def Execute(self):
if self.Surface == None:
self.PrintError('Error: no Surface.')
triangleFilter = vtk.vtkTriangleFilter()
triangleFilter.SetInput(self.Surface)
triangleFilter.Update()
self.Surface = triangleFilter.GetOutput()
if self.Loop == None:
self.PrintError('Error: no Loop.')
select = vtk.vtkImplicitSelectionLoop()
select.SetLoop(self.Loop.GetPoints())
normal = [0.0,0.0,0.0]
centroid = [0.0,0.0,0.0]
vtk.vtkPolygon().ComputeNormal(self.Loop.GetPoints(),normal)
#compute centroid and check normals
p = [0.0,0.0,0.0]
for i in range (self.Loop.GetNumberOfPoints()):
p = self.Loop.GetPoint(i)
centroid[0] += p[0]
centroid[1] += p[1]
centroid[2] += p[2]
centroid[0] = centroid[0] / self.Loop.GetNumberOfPoints()
centroid[1] = centroid[1] / self.Loop.GetNumberOfPoints()
centroid[2] = centroid[2] / self.Loop.GetNumberOfPoints()
print "loop centroid", centroid
locator = vtk.vtkPointLocator()
locator.SetDataSet(self.Surface)
locator.AutomaticOn()
locator.BuildLocator()
idsurface = locator.FindClosestPoint(centroid)
if (self.Surface.GetPointData().GetNormals() == None):
normalsFilter = vmtkscripts.vmtkSurfaceNormals()
normalsFilter.Surface = self.Surface
normalsFilter.NormalsArrayName = 'Normals'
normalsFilter.Execute()
self.Surface = normalsFilter.Surface
normalsurface = [0.0,0.0,0.0]
self.Surface.GetPointData().GetNormals().GetTuple(idsurface,normalsurface)
print "loop normal: ", normal
print "surface normal inside the loop: ", normalsurface
check = vtk.vtkMath.Dot(normalsurface,normal)
if check < 0:
normal[0] = - normal[0]
normal[1] = - normal[1]
normal[2] = - normal[2]
#compute plane
proj = float(vtk.vtkMath.Dot(self.Loop.GetPoint(0),normal))
point = [0.0,0.0,0.0]
self.Loop.GetPoint(0,point)
for i in range (self.Loop.GetNumberOfPoints()):
tmp = vtk.vtkMath.Dot(self.Loop.GetPoint(i),normal)
if tmp < proj:
proj = tmp
self.Loop.GetPoint(i,point)
origin = [0.0,0.0,0.0]
origin[0] = point[0] #- normal[0]
origin[1] = point[1] #- normal[1]
origin[2] = point[2] #- normal[2]
plane=vtk.vtkPlane()
plane.SetNormal(normal[0],normal[1],normal[2])
plane.SetOrigin(origin[0],origin[1],origin[2])
#set bool
Bool = vtk.vtkImplicitBoolean()
Bool.SetOperationTypeToDifference()
Bool.AddFunction(select)
Bool.AddFunction(plane)
clipper=vtk.vtkClipPolyData()
clipper.SetInput(self.Surface)
clipper.SetClipFunction(Bool)
clipper.GenerateClippedOutputOn()
clipper.InsideOutOff()
clipper.Update()
self.Surface = clipper.GetOutput()
# connectivity # # create pipeline # sphere = vtk.vtkSphereSource() sphere.SetRadius(1) sphere.SetPhiResolution(100) sphere.SetThetaResolution(100) selectionPoints = vtk.vtkPoints() selectionPoints.InsertPoint(0, 0.07325, 0.8417, 0.5612) selectionPoints.InsertPoint(1, 0.07244, 0.6568, 0.7450) selectionPoints.InsertPoint(2, 0.1727, 0.4597, 0.8850) selectionPoints.InsertPoint(3, 0.3265, 0.6054, 0.7309) selectionPoints.InsertPoint(4, 0.5722, 0.5848, 0.5927) selectionPoints.InsertPoint(5, 0.4305, 0.8138, 0.4189) loop = vtk.vtkImplicitSelectionLoop() loop.SetLoop(selectionPoints) extract = vtk.vtkExtractGeometry() extract.SetInputConnection(sphere.GetOutputPort()) extract.SetImplicitFunction(loop) connect = vtk.vtkConnectivityFilter() connect.SetInputConnection(extract.GetOutputPort()) connect.SetExtractionModeToClosestPointRegion() connect.SetClosestPoint(selectionPoints.GetPoint(0)) clipMapper = vtk.vtkDataSetMapper() clipMapper.SetInputConnection(connect.GetOutputPort()) backProp = vtk.vtkProperty() backProp.SetDiffuseColor(tomato) clipActor = vtk.vtkActor() clipActor.SetMapper(clipMapper) clipActor.GetProperty().SetColor(peacock)
def _extract_polygon(self, PolyData, is_clean):
self._contour_widget.EnabledOff()
print "Init Extracting"
self.setCursor(QCursor(Qt.WaitCursor))
QApplication.processEvents()
polydata_rep = self._contour_representation.GetContourRepresentationAsPolyData()
planes = self.get_frustrum()
normal = planes.GetNormals()
nor = np.array([0,0,0])
normal.GetTuple(5, nor)
#progressBar.setValue(10)
#QApplication.processEvents()
selection = vtkImplicitSelectionLoop()
selection.SetLoop(polydata_rep.GetPoints())
selection.SetNormal(nor[0], nor[1], nor[2])
#progressBar.setValue(20)
#QApplication.processEvents()
tip = vtkImplicitBoolean()
tip.AddFunction(selection)
tip.AddFunction(planes)
tip.SetOperationTypeToIntersection()
tip.Modified()
#progressBar.setValue(40)
#QApplication.processEvents()
if is_clean:
extractGeometry = vtkExtractPolyDataGeometry()
else:
extractGeometry = vtkExtractGeometry()
extractGeometry.SetInput(PolyData)
extractGeometry.SetImplicitFunction(tip)
if is_clean:
extractGeometry.ExtractInsideOff()
extractGeometry.Update()
if is_clean:
clean = vtkCleanPolyData()
clean.SetInputConnection(extractGeometry.GetOutputPort())
clean.Update()
#progressBar.setValue(80)
#QApplication.processEvents()
filter = vtkDataSetSurfaceFilter()
if is_clean:
filter.SetInputConnection(clean.GetOutputPort())
else:
filter.SetInputConnection(extractGeometry.GetOutputPort())
filter.Update()
#progressBar.setValue(90)
#QApplication.processEvents()
self.setCursor(QCursor(Qt.ArrowCursor))
QApplication.processEvents()
self.extract_action.setEnabled(False)
self.clean_action.setEnabled(False)
print "End Extracting"
return filter.GetOutput()
def cropWithCurve(self, modelNode, fidList, breastFlag, reverseNormal, setInsideOut, torsoFlag):
# This method takes in a surface scan and list of fiducials as input and computes the breast volume
# A curved posterior chest wall is constructed to create the closed breast
modelsLogic = slicer.modules.models.logic()
#Check which breast volume is being computed for
if breastFlag == True:
name = "ClosedLeftBreast"
else:
name = "ClosedRightBreast"
# Define parameters
InputModel = modelNode.GetPolyData()
breastBoundPolyData = vtk.vtkPolyData()
self.FiducialsToPolyData(fidList, breastBoundPolyData)
# Create plane of best fit from input breast boundary fiducials
plane = vtk.vtkPlane()
self.LeastSquaresPlane(modelNode, breastBoundPolyData, plane)
#creates loop from the breast boundary points
breastBound = vtk.vtkImplicitSelectionLoop()
breastBound.SetLoop(breastBoundPolyData.GetPoints())
#creates the torso model when the torso flag is set
if torsoFlag == True:
self.createTorsoModel(InputModel,breastBound)
# creates model for the plane of best fit
planeModel = vtk.vtkReverseSense()
planeModel = self.createPlaneModel(InputModel, plane, breastFlag)
splineTransform = vtk.vtkThinPlateSplineTransform()
splineTransform = self.thinPlateSplineTransform(breastBoundPolyData,plane, modelNode)
#apply spline transform to the plane visualization
planeWithSplineTransform = vtk.vtkTransformPolyDataFilter()
planeWithSplineTransform.SetInputConnection(planeModel.GetOutputPort())
planeWithSplineTransform.SetTransform(splineTransform)
#create model of the transformed plane
transformedPlaneModel = modelsLogic.AddModel(planeWithSplineTransform.GetOutputPort())
transformedPlaneModel.GetDisplayNode().SetVisibility(False)
transformedPlaneModel.SetName("transformedPlane")
# Creates cropped breast model
breastModel = self.createBreastModel(breastBound, InputModel, breastFlag, reverseNormal, setInsideOut, plane, planeWithSplineTransform)
# Creates cropped-posterior wall
posteriorWallModel = vtk.vtkPolyData()
posteriorWallModel = self.createClippedPlane(breastBound,planeWithSplineTransform)
# Creates closed breast model
appendClosedBreast = vtk.vtkAppendPolyData()
appendClosedBreast.AddInputData(breastModel) #Breasts
appendClosedBreast.AddInputData(posteriorWallModel) #Chest Wall
appendClosedBreast.Update()
# Applies cleaning filter to closed breast model
cleanClosedBreast = vtk.vtkCleanPolyData()
cleanClosedBreast.SetInputData(appendClosedBreast.GetOutput())
cleanClosedBreast.Update()
# Added closed breast model to slicer models
closedBreastModel = modelsLogic.AddModel(cleanClosedBreast.GetOutput())
closedBreastModel.GetDisplayNode().SetVisibility(True)
closedBreastModel.SetName(name)
closedBreastModel.GetDisplayNode().BackfaceCullingOff()
slicer.mrmlScene.RemoveNode(transformedPlaneModel)
return closedBreastModel
# connectivity # # create pipeline # sphere = vtk.vtkSphereSource() sphere.SetRadius(1) sphere.SetPhiResolution(100) sphere.SetThetaResolution(100) selectionPoints = vtk.vtkPoints() selectionPoints.InsertPoint(0,0.07325,0.8417,0.5612) selectionPoints.InsertPoint(1,0.07244,0.6568,0.7450) selectionPoints.InsertPoint(2,0.1727,0.4597,0.8850) selectionPoints.InsertPoint(3,0.3265,0.6054,0.7309) selectionPoints.InsertPoint(4,0.5722,0.5848,0.5927) selectionPoints.InsertPoint(5,0.4305,0.8138,0.4189) loop = vtk.vtkImplicitSelectionLoop() loop.SetLoop(selectionPoints) extract = vtk.vtkExtractGeometry() extract.SetInputConnection(sphere.GetOutputPort()) extract.SetImplicitFunction(loop) connect = vtk.vtkConnectivityFilter() connect.SetInputConnection(extract.GetOutputPort()) connect.SetExtractionModeToClosestPointRegion() connect.SetClosestPoint(selectionPoints.GetPoint(0)) clipMapper = vtk.vtkDataSetMapper() clipMapper.SetInputConnection(connect.GetOutputPort()) backProp = vtk.vtkProperty() backProp.SetDiffuseColor(tomato) clipActor = vtk.vtkActor() clipActor.SetMapper(clipMapper) clipActor.GetProperty().SetColor(peacock)
def Execute(self):
if self.Surface == None:
self.PrintError('Error: no Surface.')
triangleFilter = vtk.vtkTriangleFilter()
triangleFilter.SetInputData(self.Surface)
triangleFilter.Update()
self.Surface = triangleFilter.GetOutput()
if self.Loop == None:
self.PrintError('Error: no Loop.')
select = vtk.vtkImplicitSelectionLoop()
select.SetLoop(self.Loop.GetPoints())
normal = [0.0, 0.0, 0.0]
centroid = [0.0, 0.0, 0.0]
vtk.vtkPolygon().ComputeNormal(self.Loop.GetPoints(), normal)
#compute centroid and check normals
p = [0.0, 0.0, 0.0]
for i in range(self.Loop.GetNumberOfPoints()):
p = self.Loop.GetPoint(i)
centroid[0] += p[0]
centroid[1] += p[1]
centroid[2] += p[2]
centroid[0] = centroid[0] / self.Loop.GetNumberOfPoints()
centroid[1] = centroid[1] / self.Loop.GetNumberOfPoints()
centroid[2] = centroid[2] / self.Loop.GetNumberOfPoints()
print "loop centroid", centroid
locator = vtk.vtkPointLocator()
locator.SetDataSet(self.Surface)
locator.AutomaticOn()
locator.BuildLocator()
idsurface = locator.FindClosestPoint(centroid)
if (self.Surface.GetPointData().GetNormals() == None):
normalsFilter = vmtkscripts.vmtkSurfaceNormals()
normalsFilter.Surface = self.Surface
normalsFilter.NormalsArrayName = 'Normals'
normalsFilter.Execute()
self.Surface = normalsFilter.Surface
normalsurface = [0.0, 0.0, 0.0]
self.Surface.GetPointData().GetNormals().GetTuple(
idsurface, normalsurface)
print "loop normal: ", normal
print "surface normal inside the loop: ", normalsurface
check = vtk.vtkMath.Dot(normalsurface, normal)
if check < 0:
normal[0] = -normal[0]
normal[1] = -normal[1]
normal[2] = -normal[2]
#compute plane
proj = float(vtk.vtkMath.Dot(self.Loop.GetPoint(0), normal))
point = [0.0, 0.0, 0.0]
self.Loop.GetPoint(0, point)
for i in range(self.Loop.GetNumberOfPoints()):
tmp = vtk.vtkMath.Dot(self.Loop.GetPoint(i), normal)
if tmp < proj:
proj = tmp
self.Loop.GetPoint(i, point)
origin = [0.0, 0.0, 0.0]
origin[0] = point[0] #- normal[0]
origin[1] = point[1] #- normal[1]
origin[2] = point[2] #- normal[2]
plane = vtk.vtkPlane()
plane.SetNormal(normal[0], normal[1], normal[2])
plane.SetOrigin(origin[0], origin[1], origin[2])
#set bool
Bool = vtk.vtkImplicitBoolean()
Bool.SetOperationTypeToDifference()
Bool.AddFunction(select)
Bool.AddFunction(plane)
clipper = vtk.vtkClipPolyData()
clipper.SetInputData(self.Surface)
clipper.SetClipFunction(Bool)
clipper.GenerateClippedOutputOn()
clipper.InsideOutOff()
clipper.Update()
self.Surface = clipper.GetOutput()
