def ComputeMeanDistance(self, inputFiducials, inputModel, transform):
surfacePoints = vtk.vtkPoints()
cellId = vtk.mutable(0)
subId = vtk.mutable(0)
dist2 = vtk.mutable(0.0)
locator = vtk.vtkCellLocator()
locator.SetDataSet(inputModel.GetPolyData())
locator.SetNumberOfCellsPerBucket(1)
locator.BuildLocator()
totalDistance = 0.0
n = inputFiducials.GetNumberOfFiducials()
m = vtk.vtkMath()
for fiducialIndex in range(0, n):
originalPoint = [0, 0, 0]
inputFiducials.GetNthFiducialPosition(fiducialIndex, originalPoint)
transformedPoint = [0, 0, 0, 1]
#transform.GetTransformToParent().TransformVector(originalPoint, transformedPoint)
originalPoint.append(1)
transform.GetTransformToParent().MultiplyPoint(originalPoint, transformedPoint)
#transformedPoints.InsertNextPoint(transformedPoint)
surfacePoint = [0, 0, 0]
transformedPoint.pop()
locator.FindClosestPoint(transformedPoint, surfacePoint, cellId, subId, dist2)
totalDistance = totalDistance + math.sqrt(dist2)
return (totalDistance / n)
def ComputeMeanDistance(self, inputSourceModel, inputTargetModel, transform ):
sourcePolyData = inputSourceModel.GetPolyData()
targetPolyData = inputTargetModel.GetPolyData()
cellId = vtk.mutable(0)
subId = vtk.mutable(0)
dist2 = vtk.mutable(0.0)
locator = vtk.vtkCellLocator()
locator.SetDataSet( targetPolyData )
locator.SetNumberOfCellsPerBucket( 1 )
locator.BuildLocator()
totalDistance = 0.0
sourcePoints = sourcePolyData.GetPoints()
n = sourcePoints.GetNumberOfPoints()
m = vtk.vtkMath()
for sourcePointIndex in range(n):
sourcePointPos = [0, 0, 0]
sourcePoints.GetPoint( sourcePointIndex, sourcePointPos )
transformedSourcePointPos = [0, 0, 0, 1]
#transform.GetTransformToParent().TransformVector( sourcePointPos, transformedSourcePointPos )
sourcePointPos.append(1)
transform.GetTransformToParent().MultiplyPoint( sourcePointPos, transformedSourcePointPos )
#transformedPoints.InsertNextPoint( transformedSourcePointPos )
surfacePoint = [0, 0, 0]
transformedSourcePointPos.pop()
locator.FindClosestPoint( transformedSourcePointPos, surfacePoint, cellId, subId, dist2 )
totalDistance = totalDistance + math.sqrt(dist2)
return ( totalDistance / n )
def ComputeMeanDistance(self, inputSourceModel, inputTargetModel, transform ):
sourcePolyData = inputSourceModel.GetPolyData()
targetPolyData = inputTargetModel.GetPolyData()
cellId = vtk.mutable(0)
subId = vtk.mutable(0)
dist2 = vtk.mutable(0.0)
locator = vtk.vtkCellLocator()
locator.SetDataSet( targetPolyData )
locator.SetNumberOfCellsPerBucket( 1 )
locator.BuildLocator()
totalDistance = 0.0
sourcePoints = sourcePolyData.GetPoints()
n = sourcePoints.GetNumberOfPoints()
m = vtk.vtkMath()
for sourcePointIndex in xrange(n):
sourcePointPos = [0, 0, 0]
sourcePoints.GetPoint( sourcePointIndex, sourcePointPos )
transformedSourcePointPos = [0, 0, 0, 1]
#transform.GetTransformToParent().TransformVector( sourcePointPos, transformedSourcePointPos )
sourcePointPos.append(1)
transform.GetTransformToParent().MultiplyPoint( sourcePointPos, transformedSourcePointPos )
#transformedPoints.InsertNextPoint( transformedSourcePointPos )
surfacePoint = [0, 0, 0]
transformedSourcePointPos.pop()
locator.FindClosestPoint( transformedSourcePointPos, surfacePoint, cellId, subId, dist2 )
totalDistance = totalDistance + math.sqrt(dist2)
return ( totalDistance / n )
def ComputeMeanDistance(self, inputFiducials, inputModel, transform ):
surfacePoints = vtk.vtkPoints()
cellId = vtk.mutable(0)
subId = vtk.mutable(0)
dist2 = vtk.mutable(0.0)
locator = vtk.vtkCellLocator()
locator.SetDataSet( inputModel.GetPolyData() )
locator.SetNumberOfCellsPerBucket( 1 )
locator.BuildLocator()
totalDistance = 0.0
n = inputFiducials.GetNumberOfFiducials()
m = vtk.vtkMath()
for fiducialIndex in range( 0, n ):
originalPoint = [0, 0, 0]
inputFiducials.GetNthFiducialPosition( fiducialIndex, originalPoint )
transformedPoint = [0, 0, 0, 1]
#transform.GetTransformToParent().TransformVector( originalPoint, transformedPoint )
originalPoint.append(1)
transform.GetTransformToParent().MultiplyPoint( originalPoint, transformedPoint )
#transformedPoints.InsertNextPoint( transformedPoint )
surfacePoint = [0, 0, 0]
transformedPoint.pop()
locator.FindClosestPoint( transformedPoint, surfacePoint, cellId, subId, dist2 )
totalDistance = totalDistance + math.sqrt(dist2)
return ( totalDistance / n )
def calculateFiducialDistance(self, modelNode, fiducial):
closestFiducial = slicer.util.getNode('CP')
if not closestFiducial:
closestFiducial = slicer.vtkMRMLMarkupsFiducialNode()
closestFiducial.SetName('CP')
closestFiducial.AddFiducial(0, 0, 0)
closestFiducial.SetNthFiducialLabel(0, 'CP')
slicer.mrmlScene.AddNode(closestFiducial)
closestFiducial.SetDisplayVisibility(False)
line = slicer.util.getNode('Line')
if not line:
line = slicer.vtkMRMLModelNode()
line.SetName('Line')
linePolyData = vtk.vtkPolyData()
line.SetAndObservePolyData(linePolyData)
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetSliceIntersectionVisibility(True)
modelDisplay.SetColor(0,1,0)
slicer.mrmlScene.AddNode(modelDisplay)
line.SetAndObserveDisplayNodeID(modelDisplay.GetID())
slicer.mrmlScene.AddNode(line)
cellLocator = vtk.vtkCellLocator()
cellLocator.SetDataSet(modelNode.GetPolyData())
cellLocator.BuildLocator()
if fiducial.GetNumberOfFiducials() > 0:
ras = [0.0, 0.0, 0.0]
closestPoint = [0.0, 0.0, 0.0]
fiducial.GetNthFiducialPosition(0, ras)
distanceSquared = vtk.mutable(0.0)
subId = vtk.mutable(0)
cellId = vtk.mutable(0)
cell = vtk.vtkGenericCell()
cellLocator.FindClosestPoint(ras, closestPoint, cell, cellId, subId, distanceSquared);
distance = math.sqrt(distanceSquared)
closestFiducial.SetNthFiducialPosition(0, closestPoint[0], closestPoint[1], closestPoint[2])
closestFiducial.SetDisplayVisibility(True)
self.drawLineBetweenPoints(line, ras, closestPoint)
self.set3dViewConernerAnnotation('Distance = ' + "%.2f" % distance + 'mm')
else:
logging.warning('No fiducials in list!')
def updateScalarBarRange(self, sliceLogic, volumeNode, scalarBar, selectedLayer):
vdn = volumeNode.GetDisplayNode()
if vdn:
vcn = vdn.GetColorNode()
lut = vcn.GetLookupTable()
lut2 = vtk.vtkLookupTable()
lut2.DeepCopy(lut)
width = vtk.mutable(0)
level = vtk.mutable(0)
rangeLow = vtk.mutable(0)
rangeHigh = vtk.mutable(0)
if selectedLayer == 'background':
sliceLogic.GetBackgroundWindowLevelAndRange(width,level,rangeLow,rangeHigh)
else:
sliceLogic.GetForegroundWindowLevelAndRange(width,level,rangeLow,rangeHigh)
lut2.SetRange(level-width/2,level+width/2)
scalarBar.SetLookupTable(lut2)
def updateScalarBarRange(self, sliceLogic, volumeNode, scalarBar, selectedLayer):
vdn = volumeNode.GetDisplayNode()
if vdn:
vcn = vdn.GetColorNode()
lut = vcn.GetLookupTable()
lut2 = vtk.vtkLookupTable()
lut2.DeepCopy(lut)
width = vtk.mutable(0)
level = vtk.mutable(0)
rangeLow = vtk.mutable(0)
rangeHigh = vtk.mutable(0)
if selectedLayer == 'background':
sliceLogic.GetBackgroundWindowLevelAndRange(width,level,rangeLow,rangeHigh)
else:
sliceLogic.GetForegroundWindowLevelAndRange(width,level,rangeLow,rangeHigh)
lut2.SetRange(int(level-width/2),int(level+width/2))
scalarBar.SetLookupTable(lut2)
'''
def calculateDistance(self):
point = [0.0,0.0,0.0]
closestPoint = [0.0, 0.0, 0.0]
m = vtk.vtkMatrix4x4()
self.toolTipToTool.GetMatrixTransformToWorld(m)
point[0] = m.GetElement(0, 3)
point[1] = m.GetElement(1, 3)
point[2] = m.GetElement(2, 3)
distanceSquared = vtk.mutable(0.0)
subId = vtk.mutable(0)
cellId = vtk.mutable(0)
cell = vtk.vtkGenericCell()
self.cellLocator.FindClosestPoint(point, closestPoint, cell, cellId, subId, distanceSquared);
distance = math.sqrt(distanceSquared)
self.closestFiducial.SetNthFiducialPosition(0, closestPoint[0], closestPoint[1], closestPoint[2])
self.closestFiducial.SetDisplayVisibility(True)
self.drawLineBetweenPoints(point, closestPoint)
self.tipFiducial.SetNthFiducialLabel(0, ' %.0f' % distance + 'mm')
def calcApproachScore(self, point, skinPolyData, obstacleBspTree, skinModelNode=None):
pTarget = point
polyData = skinPolyData
nPoints = polyData.GetNumberOfPoints()
nCells = polyData.GetNumberOfCells()
pSurface=[0.0, 0.0, 0.0]
minDistancePoint = [0.0, 0.0, 0.0]
tolerance = 0.001
t = vtk.mutable(0.0)
x = [0.0, 0.0, 0.0]
pcoords = [0.0, 0.0, 0.0]
subId = vtk.mutable(0)
#print ("nPoints = %d" % (nPoints))
#print ("nCells = %d" % (nCells))
# Map surface model
if skinModelNode != None:
pointValue = vtk.vtkDoubleArray()
pointValue.SetName("Colors")
pointValue.SetNumberOfComponents(1)
pointValue.SetNumberOfTuples(nPoints)
pointValue.Reset()
pointValue.FillComponent(0,0.0);
bspTree = obstacleBspTree
cp0=[0.0, 0.0, 0.0]
cp1=[0.0, 0.0, 0.0]
cp2=[0.0, 0.0, 0.0]
accessibleArea = 0.0
inaccessibleArea = 0.0
ids=vtk.vtkIdList()
minDistance = -1;
for index in range(nCells):
cell = polyData.GetCell(index)
if cell.GetCellType() == vtk.VTK_TRIANGLE:
area = cell.ComputeArea()
polyData.GetCellPoints(index, ids)
polyData.GetPoint(ids.GetId(0), cp0)
polyData.GetPoint(ids.GetId(1), cp1)
polyData.GetPoint(ids.GetId(2), cp2)
vtk.vtkTriangle.TriangleCenter(cp0, cp1, cp2, pSurface)
iD = bspTree.IntersectWithLine(pSurface, pTarget, tolerance, t, x, pcoords, subId)
if iD < 1:
if skinModelNode != None:
d = vtk.vtkMath.Distance2BetweenPoints(pSurface, pTarget)
d = math.sqrt(d)
if d < minDistance or minDistance < 0:
minDistance = d
minDistancePoint = [pSurface[0],pSurface[1],pSurface[2]]
v = d+101
pointValue.InsertValue(ids.GetId(0), v)
pointValue.InsertValue(ids.GetId(1), v)
pointValue.InsertValue(ids.GetId(2), v)
accessibleArea = accessibleArea + area
else:
if skinModelNode != None:
v = -1.0
pointValue.InsertValue(ids.GetId(0), v)
pointValue.InsertValue(ids.GetId(1), v)
pointValue.InsertValue(ids.GetId(2), v)
inaccessibleArea = inaccessibleArea + area
else:
print ("ERROR: Non-triangular cell.")
score = accessibleArea / (accessibleArea + inaccessibleArea)
if skinModelNode != None:
skinModelNode.AddPointScalars(pointValue)
skinModelNode.SetActivePointScalars("Colors", vtk.vtkDataSetAttributes.SCALARS)
skinModelNode.Modified()
displayNode = skinModelNode.GetModelDisplayNode()
displayNode.SetActiveScalarName("Colors")
displayNode.SetScalarRange(0.0,200.0)
return (score, minDistance, minDistancePoint)
def calcApproachScore(self,
point,
skinPolyData,
obstacleBspTree,
skinModelNode=None):
pTarget = point
polyData = skinPolyData
nPoints = polyData.GetNumberOfPoints()
nCells = polyData.GetNumberOfCells()
pSurface = [0.0, 0.0, 0.0]
minDistancePoint = [0.0, 0.0, 0.0]
tolerance = 0.001
t = vtk.mutable(0.0)
x = [0.0, 0.0, 0.0]
pcoords = [0.0, 0.0, 0.0]
subId = vtk.mutable(0)
#print ("nPoints = %d" % (nPoints))
#print ("nCells = %d" % (nCells))
# Map surface model
if skinModelNode != None:
pointValue = vtk.vtkDoubleArray()
pointValue.SetName("Colors")
pointValue.SetNumberOfComponents(1)
pointValue.SetNumberOfTuples(nPoints)
pointValue.Reset()
pointValue.FillComponent(0, 0.0)
bspTree = obstacleBspTree
cp0 = [0.0, 0.0, 0.0]
cp1 = [0.0, 0.0, 0.0]
cp2 = [0.0, 0.0, 0.0]
accessibleArea = 0.0
inaccessibleArea = 0.0
ids = vtk.vtkIdList()
minDistance = -1
for index in range(nCells):
cell = polyData.GetCell(index)
if cell.GetCellType() == vtk.VTK_TRIANGLE:
area = cell.ComputeArea()
polyData.GetCellPoints(index, ids)
polyData.GetPoint(ids.GetId(0), cp0)
polyData.GetPoint(ids.GetId(1), cp1)
polyData.GetPoint(ids.GetId(2), cp2)
vtk.vtkTriangle.TriangleCenter(cp0, cp1, cp2, pSurface)
iD = bspTree.IntersectWithLine(pSurface, pTarget, tolerance, t,
x, pcoords, subId)
if iD < 1:
if skinModelNode != None:
d = vtk.vtkMath.Distance2BetweenPoints(
pSurface, pTarget)
d = math.sqrt(d)
if d < minDistance or minDistance < 0:
minDistance = d
minDistancePoint = [
pSurface[0], pSurface[1], pSurface[2]
]
v = d + 101
pointValue.InsertValue(ids.GetId(0), v)
pointValue.InsertValue(ids.GetId(1), v)
pointValue.InsertValue(ids.GetId(2), v)
accessibleArea = accessibleArea + area
else:
if skinModelNode != None:
v = -1.0
pointValue.InsertValue(ids.GetId(0), v)
pointValue.InsertValue(ids.GetId(1), v)
pointValue.InsertValue(ids.GetId(2), v)
inaccessibleArea = inaccessibleArea + area
else:
print("ERROR: Non-triangular cell.")
score = accessibleArea / (accessibleArea + inaccessibleArea)
if skinModelNode != None:
skinModelNode.AddPointScalars(pointValue)
skinModelNode.SetActivePointScalars(
"Colors", vtk.vtkDataSetAttributes.SCALARS)
skinModelNode.Modified()
displayNode = skinModelNode.GetModelDisplayNode()
displayNode.SetActiveScalarName("Colors")
displayNode.SetScalarRange(0.0, 200.0)
return (score, minDistance, minDistancePoint)
def calcApproachScore(self,
targetPointNode,
skinPolyData,
obstacleBspTree,
skinModelNode=None):
#pTargetA = targetPointNode.GetMarkupPointVector(0, 0)
tListNumber = targetPointNode.GetNumberOfFiducials()
#pTargetA = pointA
#pTargetB = pointB
#pTargetC = pointC
polyData = skinPolyData
nPoints = polyData.GetNumberOfPoints()
nCells = polyData.GetNumberOfCells()
pSurface = [0.0, 0.0, 0.0]
minDistancePoint = [0.0, 0.0, 0.0]
tolerance = 0.001
t = vtk.mutable(0.0)
x = [0.0, 0.0, 0.0]
pcoords = [0.0, 0.0, 0.0]
subId = vtk.mutable(0)
#print ("nPoints = %d" % (nPoints))
#print ("nCells = %d" % (nCells))
# Map surface model
if skinModelNode != None:
pointValue = vtk.vtkDoubleArray()
pointValue.SetName("Colors")
pointValue.SetNumberOfComponents(1)
pointValue.SetNumberOfTuples(nPoints)
pointValue.Reset()
pointValue.FillComponent(0, 0.0)
bspTree = obstacleBspTree
cp0 = [0.0, 0.0, 0.0]
cp1 = [0.0, 0.0, 0.0]
cp2 = [0.0, 0.0, 0.0]
accessibleArea = 0.0
inaccessibleArea = 0.0
ids = vtk.vtkIdList()
minDistance = -1
#iDA = 0
#iDAFlag = 0
#d = 0
for index in range(nCells):
iDA = 0
iDAFlag = 0
d = 0
i = 0
j = 0
cell = polyData.GetCell(index)
if cell.GetCellType() == vtk.VTK_TRIANGLE:
area = cell.ComputeArea()
polyData.GetCellPoints(index, ids)
polyData.GetPoint(ids.GetId(0), cp0)
polyData.GetPoint(ids.GetId(1), cp1)
polyData.GetPoint(ids.GetId(2), cp2)
vtk.vtkTriangle.TriangleCenter(cp0, cp1, cp2, pSurface)
#####
for i in range(0, tListNumber, 1):
pTargetA = targetPointNode.GetMarkupPointVector(i, 0)
iDA = bspTree.IntersectWithLine(pSurface, pTargetA,
tolerance, t, x, pcoords,
subId)
if iDA >= 1:
iDAFlag = 10
#####
if iDAFlag < 1:
if skinModelNode != None:
for j in range(0, tListNumber, 1):
pTargetA = targetPointNode.GetMarkupPointVector(
j, 0)
d += (vtk.vtkMath.Distance2BetweenPoints(
pSurface, pTargetA))
d = d / tListNumber
d = math.sqrt(d)
if 100 < d < 240:
if d < minDistance or minDistance < 0:
minDistance = d
minDistancePoint = [
pSurface[0], pSurface[1], pSurface[2]
]
v = d + 51
pointValue.InsertValue(ids.GetId(0), v)
pointValue.InsertValue(ids.GetId(1), v)
pointValue.InsertValue(ids.GetId(2), v)
accessibleArea = accessibleArea + area
else:
v = -1.0
pointValue.InsertValue(ids.GetId(0), v)
pointValue.InsertValue(ids.GetId(1), v)
pointValue.InsertValue(ids.GetId(2), v)
inaccessibleArea = inaccessibleArea + area
else:
if skinModelNode != None:
v = -1.0
pointValue.InsertValue(ids.GetId(0), v)
pointValue.InsertValue(ids.GetId(1), v)
pointValue.InsertValue(ids.GetId(2), v)
inaccessibleArea = inaccessibleArea + area
else:
print("ERROR: Non-triangular cell.")
score = accessibleArea
if skinModelNode != None:
skinModelNode.AddPointScalars(pointValue)
skinModelNode.SetActivePointScalars(
"Colors", vtk.vtkDataSetAttributes.SCALARS)
skinModelNode.Modified()
displayNode = skinModelNode.GetModelDisplayNode()
displayNode.SetActiveScalarName("Colors")
displayNode.SetScalarRange(0.0, 200.0)
return (score, minDistance, minDistancePoint)