def IntersectBaseModel(self):
transform = vtk.vtkTransform()
matrix = vtk.vtkMatrix4x4()
self.transformSelector.currentNode().GetMatrixTransformToParent(matrix)
transform.SetMatrix(matrix)
#transform.RotateX(-90.0)
# cylinder = vtk.vtkCylinderSource()
# cylinder.SetCenter(np.array([0.0, 0.0, 0.0]))
# cylinder.SetRadius(25)
# cylinder.SetHeight(60)
# cylinder.SetResolution(100)
# cylinder.Update()
originalCylinder_path = os.path.dirname(
os.path.realpath(__file__)) + "\\Models\\OriginalCylinder.stl"
originalCylinderModelNode = slicer.util.loadModel(
originalCylinder_path)
transformFilter = vtk.vtkTransformPolyDataFilter()
transformFilter.SetInputData(originalCylinderModelNode.GetPolyData())
transformFilter.SetTransform(transform)
transformFilter.ReleaseDataFlagOn()
transformFilter.Update()
modelNode = self.booleanModelSelector.currentNode()
modelNode.SetAndObservePolyData(transformFilter.GetOutput())
modelDisplayNode = modelNode.GetModelDisplayNode()
if modelDisplayNode is None:
modelDisplayNode = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(modelDisplayNode)
modelNode.SetAndObserveDisplayNodeID(modelDisplayNode.GetID())
modelDisplayNode.SetOpacity(0.2)
modelDisplayNode.SetColor(0, 1, 0)
modelNode2 = self.transientModelSelector.currentNode()
modelDisplayNode2 = self.transientModelSelector.currentNode(
).GetModelDisplayNode()
if modelDisplayNode2 is None:
modelDisplayNode2 = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode2.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(modelDisplayNode2)
modelNode2.SetAndObserveDisplayNodeID(modelDisplayNode2.GetID())
modelDisplayNode2.SetOpacity(1.0)
modelDisplayNode2.SetColor(0, 1, 0)
cylinder_path = os.path.dirname(
os.path.realpath(__file__)) + "\\Models\\cylinder.stl"
slicer.util.saveNode(modelNode, cylinder_path)
slicer.mrmlScene.RemoveNode(originalCylinderModelNode)
self.blenderBoolean()
def updateCurve(self):
if self.SourceNode and self.DestinationNode:
if self.SourceNode.GetNumberOfFiducials() < 2:
if self.CurvePoly != None:
self.CurvePoly.Initialize()
else:
if self.CurvePoly == None:
self.CurvePoly = vtk.vtkPolyData()
if self.DestinationNode.GetDisplayNodeID() == None:
modelDisplayNode = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode.SetColor(self.CurveColour)
slicer.mrmlScene.AddNode(modelDisplayNode)
self.DestinationNode.SetAndObserveDisplayNodeID(
modelDisplayNode.GetID())
if self.InterpolationMethod == 0:
self.nodesToLinear(self.SourceNode, self.CurvePoly)
elif self.InterpolationMethod == 1:
self.nodesToSpline(self.SourceNode, self.CurvePoly)
tubeFilter = vtk.vtkTubeFilter()
tubeFilter.SetInputData(self.CurvePoly)
tubeFilter.SetRadius(self.CurveThickness)
tubeFilter.SetNumberOfSides(self.CurveFaces)
tubeFilter.CappingOn()
tubeFilter.Update()
self.DestinationNode.SetAndObservePolyData(tubeFilter.GetOutput())
self.DestinationNode.Modified()
if self.DestinationNode.GetScene() == None:
slicer.mrmlScene.AddNode(self.DestinationNode)
displayNode = self.DestinationNode.GetDisplayNode()
if displayNode:
displayNode.SetActiveScalarName('')
def planeModel(self, scene, normal, origin, name, color):
""" Create a plane model node which can be viewed in the 3D View """
#A plane source
plane = vtk.vtkPlane()
plane.SetOrigin(origin)
plane.SetNormal(normal)
planeSample = vtk.vtkSampleFunction()
planeSample.SetImplicitFunction(plane)
planeSample.SetModelBounds(-100,100,-100,100,-100,100)
planeSample.SetSampleDimensions(100,100,100)
planeSample.ComputeNormalsOff()
planeContour = vtk.vtkContourFilter()
planeContour.SetInput(planeSample.GetOutput())
# Create plane model node
planeNode = slicer.vtkMRMLModelNode()
planeNode.SetScene(scene)
planeNode.SetName(name)
planeNode.SetAndObservePolyData(planeContour.GetOutput())
# Create plane display model node
planeModelDisplay = slicer.vtkMRMLModelDisplayNode()
planeModelDisplay.SetColor(color)
planeModelDisplay.SetBackfaceCulling(0)
planeModelDisplay.SetScene(scene)
scene.AddNode(planeModelDisplay)
planeNode.SetAndObserveDisplayNodeID(planeModelDisplay.GetID())
#Add to scene
planeModelDisplay.SetInputPolyData(planeContour.GetOutput())
scene.AddNode(planeNode)
return plane
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 generate3DVisualisationNode(self,
polydata,
name,
color=(1, 1, 1),
initial_pos_x=0):
#create Model Node
shape_node = slicer.vtkMRMLModelNode()
shape_node.SetAndObservePolyData(polydata)
shape_node.SetName(name)
#create display node
model_display = slicer.vtkMRMLModelDisplayNode()
model_display.SetColor(color[0], color[1], color[2])
model_display.AutoScalarRangeOff()
model_display.SetScene(slicer.mrmlScene)
model_display.SetName("Display " + name)
#create transform node
transform = vtk.vtkTransform()
transform.Translate(initial_pos_x, 0, 0)
transform_node = slicer.vtkMRMLTransformNode()
transform_node.SetName("Translation " + name)
transform_node.SetAndObserveTransformToParent(transform)
#Add Nodes to Slicer
slicer.mrmlScene.AddNode(transform_node)
slicer.mrmlScene.AddNode(model_display)
slicer.mrmlScene.AddNode(shape_node)
#Link nodes
shape_node.SetAndObserveTransformNodeID(transform_node.GetID())
shape_node.SetAndObserveDisplayNodeID(model_display.GetID())
def createSampleModelVolume(self, name, color, volumeNode=None):
if volumeNode:
self.assertTrue( volumeNode.IsA('vtkMRMLScalarVolumeNode') )
bounds = [0.0, 0.0, 0.0, 0.0, 0.0, 0.0]
volumeNode.GetRASBounds(bounds)
x = (bounds[0] + bounds[1])/2
y = (bounds[2] + bounds[3])/2
z = (bounds[4] + bounds[5])/2
radius = min(bounds[1]-bounds[0],bounds[3]-bounds[2],bounds[5]-bounds[4]) / 3.0
else:
radius = 50
x = y = z = 0
# Taken from: http://www.na-mic.org/Bug/view.php?id=1536
sphere = vtk.vtkSphereSource()
sphere.SetCenter(x, y, z)
sphere.SetRadius(radius)
modelNode = slicer.vtkMRMLModelNode()
modelNode.SetName(name)
modelNode = slicer.mrmlScene.AddNode(modelNode)
if vtk.VTK_MAJOR_VERSION <= 5:
modelNode.SetAndObservePolyData(sphere.GetOutput())
else:
modelNode.SetPolyDataConnection(sphere.GetOutputPort())
modelNode.SetHideFromEditors(0)
displayNode = slicer.vtkMRMLModelDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
displayNode.SliceIntersectionVisibilityOn()
displayNode.VisibilityOn()
displayNode.SetColor(color[0], color[1], color[2])
modelNode.SetAndObserveDisplayNodeID(displayNode.GetID())
return modelNode
def DepthMapToPointCloud(self, depthmapFilename, rgbFilename):
# Create point cloud
depthImage = imageio.imread(depthmapFilename)
rgbImage = imageio.imread(rgbFilename)
height = len(depthImage)
width = len(depthImage[0])
minimumDepth = np.amin(depthImage)
maximumDepth = np.amax(depthImage)
print(maximumDepth)
points = vtk.vtkPoints()
fx_d = self.focalLengthBox.value
fy_d = self.focalLengthBox.value
for u in range(height):
for v in range(width):
vflipped = width - (v + 1)
z = depthImage[u][vflipped]
z = z[0] / self.depthDividerBox.value
if z < 60:
#if True:
points.InsertNextPoint(
np.array([
z * (u - (height / 2)) / fx_d,
z * (v - (width / 2)) / fy_d, z
]))
# Create junk polygons so that Slicer can actually display the point cloud
polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
poly = vtk.vtkPolygon()
poly.GetPointIds().SetNumberOfIds(points.GetNumberOfPoints())
for n in range(points.GetNumberOfPoints()):
poly.GetPointIds().SetId(n, n)
polys = vtk.vtkCellArray()
polys.InsertNextCell(poly)
polydata.SetPolys(polys)
# Display the point cloud
modelNode = self.pointCloudSelector.currentNode()
modelNode.SetAndObservePolyData(polydata)
modelDisplayNode = modelNode.GetModelDisplayNode()
if modelDisplayNode is None:
modelDisplayNode = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(modelDisplayNode)
modelNode.SetAndObserveDisplayNodeID(modelDisplayNode.GetID())
modelDisplayNode.SetRepresentation(
modelDisplayNode.PointsRepresentation)
modelDisplayNode.SetPointSize(4)
modelDisplayNode.SetOpacity(0.2)
modelDisplayNode.SetColor(1, 0, 0)
return modelNode
def __init__(self, targetFiducialListNode, radius):
target = targetFiducialListNode
scene = slicer.mrmlScene
sphere = vtk.vtkSphereSource()
sphere.SetRadius(radius)
sphere.SetThetaResolution(20)
sphere.SetPhiResolution(20)
sphere.Update()
# Create model node
insertionRadiusModel = slicer.vtkMRMLModelNode()
insertionRadiusModel.SetScene(scene)
insertionRadiusModel.SetName("InsertionSphere-%s" % target.GetName())
insertionRadiusModel.SetAndObservePolyData(sphere.GetOutput())
# Create display node
insertionRadiusModelDisplay = slicer.vtkMRMLModelDisplayNode()
insertionRadiusModelDisplay.SetColor(0.8,0.8,0.8)
insertionRadiusModelDisplay.SetOpacity(0.3)
insertionRadiusModelDisplay.SliceIntersectionVisibilityOn()
insertionRadiusModelDisplay.SetScene(scene)
scene.AddNode(insertionRadiusModelDisplay)
insertionRadiusModel.SetAndObserveDisplayNodeID(insertionRadiusModelDisplay.GetID())
# Add to scene
insertionRadiusModelDisplay.SetPolyData(sphere.GetOutput())
scene.AddNode(insertionRadiusModel)
# Create insertionRadiusTransform node
insertionRadiusTransform = slicer.vtkMRMLLinearTransformNode()
insertionRadiusTransform.SetName('InsertionRadiusTransform-%s' % target.GetName())
scene.AddNode(insertionRadiusTransform)
# Translation
transformMatrix = vtk.vtkMatrix4x4()
# get coordinates from current fiducial
currentFiducialCoordinatesRAS = [0, 0, 0]
target.GetFiducialCoordinates(currentFiducialCoordinatesRAS)
transformMatrix.SetElement(0, 3, currentFiducialCoordinatesRAS[0])
transformMatrix.SetElement(1, 3, currentFiducialCoordinatesRAS[1])
transformMatrix.SetElement(2, 3, currentFiducialCoordinatesRAS[2])
insertionRadiusTransform.ApplyTransformMatrix(transformMatrix)
insertionRadiusModel.SetAndObserveTransformNodeID(insertionRadiusTransform.GetID())
self.sphere = sphere
self.insertionRadiusModel = insertionRadiusModel
self.insertionRadiusModelDisplay = insertionRadiusModelDisplay
self.insertionRadiusTransform = insertionRadiusTransform
def initializeModelNode(node): displayNode = slicer.vtkMRMLModelDisplayNode() storageNode = slicer.vtkMRMLModelStorageNode() displayNode.SetScene(slicer.mrmlScene) storageNode.SetScene(slicer.mrmlScene) slicer.mrmlScene.AddNode(displayNode) slicer.mrmlScene.AddNode(storageNode) node.SetAndObserveDisplayNodeID(displayNode.GetID()) node.SetAndObserveStorageNodeID(storageNode.GetID())
def blenderBoolean(self):
bpy.ops.wm.read_factory_settings()
for scene in bpy.data.scenes:
for obj in scene.objects:
scene.objects.unlink(obj)
# only worry about data in the startup scene
for bpy_data_iter in (bpy.data.objects, bpy.data.meshes,
bpy.data.lamps, bpy.data.cameras):
for id_data in bpy_data_iter:
bpy_data_iter.remove(id_data)
dir_path = os.path.dirname(os.path.realpath(__file__)) + "\\Models\\"
#dir_path = "D:\\w\\s\\DepthNetworkTracking\\Model\\"
airwayPath = dir_path + "airwayNoWall.stl"
cylinderPath = dir_path + "cylinder.stl"
bpy.ops.import_mesh.stl(filepath=airwayPath)
bpy.ops.import_mesh.stl(filepath=cylinderPath)
objects = bpy.data.objects
airwayNoWall = objects['airwayNoWall']
cylinder = objects['Cylinder']
airwayBoolean = airwayNoWall.modifiers.new(type="BOOLEAN",
name="bool_7")
airwayBoolean.object = cylinder
airwayBoolean.operation = 'INTERSECT'
cylinder.hide = True
bpy.context.scene.objects.active = bpy.data.objects['airwayNoWall']
bpy.ops.object.modifier_apply(apply_as='DATA',
modifier=airwayBoolean.name)
airwayNoWall.select = False
cylinder.select = True
bpy.ops.object.delete()
airwayNoWall.select = True
airwayIsolatedPath = dir_path + "airwayIsolated.stl"
bpy.ops.export_mesh.stl(filepath=airwayIsolatedPath)
outputModelPath = dir_path + "airwayIsolated.STL"
outputModelNode = slicer.util.loadModel(outputModelPath)
modelNode2 = self.transientModelSelector.currentNode()
modelDisplayNode2 = self.transientModelSelector.currentNode(
).GetModelDisplayNode()
if modelDisplayNode2 is None:
modelDisplayNode2 = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode2.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(modelDisplayNode2)
modelNode2.SetAndObserveDisplayNodeID(modelDisplayNode2.GetID())
modelDisplayNode2.SetOpacity(0.7)
modelDisplayNode2.SetColor(0, 1, 0)
modelNode2.SetAndObservePolyData(outputModelNode.GetPolyData())
slicer.mrmlScene.RemoveNode(outputModelNode)
def initializeModelNode(node):
displayNode = slicer.vtkMRMLModelDisplayNode()
storageNode = slicer.vtkMRMLModelStorageNode()
displayNode.SetScene(slicer.mrmlScene)
storageNode.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(displayNode)
slicer.mrmlScene.AddNode(storageNode)
node.SetAndObserveDisplayNodeID(displayNode.GetID())
node.SetAndObserveStorageNodeID(storageNode.GetID())
def updateModel(self):
if self.AutomaticUpdate == False:
return
if not self.ModelNode:
return
if self.ModelNode.GetDisplayNodeID() == None:
modelDisplayNode = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode.SetColor(self.ModelColor)
slicer.mrmlScene.AddNode(modelDisplayNode)
self.ModelNode.SetAndObserveDisplayNodeID(modelDisplayNode.GetID())
displayNodeID = self.ModelNode.GetDisplayNodeID()
modelDisplayNode = slicer.mrmlScene.GetNodeByID(displayNodeID)
if modelDisplayNode:
if self.SliceIntersection == True:
modelDisplayNode.SliceIntersectionVisibilityOn()
else:
modelDisplayNode.SliceIntersectionVisibilityOff()
modelDisplayNode.SetOpacity(0.5)
if self.CylinderSource == None:
self.CylinderSource = vtk.vtkCylinderSource()
self.CylinderSource.SetResolution(60)
self.CylinderSource.SetRadius(self.Diameter/2.0)
self.CylinderSource.SetHeight(self.Length)
self.CylinderSource.SetCenter(self.Offset)
self.CylinderSource.Update()
## Scale sphere to make ellipsoid
#scale = vtk.vtkTransform()
#scale.Scale(self.MinorAxis, self.MinorAxis, self.MajorAxis)
#scaleFilter = vtk.vtkTransformPolyDataFilter()
#scaleFilter.SetInputConnection(self.CylinderSource.GetOutputPort())
#scaleFilter.SetTransform(scale)
#scaleFilter.Update();
# Transform
#transform = vtk.vtkTransform()
#self.computeTransform(pTip, pTail, self.TipOffset, transform)
#transformFilter = vtk.vtkTransformPolyDataFilter()
#transformFilter.SetInputConnection(scaleFilter.GetOutputPort())
#transformFilter.SetInputConnection(self.CylinderSource.GetOutputPort())
#transformFilter.SetTransform(transform)
#transformFilter.Update();
#self.ModelNode.SetAndObservePolyData(transformFilter.GetOutput())
self.ModelNode.SetAndObservePolyData(self.CylinderSource.GetOutput())
self.ModelNode.Modified()
if self.ModelNode.GetScene() == None:
slicer.mrmlScene.AddNode(self.ModelNode)
def ExtractMesh(outputModelNode, modelNode, colorRgb, colorTolerance):
fullPolyData = modelNode.GetPolyData()
pointData = fullPolyData.GetPointData()
redValues = pointData.GetArray('ColorRed')
greenValues = pointData.GetArray('ColorGreen')
blueValues = pointData.GetArray('ColorBlue')
redMaxTolerance = colorRgb[0] + colorTolerance
redMinTolerance = colorRgb[0] - colorTolerance
greenMaxTolerance = colorRgb[1] + colorTolerance
greenMinTolerance = colorRgb[1] - colorTolerance
blueMaxTolerance = colorRgb[2] + colorTolerance
blueMinTolerance = colorRgb[2] - colorTolerance
lengthTuples = int(redValues.GetNumberOfTuples())
selectedPointIds = vtk.vtkIdTypeArray()
for pointId in range(lengthTuples):
if redValues.GetValue(
pointId) >= redMinTolerance and redValues.GetValue(
pointId) <= redMaxTolerance and greenValues.GetValue(
pointId) >= greenMinTolerance and greenValues.GetValue(
pointId
) <= greenMaxTolerance and blueValues.GetValue(
pointId
) >= blueMinTolerance and blueValues.GetValue(
pointId) <= blueMaxTolerance:
selectedPointIds.InsertNextValue(pointId)
selectedPointIds.InsertNextValue(pointId)
selectionNode = vtk.vtkSelectionNode()
selectionNode.SetFieldType(vtk.vtkSelectionNode.POINT)
selectionNode.SetContentType(vtk.vtkSelectionNode.INDICES)
selectionNode.SetSelectionList(selectedPointIds)
selectionNode.GetProperties().Set(vtk.vtkSelectionNode.CONTAINING_CELLS(),
1)
selection = vtk.vtkSelection()
selection.AddNode(selectionNode)
extractSelection = vtk.vtkExtractSelection()
extractSelection.SetInputData(0, fullPolyData)
extractSelection.SetInputData(1, selection)
extractSelection.Update()
convertToPolydata = vtk.vtkDataSetSurfaceFilter()
convertToPolydata.SetInputConnection(extractSelection.GetOutputPort())
convertToPolydata.Update()
outputModelNode.SetAndObservePolyData(convertToPolydata.GetOutput())
if not outputModelNode.GetDisplayNode():
md2 = slicer.vtkMRMLModelDisplayNode()
slicer.mrmlScene.AddNode(md2)
outputModelNode.SetAndObserveDisplayNodeID(md2.GetID())
def loadModels(self, skullModel, skullMarkersModel, pointerModel):
self.skullModel=skullModel
self.skullMarkersModel=skullMarkersModel
self.pointerModel=pointerModel
self.skull.SetName("SkullModel")
self.skull.SetAndObservePolyData(self.skullModel.GetPolyData())
slicer.mrmlScene.AddNode(self.skull)
# Add display node
modelDisplayNode = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode.SetColor(1,1,1) # White
modelDisplayNode.BackfaceCullingOff()
modelDisplayNode.SliceIntersectionVisibilityOn()
modelDisplayNode.SetSliceIntersectionThickness(4)
modelDisplayNode.SetOpacity(1) # Between 0-1, 1 being opaque
slicer.mrmlScene.AddNode(modelDisplayNode)
self.skull.SetAndObserveDisplayNodeID(modelDisplayNode.GetID())
self.skullMarkers.SetName("SkullMarkersModel")
self.skullMarkers.SetAndObservePolyData(self.skullMarkersModel.GetPolyData())
slicer.mrmlScene.AddNode(self.skullMarkers)
# Add display node
modelDisplayNode = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode.SetColor(1,0,0) # White
modelDisplayNode.BackfaceCullingOff()
modelDisplayNode.SliceIntersectionVisibilityOn()
modelDisplayNode.SetSliceIntersectionThickness(4)
modelDisplayNode.SetOpacity(1) # Between 0-1, 1 being opaque
slicer.mrmlScene.AddNode(modelDisplayNode)
self.skullMarkers.SetAndObserveDisplayNodeID(modelDisplayNode.GetID())
self.pointer.SetName("PointerModel")
self.pointer.SetAndObservePolyData(self.pointerModel.GetPolyData())
slicer.mrmlScene.AddNode(self.pointer)
# Add display node
modelDisplayNode = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode.SetColor(0,0,0) # White
modelDisplayNode.BackfaceCullingOff()
modelDisplayNode.SliceIntersectionVisibilityOn()
modelDisplayNode.SetSliceIntersectionThickness(4)
modelDisplayNode.SetOpacity(1) # Between 0-1, 1 being opaque
slicer.mrmlScene.AddNode(modelDisplayNode)
self.pointer.SetAndObserveDisplayNodeID(modelDisplayNode.GetID())
def DisplayPolyData(self, nameOfNode, polyData, overwrite=True): """ Function that Overwrites/Creates a Node to display Polydata """ n=self.CreateNewNode(nameOfNode, "vtkMRMLModelNode", overwrite=True) outputMouldModelDisplayNode = slicer.vtkMRMLModelDisplayNode() slicer.mrmlScene.AddNode(outputMouldModelDisplayNode) outputMouldModelDisplayNode.BackfaceCullingOff() n.SetAndObserveDisplayNodeID(outputMouldModelDisplayNode.GetID()) n.SetAndObservePolyData(polyData) return outputMouldModelDisplayNode
def DisplayPolyData(self, nameOfNode, polyData, overwrite=True):
""" Function that Overwrites/Creates a Node to display Polydata
"""
n = self.CreateNewNode(nameOfNode, "vtkMRMLModelNode", overwrite=True)
outputMouldModelDisplayNode = slicer.vtkMRMLModelDisplayNode()
slicer.mrmlScene.AddNode(outputMouldModelDisplayNode)
outputMouldModelDisplayNode.BackfaceCullingOff()
n.SetAndObserveDisplayNodeID(outputMouldModelDisplayNode.GetID())
n.SetAndObservePolyData(polyData)
return outputMouldModelDisplayNode
def updateAblationVolume(self):
if self.AutomaticUpdate == False:
return
if self.SourceNode and self.DestinationNode:
pTip = [0.0, 0.0, 0.0]
pTail = [0.0, 0.0, 0.0]
#self.SourceNode.GetNthFiducialPosition(0,pTip)
self.SourceNode.GetPosition1(pTip)
#self.SourceNode.GetNthFiducialPosition(1,pTail)
self.SourceNode.GetPosition2(pTail)
if self.DestinationNode.GetDisplayNodeID() == None:
modelDisplayNode = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode.SetColor(self.ModelColor)
slicer.mrmlScene.AddNode(modelDisplayNode)
self.DestinationNode.SetAndObserveDisplayNodeID(modelDisplayNode.GetID())
displayNodeID = self.DestinationNode.GetDisplayNodeID()
modelDisplayNode = slicer.mrmlScene.GetNodeByID(displayNodeID)
if modelDisplayNode != None and self.SliceIntersection == True:
modelDisplayNode.SliceIntersectionVisibilityOn()
else:
modelDisplayNode.SliceIntersectionVisibilityOff()
if self.SphereSource == None:
self.SphereSource = vtk.vtkSphereSource()
self.SphereSource.SetThetaResolution(20)
self.SphereSource.SetPhiResolution(20)
self.SphereSource.Update()
# Scale sphere to make ellipsoid
scale = vtk.vtkTransform()
scale.Scale(self.MinorAxis, self.MinorAxis, self.MajorAxis)
scaleFilter = vtk.vtkTransformPolyDataFilter()
scaleFilter.SetInputConnection(self.SphereSource.GetOutputPort())
scaleFilter.SetTransform(scale)
scaleFilter.Update();
# Transform
transform = vtk.vtkTransform()
self.computeTransform(pTip, pTail, self.TipOffset, transform)
transformFilter = vtk.vtkTransformPolyDataFilter()
transformFilter.SetInputConnection(scaleFilter.GetOutputPort())
transformFilter.SetTransform(transform)
transformFilter.Update();
self.DestinationNode.SetAndObservePolyData(transformFilter.GetOutput())
self.DestinationNode.Modified()
if self.DestinationNode.GetScene() == None:
slicer.mrmlScene.AddNode(self.DestinationNode)
def defineSphere(self):
sphereSource = vtk.vtkSphereSource()
sphereSource.SetRadius(100.0)
model = slicer.vtkMRMLModelNode()
model.SetAndObservePolyData(sphereSource.GetOutput())
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetColor(0.5,0.5,0.5)
slicer.mrmlScene.AddNode(modelDisplay)
model.SetAndObserveDisplayNodeID(modelDisplay.GetID())
modelDisplay.SetInputPolyDataConnection(sphereSource.GetOutputPort())
return model
def createModelNode(self, name, color):
scene = slicer.mrmlScene
modelNode = slicer.vtkMRMLModelNode()
modelNode.SetScene(scene)
modelNode.SetName(name)
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetColor(color)
modelDisplay.SetScene(scene)
scene.AddNode(modelDisplay)
modelNode.SetAndObserveDisplayNodeID(modelDisplay.GetID())
scene.AddNode(modelNode)
return modelNode
def createModelNode(self, name, color): scene = slicer.mrmlScene modelNode = slicer.vtkMRMLModelNode() modelNode.SetScene(scene) modelNode.SetName(name) modelDisplay = slicer.vtkMRMLModelDisplayNode() modelDisplay.SetColor(color) modelDisplay.SetScene(scene) scene.AddNode(modelDisplay) modelNode.SetAndObserveDisplayNodeID(modelDisplay.GetID()) scene.AddNode(modelNode) return modelNode
def addModelToScene(self, polyData, name): scene = slicer.mrmlScene node = slicer.vtkMRMLModelNode() node.SetScene(scene) node.SetName(name) node.SetAndObservePolyData(polyData) modelDisplay = slicer.vtkMRMLModelDisplayNode() modelDisplay.SetColor(0, 1, 0) modelDisplay.SetScene(scene) scene.AddNode(modelDisplay) node.SetAndObserveDisplayNodeID(modelDisplay.GetID()) scene.AddNode(node) return node
def enableSliceIntersection(self, state):
if self.DestinationNode.GetDisplayNodeID() == None:
modelDisplayNode = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode.SetColor(self.ModelColor)
slicer.mrmlScene.AddNode(modelDisplayNode)
self.DestinationNode.SetAndObserveDisplayNodeID(modelDisplayNode.GetID())
displayNodeID = self.DestinationNode.GetDisplayNodeID()
displayNode = slicer.mrmlScene.GetNodeByID(displayNodeID)
if displayNode != None:
if state:
displayNode.SliceIntersectionVisibilityOn()
else:
displayNode.SliceIntersectionVisibilityOff()
def gradeScrew(self, screwModel, transformFid, fidName, screwIndex):
#Reset screws
#self.clearGrade()
#Crop out head of screw
croppedScrew = self.cropScrew(screwModel, 'head')
#Clone screw model poly data
inputModel = slicer.vtkMRMLModelNode()
inputModel.SetAndObservePolyData(croppedScrew)
inputModel.SetAndObserveTransformNodeID(transformFid.GetID())
slicer.mrmlScene.AddNode(inputModel)
slicer.vtkSlicerTransformLogic.hardenTransform(inputModel)
#Create new model for output
output = slicer.vtkMRMLModelNode()
output.SetName('Grade model-%s' % fidName)
slicer.mrmlScene.AddNode(output)
#Parameters for ProbeVolumeWithModel
parameters = {}
parameters["InputVolume"] = self.__inputScalarVol.GetID()
parameters["InputModel"] = inputModel.GetID()
parameters["OutputModel"] = output.GetID()
probe = slicer.modules.probevolumewithmodel
slicer.cli.run(probe, None, parameters, wait_for_completion=True)
#Hide original screw
modelDisplay = screwModel.GetDisplayNode()
modelDisplay.SetColor(0,1,0)
modelDisplay.VisibilityOff()
#Highlight screwh head
headModel = slicer.vtkMRMLModelNode()
headModel.SetName('Head %s' % fidName)
headModel.SetAndObservePolyData(self.cropScrew(screwModel, 'shaft'))
headModel.SetAndObserveTransformNodeID(transformFid.GetID())
slicer.mrmlScene.AddNode(headModel)
headDisplay = slicer.vtkMRMLModelDisplayNode()
headDisplay.SetColor(0,1,0)
slicer.mrmlScene.AddNode(headDisplay)
headModel.SetAndObserveDisplayNodeID(headDisplay.GetID())
#Remove clone
slicer.mrmlScene.RemoveNode(inputModel)
#Grade and chart screw
self.contact(output, screwModel, fidName, screwIndex)
def gradeScrew(self, screwModel, transformFid, fidName, screwIndex):
#Reset screws
#self.clearGrade()
#Crop out head of screw
croppedScrew = self.cropScrew(screwModel, 'head')
#Clone screw model poly data
inputModel = slicer.vtkMRMLModelNode()
inputModel.SetAndObservePolyData(croppedScrew)
inputModel.SetAndObserveTransformNodeID(transformFid.GetID())
slicer.mrmlScene.AddNode(inputModel)
slicer.vtkSlicerTransformLogic.hardenTransform(inputModel)
#Create new model for output
output = slicer.vtkMRMLModelNode()
output.SetName('Grade model-%s' % fidName)
slicer.mrmlScene.AddNode(output)
#Parameters for ProbeVolumeWithModel
parameters = {}
parameters["InputVolume"] = self.__inputScalarVol.GetID()
parameters["InputModel"] = inputModel.GetID()
parameters["OutputModel"] = output.GetID()
probe = slicer.modules.probevolumewithmodel
slicer.cli.run(probe, None, parameters, wait_for_completion=True)
#Hide original screw
modelDisplay = screwModel.GetDisplayNode()
modelDisplay.SetColor(0, 1, 0)
modelDisplay.VisibilityOff()
#Highlight screwh head
headModel = slicer.vtkMRMLModelNode()
headModel.SetName('Head %s' % fidName)
headModel.SetAndObservePolyData(self.cropScrew(screwModel, 'shaft'))
headModel.SetAndObserveTransformNodeID(transformFid.GetID())
slicer.mrmlScene.AddNode(headModel)
headDisplay = slicer.vtkMRMLModelDisplayNode()
headDisplay.SetColor(0, 1, 0)
slicer.mrmlScene.AddNode(headDisplay)
headModel.SetAndObserveDisplayNodeID(headDisplay.GetID())
#Remove clone
slicer.mrmlScene.RemoveNode(inputModel)
#Grade and chart screw
self.contact(output, screwModel, fidName, screwIndex)
def addPolyDataToScene(self,polyData,name):
print "addPolyDataToScene"
self.outputDisplayNode = slicer.vtkMRMLModelDisplayNode()
self.outputDisplayNode.SetName(name+"Display")
self.outputDisplayNode.SetColor(0,0,1.0)
self.outputDisplayNode.SetOpacity(0.5)
slicer.mrmlScene.AddNode(self.outputDisplayNode)
self.outputModelNode = slicer.vtkMRMLModelNode()
self.outputModelNode.SetAndObservePolyData(polyData)
self.outputModelNode.SetAndObserveDisplayNodeID(self.outputDisplayNode.GetID())
if (self.transformGridToTargetNode):
self.outputModelNode.SetAndObserveTransformNodeID(self.transformGridToTargetNode.GetID())
self.outputModelNode.SetName(name)
slicer.mrmlScene.AddNode(self.outputModelNode)
def calculateFiducialDistance(self, modelNode, fiducial):
closestFiducial = slicer.util.getNode('CP')
if not closestFiducial:
closestFiducial = slicer.vtkMRMLMarkupsFiducialNode()
closestFiducial.SetName('CP')
closestFiducial.AddFiducial(0, 0, 0)
closestFiducial.SetNthFiducialLabel(0, 'CP')
slicer.mrmlScene.AddNode(closestFiducial)
closestFiducial.SetDisplayVisibility(False)
line = slicer.util.getNode('Line')
if not line:
line = slicer.vtkMRMLModelNode()
line.SetName('Line')
linePolyData = vtk.vtkPolyData()
line.SetAndObservePolyData(linePolyData)
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetSliceIntersectionVisibility(True)
modelDisplay.SetColor(0,1,0)
slicer.mrmlScene.AddNode(modelDisplay)
line.SetAndObserveDisplayNodeID(modelDisplay.GetID())
slicer.mrmlScene.AddNode(line)
cellLocator = vtk.vtkCellLocator()
cellLocator.SetDataSet(modelNode.GetPolyData())
cellLocator.BuildLocator()
if fiducial.GetNumberOfFiducials() > 0:
ras = [0.0, 0.0, 0.0]
closestPoint = [0.0, 0.0, 0.0]
fiducial.GetNthFiducialPosition(0, ras)
distanceSquared = vtk.mutable(0.0)
subId = vtk.mutable(0)
cellId = vtk.mutable(0)
cell = vtk.vtkGenericCell()
cellLocator.FindClosestPoint(ras, closestPoint, cell, cellId, subId, distanceSquared);
distance = math.sqrt(distanceSquared)
closestFiducial.SetNthFiducialPosition(0, closestPoint[0], closestPoint[1], closestPoint[2])
closestFiducial.SetDisplayVisibility(True)
self.drawLineBetweenPoints(line, ras, closestPoint)
self.set3dViewConernerAnnotation('Distance = ' + "%.2f" % distance + 'mm')
else:
logging.warning('No fiducials in list!')
def lineModel(self, scene, point1, point2, name, color):
""" Create a line to reflect the puncture path"""
#Line mode source
line = vtk.vtkLineSource()
line.SetPoint1(point1)#(point1[0][0], point1[0][1], point1[0][2])
line.SetPoint2(point2)#(point2[0][0], point2[0][1], point2[0][2])
# Create model node
lineModel = slicer.vtkMRMLModelNode()
lineModel.SetScene(scene)
lineModel.SetName(name)
lineModel.SetAndObservePolyData(line.GetOutput())
# Create display node
lineModelDisplay = slicer.vtkMRMLModelDisplayNode()
lineModelDisplay.SetColor(color)
lineModelDisplay.SetScene(scene)
scene.AddNode(lineModelDisplay)
lineModel.SetAndObserveDisplayNodeID(lineModelDisplay.GetID())
#Add to scene
# lineModelDisplay.SetInputPolyData(line.GetOutput())
lineModelDisplay.SetInputPolyDataConnection(line.GetOutputPort())
scene.AddNode(lineModel)
return line
def addPolyDataToScene(self, polyData, name):
print "addPolyDataToScene"
self.outputDisplayNode = slicer.vtkMRMLModelDisplayNode()
self.outputDisplayNode.SetName(name + "Display")
self.outputDisplayNode.SetColor(0, 0, 1.0)
self.outputDisplayNode.SetOpacity(0.5)
slicer.mrmlScene.AddNode(self.outputDisplayNode)
self.outputModelNode = slicer.vtkMRMLModelNode()
self.outputModelNode.SetAndObservePolyData(polyData)
self.outputModelNode.SetAndObserveDisplayNodeID(
self.outputDisplayNode.GetID())
if (self.transformGridToTargetNode):
self.outputModelNode.SetAndObserveTransformNodeID(
self.transformGridToTargetNode.GetID())
self.outputModelNode.SetName(name)
slicer.mrmlScene.AddNode(self.outputModelNode)
def ExtractMesh(outputModelNode, modelNode, colorRgb, colorTolerance):
fullPolyData = modelNode.GetPolyData()
pointData=fullPolyData.GetPointData()
redValues = pointData.GetArray('ColorRed')
greenValues = pointData.GetArray('ColorGreen')
blueValues = pointData.GetArray('ColorBlue')
redMaxTolerance = colorRgb[0] + colorTolerance
redMinTolerance = colorRgb[0] - colorTolerance
greenMaxTolerance = colorRgb[1] + colorTolerance
greenMinTolerance = colorRgb[1] - colorTolerance
blueMaxTolerance = colorRgb[2] + colorTolerance
blueMinTolerance = colorRgb[2] - colorTolerance
lengthTuples = int(redValues.GetNumberOfTuples())
selectedPointIds = vtk.vtkIdTypeArray()
for pointId in range(lengthTuples):
if redValues.GetValue(pointId) >= redMinTolerance and redValues.GetValue(pointId) <= redMaxTolerance and greenValues.GetValue(pointId) >= greenMinTolerance and greenValues.GetValue(pointId) <= greenMaxTolerance and blueValues.GetValue(pointId) >= blueMinTolerance and blueValues.GetValue(pointId) <= blueMaxTolerance:
selectedPointIds.InsertNextValue(pointId)
selectedPointIds.InsertNextValue(pointId)
selectionNode = vtk.vtkSelectionNode()
selectionNode.SetFieldType(vtk.vtkSelectionNode.POINT)
selectionNode.SetContentType(vtk.vtkSelectionNode.INDICES)
selectionNode.SetSelectionList(selectedPointIds)
selectionNode.GetProperties().Set(vtk.vtkSelectionNode.CONTAINING_CELLS(), 1);
selection = vtk.vtkSelection()
selection.AddNode(selectionNode)
extractSelection = vtk.vtkExtractSelection()
extractSelection.SetInputData(0,fullPolyData)
extractSelection.SetInputData(1,selection);
extractSelection.Update();
convertToPolydata = vtk.vtkDataSetSurfaceFilter()
convertToPolydata.SetInputConnection(extractSelection.GetOutputPort())
convertToPolydata.Update()
outputModelNode.SetAndObservePolyData(convertToPolydata.GetOutput())
if not outputModelNode.GetDisplayNode():
md2 = slicer.vtkMRMLModelDisplayNode()
slicer.mrmlScene.AddNode(md2)
outputModelNode.SetAndObserveDisplayNodeID(md2.GetID())
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 handLine(self, whichHand='Left'):
"""Create a line to show the path from the hand to the table
"""
handLineName = 'DropLine-%s' % whichHand
handLineNode = slicer.util.getNode(handLineName)
if not handLineNode:
points = vtk.vtkPoints()
polyData = vtk.vtkPolyData()
polyData.SetPoints(points)
lines = vtk.vtkCellArray()
polyData.SetLines(lines)
linesIDArray = lines.GetData()
linesIDArray.Reset()
linesIDArray.InsertNextTuple1(0)
polygons = vtk.vtkCellArray()
polyData.SetPolys(polygons)
idArray = polygons.GetData()
idArray.Reset()
idArray.InsertNextTuple1(0)
for point in ((0, 0, 0), (1, 1, 1)):
pointIndex = points.InsertNextPoint(*point)
linesIDArray.InsertNextTuple1(pointIndex)
linesIDArray.SetTuple1(0, linesIDArray.GetNumberOfTuples() - 1)
lines.SetNumberOfCells(1)
# Create handLineNode model node
handLineNode = slicer.vtkMRMLModelNode()
handLineNode.SetScene(slicer.mrmlScene)
handLineNode.SetName("DropLine-%s" % whichHand)
handLineNode.SetAndObservePolyData(polyData)
# Create display node
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetColor(1, 1, 0) # yellow
modelDisplay.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(modelDisplay)
handLineNode.SetAndObserveDisplayNodeID(modelDisplay.GetID())
# Add to slicer.mrmlScene
modelDisplay.SetInputPolyData(handLineNode.GetPolyData())
slicer.mrmlScene.AddNode(handLineNode)
return handLineNode
def handLine(self,whichHand='Left'):
"""Create a line to show the path from the hand to the table
"""
handLineName = 'DropLine-%s' % whichHand
handLineNode = slicer.util.getNode(handLineName)
if not handLineNode:
points = vtk.vtkPoints()
polyData = vtk.vtkPolyData()
polyData.SetPoints(points)
lines = vtk.vtkCellArray()
polyData.SetLines(lines)
linesIDArray = lines.GetData()
linesIDArray.Reset()
linesIDArray.InsertNextTuple1(0)
polygons = vtk.vtkCellArray()
polyData.SetPolys( polygons )
idArray = polygons.GetData()
idArray.Reset()
idArray.InsertNextTuple1(0)
for point in ( (0,0,0), (1,1,1) ):
pointIndex = points.InsertNextPoint(*point)
linesIDArray.InsertNextTuple1(pointIndex)
linesIDArray.SetTuple1( 0, linesIDArray.GetNumberOfTuples() - 1 )
lines.SetNumberOfCells(1)
# Create handLineNode model node
handLineNode = slicer.vtkMRMLModelNode()
handLineNode.SetScene(slicer.mrmlScene)
handLineNode.SetName("DropLine-%s" % whichHand)
handLineNode.SetAndObservePolyData(polyData)
# Create display node
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetColor(1,1,0) # yellow
modelDisplay.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(modelDisplay)
handLineNode.SetAndObserveDisplayNodeID(modelDisplay.GetID())
# Add to slicer.mrmlScene
modelDisplay.SetInputPolyData(handLineNode.GetPolyData())
slicer.mrmlScene.AddNode(handLineNode)
return handLineNode
def __init__(self):
self.scene = slicer.mrmlScene
self.scene.SetUndoOn()
self.scene.SaveStateForUndo(self.scene.GetNodes())
self.currentSlice = Slice('/luscinia/ProstateStudy/invivo/Patient59/loupas/RadialImagesCC_imwrite/arfi_ts3_26.57.png')
# yay, adding images to slicer
planeSource = vtk.vtkPlaneSource()
planeSource.SetCenter(self.currentSlice.x, self.currentSlice.y, self.currentSlice.z)
reader = vtk.vtkPNGReader()
reader.SetFileName(self.currentSlice.name)
# model node
self.model = slicer.vtkMRMLModelNode()
self.model.SetScene(self.scene)
self.model.SetName(self.currentSlice.name)
self.model.SetAndObservePolyData(planeSource.GetOutput())
# model display node
self.modelDisplay = slicer.vtkMRMLModelDisplayNode()
self.modelDisplay.BackfaceCullingOff() # so plane can be seen from both front and back face
self.modelDisplay.SetScene(self.scene)
self.scene.AddNode(self.modelDisplay)
# connecting model node w/ its model display node
self.model.SetAndObserveDisplayNodeID(self.modelDisplay.GetID())
# adding tiff file as texture to modelDisplay
self.modelDisplay.SetAndObserveTextureImageData(reader.GetOutput())
self.scene.AddNode(self.model)
# now doing a linear transform to set coordinates and orientation of plane
self.transform = slicer.vtkMRMLLinearTransformNode()
self.scene.AddNode(self.transform)
self.model.SetAndObserveTransformNodeID(self.transform.GetID())
vTransform = vtk.vtkTransform()
vTransform.Scale(150, 150, 150)
vTransform.RotateX(0)
vTransform.RotateY(0)
vTransform.RotateZ(0)
self.transform.SetAndObserveMatrixTransformToParent(vTransform.GetMatrix())
def selectSlice(self, index):
self.scene.Undo()
self.scene.SaveStateForUndo(self.scene.GetNodes())
imgFilePrefix = './data/test'
imgFileSuffix = '.tiff'
# yay, adding images to slicer
planeSource = vtk.vtkPlaneSource()
reader = vtk.vtkTIFFReader()
reader.SetFileName(imgFilePrefix + str(self.imageList[index]) + imgFileSuffix)
#reader.CanReadFile('imgFilePrefix + str(self.imageList[0]) + imgFileSuffix')
# model node
model = slicer.vtkMRMLModelNode()
model.SetScene(self.scene)
model.SetName("test " + str(self.imageList[index]) + "cow")
model.SetAndObservePolyData(planeSource.GetOutput())
# model display node
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.BackfaceCullingOff() # so plane can be seen from both front and back face
modelDisplay.SetScene(self.scene)
self.scene.AddNode(modelDisplay)
# connecting model node w/ its model display node
model.SetAndObserveDisplayNodeID(modelDisplay.GetID())
# adding tiff file as texture to modelDisplay
modelDisplay.SetAndObserveTextureImageData(reader.GetOutput())
self.scene.AddNode(model)
# now doing a linear transform to set coordinates and orientation of plane
transform = slicer.vtkMRMLLinearTransformNode()
self.scene.AddNode(transform)
model.SetAndObserveTransformNodeID(transform.GetID())
vTransform = vtk.vtkTransform()
vTransform.Scale(150, 150, 150)
vTransform.RotateX(self.rotateXList[index])
vTransform.RotateY(self.rotateYList[index])
vTransform.RotateZ(self.rotateZList[index])
transform.SetAndObserveMatrixTransformToParent(vTransform.GetMatrix())
def __init__(self, markupID, radius, length, position):
# We use the markupID to check whether this tool's markup has
# been removed in the onMarkupRemoved event
self.markupID = markupID
# Create a vtkCylinderSource for rendering the tool
self.toolSrc = vtk.vtkCylinderSource()
self.toolSrc.SetRadius(radius)
self.toolSrc.SetHeight(length)
# Create tool model using cylinder source
self.modelNode = slicer.vtkMRMLModelNode()
self.modelNode.HideFromEditorsOn()
self.modelNode.SetName(slicer.mrmlScene.GenerateUniqueName("Tool"))
polyData = self.toolSrc.GetOutput()
self.modelNode.SetAndObservePolyData(polyData)
slicer.mrmlScene.AddNode(self.modelNode)
# Create a DisplayNode for this node (so that it can control its
# own visibility) and have modelNode observe it
self.modelDisplay = slicer.vtkMRMLModelDisplayNode()
self.modelDisplay.SetColor(0, 1, 1) # cyan
slicer.mrmlScene.AddNode(self.modelDisplay)
self.modelNode.SetAndObserveDisplayNodeID(
self.modelDisplay.GetID())
# Create a transform for our tool model that will scale it to
# the proper radius, length, and position. Leave the orientation
# at the default.
self.transformNode = slicer.vtkMRMLLinearTransformNode()
self.transformNode.HideFromEditorsOn()
self.transformNode.SetName(
slicer.mrmlScene.GenerateUniqueName("Transform"))
self.updatePosition(position)
slicer.mrmlScene.AddNode(self.transformNode)
# apply the new transform to our tool
self.modelNode.SetAndObserveTransformNodeID(
self.transformNode.GetID())
# Set tool to be visible
self.visible = True
def updateOutputNode(polydata):
# clear scene
scene=slicer.mrmlScene
scene.Clear(0)
# create fiber node
fiber=slicer.vtkMRMLModelNode()
fiber.SetScene(scene)
fiber.SetName("QueryTract")
fiber.SetAndObservePolyData(polydata)
# create display model fiber node
fiberDisplay=slicer.vtkMRMLModelDisplayNode()
fiberDisplay.SetScene(scene)
scene.AddNode(fiberDisplay)
fiber.SetAndObserveDisplayNodeID(fiberDisplay.GetID())
# add to scene
fiberDisplay.SetInputPolyData(polydata)
scene.AddNode(fiber)
def pointModel(self, scene, point, name, color):
""" Create a point model using sphere"""
#Point
sphere = vtk.vtkSphereSource()
sphere.SetCenter(point)
sphere.SetRadius(2)
# Create model node
pointModel = slicer.vtkMRMLModelNode()
pointModel.SetScene(scene)
pointModel.SetName(name)
pointModel.SetAndObservePolyData(sphere.GetOutput())
#Create display node
pointModelDisplay = slicer.vtkMRMLModelDisplayNode()
pointModelDisplay.SetColor(color)
pointModelDisplay.SetScene(scene)
scene.AddNode(pointModelDisplay)
pointModel.SetAndObserveDisplayNodeID(pointModelDisplay.GetID())
#Add to scene
pointModelDisplay.SetInputPolyData(sphere.GetOutput())
scene.AddNode(pointModel)
def updateOutputNode(polydata):
# clear scene
scene = slicer.mrmlScene
scene.Clear(0)
# create fiber node
fiber = slicer.vtkMRMLModelNode()
fiber.SetScene(scene)
fiber.SetName("QueryTract")
fiber.SetAndObservePolyData(polydata)
# create display model fiber node
fiberDisplay = slicer.vtkMRMLModelDisplayNode()
fiberDisplay.SetScene(scene)
scene.AddNode(fiberDisplay)
fiber.SetAndObserveDisplayNodeID(fiberDisplay.GetID())
# add to scene
fiberDisplay.SetInputPolyData(polydata)
scene.AddNode(fiber)
def AddDamageTemplateModel(self,scene,LineLandmarkTransform ):
# check if already implemented
if ( self.DamageTemplateModel != None ):
print "removing", self.DamageTemplateModel.GetName()
scene.RemoveNode(self.DamageTemplateModel)
# create sphere and scale
vtkSphere = vtk.vtkSphereSource()
vtkSphere.SetRadius(1.)
vtkSphere.SetThetaResolution(16)
vtkSphere.SetPhiResolution(16)
ScaleAffineTransform = vtk.vtkTransform()
ScaleAffineTransform.Scale([self.AblationMinorAxis,self.AblationMajorAxis,self.AblationMinorAxis])
vtkEllipsoid= vtk.vtkTransformFilter()
vtkEllipsoid.SetInput(vtkSphere.GetOutput() )
vtkEllipsoid.SetTransform( ScaleAffineTransform )
vtkEllipsoid.Update()
slicertransformFilter = vtk.vtkTransformFilter()
slicertransformFilter.SetInput(vtkEllipsoid.GetOutput() )
slicertransformFilter.SetTransform( LineLandmarkTransform )
slicertransformFilter.Update()
dampolyData=slicertransformFilter.GetOutput();
# Create model node
self.DamageTemplateModel = slicer.vtkMRMLModelNode()
self.DamageTemplateModel.SetScene(scene)
#self.DamageTemplateModel.SetName(scene.GenerateUniqueName("Treatment-%s" % fiducialsNode.GetName()))
self.DamageTemplateModel.SetName( scene.GenerateUniqueName("Treatment") )
self.DamageTemplateModel.SetAndObservePolyData(dampolyData)
# Create display node
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetColor(1,1,0) # yellow
modelDisplay.SetOpacity(0.3)
modelDisplay.SetScene(scene)
scene.AddNode(modelDisplay)
self.DamageTemplateModel.SetAndObserveDisplayNodeID(modelDisplay.GetID())
# Add to scene
modelDisplay.SetInputPolyData(self.DamageTemplateModel.GetPolyData())
scene.AddNode(self.DamageTemplateModel)
def updateScene(self):
#self.scene.Undo()
#self.scene.SaveStateForUndo(self.scene.GetNodes())
self.scene.RemoveNode(self.transform)
self.scene.RemoveNode(self.modelDisplay)
self.scene.RemoveNode(self.model)
planeSource = vtk.vtkPlaneSource()
planeSource.SetCenter(self.currentSlice.x, self.currentSlice.y, self.currentSlice.z)
reader = vtk.vtkPNGReader()
reader.SetFileName(self.currentSlice.name)
# model node
self.model = slicer.vtkMRMLModelNode()
self.model.SetScene(self.scene)
self.model.SetName(self.currentSlice.name)
self.model.SetAndObservePolyData(planeSource.GetOutput())
# model display node
self.modelDisplay = slicer.vtkMRMLModelDisplayNode()
self.modelDisplay.BackfaceCullingOff() # so plane can be seen from both front and back face
self.modelDisplay.SetScene(self.scene)
self.scene.AddNode(self.modelDisplay)
# connecting model node w/ its model display node
self.model.SetAndObserveDisplayNodeID(self.modelDisplay.GetID())
# adding tiff file as texture to modelDisplay
self.modelDisplay.SetAndObserveTextureImageData(reader.GetOutput())
self.scene.AddNode(self.model)
# now doing a linear transform to set coordinates and orientation of plane
self.transform = slicer.vtkMRMLLinearTransformNode()
self.scene.AddNode(self.transform)
self.model.SetAndObserveTransformNodeID(self.transform.GetID())
vTransform = vtk.vtkTransform()
vTransform.Scale(self.currentSlice.scaling, self.currentSlice.scaling, self.currentSlice.scaling)
vTransform.RotateX(self.currentSlice.xAngle)
vTransform.RotateY(self.currentSlice.yAngle)
vTransform.RotateZ(self.currentSlice.zAngle)
self.transform.SetAndObserveMatrixTransformToParent(vTransform.GetMatrix())
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 handCursor(self, whichHand='Left'):
"""Create the mrml structure to represent a hand cursor if needed
otherwise return the current transform
whichHand : 'Left' for left color, anything else for right
also defines suffix for Transform and Cursor
"""
transformName = '%s-To-Table' % whichHand
transformNode = slicer.util.getNode(transformName)
if not transformNode:
# make the mrml
sphere = vtk.vtkSphereSource()
sphere.Update()
# Create model node
cursor = slicer.vtkMRMLModelNode()
cursor.SetScene(slicer.mrmlScene)
cursor.SetName("Cursor-%s" % whichHand)
cursor.SetAndObservePolyData(sphere.GetOutput())
# Create display node
cursorModelDisplay = slicer.vtkMRMLModelDisplayNode()
if whichHand == 'Left':
color = (1, .84313725490196079, 0) # gold (wedding ring hand)
else:
color = (0.69411764705882351, 0.47843137254901963,
0.396078431372549) # slicer skin tone
cursorModelDisplay.SetColor(color)
cursorModelDisplay.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(cursorModelDisplay)
cursor.SetAndObserveDisplayNodeID(cursorModelDisplay.GetID())
# Add to slicer.mrmlScene
cursorModelDisplay.SetInputPolyData(sphere.GetOutput())
slicer.mrmlScene.AddNode(cursor)
# Create transform node
transformNode = slicer.vtkMRMLLinearTransformNode()
transformNode.SetName(transformName)
for i in xrange(3):
transformNode.GetMatrixTransformToParent().SetElement(i, i, 10)
slicer.mrmlScene.AddNode(transformNode)
cursor.SetAndObserveTransformNodeID(transformNode.GetID())
handLineNode = self.handLine(whichHand)
return transformNode, handLineNode
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 handCursor(self,whichHand='Left'):
"""Create the mrml structure to represent a hand cursor if needed
otherwise return the current transform
whichHand : 'Left' for left color, anything else for right
also defines suffix for Transform and Cursor
"""
transformName = '%s-To-Table' % whichHand
transformNode = slicer.util.getNode(transformName)
if not transformNode:
# make the mrml
sphere = vtk.vtkSphereSource()
sphere.Update()
# Create model node
cursor = slicer.vtkMRMLModelNode()
cursor.SetScene(slicer.mrmlScene)
cursor.SetName("Cursor-%s" % whichHand)
cursor.SetAndObservePolyData(sphere.GetOutput())
# Create display node
cursorModelDisplay = slicer.vtkMRMLModelDisplayNode()
if whichHand == 'Left':
color = (1,.84313725490196079,0) # gold (wedding ring hand)
else:
color = (0.69411764705882351, 0.47843137254901963, 0.396078431372549) # slicer skin tone
cursorModelDisplay.SetColor(color)
cursorModelDisplay.SetScene(slicer.mrmlScene)
slicer.mrmlScene.AddNode(cursorModelDisplay)
cursor.SetAndObserveDisplayNodeID(cursorModelDisplay.GetID())
# Add to slicer.mrmlScene
cursorModelDisplay.SetInputPolyData(sphere.GetOutput())
slicer.mrmlScene.AddNode(cursor)
# Create transform node
transformNode = slicer.vtkMRMLLinearTransformNode()
transformNode.SetName(transformName)
for i in xrange(3):
transformNode.GetMatrixTransformToParent().SetElement(i, i, 10)
slicer.mrmlScene.AddNode(transformNode)
cursor.SetAndObserveTransformNodeID(transformNode.GetID())
handLineNode = self.handLine(whichHand)
return transformNode,handLineNode
def __init__(self, markupID, radius, length, position):
# We use the markupID to check whether this tool's markup has
# been removed in the onMarkupRemoved event
self.markupID = markupID
# Create a vtkCylinderSource for rendering the tool
self.toolSrc = vtk.vtkCylinderSource()
self.toolSrc.SetRadius(radius)
self.toolSrc.SetHeight(length)
# Create tool model using cylinder source
self.modelNode = slicer.vtkMRMLModelNode()
self.modelNode.HideFromEditorsOn()
self.modelNode.SetName(slicer.mrmlScene.GenerateUniqueName("Tool"))
polyData = self.toolSrc.GetOutput()
self.modelNode.SetAndObservePolyData(polyData)
slicer.mrmlScene.AddNode(self.modelNode)
# Create a DisplayNode for this node (so that it can control its
# own visibility) and have modelNode observe it
self.modelDisplay = slicer.vtkMRMLModelDisplayNode()
self.modelDisplay.SetColor(0,1,1) # cyan
slicer.mrmlScene.AddNode(self.modelDisplay)
self.modelNode.SetAndObserveDisplayNodeID(self.modelDisplay.GetID())
# Create a transform for our tool model that will scale it to
# the proper radius, length, and position. Leave the orientation
# at the default.
self.transformNode = slicer.vtkMRMLLinearTransformNode()
self.transformNode.HideFromEditorsOn()
self.transformNode.SetName(slicer.mrmlScene.GenerateUniqueName("Transform"))
self.updatePosition(position)
slicer.mrmlScene.AddNode(self.transformNode)
# apply the new transform to our tool
self.modelNode.SetAndObserveTransformNodeID(self.transformNode.GetID())
# Set tool to be visible
self.visible = True
def onHelloWorldButtonClicked(self):
scene = slicer.mrmlScene
inputModel = self.inputSelector.currentNode()
bounds = [0, 0, 0, 0, 0, 0]
inputModel.GetBounds(bounds)
print('Model Name is:')
print(inputModel.GetName())
X = bounds[1] - bounds[0]
Y = bounds[3] - bounds[2]
Z = bounds[5] - bounds[4]
mid = (bounds[0] + X / 2, bounds[2] + Y / 2, bounds[4] + Z / 2)
X_thick = .1 #TODO resolution input
Y_thick = .1 #TODO resolution input
Z_thick = .1 #TODO resolution input
z_slices = int(math.ceil(Z / Z_thick))
y_slices = int(math.ceil(Y / Y_thick))
x_slices = int(math.ceil(X / X_thick))
x_thick = X / x_slices
y_thick = Y / y_slices
z_thick = Z / z_slices
print('number of slices')
print((x_slices, y_slices, z_slices))
print('midpoint')
print(mid)
#TODO Bounding box calculation
imageSize = [x_slices, y_slices, z_slices]
imageSpacing = [x_thick, y_thick, z_thick]
voxelType = vtk.VTK_UNSIGNED_CHAR
imageData = vtk.vtkImageData()
imageData.SetDimensions(imageSize)
imageData.AllocateScalars(voxelType, 1)
thresholder = vtk.vtkImageThreshold()
thresholder.SetInputData(imageData)
thresholder.SetInValue(1)
thresholder.SetOutValue(1)
# Create volume node
volumeNode = slicer.vtkMRMLScalarVolumeNode()
volumeNode.SetSpacing(imageSpacing)
volumeNode.SetImageDataConnection(thresholder.GetOutputPort())
# Add volume to scene
slicer.mrmlScene.AddNode(volumeNode)
displayNode = slicer.vtkMRMLScalarVolumeDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
colorNode = slicer.util.getNode('Grey')
displayNode.SetAndObserveColorNodeID(colorNode.GetID())
volumeNode.SetAndObserveDisplayNodeID(displayNode.GetID())
volumeNode.CreateDefaultStorageNode()
#Transform the Volume to Fit Around the Model
transform = slicer.vtkMRMLLinearTransformNode()
scene.AddNode(transform)
volumeNode.SetAndObserveTransformNodeID(transform.GetID())
vTransform = vtk.vtkTransform()
vTransform.Translate(
(-X / 2 + mid[0], -Y / 2 + mid[1], -Z / 2 + mid[2]))
transform.SetAndObserveMatrixTransformToParent(vTransform.GetMatrix())
#Create a segmentation Node
segmentationNode = slicer.vtkMRMLSegmentationNode()
slicer.mrmlScene.AddNode(segmentationNode)
segmentationNode.CreateDefaultDisplayNodes()
segmentationNode.SetReferenceImageGeometryParameterFromVolumeNode(
volumeNode)
#Add the model as a segmentation
#sphereSource = vtk.vtkSphereSource()
#sphereSource.SetRadius(10)
#sphereSource.SetCenter(6,30,28)
#sphereSource.Update()
#segmentationNode.AddSegmentFromClosedSurfaceRepresentation(sphereSource.GetOutput(), "Test")
segmentID = segmentationNode.GetSegmentation().GenerateUniqueSegmentID(
"Test")
segmentationNode.AddSegmentFromClosedSurfaceRepresentation(
inputModel.GetPolyData(), segmentID)
#TODO, Unique ID
segmentationNode.SetMasterRepresentationToBinaryLabelmap()
modelLabelMap = segmentationNode.GetBinaryLabelmapRepresentation(
segmentID) #TODO Unique ID
segmentationNode.SetMasterRepresentationToBinaryLabelmap()
shape = list(modelLabelMap.GetDimensions())
shape.reverse() #why reverse?
labelArray = vtk.util.numpy_support.vtk_to_numpy(
modelLabelMap.GetPointData().GetScalars()).reshape(shape)
for n in range(1, shape[0] - 1):
labelArray[n, :, :] = numpy.maximum(labelArray[n, :, :],
labelArray[n - 1, :, :])
outputPolyData = vtk.vtkPolyData()
slicer.vtkSlicerSegmentationsModuleLogic.GetSegmentClosedSurfaceRepresentation(
segmentationNode, segmentID, outputPolyData)
# Create model node
model = slicer.vtkMRMLModelNode()
model.SetScene(scene)
model.SetName(scene.GenerateUniqueName("Model_Undercuts_Removed"))
model.SetAndObservePolyData(outputPolyData)
# Create display node
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetColor(1, 1, 0) # yellow
modelDisplay.SetBackfaceCulling(0)
modelDisplay.SetScene(scene)
scene.AddNode(modelDisplay)
model.SetAndObserveDisplayNodeID(modelDisplay.GetID())
# Add to scene
scene.AddNode(model)
def __init__(self, path, fiducialListNode):
fids = fiducialListNode
scene = slicer.mrmlScene
points = vtk.vtkPoints()
polyData = vtk.vtkPolyData()
polyData.SetPoints(points)
lines = vtk.vtkCellArray()
polyData.SetLines(lines)
linesIDArray = lines.GetData()
linesIDArray.Reset()
linesIDArray.InsertNextTuple1(0)
polygons = vtk.vtkCellArray()
polyData.SetPolys(polygons)
idArray = polygons.GetData()
idArray.Reset()
idArray.InsertNextTuple1(0)
for point in path:
pointIndex = points.InsertNextPoint(*point)
linesIDArray.InsertNextTuple1(pointIndex)
linesIDArray.SetTuple1(0, linesIDArray.GetNumberOfTuples() - 1)
lines.SetNumberOfCells(1)
# Create model node
model = slicer.vtkMRMLModelNode()
model.SetScene(scene)
model.SetName(scene.GenerateUniqueName("Path-%s" % fids.GetName()))
model.SetAndObservePolyData(polyData)
# Create display node
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetColor(1, 1, 0) # yellow
modelDisplay.SetScene(scene)
scene.AddNode(modelDisplay)
model.SetAndObserveDisplayNodeID(modelDisplay.GetID())
# Add to scene
modelDisplay.SetInputPolyData(model.GetPolyData())
scene.AddNode(model)
# Camera cursor
sphere = vtk.vtkSphereSource()
sphere.Update()
# Create model node
cursor = slicer.vtkMRMLModelNode()
cursor.SetScene(scene)
cursor.SetName(scene.GenerateUniqueName("Cursor-%s" % fids.GetName()))
cursor.SetAndObservePolyData(sphere.GetOutput())
# Create display node
cursorModelDisplay = slicer.vtkMRMLModelDisplayNode()
cursorModelDisplay.SetColor(1, 0, 0) # red
cursorModelDisplay.SetScene(scene)
scene.AddNode(cursorModelDisplay)
cursor.SetAndObserveDisplayNodeID(cursorModelDisplay.GetID())
# Add to scene
cursorModelDisplay.SetInputPolyData(sphere.GetOutput())
scene.AddNode(cursor)
# Create transform node
transform = slicer.vtkMRMLLinearTransformNode()
transform.SetName(
scene.GenerateUniqueName("Transform-%s" % fids.GetName()))
scene.AddNode(transform)
cursor.SetAndObserveTransformNodeID(transform.GetID())
self.transform = transform
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 takeUSSnapshot2(self,name):
snapshotDisp = slicer.vtkMRMLModelDisplayNode()
slicer.mrmlScene.AddNode(snapshotDisp)
snapshotDisp.SetScene(slicer.mrmlScene)
snapshotDisp.SetDisableModifiedEvent(1)
snapshotDisp.SetOpacity(1.0)
snapshotDisp.SetColor(1.0, 1.0, 1.0)
snapshotDisp.SetAmbient(1.0)
snapshotDisp.SetBackfaceCulling(0)
snapshotDisp.SetDiffuse(0)
snapshotDisp.SetSaveWithScene(0)
snapshotDisp.SetDisableModifiedEvent(0)
snapshotModel = slicer.vtkMRMLModelNode()
snapshotModel.SetName(name)
snapshotModel.SetDescription("Live Ultrasound Snapshot")
snapshotModel.SetScene(slicer.mrmlScene)
snapshotModel.SetAndObserveDisplayNodeID(snapshotDisp.GetID())
snapshotModel.SetHideFromEditors(0)
snapshotModel.SetSaveWithScene(0)
slicer.mrmlScene.AddNode(snapshotModel)
image_RAS = slicer.util.getNode("Image_Image")
dim = [0, 0, 0]
imageData = image_RAS.GetImageData()
imageData.GetDimensions(dim)
plane = vtk.vtkPlaneSource()
plane.Update()
snapshotModel.SetAndObservePolyData(plane.GetOutput())
slicePolyData = snapshotModel.GetPolyData()
slicePoints = slicePolyData.GetPoints()
# In parent transform is saved the ReferenceToRAS transform
parentTransform = vtk.vtkTransform()
parentTransform.Identity()
if not image_RAS.GetParentTransformNode() == None:
parentMatrix = vtk.vtkMatrix4x4()
parentTransformNode = image_RAS.GetParentTransformNode()
parentTransformNode.GetMatrixTransformToWorld(parentMatrix)
# aux=parentTransform.GetMatrix()
# aux.DeepCopy(parentMatrix)
# parentTransform.Update()
parentTransform.SetMatrix(parentMatrix)
inImageTransform = vtk.vtkTransform()
inImageTransform.Identity()
image_RAS.GetIJKToRASMatrix(inImageTransform.GetMatrix())
tImageToRAS = vtk.vtkTransform()
tImageToRAS.Identity()
tImageToRAS.PostMultiply()
tImageToRAS.Concatenate(inImageTransform)
tImageToRAS.Concatenate(parentTransform)
tImageToRAS.Update()
point1Image = [0.0, 0.0, 0.0, 1.0]
point2Image = [dim[0], 0.0, 0.0, 1.0]
point3Image = [0.0, dim[1], 0.0, 1.0]
point4Image = [dim[0], dim[1], 0.0, 1.0]
point1RAS = [0.0, 0.0, 0.0, 0.0]
point2RAS = [0.0, 0.0, 0.0, 0.0]
point3RAS = [0.0, 0.0, 0.0, 0.0]
point4RAS = [0.0, 0.0, 0.0, 0.0]
tImageToRAS.MultiplyPoint(point1Image, point1RAS)
tImageToRAS.MultiplyPoint(point2Image, point2RAS)
tImageToRAS.MultiplyPoint(point3Image, point3RAS)
tImageToRAS.MultiplyPoint(point4Image, point4RAS)
p1RAS = [point1RAS[0], point1RAS[1], point1RAS[2]]
p2RAS = [point2RAS[0], point2RAS[1], point2RAS[2]]
p3RAS = [point3RAS[0], point3RAS[1], point3RAS[2]]
p4RAS = [point4RAS[0], point4RAS[1], point4RAS[2]]
slicePoints.SetPoint(0, p1RAS)
slicePoints.SetPoint(1, p2RAS)
slicePoints.SetPoint(2, p3RAS)
slicePoints.SetPoint(3, p4RAS)
# # Add image texture.
image = vtk.vtkImageData()
image.DeepCopy(imageData)
modelDisplayNode = snapshotModel.GetModelDisplayNode()
modelDisplayNode.SetAndObserveTextureImageData(image)
snapshotTexture = slicer.vtkMRMLScalarVolumeNode()
snapshotTexture.SetAndObserveImageData(image)
snapshotTexture.SetName(name + "_Texture")
slicer.mrmlScene.AddNode(snapshotTexture)
snapshotTexture.CopyOrientation( image_RAS )
snapshotTextureDisplayNode = slicer.vtkMRMLScalarVolumeDisplayNode()
snapshotTextureDisplayNode.SetName(name + "_TextureDisplay")
snapshotTextureDisplayNode.SetAutoWindowLevel(0);
snapshotTextureDisplayNode.SetWindow(256);
snapshotTextureDisplayNode.SetLevel(128);
snapshotTextureDisplayNode.SetDefaultColorMap();
slicer.mrmlScene.AddNode(snapshotTextureDisplayNode)
snapshotTexture.AddAndObserveDisplayNodeID( snapshotTextureDisplayNode.GetID() )
snapshotModel.SetAttribute( "TextureNodeID", snapshotTexture.GetID() )
snapshotModelDisplayNode= snapshotModel.GetModelDisplayNode()
snapshotModelDisplayNode.SetAndObserveTextureImageData( snapshotTexture.GetImageData() )
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 computeSpline(self, spline, startVertexID, endVertexID, startPointPosition, endPointPosition, resolution):
print ("compute spline")
scene = slicer.mrmlScene
dijkstra = vtk.vtkDijkstraGraphGeodesicPath()
dijkstra.SetInputData(self.modelNode.GetPolyData())
dijkstra.SetStartVertex(startVertexID)
dijkstra.SetEndVertex(endVertexID)
dijkstra.Update()
#compute step size in according to resolution
vertices = dijkstra.GetOutput().GetPoints()
numVertices = vertices.GetNumberOfPoints()
resStepSize = float(numVertices) / (float(resolution) - 1.0)# -2 because of start and end point
print (numVertices)
print (resolution)
print (resStepSize)
equidistantIndices = []
curStep = 0
for i in range(0, int(resolution)):
curStep = (i * resStepSize) - 1
equidistantIndices.append(int(curStep + 0.5))
#create spline
splinePoints = []
points = vtk.vtkPoints()
for index in equidistantIndices:
print ("index")
print (index)
print ("position")
position = [0, 0, 0]
vertices.GetPoint(index, position)
print (position)
points.InsertNextPoint(position)
splinePoints.append(position)
spline.points = splinePoints
parametricSpline = vtk.vtkParametricSpline()
parametricSpline.SetPoints(points)
functionSource = vtk.vtkParametricFunctionSource()
functionSource.SetParametricFunction(parametricSpline)
functionSource.Update()
#create model node
splineModel = slicer.vtkMRMLModelNode()
splineModel.SetScene(scene)
splineModel.SetName("splineModel-%i" % 1) #todo
splineModel.SetAndObservePolyData(functionSource.GetOutput())
#create display node
splineModelDisplay = slicer.vtkMRMLModelDisplayNode()
splineModelDisplay.SetColor(1, 0, 0)
splineModelDisplay.SetOpacity(1)
splineModelDisplay.SetLineWidth(4)
splineModelDisplay.SliceIntersectionVisibilityOn()
splineModelDisplay.SetScene(scene)
scene.AddNode(splineModelDisplay)
splineModel.SetAndObserveDisplayNodeID(splineModelDisplay.GetID())
# add to scene
splineModelDisplay.GetPolyData = functionSource.GetOutput()
scene.AddNode(splineModel)
splineModelTransform = slicer.vtkMRMLLinearTransformNode()
splineModelTransform.SetName("SplineModelTransform-%i" % 1) # todo
scene.AddNode(splineModelTransform)
def setupScene(self): #applet specific
logging.debug('setupScene')
Guidelet.setupScene(self)
logging.debug('Create transforms')
self.cauteryTipToCautery = slicer.util.getNode('CauteryTipToCautery')
if not self.cauteryTipToCautery:
self.cauteryTipToCautery = slicer.vtkMRMLLinearTransformNode()
self.cauteryTipToCautery.SetName("CauteryTipToCautery")
m = self.readTransformFromSettings('CauteryTipToCautery')
if m:
self.cauteryTipToCautery.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.cauteryTipToCautery)
self.cauteryModelToCauteryTip = slicer.util.getNode(
'CauteryModelToCauteryTip')
if not self.cauteryModelToCauteryTip:
self.cauteryModelToCauteryTip = slicer.vtkMRMLLinearTransformNode()
self.cauteryModelToCauteryTip.SetName("CauteryModelToCauteryTip")
m = self.readTransformFromSettings('CauteryModelToCauteryTip')
if m:
self.cauteryModelToCauteryTip.SetMatrixTransformToParent(m)
self.cauteryModelToCauteryTip.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.cauteryModelToCauteryTip)
self.needleTipToNeedle = slicer.util.getNode('NeedleTipToNeedle')
if not self.needleTipToNeedle:
self.needleTipToNeedle = slicer.vtkMRMLLinearTransformNode()
self.needleTipToNeedle.SetName("NeedleTipToNeedle")
m = self.readTransformFromSettings('NeedleTipToNeedle')
if m:
self.needleTipToNeedle.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.needleTipToNeedle)
self.needleModelToNeedleTip = slicer.util.getNode(
'NeedleModelToNeedleTip')
if not self.needleModelToNeedleTip:
self.needleModelToNeedleTip = slicer.vtkMRMLLinearTransformNode()
self.needleModelToNeedleTip.SetName("NeedleModelToNeedleTip")
m = self.readTransformFromSettings('NeedleModelToNeedleTip')
if m:
self.needleModelToNeedleTip.SetMatrixTransformToParent(m)
self.needleModelToNeedleTip.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.needleModelToNeedleTip)
self.cauteryCameraToCautery = slicer.util.getNode(
'CauteryCameraToCautery')
if not self.cauteryCameraToCautery:
self.cauteryCameraToCautery = slicer.vtkMRMLLinearTransformNode()
self.cauteryCameraToCautery.SetName("CauteryCameraToCautery")
m = vtk.vtkMatrix4x4()
m.SetElement(0, 0, 0)
m.SetElement(0, 2, -1)
m.SetElement(1, 1, 0)
m.SetElement(1, 0, 1)
m.SetElement(2, 2, 0)
m.SetElement(2, 1, -1)
self.cauteryCameraToCautery.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.cauteryCameraToCautery)
self.CauteryToNeedle = slicer.util.getNode('CauteryToNeedle')
if not self.CauteryToNeedle:
self.CauteryToNeedle = slicer.vtkMRMLLinearTransformNode()
self.CauteryToNeedle.SetName("CauteryToNeedle")
slicer.mrmlScene.AddNode(self.CauteryToNeedle)
# Create transforms that will be updated through OpenIGTLink
self.cauteryToReference = slicer.util.getNode('CauteryToReference')
if not self.cauteryToReference:
self.cauteryToReference = slicer.vtkMRMLLinearTransformNode()
self.cauteryToReference.SetName("CauteryToReference")
slicer.mrmlScene.AddNode(self.cauteryToReference)
self.needleToReference = slicer.util.getNode('NeedleToReference')
if not self.needleToReference:
self.needleToReference = slicer.vtkMRMLLinearTransformNode()
self.needleToReference.SetName("NeedleToReference")
slicer.mrmlScene.AddNode(self.needleToReference)
# Cameras
logging.debug('Create cameras')
self.LeftCamera = slicer.util.getNode('Left Camera')
if not self.LeftCamera:
self.LeftCamera = slicer.vtkMRMLCameraNode()
self.LeftCamera.SetName("Left Camera")
slicer.mrmlScene.AddNode(self.LeftCamera)
self.RightCamera = slicer.util.getNode('Right Camera')
if not self.RightCamera:
self.RightCamera = slicer.vtkMRMLCameraNode()
self.RightCamera.SetName("Right Camera")
slicer.mrmlScene.AddNode(self.RightCamera)
# Models
logging.debug('Create models')
self.cauteryModel_CauteryTip = slicer.util.getNode('CauteryModel')
if not self.cauteryModel_CauteryTip:
if (self.parameterNode.GetParameter('TestMode') == 'True'):
moduleDirectoryPath = slicer.modules.lumpnav.path.replace(
'LumpNav.py', '')
slicer.util.loadModel(
qt.QDir.toNativeSeparators(
moduleDirectoryPath +
'../../../models/temporary/cautery.stl'))
self.cauteryModel_CauteryTip = slicer.util.getNode(
pattern="cautery")
else:
slicer.modules.createmodels.logic().CreateNeedle(
100, 1.0, 2.5, 0)
self.cauteryModel_CauteryTip = slicer.util.getNode(
pattern="NeedleModel")
self.cauteryModel_CauteryTip.GetDisplayNode().SetColor(
1.0, 1.0, 0)
self.cauteryModel_CauteryTip.SetName("CauteryModel")
self.needleModel_NeedleTip = slicer.util.getNode('NeedleModel')
if not self.needleModel_NeedleTip:
slicer.modules.createmodels.logic().CreateNeedle(80, 1.0, 2.5, 0)
self.needleModel_NeedleTip = slicer.util.getNode(
pattern="NeedleModel")
self.needleModel_NeedleTip.GetDisplayNode().SetColor(
0.333333, 1.0, 1.0)
self.needleModel_NeedleTip.SetName("NeedleModel")
self.needleModel_NeedleTip.GetDisplayNode(
).SliceIntersectionVisibilityOn()
# Create surface from point set
logging.debug('Create surface from point set')
self.tumorModel_Needle = slicer.util.getNode('TumorModel')
if not self.tumorModel_Needle:
self.tumorModel_Needle = slicer.vtkMRMLModelNode()
self.tumorModel_Needle.SetName("TumorModel")
sphereSource = vtk.vtkSphereSource()
sphereSource.SetRadius(0.001)
self.tumorModel_Needle.SetPolyDataConnection(
sphereSource.GetOutputPort())
slicer.mrmlScene.AddNode(self.tumorModel_Needle)
# Add display node
modelDisplayNode = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode.SetColor(0, 1, 0) # Green
modelDisplayNode.BackfaceCullingOff()
modelDisplayNode.SliceIntersectionVisibilityOn()
modelDisplayNode.SetSliceIntersectionThickness(4)
modelDisplayNode.SetOpacity(0.3) # Between 0-1, 1 being opaque
slicer.mrmlScene.AddNode(modelDisplayNode)
self.tumorModel_Needle.SetAndObserveDisplayNodeID(
modelDisplayNode.GetID())
tumorMarkups_Needle = slicer.util.getNode('T')
if not tumorMarkups_Needle:
tumorMarkups_Needle = slicer.vtkMRMLMarkupsFiducialNode()
tumorMarkups_Needle.SetName("T")
slicer.mrmlScene.AddNode(tumorMarkups_Needle)
tumorMarkups_Needle.CreateDefaultDisplayNodes()
tumorMarkups_Needle.GetDisplayNode().SetTextScale(0)
self.setAndObserveTumorMarkupsNode(tumorMarkups_Needle)
# Set up breach warning node
logging.debug('Set up breach warning')
self.breachWarningNode = slicer.util.getNode('LumpNavBreachWarning')
if not self.breachWarningNode:
self.breachWarningNode = slicer.mrmlScene.CreateNodeByClass(
'vtkMRMLBreachWarningNode')
self.breachWarningNode.SetName("LumpNavBreachWarning")
slicer.mrmlScene.AddNode(self.breachWarningNode)
self.breachWarningNode.SetPlayWarningSound(True)
self.breachWarningNode.SetWarningColor(1, 0, 0)
self.breachWarningNode.SetOriginalColor(
self.tumorModel_Needle.GetDisplayNode().GetColor())
self.breachWarningNode.SetAndObserveToolTransformNodeId(
self.cauteryTipToCautery.GetID())
self.breachWarningNode.SetAndObserveWatchedModelNodeID(
self.tumorModel_Needle.GetID())
# Set up breach warning light
import BreachWarningLight
logging.debug('Set up breach warning light')
self.breachWarningLightLogic = BreachWarningLight.BreachWarningLightLogic(
)
self.breachWarningLightLogic.setMarginSizeMm(
float(
self.parameterNode.GetParameter(
'BreachWarningLightMarginSizeMm')))
if (self.parameterNode.GetParameter('EnableBreachWarningLight') ==
'True'):
logging.debug("BreachWarningLight: active")
self.breachWarningLightLogic.startLightFeedback(
self.breachWarningNode, self.connectorNode)
else:
logging.debug("BreachWarningLight: shutdown")
self.breachWarningLightLogic.shutdownLight(self.connectorNode)
# Build transform tree
logging.debug('Set up transform tree')
self.cauteryToReference.SetAndObserveTransformNodeID(
self.ReferenceToRas.GetID())
self.cauteryCameraToCautery.SetAndObserveTransformNodeID(
self.cauteryToReference.GetID())
self.cauteryTipToCautery.SetAndObserveTransformNodeID(
self.cauteryToReference.GetID())
self.cauteryModelToCauteryTip.SetAndObserveTransformNodeID(
self.cauteryTipToCautery.GetID())
self.needleToReference.SetAndObserveTransformNodeID(
self.ReferenceToRas.GetID())
self.needleTipToNeedle.SetAndObserveTransformNodeID(
self.needleToReference.GetID())
self.needleModelToNeedleTip.SetAndObserveTransformNodeID(
self.needleTipToNeedle.GetID())
self.cauteryModel_CauteryTip.SetAndObserveTransformNodeID(
self.cauteryModelToCauteryTip.GetID())
self.needleModel_NeedleTip.SetAndObserveTransformNodeID(
self.needleModelToNeedleTip.GetID())
self.tumorModel_Needle.SetAndObserveTransformNodeID(
self.needleToReference.GetID())
self.tumorMarkups_Needle.SetAndObserveTransformNodeID(
self.needleToReference.GetID())
# self.liveUltrasoundNode_Reference.SetAndObserveTransformNodeID(self.ReferenceToRas.GetID())
# Hide slice view annotations (patient name, scale, color bar, etc.) as they
# decrease reslicing performance by 20%-100%
logging.debug('Hide slice view annotations')
import DataProbe
dataProbeUtil = DataProbe.DataProbeLib.DataProbeUtil()
dataProbeParameterNode = dataProbeUtil.getParameterNode()
dataProbeParameterNode.SetParameter('showSliceViewAnnotations', '0')
def onCompute(self):
slicer.app.processEvents()
import time
# Show the status bar
self.progressBar.show()
# Initilize various parameters
self.bone_labels = np.fromstring(self.lineedit.text,
dtype=int,
sep=',')
# Check to see if self.bone_labels is set to negative on and if so set to the default labels
if self.bone_labels[0] == -1:
# Use the minimum and maximum of the Ref_Bone_Slider (which is based on the minimum and maximum label in the first image)
self.bone_labels = range(int(self.Ref_Bone_Slider.minimum),
int(self.Ref_Bone_Slider.maximum) + 1)
self.max_bone_label = np.max(self.bone_labels)
# Find all the files in the input folder
self.files = os.listdir(self.directory_path)
# Sort the files to be in order now
self.files.sort(key=self.alphanum_key)
if self.num_files > len(self.files):
self.num_files = len(self.files)
# Initilize a list of file indicies
if self.num_files == -1:
self.file_list = range(0, len(self.files))
else:
self.file_list = range(0, int(self.num_files))
# Initilize Python list to hold all of the polydata
# One index for each bone label (ranges from 1 to 9)
polydata_list = []
for i in range(0, self.max_bone_label + 1):
polydata_list.append([])
# Load all of the images from the input folder
images_list = []
for curr_file in self.file_list:
# Update the status bar
self.progressBar.setValue(
float(curr_file) / len(self.file_list) * 100 /
10) # Use 10% of the status bar for loading the images
slicer.app.processEvents()
slicer.util.showStatusMessage("Loading Images...")
if self.files[curr_file][-3:] == 'nii':
print(str('Running file number ' + str(curr_file)))
# Load the nifti (.nii) or analyze image (.img/.hdr) using SimpleITK
filename = os.path.join(self.directory_path,
self.files[curr_file])
image = self.load_image(filename)
# It's upside-down when loaded, so add a flip filter
if self.flip_image_vertically.checked == True:
imflip = vtk.vtkImageFlip()
try:
imflip.SetInputData(image.GetOutput())
except:
imflip.SetInputData(image)
imflip.SetFilteredAxis(1)
imflip.Update()
image = imflip.GetOutput()
# If the images are flipped left/right so use a flip filter
if self.flip_image_horizontally.checked == True:
imflip = vtk.vtkImageFlip()
try:
imflip.SetInputData(image.GetOutput())
except:
imflip.SetInputData(image)
imflip.SetFilteredAxis(0)
imflip.Update()
image = imflip.GetOutput()
# Append the loaded image to the images_list
images_list.append(image)
# Temporarily push the image to Slicer (to have the correct class type for the model maker Slicer module)
if self.debug_show_images.checked == True:
image = sitk.ReadImage(filename)
sitkUtils.PushToSlicer(image,
str(curr_file),
0,
overwrite=True)
node = slicer.util.getNode(str(curr_file))
# If there is a non .nii file in the folder the images_list will be shorter than file_list
# Redefine the file_list here
self.file_list = range(0, len(images_list))
iter = 0 # For status bar
# Extract the surface from each image (i.e. the polydata)
for label in self.bone_labels:
for curr_file in self.file_list:
# Update the status bar (start at 10%)
self.progressBar.setValue(
10 + float(iter) /
(len(self.bone_labels) * len(self.file_list)) * 100 /
5) # Use 20% of the bar for this
slicer.app.processEvents()
iter = iter + 1
slicer.util.showStatusMessage("Extracting Surfaces...")
polydata = self.Extract_Surface(images_list[curr_file], label)
polydata_list[label].append(polydata)
# Create model node ("Extract_Shapes") and add to scene
if self.show_extracted_shapes.checked == True:
Extract_Shapes = slicer.vtkMRMLModelNode()
Extract_Shapes.SetAndObservePolyData(polydata)
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetSliceIntersectionVisibility(
True) # Show in slice view
modelDisplay.SetVisibility(True) # Show in 3D view
slicer.mrmlScene.AddNode(modelDisplay)
Extract_Shapes.SetAndObserveDisplayNodeID(
modelDisplay.GetID())
slicer.mrmlScene.AddNode(Extract_Shapes)
# Save each registered bone separately?
if self.Save_Extracted_Bones_Separately.checked == True:
for label in self.bone_labels:
for i in range(0, len(self.file_list)):
path = os.path.join(
self.output_directory_path,
'Bone_' + str(label) + '_position_' + str(i) + '.ply')
plyWriter = vtk.vtkPLYWriter()
plyWriter.SetFileName(path)
plyWriter.SetInputData(polydata_list[label][i])
plyWriter.Write()
print('Saved: ' + path)
# If this is set to true, stop the computation after extracting and smoothing the bones
if self.Skip_Registration.checked == True:
# Set the status bar to 100%
self.progressBar.setValue(100)
slicer.app.processEvents()
slicer.util.showStatusMessage("Skipping Registration Step...")
# Hide the status bar
self.progressBar.hide()
# Reset the status message on bottom of 3D Slicer
slicer.util.showStatusMessage(" ")
return 0
# Update the status bar (start at 30%)
self.progressBar.setValue(30 + 20) # Use 20% of the bar for this
slicer.app.processEvents()
slicer.util.showStatusMessage("Calculating Reference Shapes...")
# Don't use the mean shapes
# Use the bone shapes from volunteer 1 instead of the mean shape for each bone
# Initialize a Python list to hold the reference shapes
reference_shapes = []
# One index for each bone label (ranges from 1 to 9)
for i in range(0, self.max_bone_label + 1):
reference_shapes.append([])
# Get the bone shapes from the first volunteer and save them
for label in self.bone_labels:
reference_shapes[label].append(polydata_list[label][0])
######### Register the reference shape to each bone position #########
iter_bar = 0 # For status bar
for label in self.bone_labels:
for i in range(0, len(self.file_list)):
# Update the status bar (start at 50%)
self.progressBar.setValue(
50 + float(iter_bar) /
(len(self.bone_labels) * len(self.file_list)) * 100 /
5) # Use 20% of the bar for this
slicer.app.processEvents()
iter_bar = iter_bar + 1
slicer.util.showStatusMessage(
"Registering Reference Shapes...")
transformedSource = self.IterativeClosestPoint(
target=polydata_list[label][i],
source=reference_shapes[label][0])
# Replace the surface of file i and label with the registered reference shape for that particular bone
polydata_list[label][i] = transformedSource
iter_bar = 0 # For status bar
######### Register the reference bone (usually the radius for the wrist) for all the volunteers together #########
for label in self.bone_labels:
for i in range(0, len(self.file_list)):
# !! IMPORTANT !! Register the reference bone last (or else the bones afterwards will not register correctly)
# Skip the reference label for now (register after all the other bones are registered)
if label != self.ref_label:
# Update the status bar (start at 70%)
self.progressBar.setValue(
70 + float(iter_bar) /
(len(self.bone_labels) * len(self.file_list)) * 100 /
5) # Use 20% of the bar for this
slicer.app.processEvents()
iter_bar = iter_bar + 1
slicer.util.showStatusMessage(
"Registering Radius Together...")
polydata_list[label][i] = self.IterativeClosestPoint(
target=polydata_list[self.ref_label][0],
source=polydata_list[self.ref_label][i],
reference=polydata_list[label][i])
# Now register the reference label bones together
for i in range(0, len(self.file_list)):
polydata_list[self.ref_label][i] = self.IterativeClosestPoint(
target=polydata_list[self.ref_label][0],
source=polydata_list[self.ref_label][i],
reference=polydata_list[self.ref_label][i])
######### Save the output #########
# Should the reference bone be remove (i.e. not saved) in the final PLY surface file?
if self.Remove_Ref_Bone.checked == True:
index = np.argwhere(self.bone_labels == self.ref_label)
self.bone_labels = np.delete(self.bone_labels, index)
# Combine the surfaces of the wrist for each person and save as a .PLY file
for i in range(0, len(self.file_list)):
temp_combine_list = []
# Update the status bar (start at 90%)
self.progressBar.setValue(90 + float(i) / len(self.file_list) *
100 / 10) # Use 10% of the bar for this
slicer.app.processEvents()
iter_bar = iter_bar + 1
slicer.util.showStatusMessage("Saving Output Surfaces...")
total_points = [0]
# Get all the bones in a Python list for volunteer 'i'
for label in self.bone_labels:
temp_combine_list.append(polydata_list[label][i])
# Print the number of surface points for this bone
num_points = polydata_list[label][i].GetNumberOfPoints()
print("Bone " + str(label) + " points: " + str(num_points))
total_points.append(total_points[-1] + num_points)
print("Total Cumulative Points" + str(total_points))
# Combined the surfaces in the list into a single polydata surface
combined_polydata = self.Combine_Surfaces(temp_combine_list)
# Create model node ("ICP_Result") and add to scene
if self.show_registered_shapes.checked == True:
ICP_Result = slicer.vtkMRMLModelNode()
ICP_Result.SetAndObservePolyData(combined_polydata)
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetSliceIntersectionVisibility(
True) # Show in slice view
modelDisplay.SetVisibility(True) # Show in 3D view
slicer.mrmlScene.AddNode(modelDisplay)
ICP_Result.SetAndObserveDisplayNodeID(modelDisplay.GetID())
slicer.mrmlScene.AddNode(ICP_Result)
# Write the combined polydata surface to a .PLY file
plyWriter = vtk.vtkPLYWriter()
path = os.path.join(self.output_directory_path,
str(self.files[i][:-4]) + '_combined.ply')
plyWriter.SetFileName(path)
plyWriter.SetInputData(combined_polydata)
plyWriter.Write()
print('Saved: ' + path)
# Save each registered bone separately as well?
if self.Save_Registered_Bones_Separately.checked == True:
for label in self.bone_labels:
path = os.path.join(
self.output_directory_path,
'Position_' + str(i) + '_bone_' + str(label) + '.ply')
plyWriter.SetFileName(path)
plyWriter.SetInputData(polydata_list[label][i])
plyWriter.Write()
print('Saved: ' + path)
# Set the status bar to 100%
self.progressBar.setValue(100)
# Hide the status bar
self.progressBar.hide()
# Reset the status message on bottom of 3D Slicer
slicer.util.showStatusMessage(" ")
return 0
def updateCurve(self):
if self.AutomaticUpdate == False:
return
if self.SourceNode and self.DestinationNode:
if self.SourceNode.GetNumberOfFiducials() < 2:
if self.CurvePoly != None:
self.CurvePoly.Initialize()
self.CurveLength = 0.0
else:
if self.CurvePoly == None:
self.CurvePoly = vtk.vtkPolyData()
if self.DestinationNode.GetDisplayNodeID() == None:
modelDisplayNode = slicer.vtkMRMLModelDisplayNode()
modelDisplayNode.SetColor(self.ModelColor)
slicer.mrmlScene.AddNode(modelDisplayNode)
self.DestinationNode.SetAndObserveDisplayNodeID(
modelDisplayNode.GetID())
if self.InterpolationMethod == 0:
if self.RingMode > 0:
self.nodeToPoly(self.SourceNode, self.CurvePoly, True)
else:
self.nodeToPoly(self.SourceNode, self.CurvePoly, False)
elif self.InterpolationMethod == 1: # Cardinal Spline
if self.RingMode > 0:
self.nodeToPolyCardinalSpline(self.SourceNode,
self.CurvePoly, True)
else:
self.nodeToPolyCardinalSpline(self.SourceNode,
self.CurvePoly, False)
elif self.InterpolationMethod == 2: # Hermite Spline
if self.RingMode > 0:
self.nodeToPolyHermiteSpline(self.SourceNode,
self.CurvePoly, True)
else:
self.nodeToPolyHermiteSpline(self.SourceNode,
self.CurvePoly, False)
self.CurveLength = self.calculateLineLength(self.CurvePoly)
tubeFilter = vtk.vtkTubeFilter()
curvatureValues = vtk.vtkDoubleArray()
if self.Curvature:
## If the curvature option is ON, calculate the curvature along the curve.
(meanKappa, minKappa,
maxKappa) = self.computeCurvatures(self.CurvePoly,
curvatureValues)
self.CurvePoly.GetPointData().AddArray(curvatureValues)
self.curvatureMeanKappa = meanKappa
self.curvatureMinKappa = minKappa
self.curvatureMaxKappa = maxKappa
else:
self.curvatureMeanKappa = None
self.curvatureMinKappa = None
self.curvatureMaxKappa = None
tubeFilter.SetInputData(self.CurvePoly)
tubeFilter.SetRadius(self.TubeRadius)
tubeFilter.SetNumberOfSides(20)
tubeFilter.CappingOn()
tubeFilter.Update()
# self.DestinationNode.SetAndObservePolyData(tubeFilter.GetOutput())
self.DestinationNode.SetAndObservePolyData(self.CurvePoly)
self.DestinationNode.Modified()
if self.DestinationNode.GetScene() == None:
slicer.mrmlScene.AddNode(self.DestinationNode)
displayNode = self.DestinationNode.GetDisplayNode()
if displayNode:
if self.Curvature:
displayNode.SetActiveScalarName('Curvature')
else:
displayNode.SetActiveScalarName('')
def runSegmentation(self, elList, volume, parentPath, deetoExe, models,
createVTK):
### CHECK that both the fiducials and ct volume have been selected
if (len(elList) == 0):
# notify error
slicer.util.showStatusMessage("Error, no electrode list selected")
return
if (volume == None):
# notify error
slicer.util.showStatusMessage("Error, no volume selected")
return
### COMPUTE THE THRESHOLD the 45% of points not null(0.0)
im = volume.GetImageData()
# linearize the 3D image in a vector
vector = vtk.util.numpy_support.vtk_to_numpy(
im.GetPointData().GetScalars())
# eliminate 0.0 value from the vector
n_vector = vector[vector != 0]
# sort the intensity values
n_vector.sort()
# compute the threshold as the 45% of points not null
threshold = n_vector[int(n_vector.size * 0.45)]
### CREATE A NEW FIDUCIAL LIST CALLED ...... [TODO]
mlogic = slicer.modules.markups.logic()
###
### [TODO] Accrocchio, non so come cambiare questi parametri solo
### per il nodo corrente, invece che di default
mlogic.SetDefaultMarkupsDisplayNodeTextScale(1.3)
mlogic.SetDefaultMarkupsDisplayNodeGlyphScale(1.5)
mlogic.SetDefaultMarkupsDisplayNodeColor(0.39, 0.78, 0.78) # AZZURRO
mlogic.SetDefaultMarkupsDisplayNodeSelectedColor(0.39, 1.0,
0.39) # VERDONE
fidNode = slicer.util.getNode(mlogic.AddNewFiducialNode("recon"))
# Save the volume as has been modified
self.tmpVolumeFile = parentPath + "/Tmp/tmp.nii.gz"
self.saveNode(volume, self.tmpVolumeFile)
# Set the parameters of the progess bar and show it
self.pb.setRange(0, len(elList))
self.pb.show()
self.pb.setValue(0)
slicer.app.processEvents()
# For each electrode "e":
for i in xrange(len(elList)):
tFlag = "-l" if (elList[i].tailCheckBox.isChecked()
== True) else "-t"
hFlag = "-h" if (elList[i].headCheckBox.isChecked()
== True) else "-e"
# Construct the cmdLine to run the segmentation on "e"
cmdLine = [str(deetoExe), '-s', str(threshold), '-ct', str(self.tmpVolumeFile), \
hFlag, str(-1 * elList[i].entry[0]), str(-1 * elList[i].entry[1]), \
str(elList[i].entry[2]), tFlag, \
str(-1 * elList[i].target[0]), str(-1 * elList[i].target[1]), \
str(elList[i].target[2]), '-m'] + \
map(str, models[elList[i].model.currentText][:-1])
print cmdLine
# RUN the command line cmdLine.
# [NOTE] : I have used Popen since subprocess.check_output wont work at the moment
# It Looks a problem of returning code from deetoS
points = subprocess.Popen(
cmdLine, stdout=subprocess.PIPE).communicate()[0].splitlines()
# print points
### For each of the point returned by deeto we add it to the new markup fiducial
name = elList[i].name.text
for p in range(0, (len(points) - 1), 3):
a = fidNode.AddFiducial(float(points[p]), float(points[p + 1]),
float(points[p + 2]))
fidNode.SetNthFiducialLabel(a, name + str((p / 3) + 1))
### For each electrode we create a line from the start point to the last + 3mm
### Look for two points p1 and p3 starting from p1 and p2 (first and last point segmented
last = len(points) - 1
p1 = [float(points[0]), float(points[1]), float(points[2])]
p2 = [
float(points[last - 2]),
float(points[last - 1]),
float(points[last])
]
delta = math.sqrt(
math.pow((p1[0] - p2[0]), 2) + math.pow((p1[1] - p2[1]), 2) +
math.pow((p1[2] - p2[2]), 2))
p3 = [0.0, 0.0, 0.0]
p3[0] = p2[0] + (p2[0] - p1[0]) / delta * 3 # distance 3mm
p3[1] = p2[1] + (p2[1] - p1[1]) / delta * 3 # distance 3mm
p3[2] = p2[2] + (p2[2] - p1[2]) / delta * 3 # distance 3mm
if createVTK.checked:
### Create a vtk line
lineSource = vtk.vtkLineSource()
lineSource.SetPoint1(p1)
lineSource.SetPoint2(p3)
lineSource.SetResolution(100) ## why?
lineSource.Update()
### Create a model of the line to add to the scene
model = slicer.vtkMRMLModelNode()
model.SetName(name + "_direction")
model.SetAndObservePolyData(lineSource.GetOutput())
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetSliceIntersectionVisibility(
True) # Hide in slice view
modelDisplay.SetVisibility(True) # Show in 3D view
modelDisplay.SetColor(1, 0, 0)
modelDisplay.SetLineWidth(2)
slicer.mrmlScene.AddNode(modelDisplay)
model.SetAndObserveDisplayNodeID(modelDisplay.GetID())
slicer.mrmlScene.AddNode(model)
# Lock all markup
mlogic.SetAllMarkupsLocked(fidNode, True)
# update progress bar
self.pb.setValue(i + 1)
slicer.app.processEvents()
self.pb.hide()
