def _createPETTumorSegmentationParameterNode(self):
"""create the PETTumorSegmentation parameter node - a singleton in the scene
This is used internally by getPETTumorSegmentationParameterNode - shouldn't really
be called for any other reason.
"""
node = slicer.vtkMRMLPETTumorSegmentationParametersNode()
self.scene.AddNode(node)
# Since we are a singleton, the scene won't add our node into the scene,
# but will instead insert a copy, so we find that and return it
node = self._findPETTumorSegmentationParameterNodeInScene()
centerFiducialList = slicer.vtkMRMLFiducialListNode()
self.scene.AddNode(centerFiducialList)
node.SetCenterPointIndicatorListReference(centerFiducialList.GetID())
globalRefinementFiducialList = slicer.vtkMRMLFiducialListNode()
self.scene.AddNode(globalRefinementFiducialList)
node.SetGlobalRefinementIndicatorListReference(
globalRefinementFiducialList.GetID())
localRefinementFiducialList = slicer.vtkMRMLFiducialListNode()
self.scene.AddNode(localRefinementFiducialList)
node.SetLocalRefinementIndicatorListReference(
localRefinementFiducialList.GetID())
return node
def test_Collisions(self):
self.delayDisplay("Starting the test")
# Create models of needle and cautery, in a position that does not represent
# collision
self.createSampleModels_Collisions()
# Compute the center of mass of the target model node
tumorModelNode = slicer.mrmlScene.GetNodeByID('vtkMRMLModelNode5')
tumorModelPolyData = tumorModelNode.GetPolyData()
testingLogic = AutoTransparencyLogic()
centerFilter = testingLogic.computeCenterOfMass(tumorModelPolyData)
# Transform center to RAS coordinate system
center = []
for i,val in enumerate(centerFilter.GetCenter()):
center.append(val)
center.append(1.0)
tumorModelToRAS_transformNode = slicer.mrmlScene.GetNodeByID('vtkMRMLLinearTransformNode5')
tumorModelToRAS_vtkMatrix = vtk.vtkMatrix4x4()
tumorModelToRAS_transformNode.GetMatrixTransformToParent(tumorModelToRAS_vtkMatrix)
tumorModelToRAS_vtkMatrix.MultiplyPoint(center,center)
center.remove(1.0)
#print "Center of mass in RAS: ", center
# Get the camera node's position
cameraPosition = testingLogic.getCameraPosition()
#print "Camera position: ", cameraPosition
# Find cone dimensions
coneDimensions = testingLogic.computeConeDimensions(tumorModelPolyData, center, cameraPosition)
# Create a model of the cone and visualize it in the scene
resolution = 10
coneSource = testingLogic.createConeSource(coneDimensions, center, resolution)
coneModelNode = testingLogic.drawCone(coneSource, coneDimensions, center)
# Find the tip of cone and the center of the base of the cone, points which
# will be used as inputs for the landmark registration
coneTip = testingLogic.getConeTip(coneModelNode)
#print "coneTip"
#print coneTip
# Compute center of mass of points of cone base
coneBaseCenter = testingLogic.getCenterOfConeBase(coneSource, coneModelNode)
#print "coneBaseCenter"
#print coneBaseCenter
# Create a third point for use in landmark registration, perpendicular to a
# line drawn in the AP plane of the cone tip
pointPairThree = testingLogic.computeThirdPointsForLandmarkRegistration(cameraPosition, coneTip)
coneModelToRAS = slicer.vtkMRMLLinearTransformNode()
coneModelToRAS.SetName("coneModelToRAS")
coneModelFiducialsNode = slicer.vtkMRMLFiducialListNode()
coneModelFiducialsNode.AddFiducialWithLabelXYZSelectedVisibility('coneTip', \
coneTip[0], \
coneTip[1], \
coneTip[2], \
0, \
0)
coneModelFiducialsNode.AddFiducialWithLabelXYZSelectedVisibility('centerConeBase', \
coneBaseCenter[0], \
coneBaseCenter[1], \
coneBaseCenter[2], \
0, \
0)
coneModelFiducialsNode.AddFiducialWithLabelXYZSelectedVisibility('perpendicularPointConeAxis', \
pointPairThree.perpendicularPointCone[0], \
pointPairThree.perpendicularPointCone[1], \
pointPairThree.perpendicularPointCone[2], \
0, \
0)
rasFiducialsNode = slicer.vtkMRMLFiducialListNode()
rasFiducialsNode.AddFiducialWithLabelXYZSelectedVisibility('cameraPosition', \
cameraPosition[0], \
cameraPosition[1], \
cameraPosition[2], \
0, \
0)
rasFiducialsNode.AddFiducialWithLabelXYZSelectedVisibility('modelCOM', \
center[0], \
center[1], \
center[2], \
0, \
0)
rasFiducialsNode.AddFiducialWithLabelXYZSelectedVisibility('perpendicularPointRAS', \
pointPairThree.perpendicularPointRAS[0], \
pointPairThree.perpendicularPointRAS[1], \
pointPairThree.perpendicularPointRAS[2], \
0, \
0)
testingLogic.performLandmarkRegistion(coneModelFiducialsNode, rasFiducialsNode, coneModelToRAS)
slicer.mrmlScene.AddNode(coneModelToRAS)
coneModelNode.SetAndObserveTransformNodeID(coneModelToRAS.GetID())
# Check if collision is occcuring
cauteryModelNode = slicer.mrmlScene.GetNodeByID('vtkMRMLModelNode4')
coneCauteryCollisionDetectionFilter = \
testingLogic.setUpCollisionDetection(coneModelNode, cauteryModelNode, coneModelToRAS, self.cauteryModelToRAS)
testingLogic.checkForCollisions()
self.delayDisplay('Collision test passed!')
testBool = True
return testBool