def Smooth_Surface(self, surface):
# Take a vtk surface and run it through the smoothing pipeline
boneNormals = vtk.vtkPolyDataNormals()
try:
boneNormals.SetInputData(surface)
except:
boneNormals.SetInputConnection(surface.GetOutputPort())
boneNormals.Update()
# Clean the polydata so that the edges are shared!
cleanPolyData = vtk.vtkCleanPolyData()
cleanPolyData.SetInputConnection(boneNormals.GetOutputPort())
cleanPolyData.Update()
polydata = cleanPolyData.GetOutput()
if self.smoothing_iterations > 0:
# Apply laplacian smoothing to the surface
smoothingFilter = vtk.vtkSmoothPolyDataFilter()
smoothingFilter.SetInputData(polydata)
smoothingFilter.SetNumberOfIterations(
int(self.smoothing_iterations))
smoothingFilter.SetRelaxationFactor(self.relaxation_factor)
smoothingFilter.Update()
polydata = smoothingFilter.GetOutput()
if self.decimate_surface > 0 and self.decimate_surface < 1:
# We want to preserve topology (not let any cracks form). This may
# limit the total reduction possible, which we have specified at 80%.
deci = vtk.vtkDecimatePro()
deci.SetInputData(polydata)
deci.SetTargetReduction(self.decimate_surface)
deci.PreserveTopologyOn()
deci.Update()
polydata = deci.GetOutput()
# Clean the polydata so that the edges are shared!
cleanPolyData = vtk.vtkCleanPolyData()
cleanPolyData.SetInputData(polydata)
cleanPolyData.Update()
polydata = cleanPolyData.GetOutput()
# Generate surface normals to give a better visualization
normals = vtk.vtkPolyDataNormals()
normals.SetInputData(polydata)
normals.Update()
polydata = normals.GetOutput()
return polydata
def runLabelWise(self, targetLabelNode, obstacleModelNode, skinModelNode):
"""
Run label-wise analysis
"""
poly = skinModelNode.GetPolyData()
polyDataNormals = vtk.vtkPolyDataNormals()
polyDataNormals.SetInput(poly)
polyDataNormals.ComputeCellNormalsOn()
polyDataNormals.Update()
polyData = polyDataNormals.GetOutput()
bspTree = vtk.vtkModifiedBSPTree()
bspTree.SetDataSet(obstacleModelNode.GetPolyData())
bspTree.BuildLocator()
trans = vtk.vtkMatrix4x4()
targetLabelNode.GetIJKToRASMatrix(trans)
pos = [0.0, 0.0, 0.0, 0.0]
imageData = targetLabelNode.GetImageData()
(x0, x1, y0, y1, z0, z1) = imageData.GetExtent()
for z in range(z0, z1+1):
for y in range(y0, y1+1):
for x in range(x0, x1+1):
if imageData.GetScalarComponentAsDouble(x, y, z, 0) > 0:
trans.MultiplyPoint([x, y, z, 1.0], pos);
(score, mind, mindp) = self.calcApproachScore(pos[0:3], polyData, bspTree, None)
imageData.SetScalarComponentFromDouble(x, y, z, 0, score*100.0+1.0)
#print ("Index(%f, %f, %f) -> RAS(%f, %f, %f)" % (x, y, z, pos[0], pos[1], pos[2]))
#print ("Approach Score (<accessible area> / (<accessible area> + <inaccessible area>)) = %f" % (score))
return True
def runPointWise(self, targetPointNode, obstacleModelNode, skinModelNode):
"""
Run point-wise analysis
"""
print("runPointWise()")
tPoint = targetPointNode.GetMarkupPointVector(0, 0)
pTarget = [tPoint[0], tPoint[1], tPoint[2]]
poly = skinModelNode.GetPolyData()
polyDataNormals = vtk.vtkPolyDataNormals()
polyDataNormals.SetInput(poly)
polyDataNormals.ComputeCellNormalsOn()
polyDataNormals.Update()
polyData = polyDataNormals.GetOutput()
bspTree = vtk.vtkModifiedBSPTree()
bspTree.SetDataSet(obstacleModelNode.GetPolyData())
bspTree.BuildLocator()
(score, mind, mindp) = self.calcApproachScore(pTarget, polyData,
bspTree, skinModelNode)
print(
"Approach Score (<accessible area> / (<accessible area> + <inaccessible area>)) = %f"
% (score))
print("Minmum Distance = %f" % (mind))
return (score, mind, mindp)
def runPointWise(self, targetPointNode, obstacleModelNode, skinModelNode):
"""
Run point-wise analysis
"""
print ("runPointWise()")
tPoint = targetPointNode.GetMarkupPointVector(0, 0)
pTarget = [tPoint[0], tPoint[1], tPoint[2]]
poly = skinModelNode.GetPolyData()
polyDataNormals = vtk.vtkPolyDataNormals()
polyDataNormals.SetInput(poly)
polyDataNormals.ComputeCellNormalsOn()
polyDataNormals.Update()
polyData = polyDataNormals.GetOutput()
bspTree = vtk.vtkModifiedBSPTree()
bspTree.SetDataSet(obstacleModelNode.GetPolyData())
bspTree.BuildLocator()
(score, mind, mindp) = self.calcApproachScore(pTarget, polyData, bspTree, skinModelNode)
print ("Approach Score (<accessible area> / (<accessible area> + <inaccessible area>)) = %f" % (score))
print ("Minmum Distance = %f" % (mind))
return (score, mind, mindp)
def runLabelWise(self, targetLabelNode, obstacleModelNode, skinModelNode):
"""
Run label-wise analysis
"""
poly = skinModelNode.GetPolyData()
polyDataNormals = vtk.vtkPolyDataNormals()
polyDataNormals.SetInput(poly)
polyDataNormals.ComputeCellNormalsOn()
polyDataNormals.Update()
polyData = polyDataNormals.GetOutput()
bspTree = vtk.vtkModifiedBSPTree()
bspTree.SetDataSet(obstacleModelNode.GetPolyData())
bspTree.BuildLocator()
trans = vtk.vtkMatrix4x4()
targetLabelNode.GetIJKToRASMatrix(trans)
pos = [0.0, 0.0, 0.0, 0.0]
imageData = targetLabelNode.GetImageData()
(x0, x1, y0, y1, z0, z1) = imageData.GetExtent()
for z in range(z0, z1 + 1):
for y in range(y0, y1 + 1):
for x in range(x0, x1 + 1):
if imageData.GetScalarComponentAsDouble(x, y, z, 0) > 0:
trans.MultiplyPoint([x, y, z, 1.0], pos)
(score, mind, mindp) = self.calcApproachScore(
pos[0:3], polyData, bspTree, None)
imageData.SetScalarComponentFromDouble(
x, y, z, 0, score * 100.0 + 1.0)
#print ("Index(%f, %f, %f) -> RAS(%f, %f, %f)" % (x, y, z, pos[0], pos[1], pos[2]))
#print ("Approach Score (<accessible area> / (<accessible area> + <inaccessible area>)) = %f" % (score))
return True
def runPointWise(self, targetPointANode, obstacleModelNode, skinModelNode):
"""
Run point-wise analysis
"""
print("runPointWise()")
#tPointA = targetPointANode.GetMarkupPointVector(0, 0)
#pTargetA = [tPointA[0], tPointA[1], tPointA[2]]
#tPointB = targetPointBNode.GetMarkupPointVector(0, 0)
#pTargetB = [tPointB[0], tPointB[1], tPointB[2]]
#tPointC = targetPointCNode.GetMarkupPointVector(0, 0)
#pTargetC = [tPointC[0], tPointC[1], tPointC[2]]
poly = skinModelNode.GetPolyData()
polyDataNormals = vtk.vtkPolyDataNormals()
polyDataNormals.SetInputData(poly)
polyDataNormals.ComputeCellNormalsOn()
polyDataNormals.Update()
polyData = polyDataNormals.GetOutput()
bspTree = vtk.vtkModifiedBSPTree()
bspTree.SetDataSet(obstacleModelNode.GetPolyData())
bspTree.BuildLocator()
#(score, mind, mindp) = self.calcApproachScore(pTargetA, pTargetB, pTargetC, polyData, bspTree, skinModelNode)
#(score, mind, mindp) = self.calcApproachScore(pTargetA, polyData, bspTree, skinModelNode)
(score, mind, mindp) = self.calcApproachScore(targetPointANode,
polyData, bspTree,
skinModelNode)
print("Approach Score (<accessible area>) = %f" % (score))
print("Minmum Distance = %f" % (mind))
return (score, mind, mindp)
def GenerateMould(self, facePolydata, distanceFromMask, ROI, tubePolydata, clippedFace):
ROIExtents = self.utility.GetROIExtents(ROI)
outerFaceImplicitFunction = vtk.vtkImplicitModeller()
outerFaceImplicitFunction.SetInputConnection(facePolydata.GetOutputPort())
outerFaceImplicitFunction.SetSampleDimensions(70, 70, 70)
outerFaceImplicitFunction.SetMaximumDistance(distanceFromMask)
outerFaceImplicitFunction.SetModelBounds(ROIExtents)
outerFaceImplicitFunction.SetProcessModeToPerVoxel()
outerMaskContourFunction = vtk.vtkContourFilter()
# TODO Find out the the allowed thinkness of the plastic
THICKNESS = 3
outerMaskContourFunction.SetValue(0, THICKNESS)
outerMaskContourFunction.SetInputConnection(outerFaceImplicitFunction.GetOutputPort())
outerFaceNormalsFunction = vtk.vtkPolyDataNormals()
outerFaceNormalsFunction.AutoOrientNormalsOn()
outerFaceNormalsFunction.AddInputConnection(outerMaskContourFunction.GetOutputPort())
# Subtract the Tubes from the mask
subtractionFilter1 = vtk.vtkBooleanOperationPolyDataFilter()
subtractionFilter1.SetOperationToDifference()
subtractionFilter1.SetInputConnection(0, outerFaceNormalsFunction.GetOutputPort())
subtractionFilter1.SetInputConnection(1, tubePolydata.GetOutputPort())
# Subtract the inner face from the outer face to make the mask
subtractionFilter2 = vtk.vtkBooleanOperationPolyDataFilter()
subtractionFilter2.SetOperationToDifference()
subtractionFilter2.SetInputConnection(0, subtractionFilter1.GetOutputPort())
subtractionFilter2.SetInputConnection(1, clippedFace.GetOutputPort())
x = self.utility.DisplayPolyData("Mask", subtractionFilter2.GetOutput())
x.SetColor(0.8, 0.8, 0.8)
x.SetOpacity(1)
def applyFilters(self, state):
surface = state.inputModelNode.GetPolyData()
if state.decimation:
triangle = vtk.vtkTriangleFilter()
triangle.SetInput(surface)
decimation = vtk.vtkDecimatePro()
decimation.SetInput(triangle.GetOutput())
decimation.SetTargetReduction(state.reduction)
decimation.SetBoundaryVertexDeletion(state.boundaryDeletion)
decimation.PreserveTopologyOn()
decimation.Update()
surface = decimation.GetOutput()
if state.smoothing:
if state.smoothingMethod == "Laplace":
smoothing = vtk.vtkSmoothPolyDataFilter()
smoothing.SetInput(surface)
smoothing.SetBoundarySmoothing(state.boundarySmoothing)
smoothing.SetNumberOfIterations(state.laplaceIterations)
smoothing.SetRelaxationFactor(state.laplaceRelaxation)
smoothing.Update()
surface = smoothing.GetOutput()
elif state.smoothingMethod == "Taubin":
smoothing = vtk.vtkWindowedSincPolyDataFilter()
smoothing.SetInput(surface)
smoothing.SetBoundarySmoothing(state.boundarySmoothing)
smoothing.SetNumberOfIterations(state.taubinIterations)
smoothing.SetPassBand(state.taubinPassBand)
smoothing.Update()
surface = smoothing.GetOutput()
if state.normals:
normals = vtk.vtkPolyDataNormals()
normals.SetInput(surface)
normals.AutoOrientNormalsOn()
normals.SetFlipNormals(state.flipNormals)
normals.SetSplitting(state.splitting)
normals.SetFeatureAngle(state.featureAngle)
normals.ConsistencyOn()
normals.Update()
surface = normals.GetOutput()
if state.cleaner:
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInput(surface)
cleaner.Update()
surface = cleaner.GetOutput()
if state.connectivity:
connectivity = vtk.vtkPolyDataConnectivityFilter()
connectivity.SetInput(surface)
connectivity.SetExtractionModeToLargestRegion()
connectivity.Update()
surface = connectivity.GetOutput()
state.outputModelNode.SetAndObservePolyData(surface)
return True
def applyFilters(self, state):
surface = state.inputModelNode.GetPolyData()
if state.decimation:
triangle = vtk.vtkTriangleFilter()
triangle.SetInput(surface)
decimation = vtk.vtkDecimatePro()
decimation.SetInput(triangle.GetOutput())
decimation.SetTargetReduction(state.reduction)
decimation.SetBoundaryVertexDeletion(state.boundaryDeletion)
decimation.PreserveTopologyOn()
decimation.Update()
surface = decimation.GetOutput()
if state.smoothing:
if state.smoothingMethod == "Laplace":
smoothing = vtk.vtkSmoothPolyDataFilter()
smoothing.SetInput(surface)
smoothing.SetBoundarySmoothing(state.boundarySmoothing)
smoothing.SetNumberOfIterations(state.laplaceIterations)
smoothing.SetRelaxationFactor(state.laplaceRelaxation)
smoothing.Update()
surface = smoothing.GetOutput()
elif state.smoothingMethod == "Taubin":
smoothing = vtk.vtkWindowedSincPolyDataFilter()
smoothing.SetInput(surface)
smoothing.SetBoundarySmoothing(state.boundarySmoothing)
smoothing.SetNumberOfIterations(state.taubinIterations)
smoothing.SetPassBand(state.taubinPassBand)
smoothing.Update()
surface = smoothing.GetOutput()
if state.normals:
normals = vtk.vtkPolyDataNormals()
normals.SetInput(surface)
normals.AutoOrientNormalsOn()
normals.SetFlipNormals(state.flipNormals)
normals.SetSplitting(state.splitting)
normals.SetFeatureAngle(state.featureAngle)
normals.ConsistencyOn()
normals.Update()
surface = normals.GetOutput()
if state.cleaner:
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInput(surface)
cleaner.Update()
surface = cleaner.GetOutput()
if state.connectivity:
connectivity = vtk.vtkPolyDataConnectivityFilter()
connectivity.SetInput(surface)
connectivity.SetExtractionModeToLargestRegion()
connectivity.Update()
surface = connectivity.GetOutput()
state.outputModelNode.SetAndObservePolyData(surface)
return True
def calculateNormals(polydata, flip=False):
normalsFilter = vtk.vtkPolyDataNormals()
normalsFilter.SetInputData(polydata)
normalsFilter.AutoOrientNormalsOn()
if flip:
normalsFilter.FlipNormalsOn()
normalsFilter.Update()
return normalsFilter.GetOutput()
def MinimumDistanceMask(self,
vtkAlgorythmObject,
distanceFromMask,
ROI,
ruler,
isBubble=False):
""" Takes an algorythm object which is will send through a pipeline to
create a mask defining the minimum distance value from the skin surface
returns an algorythm object as well to preform GetOutput() -> polydata
or GetOutputPort() -> algorythm
see MinimumDistanceMask.pdf
"""
if distanceFromMask < 2:
print "WARNING: MouldLogic: MinimumDistanceMask implicit",
"modeling is very unstable below 1.5 , mask may degrade",
"and lines will become discontinuous."
Extents = self.utility.GetROIExtents(ROI)
if (isBubble):
Extents = self.utility.ExpandExtents(Extents, 100)
implicitModeller = vtk.vtkImplicitModeller()
implicitModeller.SetInputConnection(vtkAlgorythmObject.GetOutputPort())
implicitModeller.SetMaximumDistance(distanceFromMask)
implicitModeller.SetModelBounds(Extents)
implicitModeller.AdjustBoundsOn()
implicitModeller.SetAdjustBounds(10) # Removes the boundary effects
implicitModeller.CappingOff(
) # Important to create disjoint inner and outer masks
implicitModeller.SetProcessModeToPerVoxel()
implicitModeller.Update()
contourFilter = vtk.vtkContourFilter()
contourFilter.SetValue(0, distanceFromMask)
contourFilter.SetInputConnection(implicitModeller.GetOutputPort())
contourFilter.Update()
normalsFunction = vtk.vtkPolyDataNormals()
normalsFunction.FlipNormalsOn()
normalsFunction.AddInputConnection(contourFilter.GetOutputPort())
normalsFunction.Update()
implicitBoxRegion = vtk.vtkBox()
implicitBoxRegion.SetBounds(Extents)
clipper2 = vtk.vtkClipPolyData()
clipper2.InsideOutOn() # Clip the regions outside of implicit function
clipper2.SetInputConnection(normalsFunction.GetOutputPort())
clipper2.SetClipFunction(implicitBoxRegion)
clipper2.Update()
closestPoint = [0, 0, 0]
ruler.GetPosition1(closestPoint)
connectivityFilter = vtk.vtkPolyDataConnectivityFilter()
connectivityFilter.SetInputConnection(clipper2.GetOutputPort())
connectivityFilter.SetExtractionModeToClosestPointRegion()
connectivityFilter.SetClosestPoint(closestPoint)
connectivityFilter.Update()
return connectivityFilter.GetOutput()
def prepareModel( self, polyData ):
'''
'''
# import the vmtk libraries
try:
#from libvtkvmtkComputationalGeometryPython import *
#from libvtkvmtkMiscPython import *
import libvtkvmtkComputationalGeometryPython as cg
import libvtkvmtkMiscPython as m
except ImportError:
print "FAILURE: Unable to import the SlicerVmtk libraries!"
capDisplacement = 0.0
surfaceCleaner = vtk.vtkCleanPolyData()
surfaceCleaner.SetInput( polyData )
surfaceCleaner.Update()
surfaceTriangulator = vtk.vtkTriangleFilter()
surfaceTriangulator.SetInput( surfaceCleaner.GetOutput() )
surfaceTriangulator.PassLinesOff()
surfaceTriangulator.PassVertsOff()
surfaceTriangulator.Update()
# new steps for preparation to avoid problems because of slim models (f.e. at stenosis)
subdiv = vtk.vtkLinearSubdivisionFilter()
subdiv.SetInput( surfaceTriangulator.GetOutput() )
subdiv.SetNumberOfSubdivisions( 1 )
subdiv.Update()
smooth = vtk.vtkWindowedSincPolyDataFilter()
smooth.SetInput( subdiv.GetOutput() )
smooth.SetNumberOfIterations( 20 )
smooth.SetPassBand( 0.1 )
smooth.SetBoundarySmoothing( 1 )
smooth.Update()
normals = vtk.vtkPolyDataNormals()
normals.SetInput( smooth.GetOutput() )
normals.SetAutoOrientNormals( 1 )
normals.SetFlipNormals( 0 )
normals.SetConsistency( 1 )
normals.SplittingOff()
normals.Update()
surfaceCapper = m.vtkvmtkCapPolyData()
surfaceCapper.SetInput( normals.GetOutput() )
surfaceCapper.SetDisplacement( capDisplacement )
surfaceCapper.SetInPlaneDisplacement( capDisplacement )
surfaceCapper.Update()
outPolyData = vtk.vtkPolyData()
outPolyData.DeepCopy( surfaceCapper.GetOutput() )
outPolyData.Update()
return outPolyData
def autoOrientNormals(self, model):
normals = vtk.vtkPolyDataNormals()
normals.SetAutoOrientNormals(True)
normals.SetFlipNormals(False)
normals.SetSplitting(False)
normals.ConsistencyOn()
normals.SetInputData(model)
normals.Update()
normalspoint = normals.GetOutput().GetPointData().GetArray("Normals")
model.GetPointData().SetNormals(normalspoint)
def MinimumDistanceMask(self, vtkAlgorythmObject, distanceFromMask, ROI, ruler, isBubble=False):
""" Takes an algorythm object which is will send through a pipeline to
create a mask defining the minimum distance value from the skin surface
returns an algorythm object as well to preform GetOutput() -> polydata
or GetOutputPort() -> algorythm
see MinimumDistanceMask.pdf
"""
if distanceFromMask < 2:
print "WARNING: MouldLogic: MinimumDistanceMask implicit",
"modeling is very unstable below 1.5 , mask may degrade",
"and lines will become discontinuous."
Extents = self.utility.GetROIExtents(ROI)
if isBubble:
Extents = self.utility.ExpandExtents(Extents, 100)
implicitModeller = vtk.vtkImplicitModeller()
implicitModeller.SetInputConnection(vtkAlgorythmObject.GetOutputPort())
implicitModeller.SetMaximumDistance(distanceFromMask)
implicitModeller.SetModelBounds(Extents)
implicitModeller.AdjustBoundsOn()
implicitModeller.SetAdjustBounds(10) # Removes the boundary effects
implicitModeller.CappingOff() # Important to create disjoint inner and outer masks
implicitModeller.SetProcessModeToPerVoxel()
implicitModeller.Update()
contourFilter = vtk.vtkContourFilter()
contourFilter.SetValue(0, distanceFromMask)
contourFilter.SetInputConnection(implicitModeller.GetOutputPort())
contourFilter.Update()
normalsFunction = vtk.vtkPolyDataNormals()
normalsFunction.FlipNormalsOn()
normalsFunction.AddInputConnection(contourFilter.GetOutputPort())
normalsFunction.Update()
implicitBoxRegion = vtk.vtkBox()
implicitBoxRegion.SetBounds(Extents)
clipper2 = vtk.vtkClipPolyData()
clipper2.InsideOutOn() # Clip the regions outside of implicit function
clipper2.SetInputConnection(normalsFunction.GetOutputPort())
clipper2.SetClipFunction(implicitBoxRegion)
clipper2.Update()
closestPoint = [0, 0, 0]
ruler.GetPosition1(closestPoint)
connectivityFilter = vtk.vtkPolyDataConnectivityFilter()
connectivityFilter.SetInputConnection(clipper2.GetOutputPort())
connectivityFilter.SetExtractionModeToClosestPointRegion()
connectivityFilter.SetClosestPoint(closestPoint)
connectivityFilter.Update()
return connectivityFilter.GetOutput()
def marchingCubes( self, image, ijkToRasMatrix, threshold ):
transformIJKtoRAS = vtk.vtkTransform()
transformIJKtoRAS.SetMatrix( ijkToRasMatrix )
marchingCubes = vtk.vtkMarchingCubes()
marchingCubes.SetInput( image )
marchingCubes.SetValue( 0, threshold )
marchingCubes.ComputeScalarsOn()
marchingCubes.ComputeGradientsOn()
marchingCubes.ComputeNormalsOn()
marchingCubes.GetOutput().ReleaseDataFlagOn()
marchingCubes.Update()
if transformIJKtoRAS.GetMatrix().Determinant() < 0:
reverser = vtk.vtkReverseSense()
reverser.SetInput( marchingCubes.GetOutput() )
reverser.ReverseNormalsOn()
reverser.GetOutput().ReleaseDataFlagOn()
reverser.Update()
correctedOutput = reverser.GetOutput()
else:
correctedOutput = marchingCubes.GetOutput()
transformer = vtk.vtkTransformPolyDataFilter()
transformer.SetInput( correctedOutput )
transformer.SetTransform( transformIJKtoRAS )
transformer.GetOutput().ReleaseDataFlagOn()
transformer.Update()
normals = vtk.vtkPolyDataNormals()
normals.ComputePointNormalsOn()
normals.SetInput( transformer.GetOutput() )
normals.SetFeatureAngle( 60 )
normals.SetSplitting( 1 )
normals.GetOutput().ReleaseDataFlagOn()
normals.Update()
stripper = vtk.vtkStripper()
stripper.SetInput( normals.GetOutput() )
stripper.GetOutput().ReleaseDataFlagOff()
stripper.Update()
stripper.GetOutput().Update()
result = vtk.vtkPolyData()
result.DeepCopy( stripper.GetOutput() )
result.Update()
return result
def marchingCubes(self,image,ijkToRasMatrix,threshold):
transformIJKtoRAS = vtk.vtkTransform()
transformIJKtoRAS.SetMatrix(ijkToRasMatrix)
marchingCubes = vtk.vtkMarchingCubes()
marchingCubes.SetInput(image)
marchingCubes.SetValue(0,threshold)
marchingCubes.ComputeScalarsOn()
marchingCubes.ComputeGradientsOn()
marchingCubes.ComputeNormalsOn()
marchingCubes.GetOutput().ReleaseDataFlagOn()
marchingCubes.Update()
if transformIJKtoRAS.GetMatrix().Determinant() < 0:
reverser = vtk.vtkReverseSense()
reverser.SetInput(marchingCubes.GetOutput())
reverser.ReverseNormalsOn()
reverser.GetOutput().ReleaseDataFlagOn()
reverser.Update()
correctedOutput = reverser.GetOutput()
else:
correctedOutput = marchingCubes.GetOutput()
transformer = vtk.vtkTransformPolyDataFilter()
transformer.SetInput(correctedOutput)
transformer.SetTransform(transformIJKtoRAS)
transformer.GetOutput().ReleaseDataFlagOn()
transformer.Update()
normals = vtk.vtkPolyDataNormals()
normals.ComputePointNormalsOn()
normals.SetInput(transformer.GetOutput())
normals.SetFeatureAngle(60)
normals.SetSplitting(1)
normals.GetOutput().ReleaseDataFlagOn()
normals.Update()
stripper = vtk.vtkStripper()
stripper.SetInput(normals.GetOutput())
stripper.GetOutput().ReleaseDataFlagOff()
stripper.Update()
stripper.GetOutput().Update()
result = vtk.vtkPolyData()
result.DeepCopy(stripper.GetOutput())
result.Update()
return result
def CreateSegmentation(self, masterVolumeNode, outputObj):
# Create segmentation
segmentationNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentationNode")
segmentationNode.CreateDefaultDisplayNodes() # only needed for display
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(
masterVolumeNode)
addedSegmentID = segmentationNode.GetSegmentation().AddEmptySegment(
"segmentation")
# Create segment editor to get access to effects
segmentEditorWidget = slicer.qMRMLSegmentEditorWidget()
segmentEditorWidget.setMRMLScene(slicer.mrmlScene)
segmentEditorNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSegmentEditorNode")
segmentEditorWidget.setMRMLSegmentEditorNode(segmentEditorNode)
segmentEditorWidget.setSegmentationNode(segmentationNode)
segmentEditorWidget.setMasterVolumeNode(masterVolumeNode)
# Thresholding
segmentEditorWidget.setActiveEffectByName("Threshold")
effect = segmentEditorWidget.activeEffect()
effect.setParameter("MinimumThreshold", "1")
effect.setParameter("MaximumThreshold", "999")
effect.self().onApply()
# Clean up
segmentEditorWidget = None
slicer.mrmlScene.RemoveNode(segmentEditorNode)
# Make segmentation results visible in 3D
segmentationNode.CreateClosedSurfaceRepresentation()
# Make sure surface mesh cells are consistently oriented
surfaceMesh = segmentationNode.GetClosedSurfaceRepresentation(
addedSegmentID)
normals = vtk.vtkPolyDataNormals()
normals.AutoOrientNormalsOn()
normals.ConsistencyOn()
normals.SetInputData(surfaceMesh)
normals.Update()
surfaceMesh = normals.GetOutput()
# Write to OBJ file
writer = vtk.vtkOBJWriter()
writer.SetInputData(surfaceMesh)
writer.SetFileName(outputObj)
writer.Update()
def AddTubeToMask(self, maskPolydata, tube, ROI, radius, ruler):
ROIExtents = self.utility.GetROIExtents(ROI)
implicitFilter = vtk.vtkImplicitModeller()
implicitFilter.SetInput(tube)
implicitFilter.SetSampleDimensions(70, 70, 70)
implicitFilter.SetMaximumDistance(radius)
implicitFilter.SetModelBounds(ROIExtents)
implicitFilter.SetProcessModeToPerVoxel()
contourFilter = vtk.vtkContourFilter()
contourFilter.SetValue(0, radius)
implicitFilter.AdjustBoundsOn()
implicitFilter.SetAdjustBounds(1) # Removes the boundary effects
implicitFilter.CappingOff()
contourFilter.SetInputConnection(implicitFilter.GetOutputPort())
normalsFunction = vtk.vtkPolyDataNormals()
normalsFunction.AutoOrientNormalsOn()
normalsFunction.AddInputConnection(contourFilter.GetOutputPort())
unionFilter = vtk.vtkBooleanOperationPolyDataFilter()
unionFilter.SetOperationToUnion()
unionFilter.SetInput(0, normalsFunction.GetOutput())
unionFilter.SetInput(1, maskPolydata)
return unionFilter.GetOutput()
def AddTubeToMask(self, maskPolydata, tube, ROI, radius, ruler):
ROIExtents = self.utility.GetROIExtents(ROI)
implicitFilter = vtk.vtkImplicitModeller()
implicitFilter.SetInput(tube)
implicitFilter.SetSampleDimensions(70, 70, 70)
implicitFilter.SetMaximumDistance(radius)
implicitFilter.SetModelBounds(ROIExtents)
implicitFilter.SetProcessModeToPerVoxel()
contourFilter = vtk.vtkContourFilter()
contourFilter.SetValue(0, radius)
implicitFilter.AdjustBoundsOn()
implicitFilter.SetAdjustBounds(1) # Removes the boundary effects
implicitFilter.CappingOff()
contourFilter.SetInputConnection(implicitFilter.GetOutputPort())
normalsFunction = vtk.vtkPolyDataNormals()
normalsFunction.AutoOrientNormalsOn()
normalsFunction.AddInputConnection(contourFilter.GetOutputPort())
unionFilter = vtk.vtkBooleanOperationPolyDataFilter()
unionFilter.SetOperationToUnion()
unionFilter.SetInput(0, normalsFunction.GetOutput())
unionFilter.SetInput(1, maskPolydata)
return unionFilter.GetOutput()
def GenerateMould(self, facePolydata, distanceFromMask, ROI, tubePolydata,
clippedFace):
ROIExtents = self.utility.GetROIExtents(ROI)
outerFaceImplicitFunction = vtk.vtkImplicitModeller()
outerFaceImplicitFunction.SetInputConnection(
facePolydata.GetOutputPort())
outerFaceImplicitFunction.SetSampleDimensions(70, 70, 70)
outerFaceImplicitFunction.SetMaximumDistance(distanceFromMask)
outerFaceImplicitFunction.SetModelBounds(ROIExtents)
outerFaceImplicitFunction.SetProcessModeToPerVoxel()
outerMaskContourFunction = vtk.vtkContourFilter()
#TODO Find out the the allowed thinkness of the plastic
THICKNESS = 3
outerMaskContourFunction.SetValue(0, THICKNESS)
outerMaskContourFunction.SetInputConnection(
outerFaceImplicitFunction.GetOutputPort())
outerFaceNormalsFunction = vtk.vtkPolyDataNormals()
outerFaceNormalsFunction.AutoOrientNormalsOn()
outerFaceNormalsFunction.AddInputConnection(
outerMaskContourFunction.GetOutputPort())
# Subtract the Tubes from the mask
subtractionFilter1 = vtk.vtkBooleanOperationPolyDataFilter()
subtractionFilter1.SetOperationToDifference()
subtractionFilter1.SetInputConnection(
0, outerFaceNormalsFunction.GetOutputPort())
subtractionFilter1.SetInputConnection(1, tubePolydata.GetOutputPort())
# Subtract the inner face from the outer face to make the mask
subtractionFilter2 = vtk.vtkBooleanOperationPolyDataFilter()
subtractionFilter2.SetOperationToDifference()
subtractionFilter2.SetInputConnection(
0, subtractionFilter1.GetOutputPort())
subtractionFilter2.SetInputConnection(1, clippedFace.GetOutputPort())
x = self.utility.DisplayPolyData("Mask",
subtractionFilter2.GetOutput())
x.SetColor(0.8, 0.8, 0.8)
x.SetOpacity(1)
def load(self, properties):
try:
filePath = properties["fileName"]
tempDirectory = slicer.util.tempDirectory()
if not slicer.util.extractArchive(filePath, tempDirectory):
raise ValueError("Failed to extract file: " + filePath)
# Parse header
properties = {}
timestamps = []
headerSuffix = "_header.txt"
for root, dirs, filenames in os.walk(tempDirectory):
for filename in filenames:
if filename.endswith(headerSuffix):
# found header
print(filename)
internalBaseName = filename[:-len(headerSuffix)]
properties, timestamps = self.parseHeader(
os.path.join(root, filename))
break
if not properties:
raise ValueError(
"Failed to read file as TomTec UCD data file: " + filePath)
# Get node base name from filename
baseName = os.path.basename(filePath)
suffix = ".UCD.data.zip"
if baseName.endswith(suffix):
baseName = baseName[:-len(suffix)]
baseName = slicer.mrmlScene.GenerateUniqueName(baseName)
sequenceNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSequenceNode", baseName)
sequenceNode.SetIndexName("time")
sequenceNode.SetIndexUnit("ms")
sequenceNode.SetIndexType(slicer.vtkMRMLSequenceNode.NumericIndex)
for propertyName in [
"Average RR Duration", "Enddiastole time",
"Endsystole time"
]:
sequenceNode.SetAttribute(propertyName,
properties[propertyName][0])
numberOfFrames = int(properties["Number of frames"][0])
tempModelNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLModelNode", baseName + " temp")
for frameIndex in range(numberOfFrames):
# Read mesh
meshFilePath = os.path.join(
tempDirectory,
"{0}_{1:02}.ucd".format(internalBaseName, frameIndex))
reader = vtk.vtkAVSucdReader()
reader.SetFileName(meshFilePath)
reader.Update()
# TomTec UCD files store surface mesh in unstructured grid - convert it to polydata
extractSurface = vtk.vtkGeometryFilter()
extractSurface.SetInputConnection(reader.GetOutputPort())
normals = vtk.vtkPolyDataNormals()
normals.SetInputConnection(extractSurface.GetOutputPort())
normals.Update()
# Save in sequence node
tempModelNode.SetAndObserveMesh(normals.GetOutput())
addedNode = sequenceNode.SetDataNodeAtValue(
tempModelNode, timestamps[frameIndex])
import shutil
shutil.rmtree(tempDirectory, True)
slicer.mrmlScene.RemoveNode(tempModelNode)
sequenceBrowserNode = slicer.mrmlScene.AddNewNodeByClass(
"vtkMRMLSequenceBrowserNode", baseName + " browser")
sequenceBrowserNode.SetAndObserveMasterSequenceNodeID(
sequenceNode.GetID())
# Disable scalar visibility by default (there is not really anything useful to show)
proxyModelNode = sequenceBrowserNode.GetProxyNode(sequenceNode)
proxyModelNode.GetDisplayNode().SetScalarVisibility(False)
# Show sequence browser toolbar if a sequence has been loaded
slicer.modules.sequences.showSequenceBrowser(sequenceBrowserNode)
except Exception as e:
logging.error("Failed to load TomTec UCD data file: " + str(e))
import traceback
traceback.print_exc()
return False
return True
def run(self, inputModel, sModel, seedList):
"""
Run the actual algorithm
"""
self.delayDisplay('Running the aglorithm')
tri = vtk.vtkDelaunay3D()
tri.SetInputData(sModel.GetPolyData())
elev = vtk.vtkElevationFilter()
elev.SetInputConnection(tri.GetOutput())
implicitDataSet = vtk.vtkImplicitDataSet()
implicitDataSet.SetDataSet(elev.GetOutput())
triangle = vtk.vtkTriangleFilter()
triangle.SetInputData(inputModel.GetPolyData())
triangle.Update()
computeNormals = vtk.vtkPolyDataNormals()
computeNormals.SetInputData(triangle.GetOutput())
computeNormals.ComputeCellNormalsOn()
computeNormals.Update()
clip = vtk.vtkClipPolyData()
clip.SetInputData(computeNormals.GetOutput())
clip.SetClipFunction(implicitDataSet)
clip.InsideOutOff()
clip.Update()
clean = vtk.vtkCleanPolyData()
clean.SetInputData(clip.GetOutput())
clean.Update()
polydata = clean.GetOutput()
cellData = polydata.GetCellData()
normals = cellData.GetNormals()
meanNormal = [0, 0, 0]
nOfTuples = normals.GetNumberOfTuples()
for cellIndex in range(0, nOfTuples):
cellNormal = [0, 0, 0]
cell = polydata.GetCell(cellIndex)
normals.GetTuple(cellIndex, cellNormal)
meanNormal[0] = meanNormal[0] + cellNormal[0]
meanNormal[1] = meanNormal[1] + cellNormal[1]
meanNormal[2] = meanNormal[2] + cellNormal[2]
meanNormal[0] = meanNormal[0] / nOfTuples
meanNormal[1] = meanNormal[1] / nOfTuples
meanNormal[2] = meanNormal[2] / nOfTuples
print("Normal: " + str(meanNormal))
seed1 = [0, 0, 0]
seedList.GetNthFiducialPosition(0, seed1)
vector = [
seed1[0] + 50 * meanNormal[0], seed1[1] + 50 * meanNormal[1],
seed1[2] + 50 * meanNormal[2]
]
seedList.AddFiducialFromArray(vector)
# Calculate perpendicular vectors
v1 = [0, 0, 0]
v2 = [0, 0, 0]
math = vtk.vtkMath()
math.Perpendiculars(meanNormal, v2, v1, 0)
# Normalize vectors
math.Normalize(meanNormal)
math.Normalize(v1)
math.Normalize(v2)
# create matrix4x4
transform = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLLinearTransformNode')
slicer.mrmlScene.AddNode(transform)
matrix = transform.GetMatrixTransformToParent()
matrix.SetElement(0, 0, v1[0])
matrix.SetElement(1, 0, v1[1])
matrix.SetElement(2, 0, v1[2])
matrix.SetElement(3, 0, 0.0)
matrix.SetElement(0, 1, meanNormal[0])
matrix.SetElement(1, 1, meanNormal[1])
matrix.SetElement(2, 1, meanNormal[2])
matrix.SetElement(3, 1, 0.0)
matrix.SetElement(0, 2, v2[0])
matrix.SetElement(1, 2, v2[1])
matrix.SetElement(2, 2, v2[2])
matrix.SetElement(3, 2, 0.0)
matrix.SetElement(0, 3, seed1[0])
matrix.SetElement(1, 3, seed1[1])
matrix.SetElement(2, 3, seed1[2])
matrix.SetElement(3, 3, 1.0)
return True
def run(self,inputModel,sModel,seedList):
"""
Run the actual algorithm
"""
self.delayDisplay('Running the aglorithm')
tri = vtk.vtkDelaunay3D()
tri.SetInputData(sModel.GetPolyData())
elev = vtk.vtkElevationFilter()
elev.SetInputConnection(tri.GetOutput())
implicitDataSet = vtk.vtkImplicitDataSet()
implicitDataSet.SetDataSet(elev.GetOutput())
triangle = vtk.vtkTriangleFilter()
triangle.SetInputData(inputModel.GetPolyData())
triangle.Update()
computeNormals = vtk.vtkPolyDataNormals()
computeNormals.SetInputData(triangle.GetOutput())
computeNormals.ComputeCellNormalsOn()
computeNormals.Update()
clip = vtk.vtkClipPolyData()
clip.SetInputData(computeNormals.GetOutput())
clip.SetClipFunction(implicitDataSet)
clip.InsideOutOff()
clip.Update()
clean = vtk.vtkCleanPolyData()
clean.SetInputData(clip.GetOutput())
clean.Update()
polydata = clean.GetOutput()
cellData = polydata.GetCellData()
normals = cellData.GetNormals()
meanNormal = [0,0,0]
nOfTuples = normals.GetNumberOfTuples()
for cellIndex in range(0, nOfTuples):
cellNormal = [0,0,0]
cell = polydata.GetCell(cellIndex)
normals.GetTuple(cellIndex, cellNormal)
meanNormal[0] = meanNormal[0] + cellNormal[0]
meanNormal[1] = meanNormal[1] + cellNormal[1]
meanNormal[2] = meanNormal[2] + cellNormal[2]
meanNormal[0] = meanNormal[0] / nOfTuples
meanNormal[1] = meanNormal[1] / nOfTuples
meanNormal[2] = meanNormal[2] / nOfTuples
print("Normal: " + str(meanNormal))
seed1 = [0,0,0]
seedList.GetNthFiducialPosition(0,seed1)
vector = [seed1[0]+50*meanNormal[0],
seed1[1]+50*meanNormal[1],
seed1[2]+50*meanNormal[2]]
seedList.AddFiducialFromArray(vector)
# Calculate perpendicular vectors
v1 = [0,0,0]
v2 = [0,0,0]
math = vtk.vtkMath()
math.Perpendiculars(meanNormal, v2, v1, 0)
# Normalize vectors
math.Normalize(meanNormal)
math.Normalize(v1)
math.Normalize(v2)
# create matrix4x4
transform = slicer.mrmlScene.CreateNodeByClass('vtkMRMLLinearTransformNode')
slicer.mrmlScene.AddNode(transform)
matrix = transform.GetMatrixTransformToParent()
matrix.SetElement(0,0,v1[0])
matrix.SetElement(1,0,v1[1])
matrix.SetElement(2,0,v1[2])
matrix.SetElement(3,0,0.0)
matrix.SetElement(0,1,meanNormal[0])
matrix.SetElement(1,1,meanNormal[1])
matrix.SetElement(2,1,meanNormal[2])
matrix.SetElement(3,1,0.0)
matrix.SetElement(0,2,v2[0])
matrix.SetElement(1,2,v2[1])
matrix.SetElement(2,2,v2[2])
matrix.SetElement(3,2,0.0)
matrix.SetElement(0,3,seed1[0])
matrix.SetElement(1,3,seed1[1])
matrix.SetElement(2,3,seed1[2])
matrix.SetElement(3,3,1.0)
return True
def PolyDataToImageData(self,
inputPolydata_Ras,
referenceVolumeNode_Ras,
inVal=100,
outVal=0):
""" We take in an polydata and convert it to an new image data , withing the Reference Voulume node
the reference volume node is cleared with a threshold because originally the volume may contain
alot of noisy pixels
PARAM: inputPolydata_Ras: Polydata we are looking to conver vtkPolydata()
PARAM: refernceVolumeNode_Ras vtkMRMLScalarVolumeNode()
RETURN : vtkImageData
"""
""" Transform the polydata from ras to ijk using the referenceVolumeNode """
#inputPolydataTriangulated_Ijk=polyToImage.GetOutput()
transformPolydataFilter = vtk.vtkTransformPolyDataFilter()
rasToIjkMatrix = vtk.vtkMatrix4x4()
referenceVolumeNode_Ras.GetRASToIJKMatrix(rasToIjkMatrix)
rasToIjkTransform = vtk.vtkTransform()
rasToIjkTransform.SetMatrix(rasToIjkMatrix)
transformPolydataFilter.SetTransform(rasToIjkTransform)
transformPolydataFilter.SetInputData(inputPolydata_Ras)
transformPolydataFilter.Update()
inputPolydata_Ijk = transformPolydataFilter.GetOutput()
normalsFunction = vtk.vtkPolyDataNormals()
normalsFunction.SetInputData(inputPolydata_Ijk)
normalsFunction.ConsistencyOn()
trigFilter = vtk.vtkTriangleFilter()
trigFilter.SetInputConnection(normalsFunction.GetOutputPort())
stripper = vtk.vtkStripper()
stripper.SetInputConnection(trigFilter.GetOutputPort())
stripper.Update()
inputPolydataTriangulated_Ijk = stripper.GetOutput()
# Clone reference image and clear it
referenceImage_Ijk = referenceVolumeNode_Ras.GetImageData()
# Fill image with outVal (there is no volume Fill filter in VTK, therefore we need to use threshold filter)
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(outVal)
thresh.SetOutValue(outVal)
#thresh.SetOutputScalarType (vtk.VTK_UNSIGNED_CHAR)
thresh.SetInputData(referenceImage_Ijk)
thresh.Update()
whiteImage_Ijk = thresh.GetOutput()
# Convert polydata to stencil
polyToImage = vtk.vtkPolyDataToImageStencil()
polyToImage.SetInputData(inputPolydataTriangulated_Ijk)
polyToImage.SetOutputSpacing(whiteImage_Ijk.GetSpacing())
polyToImage.SetOutputOrigin(whiteImage_Ijk.GetOrigin())
polyToImage.SetOutputWholeExtent(whiteImage_Ijk.GetExtent())
polyToImage.Update()
imageStencil_Ijk = polyToImage.GetOutput()
# Convert stencil to image
imgstenc = vtk.vtkImageStencil()
imgstenc.SetInputData(whiteImage_Ijk)
imgstenc.SetStencilData(imageStencil_Ijk)
imgstenc.ReverseStencilOn()
imgstenc.SetBackgroundValue(inVal)
imgstenc.Update()
return imgstenc.GetOutput()
def PolyDataToImageData(self, inputPolydata_Ras, referenceVolumeNode_Ras, inVal=100, outVal=0):
""" We take in an polydata and convert it to an new image data , withing the Reference Voulume node
the reference volume node is cleared with a threshold because originally the volume may contain
alot of noisy pixels
PARAM: inputPolydata_Ras: Polydata we are looking to conver vtkPolydata()
PARAM: refernceVolumeNode_Ras vtkMRMLScalarVolumeNode()
RETURN : vtkImageData
"""
""" Transform the polydata from ras to ijk using the referenceVolumeNode """
#inputPolydataTriangulated_Ijk=polyToImage.GetOutput()
transformPolydataFilter=vtk.vtkTransformPolyDataFilter()
rasToIjkMatrix=vtk.vtkMatrix4x4()
referenceVolumeNode_Ras.GetRASToIJKMatrix(rasToIjkMatrix)
rasToIjkTransform = vtk.vtkTransform()
rasToIjkTransform.SetMatrix(rasToIjkMatrix)
transformPolydataFilter.SetTransform(rasToIjkTransform)
transformPolydataFilter.SetInputData(inputPolydata_Ras)
transformPolydataFilter.Update()
inputPolydata_Ijk=transformPolydataFilter.GetOutput()
normalsFunction=vtk.vtkPolyDataNormals()
normalsFunction.SetInputData(inputPolydata_Ijk)
normalsFunction.ConsistencyOn()
trigFilter=vtk.vtkTriangleFilter()
trigFilter.SetInputConnection(normalsFunction.GetOutputPort())
stripper=vtk.vtkStripper()
stripper.SetInputConnection(trigFilter.GetOutputPort())
stripper.Update()
inputPolydataTriangulated_Ijk=stripper.GetOutput()
# Clone reference image and clear it
referenceImage_Ijk = referenceVolumeNode_Ras.GetImageData()
# Fill image with outVal (there is no volume Fill filter in VTK, therefore we need to use threshold filter)
thresh = vtk.vtkImageThreshold()
thresh.ReplaceInOn()
thresh.ReplaceOutOn()
thresh.SetInValue(outVal)
thresh.SetOutValue(outVal)
#thresh.SetOutputScalarType (vtk.VTK_UNSIGNED_CHAR)
thresh.SetInputData(referenceImage_Ijk)
thresh.Update()
whiteImage_Ijk = thresh.GetOutput()
# Convert polydata to stencil
polyToImage = vtk.vtkPolyDataToImageStencil()
polyToImage.SetInputData(inputPolydataTriangulated_Ijk)
polyToImage.SetOutputSpacing(whiteImage_Ijk.GetSpacing())
polyToImage.SetOutputOrigin(whiteImage_Ijk.GetOrigin())
polyToImage.SetOutputWholeExtent(whiteImage_Ijk.GetExtent())
polyToImage.Update()
imageStencil_Ijk=polyToImage.GetOutput()
# Convert stencil to image
imgstenc = vtk.vtkImageStencil()
imgstenc.SetInputData(whiteImage_Ijk)
imgstenc.SetStencilData(imageStencil_Ijk)
imgstenc.ReverseStencilOn()
imgstenc.SetBackgroundValue(inVal)
imgstenc.Update()
return imgstenc.GetOutput()
