def generateGridPolyDataTriangular(self):
polyDataCombiner = vtk.vtkAppendPolyData()
lowerHorizontalBoundMm = self.evaluateLowerHorizontalBoundMm()
upperHorizontalBoundMm = self.evaluateUpperHorizontalBoundMm()
lowerVerticalBoundMm = self.evaluateLowerVerticalBoundMm()
upperVerticalBoundMm = self.evaluateUpperVerticalBoundMm()
# traditional 'for' loops would be very nice here... :-/
yMm = lowerVerticalBoundMm
while (yMm <= upperVerticalBoundMm):
# determine whether to offset in horizontal axis -
# this makes the triangular pattern if done on odd rows only
offsetMm = 0
oddRow = (round(yMm / self.gridSpacingVerticalMm) % 2 == 1)
if oddRow:
offsetMm = self.gridSpacingHorizontalMm / 2.0
xMm = lowerHorizontalBoundMm + offsetMm
while (xMm <= upperHorizontalBoundMm):
cylinderPolyData = self.generateCylinderPolyData(xMm, yMm)
polyDataCombiner.AddInputData(cylinderPolyData)
xMm = xMm + self.gridSpacingHorizontalMm
yMm = yMm + self.gridSpacingVerticalMm
polyDataCombiner.Update()
gridPolyData = polyDataCombiner.GetOutput()
return gridPolyData
def generateGridPolyDataTriangular(self):
polyDataCombiner = vtk.vtkAppendPolyData()
lowerHorizontalBoundMm = self.evaluateLowerHorizontalBoundMm()
upperHorizontalBoundMm = self.evaluateUpperHorizontalBoundMm()
lowerVerticalBoundMm = self.evaluateLowerVerticalBoundMm()
upperVerticalBoundMm = self.evaluateUpperVerticalBoundMm()
# traditional 'for' loops would be very nice here... :-/
yMm = lowerVerticalBoundMm
while (yMm <= upperVerticalBoundMm):
# determine whether to offset in horizontal axis -
# this makes the triangular pattern if done on odd rows only
offsetMm = 0
oddRow = (round(yMm / self.gridSpacingVerticalMm) % 2 == 1)
if oddRow:
offsetMm = self.gridSpacingHorizontalMm / 2.0
xMm = lowerHorizontalBoundMm + offsetMm
while (xMm <= upperHorizontalBoundMm):
cylinderPolyData = self.generateCylinderPolyData(xMm,yMm)
polyDataCombiner.AddInputData(cylinderPolyData)
xMm = xMm + self.gridSpacingHorizontalMm
yMm = yMm + self.gridSpacingVerticalMm
polyDataCombiner.Update()
gridPolyData = polyDataCombiner.GetOutput()
return gridPolyData
def createNeedleModelNode(self, name):
locatorModel = self.scene.CreateNodeByClass('vtkMRMLModelNode')
# Cylinder represents the locator stick
cylinder = vtk.vtkCylinderSource()
cylinder.SetRadius(1.5)
cylinder.SetHeight(100)
cylinder.SetCenter(0, 0, 0)
cylinder.Update()
# Rotate cylinder
tfilter = vtk.vtkTransformPolyDataFilter()
trans = vtk.vtkTransform()
trans.RotateX(90.0)
trans.Translate(0.0, -50.0, 0.0)
trans.Update()
if vtk.VTK_MAJOR_VERSION <= 5:
tfilter.SetInput(cylinder.GetOutput())
else:
tfilter.SetInputConnection(cylinder.GetOutputPort())
tfilter.SetTransform(trans)
tfilter.Update()
# Sphere represents the locator tip
sphere = vtk.vtkSphereSource()
sphere.SetRadius(3.0)
sphere.SetCenter(0, 0, 0)
sphere.Update()
apd = vtk.vtkAppendPolyData()
if vtk.VTK_MAJOR_VERSION <= 5:
apd.AddInput(sphere.GetOutput())
apd.AddInput(tfilter.GetOutput())
else:
apd.AddInputConnection(sphere.GetOutputPort())
apd.AddInputConnection(tfilter.GetOutputPort())
apd.Update()
locatorModel.SetAndObservePolyData(apd.GetOutput());
self.scene.AddNode(locatorModel)
locatorModel.SetScene(self.scene);
locatorModel.SetName(name)
locatorDisp = locatorModel.GetDisplayNodeID()
if locatorDisp == None:
locatorDisp = self.scene.CreateNodeByClass('vtkMRMLModelDisplayNode')
self.scene.AddNode(locatorDisp)
locatorDisp.SetScene(self.scene)
locatorModel.SetAndObserveDisplayNodeID(locatorDisp.GetID());
color = [0, 0, 0]
color[0] = 0.5
color[1] = 0.5
color[2] = 1.0
locatorDisp.SetColor(color)
return locatorModel.GetID()
def updateTipModelNode(self, tipModelNode, poly, p0, pe, radius, color,
opacity):
points = vtk.vtkPoints()
cellArray = vtk.vtkCellArray()
points.SetNumberOfPoints(2)
cellArray.InsertNextCell(2)
points.SetPoint(0, p0)
cellArray.InsertCellPoint(0)
points.SetPoint(1, pe)
cellArray.InsertCellPoint(1)
poly.Initialize()
poly.SetPoints(points)
poly.SetLines(cellArray)
tubeFilter = vtk.vtkTubeFilter()
tubeFilter.SetInputData(poly)
tubeFilter.SetRadius(radius)
tubeFilter.SetNumberOfSides(20)
tubeFilter.CappingOn()
tubeFilter.Update()
# Sphere represents the locator tip
sphere = vtk.vtkSphereSource()
sphere.SetRadius(radius * 2.0)
sphere.SetCenter(pe)
sphere.Update()
apd = vtk.vtkAppendPolyData()
if vtk.VTK_MAJOR_VERSION <= 5:
apd.AddInput(sphere.GetOutput())
apd.AddInput(tubeFilter.GetOutput())
else:
apd.AddInputConnection(sphere.GetOutputPort())
apd.AddInputConnection(tubeFilter.GetOutputPort())
apd.Update()
tipModelNode.SetAndObservePolyData(apd.GetOutput())
tipModelNode.Modified()
tipDispID = tipModelNode.GetDisplayNodeID()
if tipDispID == None:
tipDispNode = self.scene.AddNewNodeByClass(
'vtkMRMLModelDisplayNode')
tipDispNode.SetScene(self.scene)
tipModelNode.SetAndObserveDisplayNodeID(tipDispNode.GetID())
tipDispID = tipModelNode.GetDisplayNodeID()
tipDispNode = self.scene.GetNodeByID(tipDispID)
prevState = tipDispNode.StartModify()
tipDispNode.SetColor(color)
tipDispNode.SetOpacity(opacity)
tipDispNode.SliceIntersectionVisibilityOn()
tipDispNode.SetSliceDisplayModeToIntersection()
tipDispNode.EndModify(prevState)
def JoinBoundaryPoints( self, hullPoints1, hullPoints2, offset ):
if ( hullPoints1.GetNumberOfPoints() != hullPoints2.GetNumberOfPoints() ):
return
joiningAppend = vtk.vtkAppendPolyData()
numPoints = hullPoints1.GetNumberOfPoints()
for i in range( 0, numPoints ):
currPointsForSurface = vtk.vtkPoints()
point1 = [ 0, 0, 0 ]
hullPoints1.GetPoint( ( i - offset )% numPoints, point1 )
currPointsForSurface.InsertNextPoint( point1[ 0 ], point1[ 1 ], point1[ 2 ] )
point2 = [ 0, 0, 0 ]
hullPoints2.GetPoint( ( - i ) % numPoints, point2 )
currPointsForSurface.InsertNextPoint( point2[ 0 ], point2[ 1 ], point2[ 2 ] )
# Observe that the deep is flipped from the surface
# Must proceed in opposite orders
point3 = [ 0, 0, 0 ]
hullPoints1.GetPoint( ( i + 1 - offset ) % numPoints, point3 )
currPointsForSurface.InsertNextPoint( point3[ 0 ], point3[ 1 ], point3[ 2 ] )
point4 = [ 0, 0, 0 ]
hullPoints2.GetPoint( ( - ( i + 1 ) ) % numPoints, point4 )
currPointsForSurface.InsertNextPoint( point4[ 0 ], point4[ 1 ], point4[ 2 ] )
# We know what the triangles should look like, so create them manually
# Note: The order here is important - ensure the triangles face the correct way
triangle1 = vtk.vtkTriangle()
triangle1.GetPointIds().SetId( 0, 0 )
triangle1.GetPointIds().SetId( 1, 1 )
triangle1.GetPointIds().SetId( 2, 2 )
triangle2 = vtk.vtkTriangle()
triangle2.GetPointIds().SetId( 0, 3 )
triangle2.GetPointIds().SetId( 1, 2 )
triangle2.GetPointIds().SetId( 2, 1 )
triangles = vtk.vtkCellArray()
triangles.InsertNextCell( triangle1 )
triangles.InsertNextCell( triangle2 )
currPolyDataForSurface = vtk.vtkPolyData()
currPolyDataForSurface.SetPoints( currPointsForSurface )
currPolyDataForSurface.SetPolys( triangles )
joiningAppend.AddInputData( currPolyDataForSurface )
joiningAppend.Update()
return joiningAppend.GetOutput()
def createOptionalPathModel(self, pos, holeInfoList, intNumOfOptionalPath):
if intNumOfOptionalPath == 1:
self.setOptionalPathVisibility(1)
pathListRAS = []
for i in range(len(holeInfoList)):
pathListRAS.append(self.templateRAS[holeInfoList[i][3]])
print "pathListRAS: ", pathListRAS
#(not generate path -> pass, otherwise go on)
self.optModelNode = slicer.mrmlScene.GetNodeByID(self.optionalPathModelNodeID)
if self.optModelNode == None:
self.optModelNode = slicer.vtkMRMLModelNode()
self.optModelNode.SetName('AllOptionalPaths')
slicer.mrmlScene.AddNode(self.optModelNode)
self.optionalPathModelNodeID = self.optModelNode.GetID()
self.dnodeOpt = slicer.vtkMRMLModelDisplayNode()
self.dnodeOpt.SetColor(0.96,0.92,0.56)
slicer.mrmlScene.AddNode(self.dnodeOpt)
self.optModelNode.SetAndObserveDisplayNodeID(self.dnodeOpt.GetID())
optModelAppend = vtk.vtkAppendPolyData()
#for path in pathListRAS:
for index in range(len(pathListRAS)):
optLineSource = vtk.vtkLineSource()
optLineSource.SetPoint1(pos)
optLineSource.SetPoint2(pathListRAS[index])
optTubeFilter = vtk.vtkTubeFilter()
optTubeFilter.SetInputConnection(optLineSource.GetOutputPort())
optTubeFilter.SetRadius(1.0)
optTubeFilter.SetNumberOfSides(10)
optTubeFilter.CappingOn()
optTubeFilter.Update()
if vtk.VTK_MAJOR_VERSION <= 5:
optModelAppend.AddInput(optTubeFilter.GetOutput())
else:
optModelAppend.AddInputData(optTubeFilter.GetOutput())
optModelAppend.Update()
self.optModelNode.SetAndObservePolyData(optModelAppend.GetOutput())
def Combine_Surfaces(self, polydata_list):
# Combine some number of polydata together
# For example, useful for combining all the bones of a joint back together for saving to a .PLY file
# Append the meshes together
appendFilter = vtk.vtkAppendPolyData()
# Loop through each surface in the list of polydata and input into the filter
for i in range(0, len(polydata_list)):
appendFilter.AddInputData(polydata_list[i])
# Update the combinded polydata filter
appendFilter.Update()
# Get the output of the filter (i.e. combined_polydata holds the combined surfaces)
combined_polydata = appendFilter.GetOutput()
return combined_polydata
def generateGridPolyDataRectangular(self):
polyDataCombiner = vtk.vtkAppendPolyData()
lowerHorizontalBoundMm = self.evaluateLowerHorizontalBoundMm()
upperHorizontalBoundMm = self.evaluateUpperHorizontalBoundMm()
lowerVerticalBoundMm = self.evaluateLowerVerticalBoundMm()
upperVerticalBoundMm = self.evaluateUpperVerticalBoundMm()
# traditional 'for' loops would be very nice here... :-/
yMm = lowerVerticalBoundMm
while (yMm <= upperVerticalBoundMm):
xMm = lowerHorizontalBoundMm
while (xMm <= upperHorizontalBoundMm):
cylinderPolyData = self.generateCylinderPolyData(xMm, yMm)
polyDataCombiner.AddInputData(cylinderPolyData)
xMm = xMm + self.gridSpacingHorizontalMm
yMm = yMm + self.gridSpacingVerticalMm
polyDataCombiner.Update()
gridPolyData = polyDataCombiner.GetOutput()
return gridPolyData
def generateGridPolyDataRectangular(self):
polyDataCombiner = vtk.vtkAppendPolyData()
lowerHorizontalBoundMm = self.evaluateLowerHorizontalBoundMm()
upperHorizontalBoundMm = self.evaluateUpperHorizontalBoundMm()
lowerVerticalBoundMm = self.evaluateLowerVerticalBoundMm()
upperVerticalBoundMm = self.evaluateUpperVerticalBoundMm()
# traditional 'for' loops would be very nice here... :-/
yMm = lowerVerticalBoundMm
while (yMm <= upperVerticalBoundMm):
xMm = lowerHorizontalBoundMm
while (xMm <= upperHorizontalBoundMm):
cylinderPolyData = self.generateCylinderPolyData(xMm,yMm)
polyDataCombiner.AddInputData(cylinderPolyData)
xMm = xMm + self.gridSpacingHorizontalMm
yMm = yMm + self.gridSpacingVerticalMm
polyDataCombiner.Update()
gridPolyData = polyDataCombiner.GetOutput()
return gridPolyData
def createNeedleModelNode(self, name,index):
locatorModel = self.scene.CreateNodeByClass('vtkMRMLModelNode')
# Cylinder represents the locator stick
cylinder = vtk.vtkCylinderSource()
cylinder.SetRadius(1.5)
cylinder.SetHeight(100)
cylinder.SetCenter(0, 0, 0)
cylinder.Update()
# Rotate cylinder
tfilter = vtk.vtkTransformPolyDataFilter()
trans = vtk.vtkTransform()
trans.RotateX(90.0)
trans.Translate(0.0, -50.0, 0.0)
trans.Update()
if vtk.VTK_MAJOR_VERSION <= 5:
tfilter.SetInput(cylinder.GetOutput())
else:
tfilter.SetInputConnection(cylinder.GetOutputPort())
tfilter.SetTransform(trans)
tfilter.Update()
# Sphere represents the locator tip
sphere = vtk.vtkSphereSource()
sphere.SetRadius(3.0)
sphere.SetCenter(0, 0, 0)
sphere.Update()
apd = vtk.vtkAppendPolyData()
if vtk.VTK_MAJOR_VERSION <= 5:
apd.AddInput(sphere.GetOutput())
apd.AddInput(tfilter.GetOutput())
else:
apd.AddInputConnection(sphere.GetOutputPort())
apd.AddInputConnection(tfilter.GetOutputPort())
apd.Update()
locatorModel.SetAndObservePolyData(apd.GetOutput());
self.scene.AddNode(locatorModel)
locatorModel.SetScene(self.scene);
needleName = "Needle_%s" % name
locatorModel.SetName(needleName)
locatorDisp = locatorModel.GetDisplayNodeID()
if locatorDisp == None:
locatorDisp = self.scene.CreateNodeByClass('vtkMRMLModelDisplayNode')
self.scene.AddNode(locatorDisp)
locatorDisp.SetScene(self.scene)
locatorModel.SetAndObserveDisplayNodeID(locatorDisp.GetID());
color = [0, 0, 0]
color[0] = 0.5
color[1] = 0.5
color[2] = 1.0
locatorDisp.SetColor(color)
print name
if self.colorMap.get(name):
locatorDisp.SetColor(self.colorMap.get(name))
color = self.colorMap.get(name)
colorName = "background:rgb({},{},{})".format(255*color[0], 255*color[1], 255*color[2])
print colorName
self.widget.colorSelectors[index].setStyleSheet(colorName)
#qss = qt.QString("background-color: %1").arg(col.name());
return locatorModel.GetID()
print "Computing queries"
evaluated_queries = tract_querier.eval_queries(
query_file_body,
tractography_spatial_indexing,
)
query_names = evaluated_queries.keys()
print query_names
if options.query_selection != '':
selected_queries = set(options.query_selection.lower().split(','))
query_names = list(set(query_names) & set(selected_queries))
query_names.sort()
print 'save_query'
polyDataOut=vtk.vtkAppendPolyData()
for query_name in query_names:
tr_out_temp=save_query( query_name, tr, options, evaluated_queries)
if tr_out_temp is not None:
tr_polydata=tracts_to_vtkPolyData64(tr_out_temp)
polyDataOut.AddInput(tr_polydata)
updateOutputNode(polyDataOut.GetOutput())
return
def vtkMatrix_2_array(m):
import numpy
out=numpy.zeros(shape=(4,4))
for i in range(4):
for j in range(4):
out[i][j]=m.GetElement(i,j)
return out
print "Computing queries"
evaluated_queries = tract_querier.eval_queries(
query_file_body,
tractography_spatial_indexing,
)
query_names = evaluated_queries.keys()
print query_names
if options.query_selection != '':
selected_queries = set(options.query_selection.lower().split(','))
query_names = list(set(query_names) & set(selected_queries))
query_names.sort()
print 'save_query'
polyDataOut = vtk.vtkAppendPolyData()
for query_name in query_names:
tr_out_temp = save_query(query_name, tr, options, evaluated_queries)
if tr_out_temp is not None:
tr_polydata = tracts_to_vtkPolyData64(tr_out_temp)
polyDataOut.AddInput(tr_polydata)
updateOutputNode(polyDataOut.GetOutput())
return
def vtkMatrix_2_array(m):
import numpy
out = numpy.zeros(shape=(4, 4))
for i in range(4):
for j in range(4):
out[i][j] = m.GetElement(i, j)
# This module was tested on 3D Slicer version 4.3.1
def visualNeedlePath(self, pos, pointOnTemplateRAS):
if type(pointOnTemplateRAS) == list:
pass
elif type(pointOnTemplateRAS) == int:
pointOnTemplateRAS = self.templateRAS[pointOnTemplateRAS]
self.pathModelNode = slicer.mrmlScene.GetNodeByID(self.needlePathModelNodeID)
if self.pathModelNode == None:
self.pathModelNode = slicer.vtkMRMLModelNode()
self.pathModelNode.SetName('AngulatedNeedlePath')
slicer.mrmlScene.AddNode(self.pathModelNode)
self.needlePathModelNodeID = self.pathModelNode.GetID()
self.dnodeSelectedPath = slicer.vtkMRMLModelDisplayNode()
self.dnodeSelectedPath.SetColor(0, 1, 1)
slicer.mrmlScene.AddNode(self.dnodeSelectedPath)
self.pathModelNode.SetAndObserveDisplayNodeID(self.dnodeSelectedPath.GetID())
pathModelAppend = vtk.vtkAppendPolyData()
tempLineSource = vtk.vtkLineSource()
tempLineSource.SetPoint1(pos) # target in RAS
tempLineSource.SetPoint2(pointOnTemplateRAS) # point on template in RAS
tempTubeFilter = vtk.vtkTubeFilter()
tempTubeFilter.SetInputConnection(tempLineSource.GetOutputPort())
tempTubeFilter.SetRadius(1.0)
tempTubeFilter.SetNumberOfSides(18)
tempTubeFilter.CappingOn()
tempTubeFilter.Update()
self.setModelSliceIntersectionVisibilityByID(self.needlePathModelNodeID, 1)
if vtk.VTK_MAJOR_VERSION <= 5:
pathModelAppend.AddInput(tempTubeFilter.GetOutput())
else:
pathModelAppend.AddInputData(tempTubeFilter.GetOutput())
pathModelAppend.Update()
self.pathModelNode.SetAndObservePolyData(pathModelAppend.GetOutput())
#
# Reslice along with the selected needle
#
print "(target) pos: ", pos
print "pointOnTemplateRAS: ", pointOnTemplateRAS
R = pointOnTemplateRAS[0]
A = pointOnTemplateRAS[1]
S = pointOnTemplateRAS[2]
deltaR = pos[0] - R
deltaA = pos[1] - A
deltaS = pos[2] - S
pathVector = numpy.array([deltaR, deltaA, deltaS])
tR = numpy.array([1.0, 0, 0])
vectorA = numpy.cross(pathVector, tR)
vectorS = numpy.cross(pathVector, vectorA)
pathVectorNorm = numpy.linalg.norm(pathVector)
vectorANorm = numpy.linalg.norm(vectorA)
vectorSNorm = numpy.linalg.norm(vectorS)
matrix = vtk.vtkMatrix4x4()
matrix.Identity()
## TODO: if pathVector is parallel to R
matrix.SetElement(0, 0, pathVector[0]/pathVectorNorm)
matrix.SetElement(1, 0, pathVector[1]/pathVectorNorm)
matrix.SetElement(2, 0, pathVector[2]/pathVectorNorm)
matrix.SetElement(0, 1, vectorA[0]/vectorANorm)
matrix.SetElement(1, 1, vectorA[1]/vectorANorm)
matrix.SetElement(2, 1, vectorA[2]/vectorANorm)
matrix.SetElement(0, 2, vectorS[0]/vectorSNorm)
matrix.SetElement(1, 2, vectorS[1]/vectorSNorm)
matrix.SetElement(2, 2, vectorS[2]/vectorSNorm)
matrix.SetElement(0, 3, R)
matrix.SetElement(1, 3, A)
matrix.SetElement(2, 3, S)
selectNeedleNode = slicer.mrmlScene.GetNodeByID(self.selectNeedleNodeID)
if selectNeedleNode == None:
selectNeedleNode = slicer.vtkMRMLLinearTransformNode()
selectNeedleNode.SetName('SelectedNeedle')
slicer.mrmlScene.AddNode(selectNeedleNode)
self.selectNeedleNodeID = selectNeedleNode.GetID()
selectNeedleNode.SetAndObserveMatrixTransformToParent(matrix)
modelNodes = slicer.mrmlScene.GetNodesByClass("vtkMRMLModelNode")
for index in range(modelNodes.GetNumberOfItems()):
indexNode = modelNodes.GetItemAsObject(index)
if indexNode.GetTransformNodeID() == selectNeedleNode.GetID():
indexNode.SetDisplayVisibility(1)
self.selectNeedleModelNode = indexNode
print indexNode.GetID()
red = slicer.mrmlScene.GetNodeByID("vtkMRMLSliceNodeRed")
yellow = slicer.mrmlScene.GetNodeByID("vtkMRMLSliceNodeYellow")
green = slicer.mrmlScene.GetNodeByID("vtkMRMLSliceNodeGreen")
## Changed by yz, Sep/25
## If 3D Slicer includes the extension "SlicerIGT", uncomment the below code
# vrdLogic = slicer.modules.volumereslicedriver.logic()
# redDriver = vrdLogic.SetDriverForSlice(selectNeedleNode.GetID(), red)
# redMode = vrdLogic.SetModeForSlice(vrdLogic.MODE_INPLANE, red)
# yellowDriver = vrdLogic.SetDriverForSlice(selectNeedleNode.GetID(), yellow)
# yellowMode = vrdLogic.SetModeForSlice(vrdLogic.MODE_INPLANE90, yellow)
# greenDriver = vrdLogic.SetDriverForSlice(selectNeedleNode.GetID(), green)
# greenMode = vrdLogic.SetModeForSlice(vrdLogic.MODE_TRANSVERSE, green)
# vrdLogic.Modified()
return pointOnTemplateRAS
def createTemplateModel(self):
self.templatePathVectors = []
self.templatePathOrigins = []
self.tempModelNode = slicer.mrmlScene.GetNodeByID(self.templateModelNodeID)
if self.tempModelNode is None:
self.tempModelNode = slicer.vtkMRMLModelNode()
self.tempModelNode.SetName('NeedleGuideTemplate')
slicer.mrmlScene.AddNode(self.tempModelNode)
self.templateModelNodeID = self.tempModelNode.GetID()
dnode = slicer.vtkMRMLModelDisplayNode()
#dnode.SetColor(self.ModelColor)
slicer.mrmlScene.AddNode(dnode)
self.tempModelNode.SetAndObserveDisplayNodeID(dnode.GetID())
self.modelNodetag = self.tempModelNode.AddObserver(slicer.vtkMRMLTransformableNode.TransformModifiedEvent,
self.onTemplateTransformUpdated)
self.pathModelNode = slicer.mrmlScene.GetNodeByID(self.needlePathModelNodeID)
if self.pathModelNode is None:
self.pathModelNode = slicer.vtkMRMLModelNode()
self.pathModelNode.SetName('NeedleGuideNeedlePath')
slicer.mrmlScene.AddNode(self.pathModelNode)
self.needlePathModelNodeID = self.pathModelNode.GetID()
dnode = slicer.vtkMRMLModelDisplayNode()
slicer.mrmlScene.AddNode(dnode)
self.pathModelNode.SetAndObserveDisplayNodeID(dnode.GetID())
pathModelAppend = vtk.vtkAppendPolyData()
tempModelAppend = vtk.vtkAppendPolyData()
for row in self.templateConfig:
p1 = numpy.array(row[0:3])
p2 = numpy.array(row[3:6])
tempLineSource = vtk.vtkLineSource()
tempLineSource.SetPoint1(p1)
tempLineSource.SetPoint2(p2)
tempTubeFilter = vtk.vtkTubeFilter()
tempTubeFilter.SetInputConnection(tempLineSource.GetOutputPort())
tempTubeFilter.SetRadius(1.0)
tempTubeFilter.SetNumberOfSides(18)
tempTubeFilter.CappingOn()
tempTubeFilter.Update()
pathLineSource = vtk.vtkLineSource()
v = p2-p1
nl = numpy.linalg.norm(v)
n = v/nl # normal vector
l = row[6]
p3 = p1 + l * n
pathLineSource.SetPoint1(p1)
pathLineSource.SetPoint2(p3)
self.templatePathOrigins.append([row[0], row[1], row[2], 1.0])
self.templatePathVectors.append([n[0], n[1], n[2], 1.0])
self.templateMaxDepth.append(row[6])
pathTubeFilter = vtk.vtkTubeFilter()
pathTubeFilter.SetInputConnection(pathLineSource.GetOutputPort())
pathTubeFilter.SetRadius(0.8)
pathTubeFilter.SetNumberOfSides(18)
pathTubeFilter.CappingOn()
pathTubeFilter.Update()
if vtk.VTK_MAJOR_VERSION <= 5:
tempModelAppend.AddInput(tempTubeFilter.GetOutput())
pathModelAppend.AddInput(pathTubeFilter.GetOutput())
else:
tempModelAppend.AddInputData(tempTubeFilter.GetOutput())
pathModelAppend.AddInputData(pathTubeFilter.GetOutput())
tempModelAppend.Update()
self.tempModelNode.SetAndObservePolyData(tempModelAppend.GetOutput())
pathModelAppend.Update()
self.pathModelNode.SetAndObservePolyData(pathModelAppend.GetOutput())
def createNeedleModelNode(self, name):
locatorModel = self.scene.CreateNodeByClass('vtkMRMLModelNode')
# Cylinder represents the locator stick
cylinder = vtk.vtkCylinderSource()
cylinder.SetRadius(1.5)
cylinder.SetHeight(100)
cylinder.SetCenter(0, 0, 0)
cylinder.Update()
# Rotate cylinder
tfilter = vtk.vtkTransformPolyDataFilter()
trans = vtk.vtkTransform()
trans.RotateX(90.0)
trans.Translate(0.0, -50.0, 0.0)
trans.Update()
if vtk.VTK_MAJOR_VERSION <= 5:
tfilter.SetInput(cylinder.GetOutput())
else:
tfilter.SetInputConnection(cylinder.GetOutputPort())
tfilter.SetTransform(trans)
tfilter.Update()
# Sphere represents the locator tip
sphere = vtk.vtkSphereSource()
sphere.SetRadius(3.0)
sphere.SetCenter(0, 0, 0)
sphere.Update()
apd = vtk.vtkAppendPolyData()
if vtk.VTK_MAJOR_VERSION <= 5:
apd.AddInput(sphere.GetOutput())
apd.AddInput(tfilter.GetOutput())
else:
apd.AddInputConnection(sphere.GetOutputPort())
apd.AddInputConnection(tfilter.GetOutputPort())
apd.Update()
locatorModel.SetAndObservePolyData(apd.GetOutput())
self.scene.AddNode(locatorModel)
locatorModel.SetScene(self.scene)
locatorModel.SetName(name)
locatorDisp = locatorModel.GetDisplayNodeID()
if locatorDisp == None:
locatorDisp = self.scene.CreateNodeByClass(
'vtkMRMLModelDisplayNode')
self.scene.AddNode(locatorDisp)
locatorDisp.SetScene(self.scene)
locatorModel.SetAndObserveDisplayNodeID(locatorDisp.GetID())
color = [0, 0, 0]
color[0] = 0.5
color[1] = 0.5
color[2] = 1.0
locatorDisp.SetColor(color)
return locatorModel.GetID()
def createTemplateModel(self):
self.templatePathVectors = []
self.templatePathOrigins = []
tempModelNode = slicer.mrmlScene.GetNodeByID(self.templateModelNodeID)
if tempModelNode == None:
tempModelNode = slicer.vtkMRMLModelNode()
tempModelNode.SetName('NeedleGuideTemplate')
slicer.mrmlScene.AddNode(tempModelNode)
self.templateModelNodeID = tempModelNode.GetID()
dnode = slicer.vtkMRMLModelDisplayNode()
slicer.mrmlScene.AddNode(dnode)
tempModelNode.SetAndObserveDisplayNodeID(dnode.GetID())
self.modelNodetag = tempModelNode.AddObserver(slicer.vtkMRMLTransformableNode.TransformModifiedEvent,
self.onTemplateTransformUpdated)
tempModelAppend = vtk.vtkAppendPolyData()
for row in self.templateConfig:
p1 = numpy.array(row[0:3])
p2 = numpy.array(row[3:6])
tempLineSource = vtk.vtkLineSource()
tempLineSource.SetPoint1(p1)
tempLineSource.SetPoint2(p2)
tempTubeFilter = vtk.vtkTubeFilter()
tempTubeFilter.SetInputConnection(tempLineSource.GetOutputPort())
tempTubeFilter.SetRadius(1.0)
tempTubeFilter.SetNumberOfSides(18)
tempTubeFilter.CappingOn()
tempTubeFilter.Update()
pathLineSource = vtk.vtkLineSource()
v = p2-p1
nl = numpy.linalg.norm(v)
n = v/nl # normal vector
l = row[6]
p3 = p1 + l * n
pathLineSource.SetPoint1(p1)
pathLineSource.SetPoint2(p3)
self.templatePathOrigins.append([row[0], row[1], row[2], 1.0])
self.templatePathVectors.append([n[0], n[1], n[2], 1.0])
self.templateMaxDepth.append(row[6])
pathTubeFilter = vtk.vtkTubeFilter()
pathTubeFilter.SetInputConnection(pathLineSource.GetOutputPort())
pathTubeFilter.SetRadius(0.8)
pathTubeFilter.SetNumberOfSides(18)
pathTubeFilter.CappingOn()
pathTubeFilter.Update()
if vtk.VTK_MAJOR_VERSION <= 5:
tempModelAppend.AddInput(tempTubeFilter.GetOutput())
# pathModelAppend.AddInput(pathTubeFilter.GetOutput())
else:
tempModelAppend.AddInputData(tempTubeFilter.GetOutput())
# pathModelAppend.AddInputData(pathTubeFilter.GetOutput())
tempModelAppend.Update()
tempModelNode.SetAndObservePolyData(tempModelAppend.GetOutput())
def run( self, markupNode, depth, fitPlane, flip ):
"""
Run the actual algorithm
"""
# Get all of the fiducial nodes and convert to vtkPoints
points = vtk.vtkPoints()
for i in range( 0, markupNode.GetNumberOfFiducials() ):
currentCoordinates = [ 0, 0, 0 ]
markupNode.GetNthFiducialPosition( i, currentCoordinates )
points.InsertNextPoint( currentCoordinates )
# Check that there is non-zero range in all coordinate directions
pointsBounds = [ 0, 0, 0, 0, 0, 0 ]
points.GetBounds( pointsBounds )
if ( pointsBounds[0] == pointsBounds [1] or pointsBounds[2] == pointsBounds [3] or pointsBounds[4] == pointsBounds [5] ):
print "Tissue Model Creator: Points have no extent in one or more coordinate directions."
return False
# Create a polydata object from the points
# The reversiness doesn't matter - we will fix it later if it os wrong
if ( fitPlane ):
surfacePolyData = self.PointsToPlanePolyData( points, True )
else:
surfacePolyData = self.PointsToSurfacePolyData( points, True )
surfaceCleaner = vtk.vtkCleanPolyData()
surfaceCleaner.SetInputData( surfacePolyData )
surfaceCleaner.Update()
surfacePolyData = surfaceCleaner.GetOutput()
mean = self.CalculateMean( points )
surfaceBase = [ 0, 0, 0 ]
surfaceDir1 = [ 0, 0, 0 ]
surfaceDir2 = [ 0, 0, 0 ]
surfaceNormal = [ 0, 0, 0 ]
self.CalculatePlane( surfacePolyData.GetPoints(), surfaceBase, surfaceDir1, surfaceDir2, surfaceNormal )
if ( flip == True ):
surfaceNormal[ 0 ] = - surfaceNormal[ 0 ]
surfaceNormal[ 1 ] = - surfaceNormal[ 1 ]
surfaceNormal[ 2 ] = - surfaceNormal[ 2 ]
extremePointIndex = self.FindExtremePoint( surfacePolyData.GetPoints(), surfaceBase, surfaceNormal )
reverse = self.ReverseNormals( extremePointIndex, surfacePolyData, surfaceNormal )
# Reverse the normals if necessary
reverseFilter = vtk.vtkReverseSense()
reverseFilter.SetInputData( surfacePolyData )
reverseFilter.SetReverseCells( reverse )
reverseFilter.SetReverseNormals( reverse )
reverseFilter.Update()
surfacePolyData = reverseFilter.GetOutput()
untransDeepPolyData = vtk.vtkPolyData()
untransDeepPolyData.DeepCopy( surfacePolyData )
# Make the normals opposite the surface's normals
reverseFilter = vtk.vtkReverseSense()
reverseFilter.SetInputData( untransDeepPolyData )
reverseFilter.SetReverseCells( True )
reverseFilter.SetReverseNormals( True )
reverseFilter.Update()
untransDeepPolyData = reverseFilter.GetOutput()
deepTransform = vtk.vtkTransform()
deepTransform.Translate( depth * surfaceNormal[0], depth * surfaceNormal[1], depth * surfaceNormal[2] )
deepTransformFilter = vtk.vtkTransformPolyDataFilter()
deepTransformFilter.SetInputData( untransDeepPolyData )
deepTransformFilter.SetTransform( deepTransform )
deepTransformFilter.Update()
deepPolyData = deepTransformFilter.GetOutput()
surfaceHullPoints = self.GetBoundaryPoints( surfacePolyData )
deepHullPoints = self.GetBoundaryPoints( deepPolyData )
# Apparently, the joining needs an offset for the plane, but not for the surface reconstruction
if ( fitPlane ):
jointHullPolyData = self.JoinBoundaryPoints( surfaceHullPoints, deepHullPoints, 1 )
else:
jointHullPolyData = self.JoinBoundaryPoints( surfaceHullPoints, deepHullPoints, 0 )
# Append all of the polydata together
tissuePolyDataAppend = vtk.vtkAppendPolyData()
tissuePolyDataAppend.AddInputData( surfacePolyData )
tissuePolyDataAppend.AddInputData( deepPolyData )
tissuePolyDataAppend.AddInputData( jointHullPolyData )
tissuePolyDataAppend.Update()
# Clean up so the surface is closed
tissueCleaner = vtk.vtkCleanPolyData()
tissueCleaner.SetInputData( tissuePolyDataAppend.GetOutput() )
tissueCleaner.Update()
tissueModelPolyData = tissueCleaner.GetOutput()
# Add the data to a model
tissueModel = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLModelNode" )
slicer.mrmlScene.AddNode( tissueModel )
tissueModel.SetName( "TissueModel" )
tissueModel.SetAndObservePolyData( tissueModelPolyData )
tissueModel.SetScene( slicer.mrmlScene )
# Finally display the model
tissueModelDisplay = slicer.mrmlScene.CreateNodeByClass( "vtkMRMLModelDisplayNode" )
slicer.mrmlScene.AddNode( tissueModelDisplay )
tissueModel.SetAndObserveDisplayNodeID( tissueModelDisplay.GetID() )
tissueModelDisplay.SetScene( slicer.mrmlScene )
tissueModelDisplay.SetInputPolyDataConnection( tissueModel.GetPolyDataConnection() )
# Check to make sure the model is a closed surface
edgesFilter = vtk.vtkFeatureEdges()
edgesFilter.FeatureEdgesOff()
edgesFilter.BoundaryEdgesOn()
edgesFilter.NonManifoldEdgesOn()
edgesFilter.SetInputData( tissueModel.GetPolyData() )
edgesFilter.Update()
if ( edgesFilter.GetOutput().GetNumberOfCells() != 0 ):
print "Tissue Model Creator: Surface is not closed."
return False
return True
