def createGlyph(self):
self.polyData = vtk.vtkPolyData()
points = vtk.vtkPoints()
lines = vtk.vtkCellArray()
self.polyData.SetPoints( points )
self.polyData.SetLines( lines )
prevPoint = None
firstPoint = None
for x,y in ((0,0),)*4:
p = points.InsertNextPoint( x, y, 0 )
if prevPoint != None:
idList = vtk.vtkIdList()
idList.InsertNextId( prevPoint )
idList.InsertNextId( p )
self.polyData.InsertNextCell( vtk.VTK_LINE, idList )
prevPoint = p
if firstPoint == None:
firstPoint = p
# make the last line in the polydata
idList = vtk.vtkIdList()
idList.InsertNextId( p )
idList.InsertNextId( firstPoint )
self.polyData.InsertNextCell( vtk.VTK_LINE, idList )
def createGlyph(self):
self.polyData = vtk.vtkPolyData()
points = vtk.vtkPoints()
lines = vtk.vtkCellArray()
self.polyData.SetPoints( points )
self.polyData.SetLines( lines )
prevPoint = None
firstPoint = None
for x,y in ((0,0),)*4:
p = points.InsertNextPoint( x, y, 0 )
if prevPoint != None:
idList = vtk.vtkIdList()
idList.InsertNextId( prevPoint )
idList.InsertNextId( p )
self.polyData.InsertNextCell( vtk.VTK_LINE, idList )
prevPoint = p
if firstPoint == None:
firstPoint = p
# make the last line in the polydata
idList = vtk.vtkIdList()
idList.InsertNextId( p )
idList.InsertNextId( firstPoint )
self.polyData.InsertNextCell( vtk.VTK_LINE, idList )
def createGlyph(self, polyData):
"""
create a brush circle of the right radius in XY space
- assume uniform scaling between XY and RAS which
is enforced by the view interactors
"""
sliceNode = self.sliceWidget.sliceLogic().GetSliceNode()
self.rasToXY.DeepCopy(sliceNode.GetXYToRAS())
self.rasToXY.Invert()
maximum, maxIndex = 0,0
for index in range(3):
if abs(self.rasToXY.GetElement(0, index)) > maximum:
maximum = abs(self.rasToXY.GetElement(0, index))
maxIndex = index
point = [0, 0, 0, 0]
point[maxIndex] = self.radius
xyRadius = self.rasToXY.MultiplyPoint(point)
import math
xyRadius = math.sqrt( xyRadius[0]**2 + xyRadius[1]**2 + xyRadius[2]**2 )
if self.pixelMode:
xyRadius = 0.01
# make a circle paint brush
points = vtk.vtkPoints()
lines = vtk.vtkCellArray()
polyData.SetPoints(points)
polyData.SetLines(lines)
PI = 3.1415926
TWOPI = PI * 2
PIoverSIXTEEN = PI / 16
prevPoint = -1
firstPoint = -1
angle = 0
while angle <= TWOPI:
x = xyRadius * math.cos(angle)
y = xyRadius * math.sin(angle)
p = points.InsertNextPoint( x, y, 0 )
if prevPoint != -1:
idList = vtk.vtkIdList()
idList.InsertNextId(prevPoint)
idList.InsertNextId(p)
polyData.InsertNextCell( vtk.VTK_LINE, idList )
prevPoint = p
if firstPoint == -1:
firstPoint = p
angle = angle + PIoverSIXTEEN
# make the last line in the circle
idList = vtk.vtkIdList()
idList.InsertNextId(p)
idList.InsertNextId(firstPoint)
polyData.InsertNextCell( vtk.VTK_LINE, idList )
def createGlyph(self, polyData):
"""
create a brush circle of the right radius in XY space
- assume uniform scaling between XY and RAS which
is enforced by the view interactors
"""
sliceNode = self.sliceWidget.sliceLogic().GetSliceNode()
self.rasToXY.DeepCopy(sliceNode.GetXYToRAS())
self.rasToXY.Invert()
maximum, maxIndex = 0, 0
for index in range(3):
if abs(self.rasToXY.GetElement(0, index)) > maximum:
maximum = abs(self.rasToXY.GetElement(0, index))
maxIndex = index
point = [0, 0, 0, 0]
point[maxIndex] = self.radius
xyRadius = self.rasToXY.MultiplyPoint(point)
import math
xyRadius = math.sqrt(xyRadius[0]**2 + xyRadius[1]**2 + xyRadius[2]**2)
if self.pixelMode:
xyRadius = 0.01
# make a circle paint brush
points = vtk.vtkPoints()
lines = vtk.vtkCellArray()
polyData.SetPoints(points)
polyData.SetLines(lines)
PI = 3.1415926
TWOPI = PI * 2
PIoverSIXTEEN = PI / 16
prevPoint = -1
firstPoint = -1
angle = 0
while angle <= TWOPI:
x = xyRadius * math.cos(angle)
y = xyRadius * math.sin(angle)
p = points.InsertNextPoint(x, y, 0)
if prevPoint != -1:
idList = vtk.vtkIdList()
idList.InsertNextId(prevPoint)
idList.InsertNextId(p)
polyData.InsertNextCell(vtk.VTK_LINE, idList)
prevPoint = p
if firstPoint == -1:
firstPoint = p
angle = angle + PIoverSIXTEEN
# make the last line in the circle
idList = vtk.vtkIdList()
idList.InsertNextId(p)
idList.InsertNextId(firstPoint)
polyData.InsertNextCell(vtk.VTK_LINE, idList)
def calculateLineLength(self, poly):
lines = poly.GetLines()
points = poly.GetPoints()
pts = vtk.vtkIdList()
lines.GetCell(0, pts)
ip = numpy.array(points.GetPoint(pts.GetId(0)))
n = pts.GetNumberOfIds()
# Check if there is overlap between the first and last segments
# (for making sure to close the loop for spline curves)
if n > 2:
slp = numpy.array(points.GetPoint(pts.GetId(n - 2)))
# Check distance between the first point and the second last point
if numpy.linalg.norm(slp - ip) < 0.00001:
n = n - 1
length = 0.0
pp = ip
for i in range(1, n):
p = numpy.array(points.GetPoint(pts.GetId(i)))
length = length + numpy.linalg.norm(pp - p)
pp = p
return length
def getCurveLength(self, numberOfCurvePoints=-1, startPointIndex=0):
"""Get length of the curve or a section of the curve
:param n: if specified then distances up to the first n points are computed
:return: sum of distances between the curve points
"""
pointIds = vtk.vtkIdList()
self.curvePoly.GetLines().GetCell(0, pointIds)
points = self.curvePoly.GetPoints()
# Check if there is overlap between the first and last segments
# if there is, then ignore the last segment (only needed for smooth spline
# interpolation)
totalNumberOfCurvePoints = pointIds.GetNumberOfIds()
if totalNumberOfCurvePoints > 2:
firstPoint = np.array(points.GetPoint(pointIds.GetId(0)))
lastPoint = np.array(
points.GetPoint(pointIds.GetId(totalNumberOfCurvePoints - 2)))
# Check distance between the first point and the second last point
if np.linalg.norm(lastPoint - firstPoint) < 0.00001:
totalNumberOfCurvePoints -= 1
if numberOfCurvePoints < 0 or startPointIndex + numberOfCurvePoints > totalNumberOfCurvePoints:
numberOfCurvePoints = totalNumberOfCurvePoints - startPointIndex
length = 0.0
previousPoint = np.array(
points.GetPoint(pointIds.GetId(startPointIndex)))
for i in range(startPointIndex + 1,
startPointIndex + numberOfCurvePoints):
nextPoint = np.array(points.GetPoint(pointIds.GetId(i)))
length += np.linalg.norm(previousPoint - nextPoint)
previousPoint = nextPoint
return length
def convertFiducialHierarchyToVtkIdList(hierarchyNode,volumeNode):
'''
'''
outputIds = vtk.vtkIdList()
if not hierarchyNode or not volumeNode:
return outputIds
if isinstance(hierarchyNode,slicer.vtkMRMLAnnotationHierarchyNode) and isinstance(volumeNode,slicer.vtkMRMLScalarVolumeNode):
childrenNodes = vtk.vtkCollection()
image = volumeNode.GetImageData()
hierarchyNode.GetChildrenDisplayableNodes(childrenNodes)
# now we have the children which are fiducialNodes - let's loop!
for n in range(childrenNodes.GetNumberOfItems()):
currentFiducial = childrenNodes.GetItemAsObject(n)
currentCoordinatesRAS = [0,0,0]
# grab the current coordinates
currentFiducial.GetFiducialCoordinates(currentCoordinatesRAS)
# convert the RAS to IJK
currentCoordinatesIJK = Helper.ConvertRAStoIJK(volumeNode,currentCoordinatesRAS)
# strip the last element since we need a 3based tupel
currentCoordinatesIJKlist = (int(currentCoordinatesIJK[0]),int(currentCoordinatesIJK[1]),int(currentCoordinatesIJK[2]))
outputIds.InsertNextId(int(image.ComputePointId(currentCoordinatesIJKlist)))
# IdList was created, return it even if it might be empty
return outputIds
def testDefineNeighborsFunction(self):
sphereModel = self.defineSphere()
polyData = sphereModel.GetPolyData()
closestPointIndexList = [9, 35, 1]
connectedVerticesReferenceList = list()
connectedVerticesReferenceList.append([9, 2, 3, 8, 10, 15, 16])
connectedVerticesReferenceList.append(
[35, 28, 29, 34, 36, 41, 42, 21, 22, 27, 23, 30, 33, 40, 37, 43, 47, 48, 49])
connectedVerticesReferenceList.append(
[1, 7, 13, 19, 25, 31, 37, 43, 49, 6, 48, 12, 18, 24, 30, 36, 42, 5, 47, 41, 11, 17, 23, 29, 35])
connectedVerticesTestedList = list()
for i in range(0, 3):
inter = vtk.vtkIdList()
self.ShapeQuantifierCore.defineNeighbor(inter,
polyData,
closestPointIndexList[i],
i + 1)
connectedVerticesTestedList.append(inter)
list1 = list()
for j in range(0, connectedVerticesTestedList[i].GetNumberOfIds()):
list1.append(int(connectedVerticesTestedList[i].GetId(j)))
connectedVerticesTestedList[i] = list1
if connectedVerticesTestedList[i] != connectedVerticesReferenceList[i]:
print "test ",i ," AddArrayFromIdList: failed"
return False
else:
print "test ",i ," AddArrayFromIdList: succeed"
return True
def addPointToPolyData(self, polyData, ras): pid = vtk.vtkIdList() pid.SetNumberOfIds(1); temp = polyData.GetPoints().InsertNextPoint(ras[0], ras[1], ras[2]) pid.SetId(0, temp) polyData.GetVerts().InsertNextCell(pid) polyData.Modified()
def onCalculateLength(self): self.inputPolyData = self.vtkNode.GetPolyData() points = self.inputPolyData.GetPoints() lines = self.inputPolyData.GetLines() lines.InitTraversal() i = 0 for i in range(self.inputPolyData.GetNumberOfCells()): fiberLength = 0 ids = vtk.vtkIdList() lines.GetNextCell(ids) for j in range(ids.GetNumberOfIds()-1): point1 = [0,0,0] point2 = [0,0,0] points.GetPoint(ids.GetId(j), point1) points.GetPoint(ids.GetId(j+1), point2) x = point2[0] - point1[0] y = point2[1] - point1[1] z = point2[2] - point1[2] step = (x*x + y*y + z*z)**.5 fiberLength += step self.distanceTable.append(fiberLength) i += 1 min,max=self.getDistanceBound() self.thresholdMin.setValue(min) self.thresholdMin.enabled = True self.thresholdMax.setValue(max+1) self.thresholdMax.enabled = True self.applyThresholdButton.enabled = True
def convertFiducialHierarchyToVtkIdList(hierarchyNode,volumeNode):
'''
'''
outputIds = vtk.vtkIdList()
if not hierarchyNode or not volumeNode:
return outputIds
if isinstance(hierarchyNode,slicer.vtkMRMLMarkupsFiducialNode) and isinstance(volumeNode,slicer.vtkMRMLScalarVolumeNode):
image = volumeNode.GetImageData()
# now we have the children which are fiducialNodes - let's loop!
for n in range(hierarchyNode.GetNumberOfFiducials()):
currentCoordinatesRAS = [0,0,0]
# grab the current coordinates
hierarchyNode.GetNthFiducialPosition(n,currentCoordinatesRAS)
# convert the RAS to IJK
currentCoordinatesIJK = Helper.ConvertRAStoIJK(volumeNode,currentCoordinatesRAS)
# strip the last element since we need a 3based tupel
currentCoordinatesIJKlist = (int(currentCoordinatesIJK[0]),int(currentCoordinatesIJK[1]),int(currentCoordinatesIJK[2]))
outputIds.InsertNextId(int(image.ComputePointId(currentCoordinatesIJKlist)))
# IdList was created, return it even if it might be empty
return outputIds
def calculateLineLength(self, poly):
lines = poly.GetLines()
points = poly.GetPoints()
pts = vtk.vtkIdList()
lines.GetCell(0, pts)
ip = numpy.array(points.GetPoint(pts.GetId(0)))
n = pts.GetNumberOfIds()
# Check if there is overlap between the first and last segments
# (for making sure to close the loop for spline curves)
if n > 2:
slp = numpy.array(points.GetPoint(pts.GetId(n-2)))
# Check distance between the first point and the second last point
if numpy.linalg.norm(slp-ip) < 0.00001:
n = n - 1
length = 0.0
pp = ip
for i in range(1,n):
p = numpy.array(points.GetPoint(pts.GetId(i)))
length = length + numpy.linalg.norm(pp-p)
pp = p
return length
def testAddArrayFromIdListFunction(self):
sphereModel = self.defineSphere()
polyData = sphereModel.GetPolyData()
closestPointIndexList = [9, 35, 1]
for i in range(0, 3):
inter = vtk.vtkIdList()
self.ShapeQuantifierCore.defineNeighbor(inter, polyData, closestPointIndexList[i], i + 1)
self.ShapeQuantifierCore.addArrayFromIdList(inter,
sphereModel,
'Test_' + str(i + 1))
if polyData.GetPointData().HasArray('Test_' + str(i + 1)) != 1:
print "test ",i ," AddArrayFromIdList: failed"
return False
else:
print "test ",i ," AddArrayFromIdList: succeed"
return True
def addPointToPolyData(self, polyData, ras):
pid = vtk.vtkIdList()
pid.SetNumberOfIds(1);
temp = polyData.GetPoints().InsertNextPoint(ras[0], ras[1], ras[2])
pid.SetId(0, temp)
polyData.GetVerts().InsertNextCell(pid)
if self.direction > -1:
color = [0, 0, 0, 0]
tableValue = 1 + (ras[self.direction] - self.min) * self.normalizingConstant
if tableValue > 255:
tableValue = 255
elif tableValue < 0:
tableValue = 0
self.colorTable.GetColor(int(tableValue), color) # 0 -> 255
self.recordedModelNode.GetPolyData().GetPointData().GetScalars('Colors').InsertTuple(self.recordedModelNode.GetPolyData().GetPoints().GetNumberOfPoints() - 1, color)
if self.addColours:
self.showColouring()
self.addColours = False
polyData.Modified()
def PointsToPolyData(self, listOfPoints):
""" Converts 3D list of points of an array into a polyData line
The connections between this line are simply the order in which
they are provided
"""
points = vtk.vtkPoints()
idlist = vtk.vtkIdList()
numOfPoints = len(listOfPoints)
if numOfPoints == 0:
print("WARNING:No points to convert to polyData")
return vtk.vtkPolyData() #returning Blank PolyData
points.SetNumberOfPoints(numOfPoints)
for i in range(numOfPoints):
points.InsertPoint(i, listOfPoints[i]) #Add the points
idlist.InsertNextId(i)
polyData = vtk.vtkPolyData()
polyData.Allocate()
polyData.InsertNextCell(vtk.VTK_LINE, idlist)
polyData.SetPoints(points)
return polyData
def PointsToPolyData(self,listOfPoints):
""" Converts 3D list of points of an array into a polyData line
The connections between this line are simply the order in which
they are provided
"""
points=vtk.vtkPoints()
idlist = vtk.vtkIdList()
numOfPoints=len(listOfPoints)
if numOfPoints==0:
print ("WARNING:No points to convert to polyData")
return vtk.vtkPolyData() #returning Blank PolyData
points.SetNumberOfPoints(numOfPoints)
for i in range (numOfPoints):
points.InsertPoint(i, listOfPoints[i]) #Add the points
idlist.InsertNextId(i)
polyData=vtk.vtkPolyData()
polyData.Allocate()
polyData.InsertNextCell(vtk.VTK_LINE,idlist)
polyData.SetPoints(points)
return polyData
def addPointToPolyData(self, polyData, ras):
print "nuevo punto!!!"
self.pointCounter = self.pointCounter + 1;
pid = vtk.vtkIdList()
pid.SetNumberOfIds(1);
temp = polyData.GetPoints().InsertNextPoint(ras[0], ras[1], ras[2])
pid.SetId(0, temp)
polyData.GetVerts().InsertNextCell(pid)
polyData.Modified()
# check every 30 recorded points if the standard deviation is low
if (self.pointCounter%30) == 0:
sd = self.testStandardDeviation(polyData)
if sd < 1:
self.record = False
if self.pointCounter>100:
self.calculateSurface(self.recordedModelNode)
print "El standard deviation es bajo ya no se mueve"
def copyNodeContentToNewScriptedModuleNode(oldDataNode, shNode):
newDataNode = slicer.vtkMRMLScriptedModuleNode()
newDataNode.HideFromEditorsOff()
# Copy node attributes
attributeNames = vtk.vtkStringArray()
oldDataNode.GetAttributeNames(attributeNames)
for index in range(attributeNames.GetNumberOfValues()):
attributeName = attributeNames.GetValue(index)
newDataNode.SetAttribute(attributeName,
oldDataNode.GetAttribute(attributeName))
slicer.mrmlScene.AddNode(newDataNode)
newDataNode.SetName(oldDataNode.GetName())
# Copy node references
newDataNode.CopyReferences(oldDataNode)
# Move children
childItemIDs = vtk.vtkIdList()
#shNode = slicer.vtkMRMLSubjectHierarchyNode.GetSubjectHierarchyNode(slicer.mrmlScene)
shNode.GetItemChildren(shNode.GetItemByDataNode(oldDataNode), childItemIDs)
for index in range(childItemIDs.GetNumberOfIds()):
childItemID = childItemIDs.GetId(index)
shNode.ReparentItemByDataNode(childItemID, newDataNode)
return newDataNode
def convertFiducialHierarchyToVtkIdList(hierarchyNode, volumeNode):
'''
'''
outputIds = vtk.vtkIdList()
if not hierarchyNode or not volumeNode:
return outputIds
if isinstance(hierarchyNode,
slicer.vtkMRMLAnnotationHierarchyNode) and isinstance(
volumeNode, slicer.vtkMRMLScalarVolumeNode):
childrenNodes = vtk.vtkCollection()
image = volumeNode.GetImageData()
hierarchyNode.GetChildrenDisplayableNodes(childrenNodes)
# now we have the children which are fiducialNodes - let's loop!
for n in range(childrenNodes.GetNumberOfItems()):
currentFiducial = childrenNodes.GetItemAsObject(n)
currentCoordinatesRAS = [0, 0, 0]
# grab the current coordinates
currentFiducial.GetFiducialCoordinates(currentCoordinatesRAS)
# convert the RAS to IJK
currentCoordinatesIJK = Helper.ConvertRAStoIJK(
volumeNode, currentCoordinatesRAS)
# strip the last element since we need a 3based tupel
currentCoordinatesIJKlist = (int(currentCoordinatesIJK[0]),
int(currentCoordinatesIJK[1]),
int(currentCoordinatesIJK[2]))
outputIds.InsertNextId(
int(image.ComputePointId(currentCoordinatesIJKlist)))
# IdList was created, return it even if it might be empty
return outputIds
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 distanceToPoint(self, point, extrapolate):
# distanceToPoint() calculates the approximate minimum distance between
# the specified point and the closest segment of the curve.
# It calculates the minimum distance between the point and each segment
# of the curve (approxmated as a straight line) and select the segment with
# the minimum distance from the point as a closest segment.
npoint = numpy.array(point)
if self.CurvePoly == None:
return numpy.Inf
lines = self.CurvePoly.GetLines()
points = self.CurvePoly.GetPoints()
pts = vtk.vtkIdList()
lines.GetCell(0, pts)
ip = numpy.array(points.GetPoint(pts.GetId(0)))
n = pts.GetNumberOfIds()
# First point on the segment
p1 = ip
minMag2 = numpy.Inf
minIndex = -1
minErrVec = numpy.array([0.0, 0.0, 0.0])
errVec = numpy.array([0.0, 0.0, 0.0])
for i in range(1, n):
# Second point on the segment
p2 = numpy.array(points.GetPoint(pts.GetId(i)))
# Normal vector along the segment
nvec = p2 - p1
norm = numpy.linalg.norm(nvec)
if norm != 0:
nnvec = nvec / norm
# Calculate the distance between the point and the segment
mag2 = 0.0
op = npoint - p1
aproj = numpy.inner(op, nnvec)
if extrapolate and ((i == 1 and aproj < 0.0) or
(i == n - 1 and aproj > 0.0)):
# extrapolate first or last segment
errVec = op - aproj * nnvec # perpendicular
mag2 = numpy.inner(errVec, errVec) # magnitude^2
else:
if aproj < 0.0:
errVec = npoint - p1
mag2 = numpy.inner(errVec, errVec) # magnitude^2
elif aproj > norm:
errVec = npoint - p2
mag2 = numpy.inner(errVec, errVec) # magnitude^2
else:
errVec = op - aproj * nnvec # perpendicular
mag2 = numpy.inner(errVec, errVec) # magnitude^2
if mag2 < minMag2:
minMag2 = mag2
minIndex = i
minErrVec = errVec
p1 = p2
distance = numpy.sqrt(minMag2)
return (distance, minErrVec)
def computeCurvatures(self, poly, curvatureValues):
# Calculate point-by-point curvature of the curve
# Returns mean/min/max curvature
lines = poly.GetLines()
points = poly.GetPoints()
pts = vtk.vtkIdList()
lines.GetCell(0, pts)
ip = numpy.array(points.GetPoint(pts.GetId(0)))
n = pts.GetNumberOfIds()
## Check if there is overlap between the first and last segments
## (for making sure to close the loop for spline curves)
#if n > 2:
# slp = numpy.array(points.GetPoint(pts.GetId(n-2)))
# # Check distance between the first point and the second last point
# if numpy.linalg.norm(slp-ip) < 0.00001:
# n = n - 1
curvatureValues.Initialize()
curvatureValues.SetName("Curvature")
curvatureValues.SetNumberOfComponents(1)
curvatureValues.SetNumberOfTuples(n)
curvatureValues.Reset()
curvatureValues.FillComponent(0, 0.0)
minKappa = 0.0
maxKappa = 0.0
meanKappa = 0.0 # NOTE: mean is weighted by the lengh of each segment
pp = numpy.array(points.GetPoint(pts.GetId(0)))
p = numpy.array(points.GetPoint(pts.GetId(1)))
ds = numpy.linalg.norm(p - pp)
pT = (p - pp) / ds
pp = p
pm = (p + pp) / 2.0
length = 0.0 + numpy.linalg.norm(pm - pp)
curvatureValues.InsertValue(
pts.GetId(0), 0.0) # The curvature for the first cell is 0.0
for i in range(1, n - 1):
p = numpy.array(points.GetPoint(pts.GetId(i + 1)))
ds = numpy.linalg.norm(p - pp)
T = (p - pp) / ds
kappa = numpy.linalg.norm(T - pT) / ds # Curvature
curvatureValues.InsertValue(
pts.GetId(i), kappa) # The curvature for the first cell is 0.0
m = (p + pp) / 2.0
l = numpy.linalg.norm(m - pm) # length for this segment
if kappa < minKappa:
minKappa = kappa
elif kappa > maxKappa:
maxKappa = kappa
meanKappa = meanKappa + kappa * l # weighted mean
length = length + l
pp = p
pm = m
pT = T
curvatureValues.InsertValue(
pts.GetId(n - 1), 0.0) # The curvature for the last cell is 0.0
length = length + numpy.linalg.norm(pp - pm)
meanKappa = meanKappa / length
# TODO: This routin does not consider a closed loop. If a closed loop is specified,
# It needs to calculate the curveture of two ends differently.
return (meanKappa, minKappa, maxKappa)
def clipSurfaceAtEndPoints( self, networkPolyData, surfacePolyData ):
'''
Clips the surfacePolyData on the endpoints identified using the networkPolyData.
Returns a tupel of the form [clippedPolyData, endpointsPoints]
'''
# import the vmtk libraries
try:
import vtkvmtkComputationalGeometryPython as vtkvmtkComputationalGeometry
import vtkvmtkMiscPython as vtkvmtkMisc
except ImportError:
logging.error("Unable to import the SlicerVmtk libraries")
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInputData( networkPolyData )
cleaner.Update()
network = cleaner.GetOutput()
network.BuildCells()
network.BuildLinks( 0 )
endpointIds = vtk.vtkIdList()
radiusArray = network.GetPointData().GetArray( 'Radius' )
endpoints = vtk.vtkPolyData()
endpointsPoints = vtk.vtkPoints()
endpointsRadius = vtk.vtkDoubleArray()
endpointsRadius.SetName( 'Radius' )
endpoints.SetPoints( endpointsPoints )
endpoints.GetPointData().AddArray( endpointsRadius )
radiusFactor = 1.2
minRadius = 0.01
for i in range( network.GetNumberOfCells() ):
numberOfCellPoints = network.GetCell( i ).GetNumberOfPoints()
pointId0 = network.GetCell( i ).GetPointId( 0 )
pointId1 = network.GetCell( i ).GetPointId( numberOfCellPoints - 1 )
pointCells = vtk.vtkIdList()
network.GetPointCells( pointId0, pointCells )
numberOfEndpoints = endpointIds.GetNumberOfIds()
if pointCells.GetNumberOfIds() == 1:
pointId = endpointIds.InsertUniqueId( pointId0 )
if pointId == numberOfEndpoints:
point = network.GetPoint( pointId0 )
radius = radiusArray.GetValue( pointId0 )
radius = max( radius, minRadius )
endpointsPoints.InsertNextPoint( point )
endpointsRadius.InsertNextValue( radiusFactor * radius )
pointCells = vtk.vtkIdList()
network.GetPointCells( pointId1, pointCells )
numberOfEndpoints = endpointIds.GetNumberOfIds()
if pointCells.GetNumberOfIds() == 1:
pointId = endpointIds.InsertUniqueId( pointId1 )
if pointId == numberOfEndpoints:
point = network.GetPoint( pointId1 )
radius = radiusArray.GetValue( pointId1 )
radius = max( radius, minRadius )
endpointsPoints.InsertNextPoint( point )
endpointsRadius.InsertNextValue( radiusFactor * radius )
polyBall = vtkvmtkComputationalGeometry.vtkvmtkPolyBall()
#polyBall.SetInputData( endpoints )
polyBall.SetInput( endpoints )
polyBall.SetPolyBallRadiusArrayName( 'Radius' )
clipper = vtk.vtkClipPolyData()
clipper.SetInputData( surfacePolyData )
clipper.SetClipFunction( polyBall )
clipper.Update()
connectivityFilter = vtk.vtkPolyDataConnectivityFilter()
connectivityFilter.SetInputData( clipper.GetOutput() )
connectivityFilter.ColorRegionsOff()
connectivityFilter.SetExtractionModeToLargestRegion()
connectivityFilter.Update()
clippedSurface = connectivityFilter.GetOutput()
outPolyData = vtk.vtkPolyData()
outPolyData.DeepCopy( clippedSurface )
return [outPolyData, endpointsPoints]
def start(self, preview=False):
'''
'''
SlicerVmtkCommonLib.Helper.Debug("Starting Level Set Segmentation..")
# first we need the nodes
currentVolumeNode = self.__inputVolumeNodeSelector.currentNode()
currentSeedsNode = self.__seedFiducialsNodeSelector.currentNode()
currentVesselnessNode = self.__vesselnessVolumeNodeSelector.currentNode(
)
currentStoppersNode = self.__stopperFiducialsNodeSelector.currentNode()
currentLabelMapNode = self.__outputVolumeNodeSelector.currentNode()
currentModelNode = self.__outputModelNodeSelector.currentNode()
if not currentVolumeNode:
# we need a input volume node
return 0
if not currentSeedsNode:
# we need a seeds node
return 0
if not currentStoppersNode or currentStoppersNode.GetID(
) == currentSeedsNode.GetID():
# we need a current stopper node
# self.__stopperFiducialsNodeSelector.addNode()
pass
if not currentLabelMapNode or currentLabelMapNode.GetID(
) == currentVolumeNode.GetID():
# we need a current labelMap node
newLabelMapDisplayNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLLabelMapVolumeDisplayNode")
newLabelMapDisplayNode.SetScene(slicer.mrmlScene)
newLabelMapDisplayNode.SetDefaultColorMap()
slicer.mrmlScene.AddNode(newLabelMapDisplayNode)
newLabelMapNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLScalarVolumeNode")
newLabelMapNode.CopyOrientation(currentVolumeNode)
newLabelMapNode.SetScene(slicer.mrmlScene)
newLabelMapNode.SetName(
slicer.mrmlScene.GetUniqueNameByString(
self.__outputVolumeNodeSelector.baseName))
newLabelMapNode.LabelMapOn()
newLabelMapNode.SetAndObserveDisplayNodeID(
newLabelMapDisplayNode.GetID())
slicer.mrmlScene.AddNode(newLabelMapNode)
currentLabelMapNode = newLabelMapNode
self.__outputVolumeNodeSelector.setCurrentNode(currentLabelMapNode)
if not currentModelNode:
# we need a current model node, the display node is created later
newModelNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLModelNode")
newModelNode.SetScene(slicer.mrmlScene)
newModelNode.SetName(
slicer.mrmlScene.GetUniqueNameByString(
self.__outputModelNodeSelector.baseName))
slicer.mrmlScene.AddNode(newModelNode)
currentModelNode = newModelNode
self.__outputModelNodeSelector.setCurrentNode(currentModelNode)
# now we need to convert the fiducials to vtkIdLists
seeds = SlicerVmtkCommonLib.Helper.convertFiducialHierarchyToVtkIdList(
currentSeedsNode, currentVolumeNode)
# stoppers = SlicerVmtkCommonLib.Helper.convertFiducialHierarchyToVtkIdList(currentStoppersNode, currentVolumeNode)
stoppers = vtk.vtkIdList() # TODO
# the input image for the initialization
inputImage = vtk.vtkImageData()
# check if we have a vesselnessNode - this will be our input for the initialization then
if currentVesselnessNode:
# yes, there is one
inputImage.DeepCopy(currentVesselnessNode.GetImageData())
else:
# no, there is none - we use the original image
inputImage.DeepCopy(currentVolumeNode.GetImageData())
inputImage.Update()
# initialization
initImageData = vtk.vtkImageData()
# evolution
evolImageData = vtk.vtkImageData()
# perform the initialization
initImageData.DeepCopy(self.GetLogic().performInitialization(
inputImage, self.__thresholdSlider.minimumValue,
self.__thresholdSlider.maximumValue, seeds, stoppers,
0)) # TODO sidebranch ignore feature
initImageData.Update()
if not initImageData.GetPointData().GetScalars():
# something went wrong, the image is empty
SlicerVmtkCommonLib.Helper.Info(
"Segmentation failed - the output was empty..")
return -1
# check if it is a preview call
if preview:
# if this is a preview call, we want to skip the evolution
evolImageData.DeepCopy(initImageData)
else:
# no preview, run the whole thing! we never use the vesselness node here, just the original one
evolImageData.DeepCopy(self.GetLogic().performEvolution(
currentVolumeNode.GetImageData(), initImageData,
self.__iterationSpinBox.value, self.__inflationSlider.value,
self.__curvatureSlider.value, self.__attractionSlider.value,
'geodesic'))
evolImageData.Update()
# create segmentation labelMap
labelMap = vtk.vtkImageData()
labelMap.DeepCopy(self.GetLogic().buildSimpleLabelMap(
evolImageData, 0, 5))
labelMap.Update()
currentLabelMapNode.CopyOrientation(currentVolumeNode)
# propagate the label map to the node
currentLabelMapNode.SetAndObserveImageData(labelMap)
currentLabelMapNode.Modified()
# deactivate the threshold in the GUI
self.resetThresholdOnDisplayNode()
# self.onInputVolumeChanged()
# show the segmentation results in the GUI
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
if preview and currentVesselnessNode:
# if preview and a vesselnessNode was configured, show it
selectionNode.SetReferenceActiveVolumeID(
currentVesselnessNode.GetID())
else:
# if not preview, show the original volume
if currentVesselnessNode:
selectionNode.SetReferenceSecondaryVolumeID(
currentVesselnessNode.GetID())
selectionNode.SetReferenceActiveVolumeID(currentVolumeNode.GetID())
selectionNode.SetReferenceActiveLabelVolumeID(
currentLabelMapNode.GetID())
slicer.app.applicationLogic().PropagateVolumeSelection()
# generate 3D model
model = vtk.vtkPolyData()
# we need the ijkToRas transform for the marching cubes call
ijkToRasMatrix = vtk.vtkMatrix4x4()
currentLabelMapNode.GetIJKToRASMatrix(ijkToRasMatrix)
# call marching cubes
model.DeepCopy(self.GetLogic().marchingCubes(evolImageData,
ijkToRasMatrix, 0.0))
model.Update()
# propagate model to nodes
currentModelNode.SetAndObservePolyData(model)
currentModelNode.Modified()
currentModelDisplayNode = currentModelNode.GetDisplayNode()
if not currentModelDisplayNode:
# create new displayNode
currentModelDisplayNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLModelDisplayNode")
slicer.mrmlScene.AddNode(currentModelDisplayNode)
# always configure the displayNode to show the model
currentModelDisplayNode.SetInputPolyData(
currentModelNode.GetPolyData())
currentModelDisplayNode.SetColor(1.0, 0.55, 0.4) # red
currentModelDisplayNode.SetBackfaceCulling(0)
currentModelDisplayNode.SetSliceIntersectionVisibility(0)
currentModelDisplayNode.SetVisibility(1)
currentModelDisplayNode.SetOpacity(1.0)
currentModelDisplayNode.Modified()
# update the reference between model node and it's display node
currentModelNode.SetAndObserveDisplayNodeID(
currentModelDisplayNode.GetID())
currentModelNode.Modified()
# fit slice to all sliceviewers
slicer.app.applicationLogic().FitSliceToAll()
# jump all sliceViewers to the first fiducial point, if one was used
if currentSeedsNode:
currentCoordinatesRAS = [0, 0, 0]
if isinstance(currentSeedsNode,
slicer.vtkMRMLAnnotationHierarchyNode):
childrenNodes = vtk.vtkCollection()
currentSeedsNode.GetChildrenDisplayableNodes(childrenNodes)
# now we have the children, let's get the first one
currentFiducial = childrenNodes.GetItemAsObject(0)
# grab the current coordinates
currentFiducial.GetFiducialCoordinates(currentCoordinatesRAS)
elif isinstance(currentSeedsNode,
slicer.vtkMRMLAnnotationFiducialNode):
# grab the current coordinates
currentSeedsNode.GetFiducialCoordinates(currentCoordinatesRAS)
numberOfSliceNodes = slicer.mrmlScene.GetNumberOfNodesByClass(
'vtkMRMLSliceNode')
for n in xrange(numberOfSliceNodes):
sliceNode = slicer.mrmlScene.GetNthNodeByClass(
n, "vtkMRMLSliceNode")
if sliceNode:
sliceNode.JumpSliceByOffsetting(currentCoordinatesRAS[0],
currentCoordinatesRAS[1],
currentCoordinatesRAS[2])
# center 3D view(s) on the new model
if currentCoordinatesRAS:
for d in range(slicer.app.layoutManager().threeDViewCount):
threeDView = slicer.app.layoutManager().threeDWidget(
d).threeDView()
# reset the focal point
threeDView.resetFocalPoint()
# and fly to our seed point
interactor = threeDView.interactor()
renderer = threeDView.renderWindow().GetRenderers(
).GetItemAsObject(0)
interactor.FlyTo(renderer, currentCoordinatesRAS[0],
currentCoordinatesRAS[1],
currentCoordinatesRAS[2])
SlicerVmtkCommonLib.Helper.Debug("End of Level Set Segmentation..")
def onCalculateLength(self):
self.inputPolyData = self.vtkNode.GetPolyData()
points = self.inputPolyData.GetPoints()
lines = self.inputPolyData.GetLines()
lines.InitTraversal()
self.distanceTable = list()
for i in range(self.inputPolyData.GetNumberOfCells()):
fiberLength = 0
ids = vtk.vtkIdList()
lines.GetNextCell(ids)
#print(ids.GetNumberOfIds())
for j in range(ids.GetNumberOfIds() - 1):
point1 = [0, 0, 0]
point2 = [0, 0, 0]
points.GetPoint(ids.GetId(j), point1)
points.GetPoint(ids.GetId(j + 1), point2)
x = point2[0] - point1[0]
y = point2[1] - point1[1]
z = point2[2] - point1[2]
step = (x * x + y * y + z * z)**.5
fiberLength += step
self.distanceTable.append(fiberLength)
min, max = self.getDistanceBound()
self.thresholdMin.setValue(min)
self.thresholdMin.enabled = True
self.thresholdMax.setValue(max + 1)
self.thresholdMax.enabled = True
self.applyThresholdButton.enabled = True
layoutNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
layoutNodes.InitTraversal()
layoutNode = layoutNodes.GetNextItemAsObject()
layoutNode.SetViewArrangement(
slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalQuantitativeView)
chartViewNodes = slicer.mrmlScene.GetNodesByClass(
'vtkMRMLChartViewNode')
chartViewNodes.InitTraversal()
chartViewNode = chartViewNodes.GetNextItemAsObject()
arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
array.SetNumberOfTuples(10)
step = (max - min) / 10
interMin = min
interMax = min + step
for i in range(10):
numberOfFibers = 0
for length in self.distanceTable:
if length <= interMax and length >= interMin and length <= self.thresholdMax.value and length >= self.thresholdMin.value:
numberOfFibers += 1
array.SetComponent(i, 0, (interMin + interMax) / 2)
array.SetComponent(i, 1, numberOfFibers)
array.SetComponent(i, 2, 0)
interMin += step
interMax += step
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
chartNode.AddArray("Fiber Length", arrayNode.GetID())
chartViewNode.SetChartNodeID(chartNode.GetID())
chartNode.SetProperty('default', 'title', 'Length Distribution')
chartNode.SetProperty('default', 'xAxisLabel', 'Length')
chartNode.SetProperty('default', 'yAxisLabel', 'Distribution')
chartNode.SetProperty('default', 'type', 'Bar')
def onCalculateLength(self):
self.inputPolyData = self.vtkNode.GetPolyData()
points = self.inputPolyData.GetPoints()
lines = self.inputPolyData.GetLines()
lines.InitTraversal()
self.distanceTable = list()
for i in range(self.inputPolyData.GetNumberOfCells()):
fiberLength = 0
ids = vtk.vtkIdList()
lines.GetNextCell(ids)
#print(ids.GetNumberOfIds())
for j in range(ids.GetNumberOfIds() - 1):
point1 = [0,0,0]
point2 = [0,0,0]
points.GetPoint(ids.GetId(j), point1)
points.GetPoint(ids.GetId(j+1), point2)
x = point2[0] - point1[0]
y = point2[1] - point1[1]
z = point2[2] - point1[2]
step = (x*x + y*y + z*z)**.5
fiberLength += step
self.distanceTable.append(fiberLength)
min,max=self.getDistanceBound()
self.thresholdMin.setValue(min)
self.thresholdMin.enabled = True
self.thresholdMax.setValue(max+1)
self.thresholdMax.enabled = True
self.applyThresholdButton.enabled = True
layoutNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLLayoutNode')
layoutNodes.InitTraversal()
layoutNode = layoutNodes.GetNextItemAsObject()
layoutNode.SetViewArrangement(slicer.vtkMRMLLayoutNode.SlicerLayoutConventionalQuantitativeView)
chartViewNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
chartViewNodes.InitTraversal()
chartViewNode = chartViewNodes.GetNextItemAsObject()
arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
array.SetNumberOfTuples(10)
step = (max-min)/10
interMin = min
interMax = min+step
for i in range(10):
numberOfFibers = 0
for length in self.distanceTable:
if length<=interMax and length>=interMin and length<=self.thresholdMax.value and length>=self.thresholdMin.value:
numberOfFibers += 1
array.SetComponent(i,0,(interMin+interMax)/2)
array.SetComponent(i,1,numberOfFibers)
array.SetComponent(i,2,0)
interMin += step
interMax += step
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
chartNode.AddArray("Fiber Length",arrayNode.GetID())
chartViewNode.SetChartNodeID(chartNode.GetID())
chartNode.SetProperty('default', 'title', 'Length Distribution')
chartNode.SetProperty('default', 'xAxisLabel', 'Length')
chartNode.SetProperty('default', 'yAxisLabel', 'Distribution')
chartNode.SetProperty('default', 'type', 'Bar')
def onApplyThreshold(self):
min,max = self.getDistanceBound()
newPoints = vtk.vtkPoints()
newLines = vtk.vtkCellArray()
newTensors = vtk.vtkFloatArray()
newTensors.SetNumberOfComponents(9)
newScalars = vtk.vtkFloatArray()
points = self.inputPolyData.GetPoints()
lines = self.inputPolyData.GetLines()
tensors = self.inputPolyData.GetPointData().GetTensors()
lines.InitTraversal()
newId = 0
for length in self.distanceTable:
if length<=self.thresholdMax.value and length>=self.thresholdMin.value:
ids = vtk.vtkIdList()
lines.GetNextCell(ids)
newLine = vtk.vtkPolyLine()
#print(ids.GetNumberOfIds())
newLine.GetPointIds().SetNumberOfIds(ids.GetNumberOfIds())
#print(((length-min)/(max-min))*100)
for i in range(ids.GetNumberOfIds()):
newPoints.InsertNextPoint(points.GetPoint(ids.GetId(i)))
newLine.GetPointIds().SetId(i,newId)
newScalars.InsertNextValue(((length-min)/(max-min)))
newId += 1
tensorValue = [0]*9
if(tensors != None):
for j in range(9):
tensorValue[j] = tensors.GetComponent(ids.GetId(i),j)
newTensors.InsertNextTuple(tensorValue)
newLines.InsertNextCell(newLine)
self.outputPolyData = vtk.vtkPolyData()
self.outputPolyData.SetPoints(newPoints)
self.outputPolyData.SetLines(newLines)
self.outputPolyData.GetPointData().SetTensors(newTensors)
newScalars.SetName("Length")
self.outputPolyData.GetPointData().AddArray(newScalars)
self.outputNode.SetAndObservePolyData(self.outputPolyData)
chartViewNodes = slicer.mrmlScene.GetNodesByClass('vtkMRMLChartViewNode')
chartViewNodes.InitTraversal()
chartViewNode = chartViewNodes.GetNextItemAsObject()
arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
array.SetNumberOfTuples(10)
step = (max-min)/10
interMin = min
interMax = min+step
for i in range(10):
numberOfFibers = 0
for length in self.distanceTable:
if length<=interMax and length>=interMin and length<=self.thresholdMax.value and length>=self.thresholdMin.value:
numberOfFibers += 1
array.SetComponent(i,0,(interMin+interMax)/2)
array.SetComponent(i,1,numberOfFibers)
array.SetComponent(i,2,0)
interMin += step
interMax += step
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
chartNode.AddArray("Fiber Length",arrayNode.GetID())
chartViewNode.SetChartNodeID(chartNode.GetID())
chartNode.SetProperty('default', 'title', 'Length Distribution')
chartNode.SetProperty('default', 'xAxisLabel', 'Length')
chartNode.SetProperty('default', 'yAxisLabel', 'Distribution')
chartNode.SetProperty('default', 'type', 'Bar')
def findNeighbors(self, pointId):
#for i in range(0, self.moulagePolys.GetNumberOfCells()):
neighbors = vtk.vtkIdList()
self.moulagePolys.GetCell(pointId, neighbors)
return neighbors
def computeCurvatures(self, poly, curvatureValues):
# Calculate point-by-point curvature of the curve
# Returns mean/min/max curvature
lines = poly.GetLines()
points = poly.GetPoints()
pts = vtk.vtkIdList()
lines.GetCell(0, pts)
ip = numpy.array(points.GetPoint(pts.GetId(0)))
n = pts.GetNumberOfIds()
## Check if there is overlap between the first and last segments
## (for making sure to close the loop for spline curves)
#if n > 2:
# slp = numpy.array(points.GetPoint(pts.GetId(n-2)))
# # Check distance between the first point and the second last point
# if numpy.linalg.norm(slp-ip) < 0.00001:
# n = n - 1
curvatureValues.Initialize()
curvatureValues.SetName("Curvature")
curvatureValues.SetNumberOfComponents(1)
curvatureValues.SetNumberOfTuples(n)
curvatureValues.Reset()
curvatureValues.FillComponent(0,0.0)
minKappa = 0.0
maxKappa = 0.0
meanKappa = 0.0 # NOTE: mean is weighted by the lengh of each segment
pp = numpy.array(points.GetPoint(pts.GetId(0)))
p = numpy.array(points.GetPoint(pts.GetId(1)))
ds = numpy.linalg.norm(p-pp)
pT = (p-pp) / ds
pp = p
pm = (p+pp)/2.0
length = 0.0 + numpy.linalg.norm(pm-pp)
curvatureValues.InsertValue(pts.GetId(0), 0.0) # The curvature for the first cell is 0.0
for i in range(1,n-1):
p = numpy.array(points.GetPoint(pts.GetId(i+1)))
ds = numpy.linalg.norm(p-pp)
T = (p-pp) / ds
kappa = numpy.linalg.norm(T-pT) / ds # Curvature
curvatureValues.InsertValue(pts.GetId(i), kappa) # The curvature for the first cell is 0.0
m = (p+pp)/2.0
l = numpy.linalg.norm(m-pm) # length for this segment
if kappa < minKappa:
minKappa = kappa
elif kappa > maxKappa:
maxKappa = kappa
meanKappa = meanKappa + kappa * l # weighted mean
length = length + l
pp = p
pm = m
pT = T
curvatureValues.InsertValue(pts.GetId(n-1), 0.0) # The curvature for the last cell is 0.0
length = length + numpy.linalg.norm(pp-pm)
meanKappa = meanKappa / length
# TODO: This routin does not consider a closed loop. If a closed loop is specified,
# It needs to calculate the curveture of two ends differently.
return (meanKappa, minKappa, maxKappa)
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)
def distanceToPoint(self, point, extrapolate):
# distanceToPoint() calculates the approximate minimum distance between
# the specified point and the closest segment of the curve.
# It calculates the minimum distance between the point and each segment
# of the curve (approxmated as a straight line) and select the segment with
# the minimum distance from the point as a closest segment.
npoint = numpy.array(point)
if self.CurvePoly == None:
return numpy.Inf
lines = self.CurvePoly.GetLines()
points = self.CurvePoly.GetPoints()
pts = vtk.vtkIdList()
lines.GetCell(0, pts)
ip = numpy.array(points.GetPoint(pts.GetId(0)))
n = pts.GetNumberOfIds()
# First point on the segment
p1 = ip
minMag2 = numpy.Inf
minIndex = -1
minErrVec = numpy.array([0.0, 0.0, 0.0])
errVec = numpy.array([0.0, 0.0, 0.0])
for i in range(1,n):
# Second point on the segment
p2 = numpy.array(points.GetPoint(pts.GetId(i)))
# Normal vector along the segment
nvec = p2-p1
norm = numpy.linalg.norm(nvec)
if norm != 0:
nnvec = nvec / norm
# Calculate the distance between the point and the segment
mag2 = 0.0
op = npoint - p1
aproj = numpy.inner(op, nnvec)
if extrapolate and ((i == 1 and aproj < 0.0) or (i == n-1 and aproj > 0.0)):
# extrapolate first or last segment
errVec = op-aproj*nnvec # perpendicular
mag2 = numpy.inner(errVec,errVec) # magnitude^2
else:
if aproj < 0.0:
errVec = npoint - p1
mag2 = numpy.inner(errVec, errVec) # magnitude^2
elif aproj > norm:
errVec = npoint - p2
mag2 = numpy.inner(errVec, errVec) # magnitude^2
else:
errVec = op-aproj*nnvec # perpendicular
mag2 = numpy.inner(errVec,errVec) # magnitude^2
if mag2 < minMag2:
minMag2 = mag2
minIndex = i
minErrVec = errVec
p1 = p2
distance = numpy.sqrt(minMag2)
return (distance, minErrVec)
def start( self, preview=False ):
'''
'''
SlicerVmtkCommonLib.Helper.Debug( "Starting Level Set Segmentation.." )
# first we need the nodes
currentVolumeNode = self.__inputVolumeNodeSelector.currentNode()
currentSeedsNode = self.__seedFiducialsNodeSelector.currentNode()
currentVesselnessNode = self.__vesselnessVolumeNodeSelector.currentNode()
currentStoppersNode = self.__stopperFiducialsNodeSelector.currentNode()
currentLabelMapNode = self.__outputVolumeNodeSelector.currentNode()
currentModelNode = self.__outputModelNodeSelector.currentNode()
if not currentVolumeNode:
# we need a input volume node
return 0
if not currentSeedsNode:
# we need a seeds node
return 0
if not currentStoppersNode or currentStoppersNode.GetID() == currentSeedsNode.GetID():
# we need a current stopper node
# self.__stopperFiducialsNodeSelector.addNode()
pass
if not currentLabelMapNode or currentLabelMapNode.GetID() == currentVolumeNode.GetID():
# we need a current labelMap node
newLabelMapDisplayNode = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLLabelMapVolumeDisplayNode" )
newLabelMapDisplayNode.SetScene( slicer.mrmlScene )
newLabelMapDisplayNode.SetDefaultColorMap()
slicer.mrmlScene.AddNode( newLabelMapDisplayNode )
newLabelMapNode = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLScalarVolumeNode" )
newLabelMapNode.CopyOrientation( currentVolumeNode )
newLabelMapNode.SetScene( slicer.mrmlScene )
newLabelMapNode.SetName( slicer.mrmlScene.GetUniqueNameByString( self.__outputVolumeNodeSelector.baseName ) )
newLabelMapNode.LabelMapOn()
newLabelMapNode.SetAndObserveDisplayNodeID( newLabelMapDisplayNode.GetID() )
slicer.mrmlScene.AddNode( newLabelMapNode )
currentLabelMapNode = newLabelMapNode
self.__outputVolumeNodeSelector.setCurrentNode( currentLabelMapNode )
if not currentModelNode:
# we need a current model node, the display node is created later
newModelNode = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLModelNode" )
newModelNode.SetScene( slicer.mrmlScene )
newModelNode.SetName( slicer.mrmlScene.GetUniqueNameByString( self.__outputModelNodeSelector.baseName ) )
slicer.mrmlScene.AddNode( newModelNode )
currentModelNode = newModelNode
self.__outputModelNodeSelector.setCurrentNode( currentModelNode )
# now we need to convert the fiducials to vtkIdLists
seeds = SlicerVmtkCommonLib.Helper.convertFiducialHierarchyToVtkIdList( currentSeedsNode, currentVolumeNode )
# stoppers = SlicerVmtkCommonLib.Helper.convertFiducialHierarchyToVtkIdList(currentStoppersNode, currentVolumeNode)
stoppers = vtk.vtkIdList() # TODO
# the input image for the initialization
inputImage = vtk.vtkImageData()
# check if we have a vesselnessNode - this will be our input for the initialization then
if currentVesselnessNode:
# yes, there is one
inputImage.DeepCopy( currentVesselnessNode.GetImageData() )
else:
# no, there is none - we use the original image
inputImage.DeepCopy( currentVolumeNode.GetImageData() )
inputImage.Update()
# initialization
initImageData = vtk.vtkImageData()
# evolution
evolImageData = vtk.vtkImageData()
# perform the initialization
initImageData.DeepCopy( self.GetLogic().performInitialization( inputImage,
self.__thresholdSlider.minimumValue,
self.__thresholdSlider.maximumValue,
seeds,
stoppers,
0 ) ) # TODO sidebranch ignore feature
initImageData.Update()
if not initImageData.GetPointData().GetScalars():
# something went wrong, the image is empty
SlicerVmtkCommonLib.Helper.Info( "Segmentation failed - the output was empty.." )
return -1
# check if it is a preview call
if preview:
# if this is a preview call, we want to skip the evolution
evolImageData.DeepCopy( initImageData )
else:
# no preview, run the whole thing! we never use the vesselness node here, just the original one
evolImageData.DeepCopy( self.GetLogic().performEvolution( currentVolumeNode.GetImageData(),
initImageData,
self.__iterationSpinBox.value,
self.__inflationSlider.value,
self.__curvatureSlider.value,
self.__attractionSlider.value,
'geodesic' ) )
evolImageData.Update()
# create segmentation labelMap
labelMap = vtk.vtkImageData()
labelMap.DeepCopy( self.GetLogic().buildSimpleLabelMap( evolImageData, 0, 5 ) )
labelMap.Update()
currentLabelMapNode.CopyOrientation( currentVolumeNode )
# propagate the label map to the node
currentLabelMapNode.SetAndObserveImageData( labelMap )
currentLabelMapNode.Modified()
# deactivate the threshold in the GUI
self.resetThresholdOnDisplayNode()
# self.onInputVolumeChanged()
# show the segmentation results in the GUI
selectionNode = slicer.app.applicationLogic().GetSelectionNode()
if preview and currentVesselnessNode:
# if preview and a vesselnessNode was configured, show it
selectionNode.SetReferenceActiveVolumeID( currentVesselnessNode.GetID() )
else:
# if not preview, show the original volume
if currentVesselnessNode:
selectionNode.SetReferenceSecondaryVolumeID( currentVesselnessNode.GetID() )
selectionNode.SetReferenceActiveVolumeID( currentVolumeNode.GetID() )
selectionNode.SetReferenceActiveLabelVolumeID( currentLabelMapNode.GetID() )
slicer.app.applicationLogic().PropagateVolumeSelection()
# generate 3D model
model = vtk.vtkPolyData()
# we need the ijkToRas transform for the marching cubes call
ijkToRasMatrix = vtk.vtkMatrix4x4()
currentLabelMapNode.GetIJKToRASMatrix( ijkToRasMatrix )
# call marching cubes
model.DeepCopy( self.GetLogic().marchingCubes( evolImageData, ijkToRasMatrix, 0.0 ) )
model.Update()
# propagate model to nodes
currentModelNode.SetAndObservePolyData( model )
currentModelNode.Modified()
currentModelDisplayNode = currentModelNode.GetDisplayNode()
if not currentModelDisplayNode:
# create new displayNode
currentModelDisplayNode = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLModelDisplayNode" )
slicer.mrmlScene.AddNode( currentModelDisplayNode )
# always configure the displayNode to show the model
currentModelDisplayNode.SetInputPolyData( currentModelNode.GetPolyData() )
currentModelDisplayNode.SetColor( 1.0, 0.55, 0.4 ) # red
currentModelDisplayNode.SetBackfaceCulling( 0 )
currentModelDisplayNode.SetSliceIntersectionVisibility( 0 )
currentModelDisplayNode.SetVisibility( 1 )
currentModelDisplayNode.SetOpacity( 1.0 )
currentModelDisplayNode.Modified()
# update the reference between model node and it's display node
currentModelNode.SetAndObserveDisplayNodeID( currentModelDisplayNode.GetID() )
currentModelNode.Modified()
# fit slice to all sliceviewers
slicer.app.applicationLogic().FitSliceToAll()
# jump all sliceViewers to the first fiducial point, if one was used
if currentSeedsNode:
currentCoordinatesRAS = [0, 0, 0]
if isinstance( currentSeedsNode, slicer.vtkMRMLAnnotationHierarchyNode ):
childrenNodes = vtk.vtkCollection()
currentSeedsNode.GetChildrenDisplayableNodes( childrenNodes )
# now we have the children, let's get the first one
currentFiducial = childrenNodes.GetItemAsObject( 0 )
# grab the current coordinates
currentFiducial.GetFiducialCoordinates( currentCoordinatesRAS )
elif isinstance( currentSeedsNode, slicer.vtkMRMLAnnotationFiducialNode ):
# grab the current coordinates
currentSeedsNode.GetFiducialCoordinates( currentCoordinatesRAS )
numberOfSliceNodes = slicer.mrmlScene.GetNumberOfNodesByClass( 'vtkMRMLSliceNode' )
for n in xrange( numberOfSliceNodes ):
sliceNode = slicer.mrmlScene.GetNthNodeByClass( n, "vtkMRMLSliceNode" )
if sliceNode:
sliceNode.JumpSliceByOffsetting( currentCoordinatesRAS[0], currentCoordinatesRAS[1], currentCoordinatesRAS[2] )
# center 3D view(s) on the new model
if currentCoordinatesRAS:
for d in range( slicer.app.layoutManager().threeDViewCount ):
threeDView = slicer.app.layoutManager().threeDWidget( d ).threeDView()
# reset the focal point
threeDView.resetFocalPoint()
# and fly to our seed point
interactor = threeDView.interactor()
renderer = threeDView.renderWindow().GetRenderers().GetItemAsObject( 0 )
interactor.FlyTo( renderer, currentCoordinatesRAS[0], currentCoordinatesRAS[1], currentCoordinatesRAS[2] )
SlicerVmtkCommonLib.Helper.Debug( "End of Level Set Segmentation.." )
def mkVtkIdList(it):
vil = vtk.vtkIdList()
for i in it:
vil.InsertNextId(int(i))
return vil
def start( self, preview=False ):
'''
'''
SlicerVmtk4CommonLib.Helper.Debug( "Starting Centerline Computation.." )
# first we need the nodes
currentModelNode = self.__inputModelNodeSelector.currentNode()
currentSeedsNode = self.__seedFiducialsNodeSelector.currentNode()
currentOutputModelNode = self.__outputModelNodeSelector.currentNode()
currentVoronoiModelNode = self.__voronoiModelNodeSelector.currentNode()
if not currentModelNode:
# we need a input volume node
return 0
if not currentSeedsNode:
# we need a seeds node
return 0
if not currentOutputModelNode or currentOutputModelNode.GetID() == currentModelNode.GetID():
# we need a current model node, the display node is created later
newModelNode = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLModelNode" )
newModelNode.SetScene( slicer.mrmlScene )
newModelNode.SetName( slicer.mrmlScene.GetUniqueNameByString( self.__outputModelNodeSelector.baseName ) )
slicer.mrmlScene.AddNode( newModelNode )
currentOutputModelNode = newModelNode
self.__outputModelNodeSelector.setCurrentNode( currentOutputModelNode )
if not currentVoronoiModelNode or currentVoronoiModelNode.GetID() == currentModelNode.GetID() or currentVoronoiModelNode.GetID() == currentOutputModelNode.GetID():
# we need a current model node, the display node is created later
newModelNode = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLModelNode" )
newModelNode.SetScene( slicer.mrmlScene )
newModelNode.SetName( slicer.mrmlScene.GetUniqueNameByString( self.__voronoiModelNodeSelector.baseName ) )
slicer.mrmlScene.AddNode( newModelNode )
currentVoronoiModelNode = newModelNode
self.__voronoiModelNodeSelector.setCurrentNode( currentVoronoiModelNode )
# the output models
preparedModel = vtk.vtkPolyData()
model = vtk.vtkPolyData()
network = vtk.vtkPolyData()
voronoi = vtk.vtkPolyData()
currentCoordinatesRAS = [0, 0, 0]
# grab the current coordinates
currentSeedsNode.GetFiducialCoordinates( currentCoordinatesRAS )
# prepare the model
preparedModel.DeepCopy( self.GetLogic().prepareModel( currentModelNode.GetPolyData() ) )
preparedModel.Update()
# decimate the model (only for network extraction)
model.DeepCopy( self.GetLogic().decimateSurface( preparedModel ) )
model.Update()
# open the model at the seed (only for network extraction)
model.DeepCopy( self.GetLogic().openSurfaceAtPoint( model, currentCoordinatesRAS ) )
model.Update()
# extract Network
network.DeepCopy( self.GetLogic().extractNetwork( model ) )
network.Update()
#
#
# not preview mode: real computation!
if not preview:
# here we start the actual centerline computation which is mathematically more robust and accurate but takes longer than the network extraction
# clip surface at endpoints identified by the network extraction
tupel = self.GetLogic().clipSurfaceAtEndPoints( network, currentModelNode.GetPolyData() )
clippedSurface = tupel[0]
endpoints = tupel[1]
# now find the one endpoint which is closest to the seed and use it as the source point for centerline computation
# all other endpoints are the target points
sourcePoint = [0, 0, 0]
# the following arrays have the same indexes and are synchronized at all times
distancesToSeed = []
targetPoints = []
# we now need to loop through the endpoints two times
# first loop is to detect the endpoint resulting in the tiny hole we poked in the surface
# this is very close to our seed but not the correct sourcePoint
for i in range( endpoints.GetNumberOfPoints() ):
currentPoint = endpoints.GetPoint( i )
# get the euclidean distance
currentDistanceToSeed = math.sqrt( math.pow( ( currentPoint[0] - currentCoordinatesRAS[0] ), 2 ) +
math.pow( ( currentPoint[1] - currentCoordinatesRAS[1] ), 2 ) +
math.pow( ( currentPoint[2] - currentCoordinatesRAS[2] ), 2 ) )
targetPoints.append( currentPoint )
distancesToSeed.append( currentDistanceToSeed )
# now we have a list of distances with the corresponding points
# the index with the most minimal distance is the holePoint, we want to ignore it
# the index with the second minimal distance is the point closest to the seed, we want to set it as sourcepoint
# all other points are the targetpoints
# get the index of the holePoint, which we want to remove from our endPoints
holePointIndex = distancesToSeed.index( min( distancesToSeed ) )
# .. and remove it
distancesToSeed.pop( holePointIndex )
targetPoints.pop( holePointIndex )
# now find the sourcepoint
sourcePointIndex = distancesToSeed.index( min( distancesToSeed ) )
# .. and remove it after saving it as the sourcePoint
sourcePoint = targetPoints[sourcePointIndex]
distancesToSeed.pop( sourcePointIndex )
targetPoints.pop( sourcePointIndex )
# again, at this point we have a) the sourcePoint and b) a list of real targetPoints
# now create the sourceIdList and targetIdList for the actual centerline computation
sourceIdList = vtk.vtkIdList()
targetIdList = vtk.vtkIdList()
pointLocator = vtk.vtkPointLocator()
pointLocator.SetDataSet( preparedModel )
pointLocator.BuildLocator()
# locate the source on the surface
sourceId = pointLocator.FindClosestPoint( sourcePoint )
sourceIdList.InsertNextId( sourceId )
f = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLAnnotationFiducialNode" )
f.SetFiducialCoordinates( sourcePoint )
f.Initialize( slicer.mrmlScene )
f.SelectedOn()
# locate the endpoints on the surface
for p in targetPoints:
f = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLAnnotationFiducialNode" )
f.SetFiducialCoordinates( p )
f.Initialize( slicer.mrmlScene )
id = pointLocator.FindClosestPoint( p )
targetIdList.InsertNextId( id )
tupel = self.GetLogic().computeCenterlines( preparedModel, sourceIdList, targetIdList )
network.DeepCopy( tupel[0] )
voronoi.DeepCopy( tupel[1] )
#
#
# update the display of the original model in terms of opacity
currentModelDisplayNode = currentModelNode.GetDisplayNode()
if not currentModelDisplayNode:
# create new displayNode
currentModelDisplayNode = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLModelDisplayNode" )
slicer.mrmlScene.AddNode( currentModelDisplayNode )
currentModelDisplayNode.SetOpacity( 0.4 )
currentModelDisplayNode.Modified()
currentModelDisplayNode.SetModifiedSinceRead( 1 )
# update the reference between model node and it's display node
currentModelNode.SetAndObserveDisplayNodeID( currentModelDisplayNode.GetID() )
currentModelNode.Modified()
currentModelNode.SetModifiedSinceRead( 1 )
#
# finally:
# propagate output model to nodes
currentOutputModelNode.SetAndObservePolyData( network )
currentOutputModelNode.Modified()
currentOutputModelNode.SetModifiedSinceRead( 1 )
currentOutputModelDisplayNode = currentOutputModelNode.GetDisplayNode()
if not currentOutputModelDisplayNode:
# create new displayNode
currentOutputModelDisplayNode = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLModelDisplayNode" )
slicer.mrmlScene.AddNode( currentOutputModelDisplayNode )
# always configure the displayNode to show the model
currentOutputModelDisplayNode.SetPolyData( currentOutputModelNode.GetPolyData() )
currentOutputModelDisplayNode.SetColor( 0.0, 0.0, 0.4 ) # red
currentOutputModelDisplayNode.SetBackfaceCulling( 0 )
currentOutputModelDisplayNode.SetSliceIntersectionVisibility( 0 )
currentOutputModelDisplayNode.SetVisibility( 1 )
currentOutputModelDisplayNode.SetOpacity( 1.0 )
currentOutputModelDisplayNode.Modified()
currentOutputModelDisplayNode.SetModifiedSinceRead( 1 )
# update the reference between model node and it's display node
currentOutputModelNode.SetAndObserveDisplayNodeID( currentOutputModelDisplayNode.GetID() )
currentOutputModelNode.Modified()
currentOutputModelNode.SetModifiedSinceRead( 1 )
# only update the voronoi node if we are not in preview mode
if not preview:
currentVoronoiModelNode.SetAndObservePolyData( voronoi )
currentVoronoiModelNode.Modified()
currentVoronoiModelNode.SetModifiedSinceRead( 1 )
currentVoronoiModelDisplayNode = currentVoronoiModelNode.GetDisplayNode()
if not currentVoronoiModelDisplayNode:
# create new displayNode
currentVoronoiModelDisplayNode = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLModelDisplayNode" )
slicer.mrmlScene.AddNode( currentVoronoiModelDisplayNode )
# always configure the displayNode to show the model
currentVoronoiModelDisplayNode.SetPolyData( currentVoronoiModelNode.GetPolyData() )
currentVoronoiModelDisplayNode.SetScalarVisibility( 1 )
currentVoronoiModelDisplayNode.SetBackfaceCulling( 0 )
currentVoronoiModelDisplayNode.SetActiveScalarName( "Radius" )
currentVoronoiModelDisplayNode.SetAndObserveColorNodeID( slicer.mrmlScene.GetNodesByName( "Labels" ).GetItemAsObject( 0 ).GetID() )
currentVoronoiModelDisplayNode.SetSliceIntersectionVisibility( 0 )
currentVoronoiModelDisplayNode.SetVisibility( 1 )
currentVoronoiModelDisplayNode.SetOpacity( 0.5 )
currentVoronoiModelDisplayNode.Modified()
currentVoronoiModelDisplayNode.SetModifiedSinceRead( 1 )
# update the reference between model node and it's display node
currentVoronoiModelNode.SetAndObserveDisplayNodeID( currentVoronoiModelDisplayNode.GetID() )
currentVoronoiModelNode.Modified()
currentVoronoiModelNode.SetModifiedSinceRead( 1 )
SlicerVmtk4CommonLib.Helper.Debug( "End of Centerline Computation.." )
def clipSurfaceAtEndPoints(self, networkPolyData, surfacePolyData):
'''
Clips the surfacePolyData on the endpoints identified using the networkPolyData.
Returns a tupel of the form [clippedPolyData, endpointsPoints]
'''
# import the vmtk libraries
try:
from libvtkvmtkComputationalGeometryPython import *
from libvtkvmtkMiscPython import *
except ImportError:
print "FAILURE: Unable to import the SlicerVmtk4 libraries!"
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInput(networkPolyData)
cleaner.Update()
network = cleaner.GetOutput()
network.BuildCells()
network.BuildLinks(0)
endpointIds = vtk.vtkIdList()
radiusArray = network.GetPointData().GetArray('Radius')
endpoints = vtk.vtkPolyData()
endpointsPoints = vtk.vtkPoints()
endpointsRadius = vtk.vtkDoubleArray()
endpointsRadius.SetName('Radius')
endpoints.SetPoints(endpointsPoints)
endpoints.GetPointData().AddArray(endpointsRadius)
radiusFactor = 1.2
minRadius = 0.01
for i in range(network.GetNumberOfCells()):
numberOfCellPoints = network.GetCell(i).GetNumberOfPoints()
pointId0 = network.GetCell(i).GetPointId(0)
pointId1 = network.GetCell(i).GetPointId(numberOfCellPoints - 1)
pointCells = vtk.vtkIdList()
network.GetPointCells(pointId0, pointCells)
numberOfEndpoints = endpointIds.GetNumberOfIds()
if pointCells.GetNumberOfIds() == 1:
pointId = endpointIds.InsertUniqueId(pointId0)
if pointId == numberOfEndpoints:
point = network.GetPoint(pointId0)
radius = radiusArray.GetValue(pointId0)
radius = max(radius, minRadius)
endpointsPoints.InsertNextPoint(point)
endpointsRadius.InsertNextValue(radiusFactor * radius)
pointCells = vtk.vtkIdList()
network.GetPointCells(pointId1, pointCells)
numberOfEndpoints = endpointIds.GetNumberOfIds()
if pointCells.GetNumberOfIds() == 1:
pointId = endpointIds.InsertUniqueId(pointId1)
if pointId == numberOfEndpoints:
point = network.GetPoint(pointId1)
radius = radiusArray.GetValue(pointId1)
radius = max(radius, minRadius)
endpointsPoints.InsertNextPoint(point)
endpointsRadius.InsertNextValue(radiusFactor * radius)
polyBall = vtkvmtkPolyBall()
polyBall.SetInput(endpoints)
polyBall.SetPolyBallRadiusArrayName('Radius')
clipper = vtk.vtkClipPolyData()
clipper.SetInput(surfacePolyData)
clipper.SetClipFunction(polyBall)
clipper.Update()
connectivityFilter = vtk.vtkPolyDataConnectivityFilter()
connectivityFilter.SetInput(clipper.GetOutput())
connectivityFilter.ColorRegionsOff()
connectivityFilter.SetExtractionModeToLargestRegion()
connectivityFilter.Update()
clippedSurface = connectivityFilter.GetOutput()
outPolyData = vtk.vtkPolyData()
outPolyData.DeepCopy(clippedSurface)
outPolyData.Update()
return [outPolyData, endpointsPoints]
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 onApplyThreshold(self):
min, max = self.getDistanceBound()
newPoints = vtk.vtkPoints()
newLines = vtk.vtkCellArray()
newTensors = vtk.vtkFloatArray()
newTensors.SetNumberOfComponents(9)
newScalars = vtk.vtkFloatArray()
points = self.inputPolyData.GetPoints()
lines = self.inputPolyData.GetLines()
tensors = self.inputPolyData.GetPointData().GetTensors()
lines.InitTraversal()
newId = 0
for length in self.distanceTable:
if length <= self.thresholdMax.value and length >= self.thresholdMin.value:
ids = vtk.vtkIdList()
lines.GetNextCell(ids)
newLine = vtk.vtkPolyLine()
#print(ids.GetNumberOfIds())
newLine.GetPointIds().SetNumberOfIds(ids.GetNumberOfIds())
#print(((length-min)/(max-min))*100)
for i in range(ids.GetNumberOfIds()):
newPoints.InsertNextPoint(points.GetPoint(ids.GetId(i)))
newLine.GetPointIds().SetId(i, newId)
newScalars.InsertNextValue(((length - min) / (max - min)))
newId += 1
tensorValue = [0] * 9
if (tensors != None):
for j in range(9):
tensorValue[j] = tensors.GetComponent(
ids.GetId(i), j)
newTensors.InsertNextTuple(tensorValue)
newLines.InsertNextCell(newLine)
self.outputPolyData = vtk.vtkPolyData()
self.outputPolyData.SetPoints(newPoints)
self.outputPolyData.SetLines(newLines)
self.outputPolyData.GetPointData().SetTensors(newTensors)
newScalars.SetName("Length")
self.outputPolyData.GetPointData().AddArray(newScalars)
self.outputNode.SetAndObservePolyData(self.outputPolyData)
chartViewNodes = slicer.mrmlScene.GetNodesByClass(
'vtkMRMLChartViewNode')
chartViewNodes.InitTraversal()
chartViewNode = chartViewNodes.GetNextItemAsObject()
arrayNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLDoubleArrayNode())
array = arrayNode.GetArray()
array.SetNumberOfTuples(10)
step = (max - min) / 10
interMin = min
interMax = min + step
for i in range(10):
numberOfFibers = 0
for length in self.distanceTable:
if length <= interMax and length >= interMin and length <= self.thresholdMax.value and length >= self.thresholdMin.value:
numberOfFibers += 1
array.SetComponent(i, 0, (interMin + interMax) / 2)
array.SetComponent(i, 1, numberOfFibers)
array.SetComponent(i, 2, 0)
interMin += step
interMax += step
chartNode = slicer.mrmlScene.AddNode(slicer.vtkMRMLChartNode())
chartNode.AddArray("Fiber Length", arrayNode.GetID())
chartViewNode.SetChartNodeID(chartNode.GetID())
chartNode.SetProperty('default', 'title', 'Length Distribution')
chartNode.SetProperty('default', 'xAxisLabel', 'Length')
chartNode.SetProperty('default', 'yAxisLabel', 'Distribution')
chartNode.SetProperty('default', 'type', 'Bar')
def start(self, preview=False):
'''
'''
SlicerVmtk4CommonLib.Helper.Debug("Starting Centerline Computation..")
# first we need the nodes
currentModelNode = self.__inputModelNodeSelector.currentNode()
currentSeedsNode = self.__seedFiducialsNodeSelector.currentNode()
currentOutputModelNode = self.__outputModelNodeSelector.currentNode()
currentVoronoiModelNode = self.__voronoiModelNodeSelector.currentNode()
if not currentModelNode:
# we need a input volume node
return 0
if not currentSeedsNode:
# we need a seeds node
return 0
if not currentOutputModelNode or currentOutputModelNode.GetID(
) == currentModelNode.GetID():
# we need a current model node, the display node is created later
newModelNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLModelNode")
newModelNode.SetScene(slicer.mrmlScene)
newModelNode.SetName(
slicer.mrmlScene.GetUniqueNameByString(
self.__outputModelNodeSelector.baseName))
slicer.mrmlScene.AddNode(newModelNode)
currentOutputModelNode = newModelNode
self.__outputModelNodeSelector.setCurrentNode(
currentOutputModelNode)
if not currentVoronoiModelNode or currentVoronoiModelNode.GetID(
) == currentModelNode.GetID() or currentVoronoiModelNode.GetID(
) == currentOutputModelNode.GetID():
# we need a current model node, the display node is created later
newModelNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLModelNode")
newModelNode.SetScene(slicer.mrmlScene)
newModelNode.SetName(
slicer.mrmlScene.GetUniqueNameByString(
self.__voronoiModelNodeSelector.baseName))
slicer.mrmlScene.AddNode(newModelNode)
currentVoronoiModelNode = newModelNode
self.__voronoiModelNodeSelector.setCurrentNode(
currentVoronoiModelNode)
# the output models
preparedModel = vtk.vtkPolyData()
model = vtk.vtkPolyData()
network = vtk.vtkPolyData()
voronoi = vtk.vtkPolyData()
currentCoordinatesRAS = [0, 0, 0]
# grab the current coordinates
currentSeedsNode.GetFiducialCoordinates(currentCoordinatesRAS)
# prepare the model
preparedModel.DeepCopy(self.GetLogic().prepareModel(
currentModelNode.GetPolyData()))
preparedModel.Update()
# decimate the model (only for network extraction)
model.DeepCopy(self.GetLogic().decimateSurface(preparedModel))
model.Update()
# open the model at the seed (only for network extraction)
model.DeepCopy(self.GetLogic().openSurfaceAtPoint(
model, currentCoordinatesRAS))
model.Update()
# extract Network
network.DeepCopy(self.GetLogic().extractNetwork(model))
network.Update()
#
#
# not preview mode: real computation!
if not preview:
# here we start the actual centerline computation which is mathematically more robust and accurate but takes longer than the network extraction
# clip surface at endpoints identified by the network extraction
tupel = self.GetLogic().clipSurfaceAtEndPoints(
network, currentModelNode.GetPolyData())
clippedSurface = tupel[0]
endpoints = tupel[1]
# now find the one endpoint which is closest to the seed and use it as the source point for centerline computation
# all other endpoints are the target points
sourcePoint = [0, 0, 0]
# the following arrays have the same indexes and are synchronized at all times
distancesToSeed = []
targetPoints = []
# we now need to loop through the endpoints two times
# first loop is to detect the endpoint resulting in the tiny hole we poked in the surface
# this is very close to our seed but not the correct sourcePoint
for i in range(endpoints.GetNumberOfPoints()):
currentPoint = endpoints.GetPoint(i)
# get the euclidean distance
currentDistanceToSeed = math.sqrt(
math.pow((currentPoint[0] - currentCoordinatesRAS[0]), 2) +
math.pow((currentPoint[1] - currentCoordinatesRAS[1]), 2) +
math.pow((currentPoint[2] - currentCoordinatesRAS[2]), 2))
targetPoints.append(currentPoint)
distancesToSeed.append(currentDistanceToSeed)
# now we have a list of distances with the corresponding points
# the index with the most minimal distance is the holePoint, we want to ignore it
# the index with the second minimal distance is the point closest to the seed, we want to set it as sourcepoint
# all other points are the targetpoints
# get the index of the holePoint, which we want to remove from our endPoints
holePointIndex = distancesToSeed.index(min(distancesToSeed))
# .. and remove it
distancesToSeed.pop(holePointIndex)
targetPoints.pop(holePointIndex)
# now find the sourcepoint
sourcePointIndex = distancesToSeed.index(min(distancesToSeed))
# .. and remove it after saving it as the sourcePoint
sourcePoint = targetPoints[sourcePointIndex]
distancesToSeed.pop(sourcePointIndex)
targetPoints.pop(sourcePointIndex)
# again, at this point we have a) the sourcePoint and b) a list of real targetPoints
# now create the sourceIdList and targetIdList for the actual centerline computation
sourceIdList = vtk.vtkIdList()
targetIdList = vtk.vtkIdList()
pointLocator = vtk.vtkPointLocator()
pointLocator.SetDataSet(preparedModel)
pointLocator.BuildLocator()
# locate the source on the surface
sourceId = pointLocator.FindClosestPoint(sourcePoint)
sourceIdList.InsertNextId(sourceId)
f = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLAnnotationFiducialNode")
f.SetFiducialCoordinates(sourcePoint)
f.Initialize(slicer.mrmlScene)
f.SelectedOn()
# locate the endpoints on the surface
for p in targetPoints:
f = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLAnnotationFiducialNode")
f.SetFiducialCoordinates(p)
f.Initialize(slicer.mrmlScene)
id = pointLocator.FindClosestPoint(p)
targetIdList.InsertNextId(id)
tupel = self.GetLogic().computeCenterlines(preparedModel,
sourceIdList,
targetIdList)
network.DeepCopy(tupel[0])
voronoi.DeepCopy(tupel[1])
#
#
# update the display of the original model in terms of opacity
currentModelDisplayNode = currentModelNode.GetDisplayNode()
if not currentModelDisplayNode:
# create new displayNode
currentModelDisplayNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLModelDisplayNode")
slicer.mrmlScene.AddNode(currentModelDisplayNode)
currentModelDisplayNode.SetOpacity(0.4)
currentModelDisplayNode.Modified()
currentModelDisplayNode.SetModifiedSinceRead(1)
# update the reference between model node and it's display node
currentModelNode.SetAndObserveDisplayNodeID(
currentModelDisplayNode.GetID())
currentModelNode.Modified()
currentModelNode.SetModifiedSinceRead(1)
#
# finally:
# propagate output model to nodes
currentOutputModelNode.SetAndObservePolyData(network)
currentOutputModelNode.Modified()
currentOutputModelNode.SetModifiedSinceRead(1)
currentOutputModelDisplayNode = currentOutputModelNode.GetDisplayNode()
if not currentOutputModelDisplayNode:
# create new displayNode
currentOutputModelDisplayNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLModelDisplayNode")
slicer.mrmlScene.AddNode(currentOutputModelDisplayNode)
# always configure the displayNode to show the model
currentOutputModelDisplayNode.SetPolyData(
currentOutputModelNode.GetPolyData())
currentOutputModelDisplayNode.SetColor(0.0, 0.0, 0.4) # red
currentOutputModelDisplayNode.SetBackfaceCulling(0)
currentOutputModelDisplayNode.SetSliceIntersectionVisibility(0)
currentOutputModelDisplayNode.SetVisibility(1)
currentOutputModelDisplayNode.SetOpacity(1.0)
currentOutputModelDisplayNode.Modified()
currentOutputModelDisplayNode.SetModifiedSinceRead(1)
# update the reference between model node and it's display node
currentOutputModelNode.SetAndObserveDisplayNodeID(
currentOutputModelDisplayNode.GetID())
currentOutputModelNode.Modified()
currentOutputModelNode.SetModifiedSinceRead(1)
# only update the voronoi node if we are not in preview mode
if not preview:
currentVoronoiModelNode.SetAndObservePolyData(voronoi)
currentVoronoiModelNode.Modified()
currentVoronoiModelNode.SetModifiedSinceRead(1)
currentVoronoiModelDisplayNode = currentVoronoiModelNode.GetDisplayNode(
)
if not currentVoronoiModelDisplayNode:
# create new displayNode
currentVoronoiModelDisplayNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLModelDisplayNode")
slicer.mrmlScene.AddNode(currentVoronoiModelDisplayNode)
# always configure the displayNode to show the model
currentVoronoiModelDisplayNode.SetPolyData(
currentVoronoiModelNode.GetPolyData())
currentVoronoiModelDisplayNode.SetScalarVisibility(1)
currentVoronoiModelDisplayNode.SetBackfaceCulling(0)
currentVoronoiModelDisplayNode.SetActiveScalarName("Radius")
currentVoronoiModelDisplayNode.SetAndObserveColorNodeID(
slicer.mrmlScene.GetNodesByName("Labels").GetItemAsObject(
0).GetID())
currentVoronoiModelDisplayNode.SetSliceIntersectionVisibility(0)
currentVoronoiModelDisplayNode.SetVisibility(1)
currentVoronoiModelDisplayNode.SetOpacity(0.5)
currentVoronoiModelDisplayNode.Modified()
currentVoronoiModelDisplayNode.SetModifiedSinceRead(1)
# update the reference between model node and it's display node
currentVoronoiModelNode.SetAndObserveDisplayNodeID(
currentVoronoiModelDisplayNode.GetID())
currentVoronoiModelNode.Modified()
currentVoronoiModelNode.SetModifiedSinceRead(1)
SlicerVmtk4CommonLib.Helper.Debug("End of Centerline Computation..")
