def AddDamageTemplateModel(self,scene,LineLandmarkTransform ):
# check if already implemented
if ( self.DamageTemplateModel != None ):
print "removing", self.DamageTemplateModel.GetName()
scene.RemoveNode(self.DamageTemplateModel)
# create sphere and scale
vtkSphere = vtk.vtkSphereSource()
vtkSphere.SetRadius(1.)
vtkSphere.SetThetaResolution(16)
vtkSphere.SetPhiResolution(16)
ScaleAffineTransform = vtk.vtkTransform()
ScaleAffineTransform.Scale([self.AblationMinorAxis,self.AblationMajorAxis,self.AblationMinorAxis])
vtkEllipsoid= vtk.vtkTransformFilter()
vtkEllipsoid.SetInput(vtkSphere.GetOutput() )
vtkEllipsoid.SetTransform( ScaleAffineTransform )
vtkEllipsoid.Update()
slicertransformFilter = vtk.vtkTransformFilter()
slicertransformFilter.SetInput(vtkEllipsoid.GetOutput() )
slicertransformFilter.SetTransform( LineLandmarkTransform )
slicertransformFilter.Update()
dampolyData=slicertransformFilter.GetOutput();
# Create model node
self.DamageTemplateModel = slicer.vtkMRMLModelNode()
self.DamageTemplateModel.SetScene(scene)
#self.DamageTemplateModel.SetName(scene.GenerateUniqueName("Treatment-%s" % fiducialsNode.GetName()))
self.DamageTemplateModel.SetName( scene.GenerateUniqueName("Treatment") )
self.DamageTemplateModel.SetAndObservePolyData(dampolyData)
# Create display node
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetColor(1,1,0) # yellow
modelDisplay.SetOpacity(0.3)
modelDisplay.SetScene(scene)
scene.AddNode(modelDisplay)
self.DamageTemplateModel.SetAndObserveDisplayNodeID(modelDisplay.GetID())
# Add to scene
modelDisplay.SetInputPolyData(self.DamageTemplateModel.GetPolyData())
scene.AddNode(self.DamageTemplateModel)
def generateCylinderPolyData(self, x, y):
cylinderHeightMm = 80
cylinderRadiusMm = 1
cylinderSource = vtk.vtkCylinderSource()
cylinderSource.SetHeight(cylinderHeightMm)
cylinderSource.SetRadius(cylinderRadiusMm)
renderDepthMm = -cylinderHeightMm # negative because in graphics, negative is depth, positive goes toward the user
transform = vtk.vtkTransform()
transform.Translate(x, y, renderDepthMm)
transform.RotateX(90) # rotate so that the cylinder follows the z axis
transformFilter = vtk.vtkTransformFilter()
transformFilter.SetTransform(transform)
transformFilter.SetInputConnection(cylinderSource.GetOutputPort(0))
transformFilter.Update()
polyData = transformFilter.GetOutput()
return polyData
def generateCylinderPolyData(self,x,y): cylinderHeightMm = 80 cylinderRadiusMm = 1 cylinderSource = vtk.vtkCylinderSource() cylinderSource.SetHeight(cylinderHeightMm) cylinderSource.SetRadius(cylinderRadiusMm) renderDepthMm = -cylinderHeightMm # negative because in graphics, negative is depth, positive goes toward the user transform = vtk.vtkTransform() transform.Translate(x,y,renderDepthMm) transform.RotateX(90) # rotate so that the cylinder follows the z axis transformFilter = vtk.vtkTransformFilter() transformFilter.SetTransform(transform) transformFilter.SetInputConnection(cylinderSource.GetOutputPort(0)) transformFilter.Update() polyData = transformFilter.GetOutput() return polyData
def AddApplicatorTrajectoryModel(self,scene,LineLandmarkTransform ):
# check if already implemented
if ( self.ApplicatorTrajectoryModel != None ):
print "removing", self.ApplicatorTrajectoryModel.GetName()
scene.RemoveNode(self.ApplicatorTrajectoryModel)
# Define applicator tip
vtkCylinder = vtk.vtkCylinderSource()
vtkCylinder.SetHeight(10.*self.DiffusingTipLength);
vtkCylinder.SetRadius(0.1*self.DiffusingTipRadius);
vtkCylinder.SetCenter(0.0, 10.*self.DiffusingTipLength/2.0, 0.0);
vtkCylinder.SetResolution(16);
# transform
slicertransformFilter = vtk.vtkTransformFilter()
slicertransformFilter.SetInput(vtkCylinder.GetOutput() )
slicertransformFilter.SetTransform( LineLandmarkTransform )
slicertransformFilter.Update()
apppolyData=slicertransformFilter.GetOutput();
# add to scene
self.ApplicatorTrajectoryModel = slicer.vtkMRMLModelNode()
self.ApplicatorTrajectoryModel.SetScene(scene)
#self.ApplicatorTrajectoryModel.SetName(scene.GenerateUniqueName("Applicator-%s" % fiducialsNode.GetName()))
self.ApplicatorTrajectoryModel.SetName("ApplicatorTrajectory" )
self.ApplicatorTrajectoryModel.SetAndObservePolyData(apppolyData)
# Create display node
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetColor(1,0.5,0) # red
modelDisplay.SetScene(scene)
scene.AddNode(modelDisplay)
self.ApplicatorTrajectoryModel.SetAndObserveDisplayNodeID(modelDisplay.GetID())
# Add to scene
modelDisplay.SetInputPolyData(self.ApplicatorTrajectoryModel.GetPolyData())
scene.AddNode(self.ApplicatorTrajectoryModel)
def CreateSlit(self, normal, pathPolydata, ruler, ROI, slitSize):
""" Here we are going to create a boxSource , the size of the 2*ROI in the X,Y
and the size of the slit Size in the Z.
We are then going to translate the box source to its correct location in slicer
As always to visualize , a DEBUG option can be set at the top.
x is L->R, y is P->A, z is I->S
"""
# Cube Creation
roiPoints = self.utility.GetROIPoints(ROI)
frontExtentIndex = self.utility.GetClosestExtent(ruler, ROI)
backExtentIndex = self.utility.GetOppositeExtent(frontExtentIndex)
pointA = numpy.array(roiPoints[frontExtentIndex])
pointB = numpy.array(roiPoints[backExtentIndex])
yDist = numpy.linalg.norm(pointA - pointB)
numPoints = pathPolydata.GetNumberOfPoints()
pointA = numpy.array(pathPolydata.GetPoint(0))
pointB = numpy.array(pathPolydata.GetPoint(numPoints - 1))
xDist = numpy.linalg.norm(pointA - pointB)
zDist = slitSize # Rewording the parameter to make it easier to understand
slitCube = vtk.vtkCubeSource()
slitCube.SetBounds(0, xDist, -yDist, yDist, -zDist / 2, zDist / 2) # (Xmin, Xmax, Ymin, Ymax,Zmin, Zmax)
# Transforming Cube
transformFilter = vtk.vtkTransformFilter()
transform = vtk.vtkTransform()
matrix = vtk.vtkMatrix4x4()
pointA = numpy.array(pathPolydata.GetPoint(0))
pointB = numpy.array(pathPolydata.GetPoint(numPoints - 1))
xVector = pointA - pointB
xDist = numpy.linalg.norm(pointA - pointB)
xUnitVector = (xVector[0] / xDist, xVector[1] / xDist, xVector[2] / xDist)
yVector = self.utility.GetRulerVector(ruler)
yDist = numpy.linalg.norm(yVector)
yUnitVector = (yVector[0] / yDist, yVector[1] / yDist, yVector[2] / yDist)
zVector = numpy.cross(xVector, yVector)
zDist = numpy.linalg.norm(zVector)
zUnitVector = (zVector[0] / zDist, zVector[1] / zDist, zVector[2] / zDist)
origin = pointA = numpy.array(pathPolydata.GetPoint(numPoints - 1))
matrix.DeepCopy(
(
xUnitVector[0],
yUnitVector[0],
zUnitVector[0],
origin[0],
xUnitVector[1],
yUnitVector[1],
zUnitVector[1],
origin[1],
xUnitVector[2],
yUnitVector[2],
zUnitVector[2],
origin[2],
0,
0,
0,
1,
)
)
transform.SetMatrix(matrix)
transformFilter.SetTransform(transform)
transformFilter.SetInputConnection(slitCube.GetOutputPort())
transformFilter.Update()
self.slitPlanes.append(transformFilter.GetOutput())
if len(self.slitPlanes) == self.numberOfPaths and self.DEBUG_SLITPLANES == True:
for i in range(self.numberOfPaths):
self.utility.DisplayPolyData("Slit" + str(i), self.slitPlanes[i])
return transformFilter.GetOutput()
def CreateSlit(self, normal, pathPolydata, ruler, ROI, slitSize):
""" Here we are going to create a boxSource , the size of the 2*ROI in the X,Y
and the size of the slit Size in the Z.
We are then going to translate the box source to its correct location in slicer
As always to visualize , a DEBUG option can be set at the top.
x is L->R, y is P->A, z is I->S
"""
#Cube Creation
roiPoints = self.utility.GetROIPoints(ROI)
frontExtentIndex = self.utility.GetClosestExtent(ruler, ROI)
backExtentIndex = self.utility.GetOppositeExtent(frontExtentIndex)
pointA = numpy.array(roiPoints[frontExtentIndex])
pointB = numpy.array(roiPoints[backExtentIndex])
yDist = numpy.linalg.norm(pointA - pointB)
numPoints = pathPolydata.GetNumberOfPoints()
pointA = numpy.array(pathPolydata.GetPoint(0))
pointB = numpy.array(pathPolydata.GetPoint(numPoints - 1))
xDist = numpy.linalg.norm(pointA - pointB)
zDist = slitSize #Rewording the parameter to make it easier to understand
slitCube = vtk.vtkCubeSource()
slitCube.SetBounds(0, xDist, -yDist, yDist, -zDist / 2,
zDist / 2) # (Xmin, Xmax, Ymin, Ymax,Zmin, Zmax)
#Transforming Cube
transformFilter = vtk.vtkTransformFilter()
transform = vtk.vtkTransform()
matrix = vtk.vtkMatrix4x4()
pointA = numpy.array(pathPolydata.GetPoint(0))
pointB = numpy.array(pathPolydata.GetPoint(numPoints - 1))
xVector = pointA - pointB
xDist = numpy.linalg.norm(pointA - pointB)
xUnitVector = (xVector[0] / xDist, xVector[1] / xDist,
xVector[2] / xDist)
yVector = self.utility.GetRulerVector(ruler)
yDist = numpy.linalg.norm(yVector)
yUnitVector = (yVector[0] / yDist, yVector[1] / yDist,
yVector[2] / yDist)
zVector = numpy.cross(xVector, yVector)
zDist = numpy.linalg.norm(zVector)
zUnitVector = (zVector[0] / zDist, zVector[1] / zDist,
zVector[2] / zDist)
origin = pointA = numpy.array(pathPolydata.GetPoint(numPoints - 1))
matrix.DeepCopy(
(xUnitVector[0], yUnitVector[0], zUnitVector[0], origin[0],
xUnitVector[1], yUnitVector[1], zUnitVector[1], origin[1],
xUnitVector[2], yUnitVector[2], zUnitVector[2], origin[2], 0, 0,
0, 1))
transform.SetMatrix(matrix)
transformFilter.SetTransform(transform)
transformFilter.SetInputConnection(slitCube.GetOutputPort())
transformFilter.Update()
self.slitPlanes.append(transformFilter.GetOutput())
if len(self.slitPlanes
) == self.numberOfPaths and self.DEBUG_SLITPLANES == True:
for i in range(self.numberOfPaths):
self.utility.DisplayPolyData("Slit" + str(i),
self.slitPlanes[i])
return transformFilter.GetOutput()
