def setupMRMLTracking(self):
if not hasattr(self, "trackingDevice"):
""" set up the mrml parts or use existing """
nodes = slicer.mrmlScene.GetNodesByName('trackingDevice')
if nodes.GetNumberOfItems() > 0:
self.trackingDevice = nodes.GetItemAsObject(0)
nodes = slicer.mrmlScene.GetNodesByName('tracker')
self.tracker = nodes.GetItemAsObject(0)
else:
# trackingDevice cursor
self.cube = vtk.vtkCubeSource()
self.cube.SetXLength(30)
self.cube.SetYLength(70)
self.cube.SetZLength(5)
self.cube.Update()
# display node
self.modelDisplay = slicer.vtkMRMLModelDisplayNode()
self.modelDisplay.SetColor(1,1,0) # yellow
slicer.mrmlScene.AddNode(self.modelDisplay)
# self.modelDisplay.SetPolyData(self.cube.GetOutputPort())
# Create model node
self.trackingDevice = slicer.vtkMRMLModelNode()
self.trackingDevice.SetScene(slicer.mrmlScene)
self.trackingDevice.SetName("trackingDevice")
self.trackingDevice.SetAndObservePolyData(self.cube.GetOutputDataObject(0))
self.trackingDevice.SetAndObserveDisplayNodeID(self.modelDisplay.GetID())
slicer.mrmlScene.AddNode(self.trackingDevice)
# tracker
self.tracker = slicer.vtkMRMLLinearTransformNode()
self.tracker.SetName('tracker')
slicer.mrmlScene.AddNode(self.tracker)
self.trackingDevice.SetAndObserveTransformNodeID(self.tracker.GetID())
def createBox(X, Y, Z, name):
miterBox = slicer.mrmlScene.CreateNodeByClass('vtkMRMLModelNode')
miterBox.SetName(slicer.mrmlScene.GetUniqueNameByString(name))
slicer.mrmlScene.AddNode(miterBox)
miterBox.CreateDefaultDisplayNodes()
miterBoxSource = vtk.vtkCubeSource()
miterBoxSource.SetXLength(X)
miterBoxSource.SetYLength(Y)
miterBoxSource.SetZLength(Z)
triangleFilter = vtk.vtkTriangleFilter()
triangleFilter.SetInputConnection(miterBoxSource.GetOutputPort())
#triangleFilter.Update()
miterBox.SetPolyDataConnection(triangleFilter.GetOutputPort())
return miterBox
def cropPoints(self, input):
#Get bounds of screw
bounds = input.GetPolyData().GetBounds()
#Create a cube with bounds equal to that of the screw minus the head (-17)
cropCube = vtk.vtkCubeSource()
cropCube.SetBounds(bounds[0],bounds[1],bounds[2],bounds[3]-17,bounds[4],bounds[5])
#Select points on screw within cube
select = vtk.vtkSelectEnclosedPoints()
select.SetInput(input.GetPolyData())
select.SetSurface(cropCube.GetOutput())
select.Update()
return select
def cropPoints(self, input):
#Get bounds of screw
bounds = input.GetPolyData().GetBounds()
#Create a cube with bounds equal to that of the screw minus the head (-17)
cropCube = vtk.vtkCubeSource()
cropCube.SetBounds(bounds[0],bounds[1],bounds[2],bounds[3]-17,bounds[4],bounds[5])
#Select points on screw within cube
select = vtk.vtkSelectEnclosedPoints()
select.SetInput(input.GetPolyData())
select.SetSurface(cropCube.GetOutput())
select.Update()
return select
def startTransformMapping(self, groundTruthTransformNode, mappedTransformNode, outputVisitedPointsModelNode, positionErrorTransformNode, orientationErrorTransformNode):
self.removeObservers()
self.groundTruthTransformNode = groundTruthTransformNode
self.mappedTransformNode = mappedTransformNode
self.outputVisitedPointsModelNode = outputVisitedPointsModelNode
self.positionErrorTransformNode = positionErrorTransformNode
self.orientationErrorTransformNode = orientationErrorTransformNode
self.positionErrorMagnitudeList = []
self.orientationErrorMagnitudeList = []
if self.outputVisitedPointsModelNode:
if not self.outputVisitedPointsModelNode.GetDisplayNode():
modelDisplay = slicer.vtkMRMLModelDisplayNode()
#modelDisplay.SetSliceIntersectionVisibility(False) # Show in slice view
#modelDisplay.SetEdgeVisibility(True) # Hide in 3D view
modelDisplay.SetEdgeVisibility(True)
slicer.mrmlScene.AddNode(modelDisplay)
self.outputVisitedPointsModelNode.SetAndObserveDisplayNodeID(modelDisplay.GetID())
self.visitedPoints = vtk.vtkPoints()
self.visitedPointsPolydata = vtk.vtkPolyData()
self.visitedPointsPolydata.SetPoints(self.visitedPoints)
glyph = vtk.vtkPolyData()
cubeSource = vtk.vtkCubeSource()
cubeSource.SetXLength(self.minimumSamplingDistance)
cubeSource.SetYLength(self.minimumSamplingDistance)
cubeSource.SetZLength(self.minimumSamplingDistance)
self.visitedPointsGlyph3d = vtk.vtkGlyph3D()
self.visitedPointsGlyph3d.SetSourceConnection(cubeSource.GetOutputPort())
self.visitedPointsGlyph3d.SetInputData(self.visitedPointsPolydata)
self.visitedPointsGlyph3d.Update()
self.outputVisitedPointsModelNode.SetPolyDataConnection(self.visitedPointsGlyph3d.GetOutputPort())
self.initializeErrorTransform(self.positionErrorTransformNode)
self.initializeErrorTransform(self.orientationErrorTransformNode)
# Start the updates
self.addObservers()
self.onGroundTruthTransformNodeModified(0,0)
def tableCursor(self, dimensions=(900, 30, 600)):
"""Create the mrml structure to represent the table if needed
otherwise return the current transform
dimensions : left-right, up-down, in-out size of table
"""
transformName = 'Table-To-Camera'
transformNode = slicer.util.getNode(transformName)
if not transformNode:
# make the mrml
box = vtk.vtkCubeSource()
box.SetXLength(dimensions[0])
box.SetYLength(dimensions[1])
box.SetZLength(dimensions[2])
box.SetCenter(0, -dimensions[1] / 2., 0)
box.Update()
# Create model node
cursor = slicer.vtkMRMLModelNode()
cursor.SetScene(slicer.mrmlScene)
cursor.SetName("Cursor-Table")
cursor.SetAndObservePolyData(box.GetOutput())
# Create display node
cursorModelDisplay = slicer.vtkMRMLModelDisplayNode()
cursorModelDisplay.SetColor(
(0.86274509803921573, ) * 3) # 'gainsboro'
cursorModelDisplay.SetOpacity(0.5)
cursorModelDisplay.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(cursorModelDisplay)
cursor.SetAndObserveDisplayNodeID(cursorModelDisplay.GetID())
# Add to slicer.mrmlScene
cursorModelDisplay.SetInputPolyData(box.GetOutput())
slicer.mrmlScene.AddNode(cursor)
# Create transform node
transformNode = slicer.vtkMRMLLinearTransformNode()
transformNode.SetName(transformName)
slicer.mrmlScene.AddNode(transformNode)
tableToCamera = vtk.vtkMatrix4x4()
tableToCamera.SetElement(1, 3, -100)
transformNode.GetMatrixTransformToParent().DeepCopy(tableToCamera)
cursor.SetAndObserveTransformNodeID(transformNode.GetID())
return transformNode
def startTransformMapping(self, groundTruthTransformNode, mappedTransformNode, outputVisitedPointsModelNode, positionErrorTransformNode, orientationErrorTransformNode):
self.removeObservers()
self.groundTruthTransformNode = groundTruthTransformNode
self.mappedTransformNode = mappedTransformNode
self.outputVisitedPointsModelNode = outputVisitedPointsModelNode
self.positionErrorTransformNode = positionErrorTransformNode
self.orientationErrorTransformNode = orientationErrorTransformNode
self.positionErrorMagnitudeList = []
self.orientationErrorMagnitudeList = []
if self.outputVisitedPointsModelNode:
if not self.outputVisitedPointsModelNode.GetDisplayNode():
modelDisplay = slicer.vtkMRMLModelDisplayNode()
#modelDisplay.SetSliceIntersectionVisibility(False) # Show in slice view
#modelDisplay.SetEdgeVisibility(True) # Hide in 3D view
modelDisplay.SetEdgeVisibility(True)
slicer.mrmlScene.AddNode(modelDisplay)
self.outputVisitedPointsModelNode.SetAndObserveDisplayNodeID(modelDisplay.GetID())
self.visitedPoints = vtk.vtkPoints()
self.visitedPointsPolydata = vtk.vtkPolyData()
self.visitedPointsPolydata.SetPoints(self.visitedPoints)
glyph = vtk.vtkPolyData()
cubeSource = vtk.vtkCubeSource()
cubeSource.SetXLength(self.minimumSamplingDistance)
cubeSource.SetYLength(self.minimumSamplingDistance)
cubeSource.SetZLength(self.minimumSamplingDistance)
self.visitedPointsGlyph3d = vtk.vtkGlyph3D()
self.visitedPointsGlyph3d.SetSourceConnection(cubeSource.GetOutputPort())
self.visitedPointsGlyph3d.SetInputData(self.visitedPointsPolydata)
self.visitedPointsGlyph3d.Update()
self.outputVisitedPointsModelNode.SetPolyDataConnection(self.visitedPointsGlyph3d.GetOutputPort())
self.initializeErrorTransform(self.positionErrorTransformNode)
self.initializeErrorTransform(self.orientationErrorTransformNode)
# Start the updates
self.addObservers()
self.onGroundTruthTransformNodeModified(0,0)
def tableCursor(self,dimensions=(900,30,600)):
"""Create the mrml structure to represent the table if needed
otherwise return the current transform
dimensions : left-right, up-down, in-out size of table
"""
transformName = 'Table-To-Camera'
transformNode = slicer.util.getNode(transformName)
if not transformNode:
# make the mrml
box = vtk.vtkCubeSource()
box.SetXLength(dimensions[0])
box.SetYLength(dimensions[1])
box.SetZLength(dimensions[2])
box.SetCenter(0,-dimensions[1]/2.,0)
box.Update()
# Create model node
cursor = slicer.vtkMRMLModelNode()
cursor.SetScene(slicer.mrmlScene)
cursor.SetName("Cursor-Table")
cursor.SetAndObservePolyData(box.GetOutput())
# Create display node
cursorModelDisplay = slicer.vtkMRMLModelDisplayNode()
cursorModelDisplay.SetColor((0.86274509803921573,)*3) # 'gainsboro'
cursorModelDisplay.SetOpacity(0.5)
cursorModelDisplay.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(cursorModelDisplay)
cursor.SetAndObserveDisplayNodeID(cursorModelDisplay.GetID())
# Add to slicer.mrmlScene
cursorModelDisplay.SetInputPolyData(box.GetOutput())
slicer.mrmlScene.AddNode(cursor)
# Create transform node
transformNode = slicer.vtkMRMLLinearTransformNode()
transformNode.SetName(transformName)
slicer.mrmlScene.AddNode(transformNode)
tableToCamera = vtk.vtkMatrix4x4()
tableToCamera.SetElement(1, 3, -100)
transformNode.GetMatrixTransformToParent().DeepCopy(tableToCamera)
cursor.SetAndObserveTransformNodeID(transformNode.GetID())
return transformNode
def transform(self,cmd):
if not hasattr(self,'p'):
self.p = numpy.zeros(3)
self.dpdt = numpy.zeros(3)
self.d2pdt2 = numpy.zeros(3)
self.o = numpy.zeros(3)
self.dodt = numpy.zeros(3)
self.d2odt2 = numpy.zeros(3)
p = urlparse.urlparse(cmd)
q = urlparse.parse_qs(p.query)
self.logMessage (q)
dt = float(q['interval'][0])
self.d2pdt2 = 1000 * numpy.array([float(q['x'][0]), float(q['y'][0]), float(q['z'][0])])
if not hasattr(self,'g0'):
self.g0 = self.d2pdt2
self.d2pdt2 = self.d2pdt2 - self.g0
self.dpdt = self.dpdt + dt * self.d2pdt2
self.p = self.p + dt * self.dpdt
# TODO: integrate rotations
if not hasattr(self, "idevice"):
""" set up the mrml parts or use existing """
nodes = slicer.mrmlScene.GetNodesByName('idevice')
if nodes.GetNumberOfItems() > 0:
self.idevice = nodes.GetItemAsObject(0)
nodes = slicer.mrmlScene.GetNodesByName('tracker')
self.tracker = nodes.GetItemAsObject(0)
else:
# idevice cursor
self.cube = vtk.vtkCubeSource()
self.cube.SetXLength(30)
self.cube.SetYLength(70)
self.cube.SetZLength(5)
self.cube.Update()
# display node
self.modelDisplay = slicer.vtkMRMLModelDisplayNode()
self.modelDisplay.SetColor(1,1,0) # yellow
slicer.mrmlScene.AddNode(self.modelDisplay)
self.modelDisplay.SetPolyData(self.cube.GetOutput())
# Create model node
self.idevice = slicer.vtkMRMLModelNode()
self.idevice.SetScene(slicer.mrmlScene)
self.idevice.SetName("idevice")
self.idevice.SetAndObservePolyData(self.cube.GetOutput())
self.idevice.SetAndObserveDisplayNodeID(self.modelDisplay.GetID())
slicer.mrmlScene.AddNode(self.idevice)
# tracker
self.tracker = slicer.vtkMRMLLinearTransformNode()
self.tracker.SetName('tracker')
slicer.mrmlScene.AddNode(self.tracker)
self.idevice.SetAndObserveTransformNodeID(self.tracker.GetID())
m = self.tracker.GetMatrixTransformToParent()
m.Identity()
up = numpy.zeros(3)
up[2] = 1
d = self.d2pdt2
dd = d / numpy.sqrt(numpy.dot(d,d))
xx = numpy.cross(dd,up)
yy = numpy.cross(dd,xx)
for row in xrange(3):
m.SetElement(row,0, dd[row])
m.SetElement(row,1, xx[row])
m.SetElement(row,2, yy[row])
#m.SetElement(row,3, self.p[row])
return ( "got it" )
# This module was tested on 3D Slicer version 4.3.1
def CreateSlit(self, normal, pathPolydata, ruler, ROI, slitSize):
""" Here we are going to create a boxSource , the size of the 2*ROI in the X,Y
and the size of the slit Size in the Z.
We are then going to translate the box source to its correct location in slicer
As always to visualize , a DEBUG option can be set at the top.
x is L->R, y is P->A, z is I->S
"""
# Cube Creation
roiPoints = self.utility.GetROIPoints(ROI)
frontExtentIndex = self.utility.GetClosestExtent(ruler, ROI)
backExtentIndex = self.utility.GetOppositeExtent(frontExtentIndex)
pointA = numpy.array(roiPoints[frontExtentIndex])
pointB = numpy.array(roiPoints[backExtentIndex])
yDist = numpy.linalg.norm(pointA - pointB)
numPoints = pathPolydata.GetNumberOfPoints()
pointA = numpy.array(pathPolydata.GetPoint(0))
pointB = numpy.array(pathPolydata.GetPoint(numPoints - 1))
xDist = numpy.linalg.norm(pointA - pointB)
zDist = slitSize # Rewording the parameter to make it easier to understand
slitCube = vtk.vtkCubeSource()
slitCube.SetBounds(0, xDist, -yDist, yDist, -zDist / 2, zDist / 2) # (Xmin, Xmax, Ymin, Ymax,Zmin, Zmax)
# Transforming Cube
transformFilter = vtk.vtkTransformFilter()
transform = vtk.vtkTransform()
matrix = vtk.vtkMatrix4x4()
pointA = numpy.array(pathPolydata.GetPoint(0))
pointB = numpy.array(pathPolydata.GetPoint(numPoints - 1))
xVector = pointA - pointB
xDist = numpy.linalg.norm(pointA - pointB)
xUnitVector = (xVector[0] / xDist, xVector[1] / xDist, xVector[2] / xDist)
yVector = self.utility.GetRulerVector(ruler)
yDist = numpy.linalg.norm(yVector)
yUnitVector = (yVector[0] / yDist, yVector[1] / yDist, yVector[2] / yDist)
zVector = numpy.cross(xVector, yVector)
zDist = numpy.linalg.norm(zVector)
zUnitVector = (zVector[0] / zDist, zVector[1] / zDist, zVector[2] / zDist)
origin = pointA = numpy.array(pathPolydata.GetPoint(numPoints - 1))
matrix.DeepCopy(
(
xUnitVector[0],
yUnitVector[0],
zUnitVector[0],
origin[0],
xUnitVector[1],
yUnitVector[1],
zUnitVector[1],
origin[1],
xUnitVector[2],
yUnitVector[2],
zUnitVector[2],
origin[2],
0,
0,
0,
1,
)
)
transform.SetMatrix(matrix)
transformFilter.SetTransform(transform)
transformFilter.SetInputConnection(slitCube.GetOutputPort())
transformFilter.Update()
self.slitPlanes.append(transformFilter.GetOutput())
if len(self.slitPlanes) == self.numberOfPaths and self.DEBUG_SLITPLANES == True:
for i in range(self.numberOfPaths):
self.utility.DisplayPolyData("Slit" + str(i), self.slitPlanes[i])
return transformFilter.GetOutput()
def CreateSlit(self, normal, pathPolydata, ruler, ROI, slitSize):
""" Here we are going to create a boxSource , the size of the 2*ROI in the X,Y
and the size of the slit Size in the Z.
We are then going to translate the box source to its correct location in slicer
As always to visualize , a DEBUG option can be set at the top.
x is L->R, y is P->A, z is I->S
"""
#Cube Creation
roiPoints = self.utility.GetROIPoints(ROI)
frontExtentIndex = self.utility.GetClosestExtent(ruler, ROI)
backExtentIndex = self.utility.GetOppositeExtent(frontExtentIndex)
pointA = numpy.array(roiPoints[frontExtentIndex])
pointB = numpy.array(roiPoints[backExtentIndex])
yDist = numpy.linalg.norm(pointA - pointB)
numPoints = pathPolydata.GetNumberOfPoints()
pointA = numpy.array(pathPolydata.GetPoint(0))
pointB = numpy.array(pathPolydata.GetPoint(numPoints - 1))
xDist = numpy.linalg.norm(pointA - pointB)
zDist = slitSize #Rewording the parameter to make it easier to understand
slitCube = vtk.vtkCubeSource()
slitCube.SetBounds(0, xDist, -yDist, yDist, -zDist / 2,
zDist / 2) # (Xmin, Xmax, Ymin, Ymax,Zmin, Zmax)
#Transforming Cube
transformFilter = vtk.vtkTransformFilter()
transform = vtk.vtkTransform()
matrix = vtk.vtkMatrix4x4()
pointA = numpy.array(pathPolydata.GetPoint(0))
pointB = numpy.array(pathPolydata.GetPoint(numPoints - 1))
xVector = pointA - pointB
xDist = numpy.linalg.norm(pointA - pointB)
xUnitVector = (xVector[0] / xDist, xVector[1] / xDist,
xVector[2] / xDist)
yVector = self.utility.GetRulerVector(ruler)
yDist = numpy.linalg.norm(yVector)
yUnitVector = (yVector[0] / yDist, yVector[1] / yDist,
yVector[2] / yDist)
zVector = numpy.cross(xVector, yVector)
zDist = numpy.linalg.norm(zVector)
zUnitVector = (zVector[0] / zDist, zVector[1] / zDist,
zVector[2] / zDist)
origin = pointA = numpy.array(pathPolydata.GetPoint(numPoints - 1))
matrix.DeepCopy(
(xUnitVector[0], yUnitVector[0], zUnitVector[0], origin[0],
xUnitVector[1], yUnitVector[1], zUnitVector[1], origin[1],
xUnitVector[2], yUnitVector[2], zUnitVector[2], origin[2], 0, 0,
0, 1))
transform.SetMatrix(matrix)
transformFilter.SetTransform(transform)
transformFilter.SetInputConnection(slitCube.GetOutputPort())
transformFilter.Update()
self.slitPlanes.append(transformFilter.GetOutput())
if len(self.slitPlanes
) == self.numberOfPaths and self.DEBUG_SLITPLANES == True:
for i in range(self.numberOfPaths):
self.utility.DisplayPolyData("Slit" + str(i),
self.slitPlanes[i])
return transformFilter.GetOutput()
def transform(self, cmd):
if not hasattr(self, 'p'):
self.p = numpy.zeros(3)
self.dpdt = numpy.zeros(3)
self.d2pdt2 = numpy.zeros(3)
self.o = numpy.zeros(3)
self.dodt = numpy.zeros(3)
self.d2odt2 = numpy.zeros(3)
p = urlparse.urlparse(cmd)
q = urlparse.parse_qs(p.query)
self.logMessage(q)
dt = float(q['interval'][0])
self.d2pdt2 = 1000 * numpy.array(
[float(q['x'][0]),
float(q['y'][0]),
float(q['z'][0])])
if not hasattr(self, 'g0'):
self.g0 = self.d2pdt2
self.d2pdt2 = self.d2pdt2 - self.g0
self.dpdt = self.dpdt + dt * self.d2pdt2
self.p = self.p + dt * self.dpdt
# TODO: integrate rotations
if not hasattr(self, "idevice"):
""" set up the mrml parts or use existing """
nodes = slicer.mrmlScene.GetNodesByName('idevice')
if nodes.GetNumberOfItems() > 0:
self.idevice = nodes.GetItemAsObject(0)
nodes = slicer.mrmlScene.GetNodesByName('tracker')
self.tracker = nodes.GetItemAsObject(0)
else:
# idevice cursor
self.cube = vtk.vtkCubeSource()
self.cube.SetXLength(30)
self.cube.SetYLength(70)
self.cube.SetZLength(5)
self.cube.Update()
# display node
self.modelDisplay = slicer.vtkMRMLModelDisplayNode()
self.modelDisplay.SetColor(1, 1, 0) # yellow
slicer.mrmlScene.AddNode(self.modelDisplay)
self.modelDisplay.SetPolyData(self.cube.GetOutput())
# Create model node
self.idevice = slicer.vtkMRMLModelNode()
self.idevice.SetScene(slicer.mrmlScene)
self.idevice.SetName("idevice")
self.idevice.SetAndObservePolyData(self.cube.GetOutput())
self.idevice.SetAndObserveDisplayNodeID(
self.modelDisplay.GetID())
slicer.mrmlScene.AddNode(self.idevice)
# tracker
self.tracker = slicer.vtkMRMLLinearTransformNode()
self.tracker.SetName('tracker')
slicer.mrmlScene.AddNode(self.tracker)
self.idevice.SetAndObserveTransformNodeID(self.tracker.GetID())
m = self.tracker.GetMatrixTransformToParent()
m.Identity()
up = numpy.zeros(3)
up[2] = 1
d = self.d2pdt2
dd = d / numpy.sqrt(numpy.dot(d, d))
xx = numpy.cross(dd, up)
yy = numpy.cross(dd, xx)
for row in xrange(3):
m.SetElement(row, 0, dd[row])
m.SetElement(row, 1, xx[row])
m.SetElement(row, 2, yy[row])
#m.SetElement(row,3, self.p[row])
return ("got it")
def createTumorFromMarkups(self):
logging.debug('createTumorFromMarkups')
#self.tumorMarkups_Needle.SetDisplayVisibility(0)
# Create polydata point set from markup points
points = vtk.vtkPoints()
cellArray = vtk.vtkCellArray()
numberOfPoints = self.tumorMarkups_Needle.GetNumberOfFiducials()
if numberOfPoints > 0:
self.deleteLastFiducialButton.setEnabled(True)
self.deleteAllFiducialsButton.setEnabled(True)
self.deleteLastFiducialDuringNavigationButton.setEnabled(True)
# Surface generation algorithms behave unpredictably when there are not enough points
# return if there are very few points
if numberOfPoints < 1:
return
points.SetNumberOfPoints(numberOfPoints)
new_coord = [0.0, 0.0, 0.0]
for i in range(numberOfPoints):
self.tumorMarkups_Needle.GetNthFiducialPosition(i, new_coord)
points.SetPoint(i, new_coord)
cellArray.InsertNextCell(numberOfPoints)
for i in range(numberOfPoints):
cellArray.InsertCellPoint(i)
pointPolyData = vtk.vtkPolyData()
pointPolyData.SetLines(cellArray)
pointPolyData.SetPoints(points)
delaunay = vtk.vtkDelaunay3D()
if numberOfPoints < 10:
logging.debug("use glyphs")
sphere = vtk.vtkCubeSource()
glyph = vtk.vtkGlyph3D()
glyph.SetInputData(pointPolyData)
glyph.SetSourceConnection(sphere.GetOutputPort())
#glyph.SetVectorModeToUseNormal()
#glyph.SetScaleModeToScaleByVector()
#glyph.SetScaleFactor(0.25)
delaunay.SetInputConnection(glyph.GetOutputPort())
else:
delaunay.SetInputData(pointPolyData)
surfaceFilter = vtk.vtkDataSetSurfaceFilter()
surfaceFilter.SetInputConnection(delaunay.GetOutputPort())
smoother = vtk.vtkButterflySubdivisionFilter()
smoother.SetInputConnection(surfaceFilter.GetOutputPort())
smoother.SetNumberOfSubdivisions(3)
smoother.Update()
forceConvexShape = True
if (forceConvexShape == True):
delaunaySmooth = vtk.vtkDelaunay3D()
delaunaySmooth.SetInputData(smoother.GetOutput())
delaunaySmooth.Update()
smoothSurfaceFilter = vtk.vtkDataSetSurfaceFilter()
smoothSurfaceFilter.SetInputConnection(
delaunaySmooth.GetOutputPort())
self.tumorModel_Needle.SetPolyDataConnection(
smoothSurfaceFilter.GetOutputPort())
else:
self.tumorModel_Needle.SetPolyDataConnection(
smoother.GetOutputPort())
self.tumorModel_Needle.Modified()
def createTumorFromMarkups(self):
logging.debug("createTumorFromMarkups")
# self.tumorMarkups_Needle.SetDisplayVisibility(0)
# Create polydata point set from markup points
points = vtk.vtkPoints()
cellArray = vtk.vtkCellArray()
numberOfPoints = self.tumorMarkups_Needle.GetNumberOfFiducials()
if numberOfPoints > 0:
self.deleteLastFiducialButton.setEnabled(True)
self.deleteAllFiducialsButton.setEnabled(True)
self.deleteLastFiducialDuringNavigationButton.setEnabled(True)
# Surface generation algorithms behave unpredictably when there are not enough points
# return if there are very few points
if numberOfPoints < 1:
return
points.SetNumberOfPoints(numberOfPoints)
new_coord = [0.0, 0.0, 0.0]
for i in range(numberOfPoints):
self.tumorMarkups_Needle.GetNthFiducialPosition(i, new_coord)
points.SetPoint(i, new_coord)
cellArray.InsertNextCell(numberOfPoints)
for i in range(numberOfPoints):
cellArray.InsertCellPoint(i)
pointPolyData = vtk.vtkPolyData()
pointPolyData.SetLines(cellArray)
pointPolyData.SetPoints(points)
delaunay = vtk.vtkDelaunay3D()
if numberOfPoints < 10:
logging.debug("use glyphs")
sphere = vtk.vtkCubeSource()
glyph = vtk.vtkGlyph3D()
glyph.SetInputData(pointPolyData)
glyph.SetSourceConnection(sphere.GetOutputPort())
# glyph.SetVectorModeToUseNormal()
# glyph.SetScaleModeToScaleByVector()
# glyph.SetScaleFactor(0.25)
delaunay.SetInputConnection(glyph.GetOutputPort())
else:
delaunay.SetInputData(pointPolyData)
surfaceFilter = vtk.vtkDataSetSurfaceFilter()
surfaceFilter.SetInputConnection(delaunay.GetOutputPort())
smoother = vtk.vtkButterflySubdivisionFilter()
smoother.SetInputConnection(surfaceFilter.GetOutputPort())
smoother.SetNumberOfSubdivisions(3)
smoother.Update()
forceConvexShape = True
if forceConvexShape == True:
delaunaySmooth = vtk.vtkDelaunay3D()
delaunaySmooth.SetInputData(smoother.GetOutput())
delaunaySmooth.Update()
smoothSurfaceFilter = vtk.vtkDataSetSurfaceFilter()
smoothSurfaceFilter.SetInputConnection(delaunaySmooth.GetOutputPort())
self.tumorModel_Needle.SetPolyDataConnection(smoothSurfaceFilter.GetOutputPort())
else:
self.tumorModel_Needle.SetPolyDataConnection(smoother.GetOutputPort())
self.tumorModel_Needle.Modified()
