicerNodeSelectorWidget()
self._topFrame = slicer.vtkSlicerModuleCollapsibleFrame()
self._startButton = slicer.vtkKWPushButton()
self._checkButton = slicer.vtkKWCheckButton()
self._helper = VMTKBranchSplittingHelper(self)
self._logic = VMTKBranchSplittingLogic(self)
self._updating = 0
def Destructor(self):
self._helper = None
self._logic = None
def RemoveMRMLNodeObservers(self):
pass
def RemoveLogicObservers(self):
pass
def AddGUIObservers(self):
self._startButtonTag = self.AddObserverByNumber(
self._startButton, vtkKWPushButton_InvokedEvent)
def RemoveGUIObservers(self):
pass
def ProcessGUIEvents(self, caller, event):
if not self._updating:
if caller == self._startButton and event == vtkKWPushButton_InvokedEvent:
self.Splitting()
def Splitting(self):
inCeLine = self._inCenterLineSelector.GetSelected()
inModel = self._inModelSelector.GetSelected()
outModel = self._outModelSelector.GetSelected()
split = self._checkButton.GetSelectedState()
vmtkFound = self.CheckForVmtkLibrary()
if inCeLine and inModel and outModel and vmtkFound:
result = slicer.vtkPolyData()
r = self._logic.branchSplitting(inCeLine.GetPolyData(),
inModel.GetPolyData())
result.DeepCopy(r)
result.Update()
outModel.SetAndObservePolyData(result)
outModel.SetModifiedSinceRead(1)
displayNode = outModel.GetModelDisplayNode()
if not displayNode:
displayNode = slicer.vtkMRMLModelDisplayNode()
displayNode.SetPolyData(outModel.GetPolyData())
displayNode.SetColor(1, 0, 0)
displayNode.SetScalarVisibility(1)
displayNode.SetActiveScalarName(self._logic._GroupIdsArrayName)
displayNode.SetAndObserveColorNodeID(
self.GetLogic().GetMRMLScene().GetNodesByName(
"Labels").GetItemAsObject(0).GetID())
displayNode.SetVisibility(1)
displayNode.SetOpacity(1.0)
self.GetLogic().GetMRMLScene().AddNode(displayNode)
outModel.SetAndObserveDisplayNodeID(displayNode.GetID())
dNode = inModel.GetModelDisplayNode()
dNode.SetOpacity(0.0)
inModel.SetAndObserveDisplayNodeID(dNode.GetID())
if split == 1:
ctr = 0
newPdList = self._logic.splitModels(result)
for i in newPdList:
if i.GetNumberOfCells() == 0:
continue
self._helper.debug("Number of Cells are: " +
str(i.GetNumberOfCells()))
ctr += 1
scene = self.GetLogic().GetMRMLScene()
newNode = slicer.vtkMRMLModelNode()
newNode.SetName("VMTKBranchSplittingOut_Branch" + str(ctr))
newNode.SetScene(scene)
newNode.SetAndObservePolyData(i)
scene.AddNode(newNode)
dn = slicer.vtkMRMLModelDisplayNode()
dn.SetPolyData(newNode.GetPolyData())
dn.SetColor(random.random(), random.random(),
random.random())
dn.SetBackfaceCulling(0)
dn.SetSliceIntersectionVisibility(1)
dn.SetVisibility(1)
dn.SetOpacity(1.0)
scene.AddNode(dn)
newNode.SetAndObserveDisplayNodeID(dn.GetName())
def CheckForVmtkLibrary(self):
try:
t = slicer.vtkvmtkFastMarchingUpwindGradientImageFilter()
except Exception:
d = slicer.vtkKWMessageDialog()
d.SetParent(slicer.ApplicationGUI.GetMainSlicerWindow())
d.SetMasterWindow(slicer.ApplicationGUI.GetMainSlicerWindow())
d.SetStyleToMessage()
d.SetText(
"VmtkSlicerModule not found! Please install the VmtkSlicerModule extension to use this module!"
)
d.Create()
d.Invoke()
return 0
return 1
def UpdateMRML(self):
if not self._updating:
self._updating = 1
self._updating = 0
def UpdateGUI(self):
if not self._updating:
self._updating = 1
self._updating = 0
def ProcessMRMLEvents(self, caller, event):
if caller == self.GetLogic().GetMRMLScene(
) and event == vtkMRMLScene_CloseEvent:
self.OnSceneClose()
elif caller == self.GetScriptedModuleNode():
self.UpdateGUI()
def BuildGUI(self):
self.GetUIPanel().AddPage("BranchSplitting", "BranchSplitting", "")
self._centerlinePage = self.GetUIPanel().GetPageWidget(
"BranchSplitting")
helpText = "**Branch Splitting using VMTK**, developed by Johannes Schick."
aboutText = "This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer community."
self._helpAboutFrame = self.BuildHelpAndAboutFrame(
self._centerlinePage, helpText, aboutText)
self._helper.debug("Creating BranchSplitting GUI")
self._moduleFrame.SetParent(self._centerlinePage)
self._moduleFrame.Create()
self._moduleFrame.SetLabelText("VMTKBranchSplitting")
self._moduleFrame.ExpandFrame()
slicer.TkCall(
"pack %s -side top -anchor nw -fill x -padx 2 -pady 2 -in %s" %
(self._moduleFrame.GetWidgetName(),
self._centerlinePage.GetWidgetName()))
self._topFrame.SetParent(self._moduleFrame.GetFrame())
self._topFrame.Create()
self._topFrame.SetLabelText("Input/Output")
self._topFrame.ExpandFrame()
slicer.TkCall("pack %s -side top -anchor nw -fill x -padx 2 -pady 2" %
self._topFrame.GetWidgetName())
self._inModelSelector.SetNodeClass("vtkMRMLModelNode", "", "", "")
self._inModelSelector.SetParent(self._topFrame.GetFrame())
self._inModelSelector.Create()
self._inModelSelector.SetMRMLScene(self.GetLogic().GetMRMLScene())
self._inModelSelector.UpdateMenu()
self._inModelSelector.SetBorderWidth(2)
self._inModelSelector.SetLabelText("Input Model: ")
self._inModelSelector.SetBalloonHelpString(
"select an input model from the current mrml scene.")
slicer.TkCall("pack %s -side top -anchor e -padx 20 -pady 4" %
self._inModelSelector.GetWidgetName())
self._inCenterLineSelector.SetNodeClass("vtkMRMLModelNode", "", "", "")
self._inCenterLineSelector.SetParent(self._topFrame.GetFrame())
self._inCenterLineSelector.Create()
self._inCenterLineSelector.SetMRMLScene(self.GetLogic().GetMRMLScene())
self._inCenterLineSelector.UpdateMenu()
self._inCenterLineSelector.SetBorderWidth(2)
self._inCenterLineSelector.SetLabelText("Input Centerline: ")
self._inCenterLineSelector.SetBalloonHelpString(
"select an input model from the current mrml scene.")
slicer.TkCall("pack %s -side top -anchor e -padx 20 -pady 4" %
self._inCenterLineSelector.GetWidgetName())
self._outModelSelector.SetNodeClass("vtkMRMLModelNode", "", "1",
"VMTKBranchSplittingOut")
self._outModelSelector.SetNewNodeEnabled(1)
self._outModelSelector.SetParent(self._topFrame.GetFrame())
self._outModelSelector.Create()
self._outModelSelector.SetMRMLScene(self.GetLogic().GetMRMLScene())
self._outModelSelector.UpdateMenu()
self._outModelSelector.SetBorderWidth(2)
self._outModelSelector.SetLabelText("Branch Output Model: ")
self._outModelSelector.SetBalloonHelpString(
"select an output model from the current mrml scene.")
slicer.TkCall("pack %s -side top -anchor e -padx 20 -pady 4" %
self._outModelSelector.GetWidgetName())
self._checkButton.SetParent(self._topFrame.GetFrame())
self._checkButton.Create()
self._checkButton.SetEnabled(1)
self._checkButton.SetText("Split into models")
self._checkButton.SetBalloonHelpString(
"Split model into different surface models")
slicer.TkCall("pack %s -side top -anchor e -padx 2 -pady 2" %
self._checkButton.GetWidgetName())
self._startButton.SetParent(self._topFrame.GetFrame())
self._startButton.Create()
self._startButton.SetEnabled(1)
self._startButton.SetText("Split Branchs")
self._startButton.SetBalloonHelpString(
"Click to start the network extraction")
slicer.TkCall("pack %s -side top -anchor e -padx 2 -pady 2" %
self._startButton.GetWidgetName())
#self.CreateOutModelNodes()
self._helper.debug("Done Creating BranchSplitting GUI")
def TearDownGUI(self):
if self.GetUIPanel().GetUserInterfaceManager():
self.GetUIPanel().RemovePage("BranchSplitting")
def GetHelper(self):
return self._helper
def GetMyLogic(self):
return self._logic
class VMTKBranchSplittingGUI(ScriptedModuleGUI):
def __init__(self):
ScriptedModuleGUI.__init__(self)
self.SetCategory("Vascular Modeling Toolkit")
self.SetGUIName("Branch Splitting using VMTK")
self._moduleFrame = slicer.vtkSlicerModuleCollapsibleFrame()
self._inCenterLineSelector = slicer.vtkSlicerNodeSelectorWidget()
self._inModelSelector = slicer.vtkSlicerNodeSelectorWidget()
self._outModelSelector = slicer.vtkSlicerNodeSelectorWidget()
self._topFrame = slicer.vtkSlicerModuleCollapsibleFrame()
self._startButton = slicer.vtkKWPushButton()
self._checkButton = slicer.vtkKWCheckButton()
self._helper = VMTKBranchSplittingHelper(self)
self._logic = VMTKBranchSplittingLogic(self)
self._updating = 0
def Destructor(self):
self._helper = None
self._logic = None
def RemoveMRMLNodeObservers(self):
pass
def RemoveLogicObservers(self):
pass
def AddGUIObservers(self):
self._startButtonTag = self.AddObserverByNumber(self._startButton,vtkKWPushButton_InvokedEvent)
def RemoveGUIObservers(self):
pass
def ProcessGUIEvents(self,caller,event):
if not self._updating:
if caller == self._startButton and event == vtkKWPushButton_InvokedEvent:
self.Splitting()
def Splitting(self):
inCeLine = self._inCenterLineSelector.GetSelected()
inModel = self._inModelSelector.GetSelected()
outModel = self._outModelSelector.GetSelected()
split = self._checkButton.GetSelectedState()
vmtkFound=self.CheckForVmtkLibrary()
if inCeLine and inModel and outModel and vmtkFound:
result = slicer.vtkPolyData()
r=self._logic.branchSplitting(inCeLine.GetPolyData(),inModel.GetPolyData())
result.DeepCopy(r)
result.Update()
outModel.SetAndObservePolyData(result)
outModel.SetModifiedSinceRead(1)
displayNode = outModel.GetModelDisplayNode()
if not displayNode:
displayNode = slicer.vtkMRMLModelDisplayNode()
displayNode.SetPolyData(outModel.GetPolyData())
displayNode.SetColor(1, 0, 0)
displayNode.SetScalarVisibility(1)
displayNode.SetActiveScalarName(self._logic._GroupIdsArrayName)
displayNode.SetAndObserveColorNodeID(self.GetLogic().GetMRMLScene().GetNodesByName("Labels").GetItemAsObject(0).GetID())
displayNode.SetVisibility(1)
displayNode.SetOpacity(1.0)
self.GetLogic().GetMRMLScene().AddNode(displayNode)
outModel.SetAndObserveDisplayNodeID(displayNode.GetID())
dNode = inModel.GetModelDisplayNode()
dNode.SetOpacity(0.0)
inModel.SetAndObserveDisplayNodeID(dNode.GetID())
if split == 1:
ctr=0
newPdList=self._logic.splitModels(result)
for i in newPdList:
if i.GetNumberOfCells() == 0:
continue
self._helper.debug("Number of Cells are: "+str(i.GetNumberOfCells()))
ctr+=1
scene=self.GetLogic().GetMRMLScene()
newNode=slicer.vtkMRMLModelNode()
newNode.SetName("VMTKBranchSplittingOut_Branch"+str(ctr))
newNode.SetScene(scene)
newNode.SetAndObservePolyData(i)
scene.AddNode(newNode)
dn=slicer.vtkMRMLModelDisplayNode()
dn.SetPolyData(newNode.GetPolyData())
dn.SetColor(random.random() ,random.random() ,random.random() )
dn.SetBackfaceCulling(0)
dn.SetSliceIntersectionVisibility(1)
dn.SetVisibility(1)
dn.SetOpacity(1.0)
scene.AddNode(dn)
newNode.SetAndObserveDisplayNodeID(dn.GetName())
def CheckForVmtkLibrary(self):
try:
t = slicer.vtkvmtkFastMarchingUpwindGradientImageFilter()
except Exception:
d = slicer.vtkKWMessageDialog()
d.SetParent(slicer.ApplicationGUI.GetMainSlicerWindow())
d.SetMasterWindow(slicer.ApplicationGUI.GetMainSlicerWindow())
d.SetStyleToMessage()
d.SetText("VmtkSlicerModule not found! Please install the VmtkSlicerModule extension to use this module!")
d.Create()
d.Invoke()
return 0
return 1
def UpdateMRML(self):
if not self._updating:
self._updating = 1
self._updating = 0
def UpdateGUI(self):
if not self._updating:
self._updating = 1
self._updating = 0
def ProcessMRMLEvents(self,caller,event):
if caller == self.GetLogic().GetMRMLScene() and event == vtkMRMLScene_CloseEvent:
self.OnSceneClose()
elif caller == self.GetScriptedModuleNode():
self.UpdateGUI()
def BuildGUI(self):
self.GetUIPanel().AddPage("BranchSplitting","BranchSplitting","")
self._centerlinePage = self.GetUIPanel().GetPageWidget("BranchSplitting")
helpText = "**Branch Splitting using VMTK**, developed by Johannes Schick."
aboutText = "This work is supported by NA-MIC, NAC, BIRN, NCIGT, and the Slicer community."
self._helpAboutFrame = self.BuildHelpAndAboutFrame(self._centerlinePage,helpText,aboutText)
self._helper.debug("Creating BranchSplitting GUI")
self._moduleFrame.SetParent(self._centerlinePage)
self._moduleFrame.Create()
self._moduleFrame.SetLabelText("VMTKBranchSplitting")
self._moduleFrame.ExpandFrame()
slicer.TkCall("pack %s -side top -anchor nw -fill x -padx 2 -pady 2 -in %s" % (self._moduleFrame.GetWidgetName(),self._centerlinePage.GetWidgetName()))
self._topFrame.SetParent(self._moduleFrame.GetFrame())
self._topFrame.Create()
self._topFrame.SetLabelText("Input/Output")
self._topFrame.ExpandFrame()
slicer.TkCall("pack %s -side top -anchor nw -fill x -padx 2 -pady 2" % self._topFrame.GetWidgetName())
self._inModelSelector.SetNodeClass("vtkMRMLModelNode","","","")
self._inModelSelector.SetParent(self._topFrame.GetFrame())
self._inModelSelector.Create()
self._inModelSelector.SetMRMLScene(self.GetLogic().GetMRMLScene())
self._inModelSelector.UpdateMenu()
self._inModelSelector.SetBorderWidth(2)
self._inModelSelector.SetLabelText("Input Model: ")
self._inModelSelector.SetBalloonHelpString("select an input model from the current mrml scene.")
slicer.TkCall("pack %s -side top -anchor e -padx 20 -pady 4" % self._inModelSelector.GetWidgetName())
self._inCenterLineSelector.SetNodeClass("vtkMRMLModelNode","","","")
self._inCenterLineSelector.SetParent(self._topFrame.GetFrame())
self._inCenterLineSelector.Create()
self._inCenterLineSelector.SetMRMLScene(self.GetLogic().GetMRMLScene())
self._inCenterLineSelector.UpdateMenu()
self._inCenterLineSelector.SetBorderWidth(2)
self._inCenterLineSelector.SetLabelText("Input Centerline: ")
self._inCenterLineSelector.SetBalloonHelpString("select an input model from the current mrml scene.")
slicer.TkCall("pack %s -side top -anchor e -padx 20 -pady 4" % self._inCenterLineSelector.GetWidgetName())
self._outModelSelector.SetNodeClass("vtkMRMLModelNode","","1","VMTKBranchSplittingOut")
self._outModelSelector.SetNewNodeEnabled(1)
self._outModelSelector.SetParent(self._topFrame.GetFrame())
self._outModelSelector.Create()
self._outModelSelector.SetMRMLScene(self.GetLogic().GetMRMLScene())
self._outModelSelector.UpdateMenu()
self._outModelSelector.SetBorderWidth(2)
self._outModelSelector.SetLabelText("Branch Output Model: ")
self._outModelSelector.SetBalloonHelpString("select an output model from the current mrml scene.")
slicer.TkCall("pack %s -side top -anchor e -padx 20 -pady 4" % self._outModelSelector.GetWidgetName())
self._checkButton.SetParent(self._topFrame.GetFrame())
self._checkButton.Create()
self._checkButton.SetEnabled(1)
self._checkButton.SetText("Split into models")
self._checkButton.SetBalloonHelpString("Split model into different surface models")
slicer.TkCall("pack %s -side top -anchor e -padx 2 -pady 2" % self._checkButton.GetWidgetName())
self._startButton.SetParent(self._topFrame.GetFrame())
self._startButton.Create()
self._startButton.SetEnabled(1)
self._startButton.SetText("Split Branchs")
self._startButton.SetBalloonHelpString("Click to start the network extraction")
slicer.TkCall("pack %s -side top -anchor e -padx 2 -pady 2" % self._startButton.GetWidgetName())
#self.CreateOutModelNodes()
self._helper.debug("Done Creating BranchSplitting GUI")
def TearDownGUI(self):
if self.GetUIPanel().GetUserInterfaceManager():
self.GetUIPanel().RemovePage("BranchSplitting")
def GetHelper(self):
return self._helper
def GetMyLogic(self):
return self._logic