def FM(self):
inVolume = self._inVolumeSelector.GetSelected()
outVolume = self._outVolumeSelector.GetSelected()
seeds = self._seedsSelector.GetSelected()
targetSeeds = self._targetSeedsSelector.GetSelected()
vmtkFound = self.CheckForVmtkLibrary()
if inVolume and outVolume and seeds and vmtkFound:
extentValues = self._thresholdExtent.GetExtent()
sourceSeedIds = slicer.vtkIdList()
targetSeedIds = slicer.vtkIdList()
image = inVolume.GetImageData()
rasToIjkMatrix = slicer.vtkMatrix4x4()
inVolume.GetRASToIJKMatrix(rasToIjkMatrix)
for i in range(seeds.GetNumberOfFiducials()):
rasPt = seeds.GetNthFiducialXYZ(i)
rasPt.append(1)
ijkPt = rasToIjkMatrix.MultiplyPoint(*rasPt)
sourceSeedIds.InsertNextId(image.ComputePointId(int(ijkPt[0]),int(ijkPt[1]),int(ijkPt[2])))
inValue = 0
outValue = 5
sideBranchSwitch=0
if targetSeeds:
if targetSeeds.GetID()!=seeds.GetID():
#only run if different fiducial lists
self._helper.debug("Using target points..")
for i in range(targetSeeds.GetNumberOfFiducials()):
rasPt = targetSeeds.GetNthFiducialXYZ(i)
rasPt.append(1)
ijkPt = rasToIjkMatrix.MultiplyPoint(*rasPt)
targetSeedIds.InsertNextId(image.ComputePointId(int(ijkPt[0]),int(ijkPt[1]),int(ijkPt[2])))
if self._sbCheckButton.GetSelectedState():
sideBranchSwitch=1 # allow side branches only if targetseeds are available
# switch thresholds for labelmap when using target points
inValue = 5
outValue = 0
result = self._logic.ExecuteFM(inVolume.GetImageData(),extentValues[0],extentValues[1],sourceSeedIds,targetSeedIds,sideBranchSwitch)
#self._helper.debug(result)
ijkToRasMatrix = slicer.vtkMatrix4x4()
inVolume.GetIJKToRASMatrix(ijkToRasMatrix)
self.CreateOutVolumeNode()
#outVolume.LabelMapOn()
outVolume.SetAndObserveImageData(result)
outVolume.SetIJKToRASMatrix(ijkToRasMatrix)
outVolume.SetModifiedSinceRead(1)
scene = self.GetLogic().GetMRMLScene()
newDisplayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
newDisplayNode.SetScene(scene)
newDisplayNode.SetDefaultColorMap()
slicer.MRMLScene.AddNodeNoNotify(newDisplayNode)
labelMap = slicer.vtkMRMLScalarVolumeNode()
labelMap.SetName("VMTKInitializationLabelMap")
labelMap.SetAndObserveImageData(self._logic.BuildSimpleLabelMap(result,inValue,outValue))
labelMap.SetIJKToRASMatrix(ijkToRasMatrix)
labelMap.LabelMapOn()
labelMap.SetAndObserveDisplayNodeID(newDisplayNode.GetID())
labelMap.SetModifiedSinceRead(1)
scene.AddNode(labelMap)
slicer.ApplicationLogic.GetSelectionNode().SetReferenceActiveLabelVolumeID(labelMap.GetID())
slicer.ApplicationLogic.PropagateVolumeSelection()
displayNode = inVolume.GetDisplayNode() # reset threshold for visualization
extentValues = self._thresholdExtent.GetExtentRange()
displayNode.SetLowerThreshold(extentValues[0])
displayNode.SetUpperThreshold(extentValues[1])
displayNode.SetApplyThreshold(1)
if self._vrCheckButton.GetSelectedState():
self._helper.HideVR()
if targetSeeds:
self._helper.VolumeRendering(outVolume,'red',targetSeeds.GetID()==seeds.GetID(),sideBranchSwitch)
else:
self._helper.VolumeRendering(outVolume,'red',1)
self._helper.ShowVR()
else:
self._helper.HideVR()
self._helper.GenerateModel(outVolume,'red')
def GAC(self):
origVolume = self._inVolumeSelector.GetSelected()
segmentationVolume = self._outVolumeSelector.GetSelected()
outVolume = self._outEvolVolumeSelector.GetSelected()
seeds = self._seedsSelector.GetSelected()
targetSeeds = self._targetSeedsSelector.GetSelected()
vmtkFound = self.CheckForVmtkLibrary()
if origVolume and segmentationVolume and outVolume and vmtkFound:
numberOfIterations = int(self._iterationsSpinbox.GetWidget().GetValue())
propagationScaling = self._propagationScale.GetValue()
curvatureScaling = self._curvatureScale.GetValue()
advectionScaling = self._advectionScale.GetValue()
if (self._evolMethod.GetWidget().GetWidget(0).GetSelectedState()==1):
result = self._logic.ExecuteGAC(origVolume.GetImageData(),segmentationVolume.GetImageData(),numberOfIterations,propagationScaling,curvatureScaling,advectionScaling,'geodesic')
else:
result = self._logic.ExecuteGAC(origVolume.GetImageData(),segmentationVolume.GetImageData(),numberOfIterations,propagationScaling,curvatureScaling,advectionScaling,'curves')
ijkToRasMatrix = slicer.vtkMatrix4x4()
origVolume.GetIJKToRASMatrix(ijkToRasMatrix)
#outVolume.LabelMapOn()
outVolume.SetAndObserveImageData(result)
outVolume.SetIJKToRASMatrix(ijkToRasMatrix)
outVolume.SetModifiedSinceRead(1)
inValue = 0
outValue = 5
if seeds and targetSeeds:
if targetSeeds.GetID()!=seeds.GetID():
# switch thresholds for labelmap when using target points
inValue = 5
outValue = 0
scene = self.GetLogic().GetMRMLScene()
newDisplayNode = slicer.vtkMRMLLabelMapVolumeDisplayNode()
newDisplayNode.SetScene(scene)
newDisplayNode.SetDefaultColorMap()
slicer.MRMLScene.AddNodeNoNotify(newDisplayNode)
labelMap = slicer.vtkMRMLScalarVolumeNode()
labelMap.SetName("VMTKEvolutionLabelMap")
labelMap.SetAndObserveImageData(self._logic.BuildSimpleLabelMap(result,inValue,outValue))
labelMap.SetIJKToRASMatrix(ijkToRasMatrix)
labelMap.LabelMapOn()
labelMap.SetAndObserveDisplayNodeID(newDisplayNode.GetID())
scene.AddNode(labelMap)
slicer.ApplicationLogic.GetSelectionNode().SetReferenceActiveLabelVolumeID(labelMap.GetID())
slicer.ApplicationLogic.GetSelectionNode().SetReferenceActiveVolumeID(origVolume.GetID())
slicer.ApplicationLogic.PropagateVolumeSelection()
#slicer.ApplicationLogic.GetSelectionNode().SetReferenceActiveLabelVolumeID(outVolume.GetID())
#slicer.ApplicationLogic.PropagateVolumeSelection()
if self._outInitModelDisplay != None: # deactivate old init model if it exists
#nodeId = self.GetLogic().GetMRMLScene().GetNodeByID(self._outInitModelDisplay.GetID())
#if nodeId:
#if self.GetLogic().GetMRMLScene().IsNodePresent(nodeId):
self._helper.debug("hiding old model..")
self._outInitModelDisplay.SetVisibility(0)
self._outInitModelDisplay.SetModifiedSinceRead(1)
if self._vrCheckButton.GetSelectedState():
self._helper.HideVR()
if targetSeeds:
self._helper.VolumeRendering(outVolume,'blue',targetSeeds.GetID()==seeds.GetID())
else:
self._helper.VolumeRendering(outVolume,'blue',1)
#self._helper.VolumeRendering(outVolume,'blue')
self._helper.ShowVR()
else:
self._helper.HideVR()
self._helper.GenerateModel(outVolume,'blue')