def onApplyParameters(self):
segmentationParameters = self.getPETTumorSegmentationParameterNode()
if not segmentationParameters: return
paramsNode = self.scriptedEffect.parameterSetNode()
volumeID = paramsNode.GetMasterVolumeNode().GetID()
segmentationID = paramsNode.GetSegmentationNode().GetID()
selectedSegmentID = paramsNode.GetSelectedSegmentID()
segment = paramsNode.GetSegmentationNode().GetSegmentation(
).GetSegment(selectedSegmentID)
priorSegmentationExists = segment.HasTag(
'PETTumorSegmentation.SegmentationId')
oldVolumeID = segmentationParameters.GetPETVolumeReference()
oldSegmentationID = segmentationParameters.GetSegmentationReference()
oldSelectedSegmentID = segmentationParameters.GetSelectedSegmentID()
if (volumeID != oldVolumeID or segmentationID != oldSegmentationID):
self.reset()
segmentationParameters = self.getPETTumorSegmentationParameterNode()
if not segmentationParameters: return
if not self.vtkSegmentationLogic:
self.vtkSegmentationLogic = slicer.vtkSlicerPETTumorSegmentationLogic(
)
centerPointFiducialsNode = self.scene.GetNodeByID(
str(segmentationParameters.GetCenterPointIndicatorListReference()))
centerPointFiducials = slicer.vtkMRMLFiducialListNode.SafeDownCast(
centerPointFiducialsNode)
if (centerPointFiducials.GetNumberOfFiducials() == 0
or selectedSegmentID != oldSelectedSegmentID):
# there is no segmentation which could be changed by updated paramters
return
self.saveStateForUndo()
# run segmentation algorithm with changed parameters
self.updateMRMLFromGUI()
self._showDebugInfo(segmentationParameters)
self.vtkSegmentationLogic.Apply(segmentationParameters, None)
self.updateCurrentSegmentationID()
def onApplyMouseClick(self, rasCoorinate):
segmentationParameters = self.getPETTumorSegmentationParameterNode()
if not segmentationParameters: return
paramsNode = self.scriptedEffect.parameterSetNode()
volumeID = paramsNode.GetMasterVolumeNode().GetID()
segmentationID = paramsNode.GetSegmentationNode().GetID()
selectedSegmentID = paramsNode.GetSelectedSegmentID()
segment = paramsNode.GetSegmentationNode().GetSegmentation(
).GetSegment(selectedSegmentID)
priorSegmentationExists = segment.HasTag(
'PETTumorSegmentation.SegmentationId')
oldVolumeID = segmentationParameters.GetPETVolumeReference()
oldSegmentationID = segmentationParameters.GetSegmentationReference()
oldSelectedSegmentID = segmentationParameters.GetSelectedSegmentID()
if (volumeID != oldVolumeID or segmentationID != oldSegmentationID):
self.reset()
segmentationParameters = self.getPETTumorSegmentationParameterNode()
if not segmentationParameters: return
if not self.vtkSegmentationLogic:
self.vtkSegmentationLogic = slicer.vtkSlicerPETTumorSegmentationLogic(
)
self.saveStateForUndo()
self.updateMRMLFromGUI()
#Get the fiducial nodes
centerPointFiducialsNode = self.scene.GetNodeByID(
str(segmentationParameters.GetCenterPointIndicatorListReference()))
centerPointFiducials = slicer.vtkMRMLFiducialListNode.SafeDownCast(
centerPointFiducialsNode)
globalRefinementFiducialNode = self.scene.GetNodeByID(
str(segmentationParameters.
GetGlobalRefinementIndicatorListReference()))
globalRefinementFiducial = slicer.vtkMRMLFiducialListNode.SafeDownCast(
globalRefinementFiducialNode)
localRefinementFiducialNode = self.scene.GetNodeByID(
str(segmentationParameters.
GetLocalRefinementIndicatorListReference()))
localRefinementFiducial = slicer.vtkMRMLFiducialListNode.SafeDownCast(
localRefinementFiducialNode)
#Set the current segment information and volumes
segmentationParameters.SetPETVolumeReference(volumeID)
segmentationParameters.SetSegmentationReference(segmentationID)
segmentationParameters.SetSelectedSegmentID(selectedSegmentID)
#If there are no center points, then the click should make a new center point and segmentation.
#If the label has changed, go with this and remove center points to start a new segmentation.
#If no refinement mode is on, remove points and start a new segmentation.
if (centerPointFiducials.GetNumberOfFiducials() == 0
or selectedSegmentID != oldSelectedSegmentID
or segmentationParameters.GetNoRefinementOn()
): # initialize segmentation
# clear old data
segmentationParameters.ClearInitialLabelMap()
if (centerPointFiducials.GetNumberOfFiducials() != 0):
globalRefinementFiducial.RemoveAllFiducials()
localRefinementFiducial.RemoveAllFiducials()
centerPointFiducials.RemoveAllFiducials()
#add the new center point
centerPointFiducials.AddFiducialWithXYZ(rasCoorinate[0],
rasCoorinate[1],
rasCoorinate[2], False)
self.vtkSegmentationLogic.Apply(segmentationParameters, None)
else:
#If global refinement is active, then the existing segmentation should be refined globally.
if (segmentationParameters.GetGlobalRefinementOn()
): # perform global refinement, unless new label
#Only one global refinement point at a time
globalRefinementFiducial.RemoveAllFiducials()
globalRefinementFiducial.AddFiducialWithXYZ(
rasCoorinate[0], rasCoorinate[1], rasCoorinate[2], False)
self.vtkSegmentationLogic.ApplyGlobalRefinement(
segmentationParameters, None)
#If local refinement is active, then the existing segmentation should be refined localy.
elif (segmentationParameters.GetLocalRefinementOn()
): # perform local refinement, unless new label
localRefinementFiducial.AddFiducialWithXYZ(
rasCoorinate[0], rasCoorinate[1], rasCoorinate[2], False)
self.vtkSegmentationLogic.ApplyLocalRefinement(
segmentationParameters, None)
# run segmentation algorithm
#self._showDebugInfo(segmentationParameters)
#self.vtkSegmentationLogic.Apply( segmentationParameters, None )
self.updateCurrentSegmentationID()