def onCircularROIBtn(self):
self.markups = slicer.util.getNode("F")
self.sphere = vtk.vtkSphereSource()
self.UpdateSphere(0, 0)
scene = slicer.mrmlScene
# Create model node
model = slicer.vtkMRMLModelNode()
model.SetAndObservePolyData(self.sphere.GetOutput())
# self.modelDisplay.SetColor(1, 1, 0) # yellows
# self.modelDisplay.SetBackfaceCulling(0)
# Create display node
self.modelDisplay = slicer.vtkMRMLModelDisplayNode()
self.modelDisplay.SetSliceIntersectionVisibility(True)
self.modelDisplay.SetVisibility(True)
scene.AddNode(self.modelDisplay)
model.SetAndObserveDisplayNodeID(self.modelDisplay.GetID())
# Add to scene
self.modelDisplay.SetInputPolyDataConnection(model.GetPolyDataConnection())
scene.AddNode(model)
self.markups.AddObserver("ModifiedEvent", self.UpdateSphere, 2)
def merge_models(self, modelA, modelB, modelC):
scene = slicer.mrmlScene
# Create model node
mergedModel = slicer.vtkMRMLModelNode()
mergedModel.SetScene(scene)
mergedModel.SetName(modelName)
dnode = slicer.vtkMRMLModelDisplayNode()
snode = slicer.vtkMRMLModelStorageNode()
mergedModel.SetAndObserveDisplayNodeID(dnode.GetID())
mergedModel.SetAndObserveStorageNodeID(snode.GetID())
scene.AddNode(dnode)
scene.AddNode(snode)
scene.AddNode(mergedModel)
# Get transformed poly data from input models
modelA_polydata = self.getTransformedPolyDataFromModel(self.modelA)
modelB_polydata = self.getTransformedPolyDataFromModel(self.modelB)
modelC_polydata = self.getTransformedPolyDataFromModel(self.modelC)
# Append poly data
appendFilter = vtk.vtkAppendPolyData()
appendFilter.AddInputData(modelA_polydata)
appendFilter.AddInputData(modelB_polydata)
appendFilter.AddInputData(modelC_polydata)
appendFilter.Update();
# Output
mergedModel.SetAndObservePolyData(appendFilter.GetOutput());
mergedModel.SetAndObserveDisplayNodeID(dnode.GetID());
return mergedModel
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 copyAndHardenModel(self,originalModel):
# copy model
outputModel = slicer.vtkMRMLModelNode()
fullPolyData = originalModel.GetPolyData()
outputModel.SetAndObservePolyData(fullPolyData)
md2 = slicer.vtkMRMLModelDisplayNode()
slicer.mrmlScene.AddNode(outputModel)
slicer.mrmlScene.AddNode(md2)
outputModel.SetAndObserveDisplayNodeID(md2.GetID())
md2.SetVisibility(0)
# apply transforms tree to copied model
parent_transform = originalModel.GetParentTransformNode()
try:
t = slicer.util.getNode('DefinedTransform')
identityTransform = vtk.vtkMatrix4x4()
t.SetMatrixTransformToParent(identityTransform)
except:
t=slicer.vtkMRMLLinearTransformNode()
t.SetName('DefinedTransform')
slicer.mrmlScene.AddNode(t)
t.SetAndObserveTransformNodeID(parent_transform.GetID())
t.HardenTransform()
outputModel.SetAndObserveTransformNodeID(t.GetID())
outputModel.HardenTransform()
return outputModel,t
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())
lineModelDisplay.SetInputPolyDataConnection(line.GetOutputPort())
scene.AddNode(lineModel)
return line
def arrowModel(self, scene, point1, point2, name, color):
""" Create a line to reflect the puncture path"""
#Line mode source
arrow = vtk.vtkLineSource()
#arrow.SetShaftRadius(0.01)
#arrow.SetTipLength(.9)
arrow.SetPoint1(point1) #(point1[0][0], point1[0][1], point1[0][2])
arrow.SetPoint2(point2) #(point2[0][0], point2[0][1], point2[0][2])
tubes = vtk.vtkTubeFilter()
tubes.SetInputConnection(arrow.GetOutputPort())
tubes.SetRadius(0.8)
tubes.SetNumberOfSides(6)
# Create model node
arrowModel = slicer.vtkMRMLModelNode()
arrowModel.SetScene(scene)
arrowModel.SetName(name)
arrowModel.SetAndObservePolyData(tubes.GetOutput())
# Create display node
arrowModelDisplay = slicer.vtkMRMLModelDisplayNode()
arrowModelDisplay.SetColor(color)
arrowModelDisplay.SetScene(scene)
scene.AddNode(arrowModelDisplay)
arrowModel.SetAndObserveDisplayNodeID(arrowModelDisplay.GetID())
arrowModelDisplay.SetInputPolyDataConnection(tubes.GetOutputPort())
scene.AddNode(arrowModel)
return arrow
def createSampleModelNode(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: https://mantisarchive.slicer.org/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)
modelNode.SetPolyDataConnection(sphere.GetOutputPort())
modelNode.SetHideFromEditors(0)
displayNode = slicer.vtkMRMLModelDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
displayNode.Visibility2DOn()
displayNode.VisibilityOn()
displayNode.SetColor(color[0], color[1], color[2])
modelNode.SetAndObserveDisplayNodeID(displayNode.GetID())
return modelNode
def onApplyButtonClicked(self):
"""
Real algorithm should be in class VascularWallLogic.
"""
logging.info("applyButton is clicked.")
# Create models for sphere
self.sphere = vtk.vtkSphereSource()
# Model node
model = slicer.vtkMRMLModelNode()
model.SetAndObservePolyData(self.sphere.GetOutput())
# Display node
self.modelDisplay = slicer.vtkMRMLModelDisplayNode()
self.modelDisplay.SetSliceIntersectionVisibility(True)
self.modelDisplay.SetVisibility(self.showCheckBox.isChecked())
self.modelDisplay.SetOpacity(0.5)
self.modelDisplay.SetRepresentation(1)
slicer.mrmlScene.AddNode(self.modelDisplay)
model.SetAndObserveDisplayNodeID(self.modelDisplay.GetID())
# Add to scene
self.modelDisplay.SetInputPolyDataConnection(
model.GetPolyDataConnection())
slicer.mrmlScene.AddNode(model)
# Callback
self.UpdateSphere(0, 0)
self.rulerSelector.currentNode().AddObserver(
'ModifiedEvent', self.UpdateSphere)
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())
planeContour.SetInputData(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())
planeModelDisplay.SetInputPolyDataConnection(
planeContour.GetOutputPort())
scene.AddNode(planeNode)
return plane
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 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 showColorMap(self):
# Get PolyData from Segment 1
self.segment1.CreateClosedSurfaceRepresentation()
ss1 = self.segment1.GetSegmentation()
str1 = ss1.GetNthSegmentID(0)
pl1 = vtk.vtkPolyData()
pl1 = self.segment1.GetClosedSurfaceRepresentation(str1)
# Get PolyData from Segment 2
self.segment2.CreateClosedSurfaceRepresentation()
ss2 = self.segment2.GetSegmentation()
str2 = ss2.GetNthSegmentID(0)
pl2 = vtk.vtkPolyData()
pl2 = self.segment2.GetClosedSurfaceRepresentation(str2)
# Compute distance
distanceFilter = vtk.vtkDistancePolyDataFilter()
distanceFilter.SetInputData(0, pl1)
distanceFilter.SetInputData(1, pl2)
distanceFilter.SignedDistanceOff()
distanceFilter.Update()
# Center 3D view
#slicer.app.layoutManager().tableWidget(0).setVisible(False)
layoutManager = slicer.app.layoutManager()
threeDWidget = layoutManager.threeDWidget(0)
threeDView = threeDWidget.threeDView()
threeDView.resetFocalPoint()
# Output model
model = slicer.vtkMRMLModelNode()
slicer.mrmlScene.AddNode(model)
model.SetName('DistanceModelNode')
model.SetAndObservePolyData(distanceFilter.GetOutput())
self.distanceColorMap_display = slicer.vtkMRMLModelDisplayNode()
slicer.mrmlScene.AddNode(self.distanceColorMap_display)
model.SetAndObserveDisplayNodeID(self.distanceColorMap_display.GetID())
self.distanceColorMap_display.SetActiveScalarName('Distance')
self.distanceColorMap_display.SetAndObserveColorNodeID(
'vtkMRMLColorTableNodeFileDivergingBlueRed.txt')
self.distanceColorMap_display.SetScalarVisibility(True)
self.distanceColorMap_display.SetScalarRangeFlag(
0) # Set scalar range mode to Manual
self.distanceColorMap_display.SetScalarRange(0.0, 10.0)
[rmin, rmax] = self.distanceColorMap_display.GetScalarRange()
print(rmin)
print(rmax)
# Scalar bar
self.updateScalarBarRange(0.0, 10.0)
self.updateScalarBarVisibility(True)
# Deactivate visibility of segments (deberia actualizarse el checkbox del GUI pero no lo consigo)
self.updateSegment1Visibility(False)
self.updateSegment2Visibility(False)
def onApplyButton(self):
print("Transducer parameters >> /n")
print("ROC:" + str(self.ROC.value))
print("Width:" + str(self.width.value))
print("ROC:" + str(self.freq.value))
skull, skull_actor = hlp.read_skull_vtk(
"/Users/home/Desktop/Simulation/Simulation/SMA_matlab_skull_transform0.vtk",
0.5, [0.8, 0.8, 0.8])
model = slicer.vtkMRMLModelNode()
model.SetAndObservePolyData(skull)
## set model node properties
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetColor(0.8, 0.8, 0.8)
modelDisplay.BackfaceCullingOff()
modelDisplay.SetOpacity(0.5)
modelDisplay.SetPointSize(3)
## mode node display
modelDisplay.SetSliceIntersectionVisibility(True)
modelDisplay.SetVisibility(True)
slicer.mrmlScene.AddNode(modelDisplay)
model.SetAndObserveDisplayNodeID(modelDisplay.GetID())
modelDisplay.SetInputPolyDataConnection(model.GetPolyDataConnection())
## model node set name
slicer.mrmlScene.AddNode(model).SetName("Skull")
## read vtk object convert to vtkimage
result_image = hlp.vtk_grid2image(
"/Users/home/Desktop/Simulation/Simulation/SMA_full_0.vtk")
result_volume = slicer.vtkMRMLScalarVolumeNode()
result_volume.SetAndObserveImageData(result_image)
## image to 2D scene
defaultVolumeDisplayNode = slicer.mrmlScene.CreateNodeByClass(
"vtkMRMLScalarVolumeDisplayNode")
defaultVolumeDisplayNode.AutoWindowLevelOn()
defaultVolumeDisplayNode.SetVisibility(True)
defaultVolumeDisplayNode.AddWindowLevelPresetFromString(
"ColdToHotRainbow")
slicer.mrmlScene.AddDefaultNode(defaultVolumeDisplayNode)
result_volume.SetAndObserveDisplayNodeID(
defaultVolumeDisplayNode.GetID())
defaultVolumeDisplayNode.SetInputImageDataConnection(
result_volume.GetImageDataConnection())
## volume node set name
slicer.mrmlScene.AddNode(result_volume).SetName("simulation_result")
## volume rendering
hlp.showVolumeRendering(result_volume)
slicer.mrmlScene.AddObserver(slicer.vtkMRMLScene.NodeAddedEvent,
hlp.onNodeAdded)
def defineSphere(self):
sphereSource = vtk.vtkSphereSource()
sphereSource.SetRadius(100.0)
model = slicer.vtkMRMLModelNode()
model.SetAndObservePolyData(sphereSource.GetOutput())
modelDisplay = slicer.vtkMRMLModelDisplayNode()
slicer.mrmlScene.AddNode(modelDisplay)
model.SetAndObserveDisplayNodeID(modelDisplay.GetID())
modelDisplay.SetInputPolyDataConnection(sphereSource.GetOutputPort())
return model
def createAndConfigureClippingModelDisplayNode(self):
self.clippingModelDisplayNode = slicer.vtkMRMLModelDisplayNode()
self.clippingModelDisplayNode.SetSliceIntersectionThickness(3)
self.clippingModelDisplayNode.SetColor(self.labelValueToRGB(self.outputLabelValue) if self.outputLabelValue
else [0.200, 0.800, 0.000])
self.clippingModelDisplayNode.BackfaceCullingOff()
self.clippingModelDisplayNode.SliceIntersectionVisibilityOn()
self.clippingModelDisplayNode.SetOpacity(0.3)
slicer.mrmlScene.AddNode(self.clippingModelDisplayNode)
self.clippingModelNode.SetAndObserveDisplayNodeID(self.clippingModelDisplayNode.GetID())
def drawCone(self, coneSource, coneDimensions, center):
coneModelNode = slicer.vtkMRMLModelNode()
slicer.mrmlScene.AddNode(coneModelNode)
coneModelNode.SetName('ConeModel')
coneModelNodeToUpdate = coneModelNode
coneSource.Update()
coneModelNodeToUpdate.SetAndObservePolyData(coneSource.GetOutput())
if coneModelNodeToUpdate.GetDisplayNode() is None:
displayNode = slicer.vtkMRMLModelDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
displayNode.SetName('ConeModelDisplay')
coneModelNodeToUpdate.SetAndObserveDisplayNodeID(displayNode.GetID())
return coneModelNode
def __init__(self):
self.sendDataOK = False
self.OSC_active = False
self.line = slicer.util.getNode('Line')
if not self.line:
self.line = slicer.vtkMRMLModelNode()
self.line.SetName('Line')
linePolyData = vtk.vtkPolyData()
self.line.SetAndObservePolyData(linePolyData)
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetSliceIntersectionVisibility(True)
modelDisplay.SetColor(0,1,0)
slicer.mrmlScene.AddNode(modelDisplay)
self.line.SetAndObserveDisplayNodeID(modelDisplay.GetID())
slicer.mrmlScene.AddNode(self.line)
def createAndConfigureSegmentModelDisplayNode(self):
self.segmentModelNode = slicer.vtkMRMLModelNode()
prefix = "{}-".format(self.seriesNumber) if self.seriesNumber else ""
self.segmentModelNode.SetName('%sSurfaceCut-MODEL' % prefix)
slicer.mrmlScene.AddNode(self.segmentModelNode)
self.segmentModelDisplayNode = slicer.vtkMRMLModelDisplayNode()
self.segmentModelDisplayNode.SetSliceIntersectionThickness(3)
# self.refreshViewNodeIDs
self.segmentModelDisplayNode.SetColor(self.labelValueToRGB(self.outputLabelValue) if self.outputLabelValue
else [0.200, 0.800, 0.000])
self.segmentModelDisplayNode.BackfaceCullingOff()
self.segmentModelDisplayNode.SliceIntersectionVisibilityOn()
self.segmentModelDisplayNode.SetOpacity(0.3)
slicer.mrmlScene.AddNode(self.segmentModelDisplayNode)
self.segmentModelNode.SetAndObserveDisplayNodeID(self.segmentModelDisplayNode.GetID())
def renderSegmentedData(self, modelNode, outputModelNode, selectedTexture):
fullPolyData = modelNode.GetPolyData()
pointData=fullPolyData.GetPointData()
data = np.load('C:/Users/Brand/OneDrive/Documents/CISC 472/test segmentation_model/classified_texture.pkl')
size_of_data = data.shape
print(size_of_data)
print(int(data[1][0]))
print(' ')
print(selectedTexture)
segmentedPointIds = vtk.vtkIdTypeArray()
print('begin classifiacation')
for point in range(size_of_data[1]):
if int(data[1][point]) == selectedTexture:
segmentedPointIds.InsertNextValue(int(data[0][point]))
segmentedPointIds.InsertNextValue(int(data[0][point]))
print('calssification done')
selectionNode = vtk.vtkSelectionNode()
selectionNode.SetFieldType(vtk.vtkSelectionNode.POINT)
selectionNode.SetContentType(vtk.vtkSelectionNode.INDICES)
selectionNode.SetSelectionList(segmentedPointIds)
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())
print('done?')
return 0
def drawPlane(self, m, V_norm):
scene = slicer.mrmlScene
#create a plane to cut,here it cuts in the XZ direction (xz normal=(1,0,0);XY =(0,0,1),YZ =(0,1,0)
planex=vtk.vtkPlane()
planex.SetOrigin(m[0],m[1],m[2])
planex.SetNormal(V_norm[0],V_norm[1],V_norm[2])
renderer = slicer.app.layoutManager().threeDWidget(0).threeDView().renderWindow().GetRenderers().GetFirstRenderer()
viewSize = renderer.ComputeVisiblePropBounds()
#viewSize = (-50.0, 50.0, -50.0, 50.0, -50.0, 50.0)
planexSample = vtk.vtkSampleFunction()
planexSample.SetImplicitFunction(planex)
planexSample.SetModelBounds(viewSize)
#planexSample.SetSampleDimensions(200,200,200)
planexSample.ComputeNormalsOff()
plane1 = vtk.vtkContourFilter()
plane1.SetInputConnection(planexSample.GetOutputPort())
# Create model Plane A node
planeA = slicer.vtkMRMLModelNode()
planeA.SetScene(scene)
planeA.SetName("X-Y Plane")
planeA.SetAndObservePolyData(plane1.GetOutput())
# Create display model Plane A node
planeAModelDisplay = slicer.vtkMRMLModelDisplayNode()
planeAModelDisplay.SetColor(0.145,0.77,0.596)
planeAModelDisplay.BackfaceCullingOff()
planeAModelDisplay.SetScene(scene)
scene.AddNode(planeAModelDisplay)
planeA.SetAndObserveDisplayNodeID(planeAModelDisplay.GetID())
#Add to scene
planeAModelDisplay.SetInputPolyDataConnection(plane1.GetOutputPort())
scene.AddNode(planeA)
# adjust center of 3d view to plane
layoutManager = slicer.app.layoutManager()
threeDWidget = layoutManager.threeDWidget(0)
threeDView = threeDWidget.threeDView()
threeDView.resetFocalPoint()
def run(self):
"""
Run the actual algorithm
"""
#generating Nodes for displaying a new model
modelNode = slicer.vtkMRMLModelNode()
dispNode = slicer.vtkMRMLModelDisplayNode()
transform = slicer.vtkMRMLLinearTransformNode()
#Display node characteristics
dispNode.SetVisibility(True)
dispNode.SetSliceIntersectionVisibility(True)
dispNode.SetOpacity(1)
dispNode.SetColor(1, 1, 0)
dispNode.SetScene(slicer.mrmlScene)
#generate sphere data
sphere = vtk.vtkSphereSource()
sphere.SetCenter(10,10,10)
sphere.SetRadius(40)
sphere.Update()
#adding necessary nodes to the Scene
slicer.mrmlScene.AddNode(dispNode)
slicer.mrmlScene.AddNode(transform)
slicer.mrmlScene.AddNode(modelNode)
#model node name and associations!
modelNode.SetName("SphereModelNode")
modelNode.SetScene(slicer.mrmlScene)
modelNode.SetAndObserveTransformNodeID(transform.GetID())
modelNode.SetAndObserveDisplayNodeID(dispNode.GetID())
apd = vtk.vtkAppendPolyData()
apd.AddInputData(sphere.GetOutput())
apd.Update()
#adding model node poly data! Here there are sphere's data!!!
modelNode.SetAndObservePolyData(apd.GetOutput())
#update the scene
slicer.mrmlScene.Modified()
return True
def plotLineZaxis(self):
# Create a vtkPoints object and store the points in it
self.pos = [0.0, 0.0, 0.0, 0.0]
self.targetFiducial.GetNthFiducialWorldCoordinates(0, self.pos)
targetP = [self.pos[i] for i in (0,1,2)]
self.surfPoint = [0.0, 0.0, 0.0, 0.0]
self.surfaceFiducial.GetNthFiducialWorldCoordinates(0, self.surfPoint)
surfaceP = [self.surfPoint[i] for i in (0,1,2)]
self.zVector = np.subtract(targetP,surfaceP)
points = vtk.vtkPoints()
points.InsertNextPoint(targetP)
points.InsertNextPoint(surfaceP)
# Create line
line = vtk.vtkLine()
line.GetPointIds().SetId(0,0)
line.GetPointIds().SetId(1,1)
lineCellArray = vtk.vtkCellArray()
lineCellArray.InsertNextCell(line)
self.lineNode = slicer.vtkMRMLModelNode()
self.lineNode.SetName('LineZ')
linePolyData = vtk.vtkPolyData()
self.lineNode.SetAndObservePolyData(linePolyData)
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetSliceIntersectionVisibility(True)
modelDisplay.SetColor(1,1,1)
slicer.mrmlScene.AddNode(modelDisplay)
self.lineNode.SetAndObserveDisplayNodeID(modelDisplay.GetID())
slicer.mrmlScene.AddNode(self.lineNode)
self.lineNode.GetPolyData().SetPoints(points)
self.lineNode.GetPolyData().SetLines(lineCellArray)
#self.lineNode.SetAndObserveTransformNodeID(self.boxToReference.GetID())
self.drawPlane(surfaceP, self.zVector)
self.definePlaneAxis(surfaceP, self.zVector)
def TextureMappedPlane(self, obj, event):
# use dummy image data here
e = vtk.vtkImageEllipsoidSource()
scene = slicer.mrmlScene
# Create model node
model = slicer.vtkMRMLModelNode()
model.SetScene(scene)
model.SetName(scene.GenerateUniqueName("2DImageModel"))
planeSource = vtk.vtkPlaneSource()
model.SetAndObservePolyData(planeSource.GetOutput())
# 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())
modelDisplay.SetSliceIntersectionVisibility(True)
modelDisplay.SetVisibility(True)
# Add to scene
modelDisplay.SetTextureImageDataConnection(e.GetOutputPort())
# modelDisplay.SetInputPolyDataConnection(model.GetPolyDataConnection())
scene.AddNode(model)
transform = slicer.vtkMRMLLinearTransformNode()
scene.AddNode(transform)
model.SetAndObserveTransformNodeID(transform.GetID())
vTransform = vtk.vtkTransform()
vTransform.Scale(50, 50, 50)
vTransform.RotateX(30)
# transform.SetAndObserveMatrixTransformToParent(vTransform.GetMatrix())
transform.SetMatrixTransformToParent(vTransform.GetMatrix())
def setupMRMLTracking(self):
"""
For the tracking endpoint this creates a kind of 'cursor' in the scene.
Adds "trackingDevice" (model node) to 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 drawPlane(self, m, V_norm):
scene = slicer.mrmlScene
#create a plane to cut,here it cuts in the XZ direction (xz normal=(1,0,0);XY =(0,0,1),YZ =(0,1,0)
planex = vtk.vtkPlane()
planex.SetOrigin(m[0], m[1], m[2])
planex.SetNormal(V_norm[0], V_norm[1], V_norm[2])
renderer = slicer.app.layoutManager().threeDWidget(
0).threeDView().renderWindow().GetRenderers().GetFirstRenderer()
viewSize = renderer.ComputeVisiblePropBounds()
planexSample = vtk.vtkSampleFunction()
planexSample.SetImplicitFunction(planex)
planexSample.SetModelBounds(viewSize)
planexSample.SetSampleDimensions(50, 50, 50)
planexSample.ComputeNormalsOff()
plane1 = vtk.vtkContourFilter()
plane1.SetInputConnection(planexSample.GetOutputPort())
# Create model Plane A node
planeA = slicer.vtkMRMLModelNode()
planeA.SetScene(scene)
planeA.SetName("Symmetry Plane")
planeA.SetAndObservePolyData(plane1.GetOutput())
# Create display model Plane A node
planeAModelDisplay = slicer.vtkMRMLModelDisplayNode()
planeAModelDisplay.SetColor(0, 170, 127)
planeAModelDisplay.BackfaceCullingOff()
planeAModelDisplay.SetScene(scene)
scene.AddNode(planeAModelDisplay)
planeA.SetAndObserveDisplayNodeID(planeAModelDisplay.GetID())
#Add to scene
planeAModelDisplay.SetInputPolyDataConnection(plane1.GetOutputPort())
scene.AddNode(planeA)
# adjust center of 3d view to plane
layoutManager = slicer.app.layoutManager()
threeDWidget = layoutManager.threeDWidget(0)
threeDView = threeDWidget.threeDView()
threeDView.resetFocalPoint()
return plane1
def __init__(self):
self.coord = []
self.resNameRegion = []
self.segmentationNode = slicer.vtkMRMLModelDisplayNode()
self.index = []
self.position = []
self.visu = []
self.subject_index = 0
self.min_column = 1
self.max_column = 79
self.path_to_json = './Resources/nodeGraph_3D.json'
self.jep = JEP.json_extract_properties()
# Initialize an empty filtered VisuHierarchy Map
self.filteredVisuHierarchy = {}
self.visuHierarchyMap = []
self.checked_regions = []
self.node_color_map = None
self.connect_color_map = None
self.user_table = None
self.vtk_spheres = []
self.line_actors = []
self.tube_actors = []
self.header = False
self.connection_d = False
self.connection_matrix = None
self.node_size = 7
self.min_size = 1
self.max_size = 7
self.min_strength = 0
self.max_strength = 7
self.node_min = 0
self.node_max = 0.6
self.line_min = 0
self.line_max = 1
self.f = 0.000033
self.C = 10.0
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())
pointModelDisplay.SetInputPolyDataConnection(sphere.GetOutputPort())
scene.AddNode(pointModel)
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
if vtk.VTK_MAJOR_VERSION <= 5:
# shall not be needed.
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()))
if vtk.VTK_MAJOR_VERSION <= 5:
cursor.SetAndObservePolyData(sphere.GetOutput())
else:
cursor.SetPolyDataConnection(sphere.GetOutputPort())
# 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
if vtk.VTK_MAJOR_VERSION <= 5:
# Shall not be needed.
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 __init__(self):
self.toolTipToTool = slicer.util.getNode('toolTipToTool')
self.pointerTipToReference = None
self.targetCreatedTransformed = False
self.firstFiducial = True
if not self.toolTipToTool:
self.toolTipToTool=slicer.vtkMRMLLinearTransformNode()
self.toolTipToTool.SetName("toolTipToTool")
m = vtk.vtkMatrix4x4()
m.SetElement( 0, 0, 1 ) # Row 1
m.SetElement( 0, 1, 0 )
m.SetElement( 0, 2, 0 )
m.SetElement( 0, 3, 0 )
m.SetElement( 1, 0, 0 ) # Row 2
m.SetElement( 1, 1, 1 )
m.SetElement( 1, 2, 0 )
m.SetElement( 1, 3, 0 )
m.SetElement( 2, 0, 0 ) # Row 3
m.SetElement( 2, 1, 0 )
m.SetElement( 2, 2, 1 )
m.SetElement( 2, 3, 0 )
self.toolTipToTool.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.toolTipToTool)
self.line = slicer.util.getNode('Line')
if not self.line:
self.line = slicer.vtkMRMLModelNode()
self.line.SetName('Line')
linePolyData = vtk.vtkPolyData()
self.line.SetAndObservePolyData(linePolyData)
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetSliceIntersectionVisibility(True)
modelDisplay.SetColor(0,1,0)
slicer.mrmlScene.AddNode(modelDisplay)
self.line.SetAndObserveDisplayNodeID(modelDisplay.GetID())
slicer.mrmlScene.AddNode(self.line)
# VTK objects
self.transformPolyDataFilter = vtk.vtkTransformPolyDataFilter()
self.cellLocator = vtk.vtkCellLocator()
# 3D View
threeDWidget = slicer.app.layoutManager().threeDWidget(0)
self.threeDView = threeDWidget.threeDView()
self.callbackObserverTag = -1
self.observerTag=None
# Output Distance Label
self.outputDistanceLabel=None
import Viewpoint # Viewpoint Module must have been added to Slicer
self.viewpointLogic = Viewpoint.ViewpointLogic()
# Camera transformations
self.needleCameraToNeedle = slicer.util.getNode('needleCameraToNeedle')
if not self.needleCameraToNeedle:
self.needleCameraToNeedle=slicer.vtkMRMLLinearTransformNode()
self.needleCameraToNeedle.SetName("needleCameraToNeedle")
matrixNeedleCamera = vtk.vtkMatrix4x4()
matrixNeedleCamera.SetElement( 0, 0, -0.05 ) # Row 1
matrixNeedleCamera.SetElement( 0, 1, 0.09 )
matrixNeedleCamera.SetElement( 0, 2, -0.99 )
matrixNeedleCamera.SetElement( 0, 3, 60.72 )
matrixNeedleCamera.SetElement( 1, 0, -0.01 ) # Row 2
matrixNeedleCamera.SetElement( 1, 1, 1 )
matrixNeedleCamera.SetElement( 1, 2, 0.09 )
matrixNeedleCamera.SetElement( 1, 3, 12.17 )
matrixNeedleCamera.SetElement( 2, 0, 1 ) # Row 3
matrixNeedleCamera.SetElement( 2, 1, 0.01 )
matrixNeedleCamera.SetElement( 2, 2, -0.05 )
matrixNeedleCamera.SetElement( 2, 3, -7.26 )
self.needleCameraToNeedle.SetMatrixTransformToParent(matrixNeedleCamera)
slicer.mrmlScene.AddNode(self.needleCameraToNeedle)
self.pointerCameraToPointer = slicer.util.getNode('pointerCameraToPointer')
if not self.pointerCameraToPointer:
self.pointerCameraToPointer=slicer.vtkMRMLLinearTransformNode()
self.pointerCameraToPointer.SetName("pointerCameraToPointer")
matrixPointerCamera = vtk.vtkMatrix4x4()
matrixPointerCamera.SetElement( 0, 0, -0.05 ) # Row 1
matrixPointerCamera.SetElement( 0, 1, 0.09 )
matrixPointerCamera.SetElement( 0, 2, -0.99 )
matrixPointerCamera.SetElement( 0, 3, 121.72 )
matrixPointerCamera.SetElement( 1, 0, -0.01 ) # Row 2
matrixPointerCamera.SetElement( 1, 1, 1 )
matrixPointerCamera.SetElement( 1, 2, 0.09 )
matrixPointerCamera.SetElement( 1, 3, 17.17 )
matrixPointerCamera.SetElement( 2, 0, 1 ) # Row 3
matrixPointerCamera.SetElement( 2, 1, 0.01 )
matrixPointerCamera.SetElement( 2, 2, -0.05 )
matrixPointerCamera.SetElement( 2, 3, -7.26 )
self.pointerCameraToPointer.SetMatrixTransformToParent(matrixPointerCamera)
slicer.mrmlScene.AddNode(self.pointerCameraToPointer)
# Tranformations to fix models orientation
self.needleModelToNeedleTip = slicer.util.getNode('needleModelToNeedleTip')
if not self.needleModelToNeedleTip:
self.needleModelToNeedleTip=slicer.vtkMRMLLinearTransformNode()
self.needleModelToNeedleTip.SetName("needleModelToNeedleTip")
matrixNeedleModel = vtk.vtkMatrix4x4()
matrixNeedleModel.SetElement( 0, 0, -1 ) # Row 1
matrixNeedleModel.SetElement( 0, 1, 0 )
matrixNeedleModel.SetElement( 0, 2, 0 )
matrixNeedleModel.SetElement( 0, 3, 0 )
matrixNeedleModel.SetElement( 1, 0, 0 ) # Row 2
matrixNeedleModel.SetElement( 1, 1, 1 )
matrixNeedleModel.SetElement( 1, 2, 0 )
matrixNeedleModel.SetElement( 1, 3, 0 )
matrixNeedleModel.SetElement( 2, 0, 0 ) # Row 3
matrixNeedleModel.SetElement( 2, 1, 0 )
matrixNeedleModel.SetElement( 2, 2, -1 )
matrixNeedleModel.SetElement( 2, 3, 0 )
self.needleModelToNeedleTip.SetMatrixTransformToParent(matrixNeedleModel)
slicer.mrmlScene.AddNode(self.needleModelToNeedleTip)
self.pointerModelToPointerTip = slicer.util.getNode('pointerModelToPointerTip')
if not self.pointerModelToPointerTip:
self.pointerModelToPointerTip=slicer.vtkMRMLLinearTransformNode()
self.pointerModelToPointerTip.SetName("pointerModelToPointerTip")
matrixPointerModel = vtk.vtkMatrix4x4()
matrixPointerModel.SetElement( 0, 0, 0 ) # Row 1
matrixPointerModel.SetElement( 0, 1, 0 )
matrixPointerModel.SetElement( 0, 2, 1 )
matrixPointerModel.SetElement( 0, 3, 0 )
matrixPointerModel.SetElement( 1, 0, 0 ) # Row 2
matrixPointerModel.SetElement( 1, 1, 1 )
matrixPointerModel.SetElement( 1, 2, 0 )
matrixPointerModel.SetElement( 1, 3, 0 )
matrixPointerModel.SetElement( 2, 0, -1 ) # Row 3
matrixPointerModel.SetElement( 2, 1, 0 )
matrixPointerModel.SetElement( 2, 2, 0 )
matrixPointerModel.SetElement( 2, 3, 0 )
self.pointerModelToPointerTip.SetMatrixTransformToParent(matrixPointerModel)
slicer.mrmlScene.AddNode(self.pointerModelToPointerTip)
self.fRBLToSLPR = slicer.util.getNode('FRBLToSLPR')
if not self.fRBLToSLPR:
self.fRBLToSLPR = slicer.vtkMRMLLinearTransformNode()
self.fRBLToSLPR.SetName('FRBLToSLPR')
slicer.mrmlScene.AddNode(self.fRBLToSLPR)
# Create fiducials to orientate model
self.fiducialsFRBL = slicer.util.getNode('FiducialsFRBL')
if not self.fiducialsFRBL:
self.fiducialsFRBL = slicer.vtkMRMLMarkupsFiducialNode()
self.fiducialsFRBL.SetName('FiducialsFRBL')
slicer.mrmlScene.AddNode(self.fiducialsFRBL)
self.fiducialsFRBL.SetDisplayVisibility(False)
self.fiducialsSLPR = slicer.util.getNode('FiducialsSLPR')
if not self.fiducialsSLPR:
self.fiducialsSLPR = slicer.vtkMRMLMarkupsFiducialNode()
self.fiducialsSLPR.SetName('FiducialsSLPR')
self.fiducialsSLPR.AddFiducial(0, 100, 0)
self.fiducialsSLPR.SetNthFiducialLabel(0, 'S')
self.fiducialsSLPR.AddFiducial(-100, 0, 0)
self.fiducialsSLPR.SetNthFiducialLabel(1, 'L')
self.fiducialsSLPR.AddFiducial(0, -100, 0)
self.fiducialsSLPR.SetNthFiducialLabel(2, 'P')
self.fiducialsSLPR.AddFiducial(100, 0, 0)
self.fiducialsSLPR.SetNthFiducialLabel(3, 'R')
slicer.mrmlScene.AddNode(self.fiducialsSLPR)
self.fiducialsSLPR.SetDisplayVisibility(False)
def createModels(self):
self.deleteModels()
self.labelScores = []
self.selectedLableList = []
if self.calcinationType == 0 and self.volumeNode and self.roiNode:
#print 'in Heart Create Models'
slicer.vtkSlicerCropVolumeLogic().CropVoxelBased(self.roiNode, self.volumeNode, self.croppedNode)
croppedImage = sitk.ReadImage( sitkUtils.GetSlicerITKReadWriteAddress(self.croppedNode.GetName()))
thresholdImage = sitk.BinaryThreshold(croppedImage,self.ThresholdMin, self.ThresholdMax, 1, 0)
connectedCompImage =sitk.ConnectedComponent(thresholdImage, True)
relabelImage =sitk.RelabelComponent(connectedCompImage)
labelStatFilter =sitk.LabelStatisticsImageFilter()
labelStatFilter.Execute(croppedImage, relabelImage)
if relabelImage.GetPixelID() != sitk.sitkInt16:
relabelImage = sitk.Cast( relabelImage, sitk.sitkInt16 )
sitk.WriteImage( relabelImage, sitkUtils.GetSlicerITKReadWriteAddress(self.labelsNode.GetName()))
nLabels = labelStatFilter.GetNumberOfLabels()
#print "Number of labels = ", nLabels
self.totalScore = 0
count = 0
for n in range(0,nLabels):
max = labelStatFilter.GetMaximum(n);
size = labelStatFilter.GetCount(n)
score = self.computeScore(max)
if size*self.voxelVolume > self.MaximumLesionSize:
continue
if size*self.voxelVolume < self.MinimumLesionSize:
nLabels = n+1
break
#print "label = ", n, " max = ", max, " score = ", score, " voxels = ", size
self.labelScores.append(score)
self.selectedLableList.append(0)
self.marchingCubes.SetInputData(self.labelsNode.GetImageData())
self.marchingCubes.SetValue(0, n)
self.marchingCubes.Update()
self.transformPolyData.SetInputData(self.marchingCubes.GetOutput())
mat = vtk.vtkMatrix4x4()
self.labelsNode.GetIJKToRASMatrix(mat)
trans = vtk.vtkTransform()
trans.SetMatrix(mat)
self.transformPolyData.SetTransform(trans)
self.transformPolyData.Update()
poly = vtk.vtkPolyData()
poly.DeepCopy(self.transformPolyData.GetOutput())
modelNode = slicer.vtkMRMLModelNode()
slicer.mrmlScene.AddNode(modelNode)
dnode = slicer.vtkMRMLModelDisplayNode()
slicer.mrmlScene.AddNode(dnode)
modelNode.AddAndObserveDisplayNodeID(dnode.GetID())
modelNode.SetAndObservePolyData(poly)
ct=slicer.mrmlScene.GetNodeByID('vtkMRMLColorTableNodeLabels')
rgb = [0,0,0]
ct.GetLookupTable().GetColor(count+1,rgb)
dnode.SetColor(rgb)
self.addLabel(count, rgb, score)
self.modelNodes.append(modelNode)
self.selectedLables[poly] = n
count = count+1
#a = slicer.util.array(tn.GetID())
#sa = sitk.GetImageFromArray(a)
self.scoreField.setText(self.totalScore)
else:
print "not implemented"
def createModels(self):
self.deleteModels()
for sr in self.summary_reports:
self.labelScores[sr]=[]
self.selectedLabelList = []
if self.calcificationType == 0 and self.volumeNode and self.roiNode:
#print 'in Heart Create Models'
slicer.vtkSlicerCropVolumeLogic().CropVoxelBased(self.roiNode, self.volumeNode, self.croppedNode)
croppedImage = sitk.ReadImage( sitkUtils.GetSlicerITKReadWriteAddress(self.croppedNode.GetName()))
thresholdImage = sitk.BinaryThreshold(croppedImage,self.ThresholdMin, self.ThresholdMax, 1, 0)
connectedCompImage =sitk.ConnectedComponent(thresholdImage, True)
relabelImage =sitk.RelabelComponent(connectedCompImage)
labelStatFilter =sitk.LabelStatisticsImageFilter()
labelStatFilter.Execute(croppedImage, relabelImage)
if relabelImage.GetPixelID() != sitk.sitkInt16:
relabelImage = sitk.Cast( relabelImage, sitk.sitkInt16 )
sitk.WriteImage( relabelImage, sitkUtils.GetSlicerITKReadWriteAddress(self.labelsNode.GetName()))
nLabels = labelStatFilter.GetNumberOfLabels()
#print "Number of labels = ", nLabels
self.totalScore = 0
count = 0
#Computation of the score follows this paper:
#C. H McCollough, Radiology, 243(2), 2007
for n in range(0,nLabels):
max = labelStatFilter.GetMaximum(n)
mean = labelStatFilter.GetMean(n)
size = labelStatFilter.GetCount(n)
volume = size*self.voxelVolume
if volume > self.MaximumLesionSize:
continue
if volume < self.MinimumLesionSize:
nLabels = n+1
break
density_score = self.computeDensityScore(max)
#Agatston score is \sum_i area_i * density_score_i
#For now we assume that all the plaques have the same density score
score = size*(self.sx*self.sy)*density_score
mass_score = mean*volume
#print "label = ", n, " max = ", max, " score = ", score, " voxels = ", size
self.labelScores["Agatston Score"].append(score)
self.labelScores["Mass Score"].append(mass_score)
self.labelScores["Volume"].append(volume)
self.selectedLabelList.append(0)
self.marchingCubes.SetInputData(self.labelsNode.GetImageData())
self.marchingCubes.SetValue(0, n)
self.marchingCubes.Update()
self.transformPolyData.SetInputData(self.marchingCubes.GetOutput())
mat = vtk.vtkMatrix4x4()
self.labelsNode.GetIJKToRASMatrix(mat)
trans = vtk.vtkTransform()
trans.SetMatrix(mat)
self.transformPolyData.SetTransform(trans)
self.transformPolyData.Update()
poly = vtk.vtkPolyData()
poly.DeepCopy(self.transformPolyData.GetOutput())
modelNode = slicer.vtkMRMLModelNode()
slicer.mrmlScene.AddNode(modelNode)
dnode = slicer.vtkMRMLModelDisplayNode()
slicer.mrmlScene.AddNode(dnode)
modelNode.AddAndObserveDisplayNodeID(dnode.GetID())
modelNode.SetAndObservePolyData(poly)
ct=slicer.mrmlScene.GetNodeByID('vtkMRMLColorTableNodeLabels')
rgb = [0,0,0]
ct.GetLookupTable().GetColor(count+1,rgb)
dnode.SetColor(rgb)
#Enable Slice intersection
dnode.SetSliceDisplayMode(0)
dnode.SetSliceIntersectionVisibility(1)
self.addLabel(count, rgb, [score,mass_score,volume,mean,max])
count = count+1
self.modelNodes.append(modelNode)
self.selectedLabels[poly] = n
#a = slicer.util.array(tn.GetID())
#sa = sitk.GetImageFromArray(a)
for sr in self.summary_reports:
self.scoreField[sr].setText(self.totalScores[sr])
else:
print ("not implemented")
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)
print (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 setAndObserveDisplayNode(node):
displayNode = slicer.vtkMRMLModelDisplayNode()
slicer.mrmlScene.AddNode(displayNode)
node.SetAndObserveDisplayNodeID(displayNode.GetID())
return displayNode
def __init__(self):
self.toolTipToTool = slicer.util.getNode('toolTipToTool')
if not self.toolTipToTool:
self.toolTipToTool=slicer.vtkMRMLLinearTransformNode()
self.toolTipToTool.SetName("toolTipToTool")
m = vtk.vtkMatrix4x4()
m.SetElement( 0, 0, 1 ) # Row 1
m.SetElement( 0, 1, 0 )
m.SetElement( 0, 2, 0 )
m.SetElement( 0, 3, 0 )
m.SetElement( 1, 0, 0 ) # Row 2
m.SetElement( 1, 1, 1 )
m.SetElement( 1, 2, 0 )
m.SetElement( 1, 3, 0 )
m.SetElement( 2, 0, 0 ) # Row 3
m.SetElement( 2, 1, 0 )
m.SetElement( 2, 2, 1 )
m.SetElement( 2, 3, 0 )
self.toolTipToTool.SetMatrixTransformToParent(m)
slicer.mrmlScene.AddNode(self.toolTipToTool)
self.toolToReference = slicer.util.getNode('toolToReference')
if not self.toolToReference:
self.toolToReference=slicer.vtkMRMLLinearTransformNode()
self.toolToReference.SetName("toolToReference")
matrixRef = vtk.vtkMatrix4x4()
matrixRef.SetElement( 0, 0, 1 ) # Row 1
matrixRef.SetElement( 0, 1, 0 )
matrixRef.SetElement( 0, 2, 0 )
matrixRef.SetElement( 0, 3, 0 )
matrixRef.SetElement( 1, 0, 0 ) # Row 2
matrixRef.SetElement( 1, 1, 1 )
matrixRef.SetElement( 1, 2, 0 )
matrixRef.SetElement( 1, 3, 0 )
matrixRef.SetElement( 2, 0, 0 ) # Row 3
matrixRef.SetElement( 2, 1, 0 )
matrixRef.SetElement( 2, 2, 1 )
matrixRef.SetElement( 2, 3, 0 )
self.toolToReference.SetMatrixTransformToParent(matrixRef)
slicer.mrmlScene.AddNode(self.toolToReference)
self.tipFiducial = slicer.util.getNode('Tip')
if not self.tipFiducial:
self.tipFiducial = slicer.vtkMRMLMarkupsFiducialNode()
self.tipFiducial.SetName('Tip')
self.tipFiducial.AddFiducial(0, 0, 0)
self.tipFiducial.SetNthFiducialLabel(0, '')
slicer.mrmlScene.AddNode(self.tipFiducial)
self.tipFiducial.SetDisplayVisibility(True)
self.tipFiducial.GetDisplayNode().SetGlyphType(1) # Vertex2D
self.tipFiducial.GetDisplayNode().SetTextScale(1.3)
self.tipFiducial.GetDisplayNode().SetSelectedColor(1,1,1)
self.targetFiducial = slicer.util.getNode('Target')
if not self.targetFiducial:
self.targetFiducial = slicer.vtkMRMLMarkupsFiducialNode()
self.targetFiducial.SetName('Target')
self.targetFiducial.AddFiducial(0, 0, 0)
self.targetFiducial.SetNthFiducialLabel(0, '')
slicer.mrmlScene.AddNode(self.targetFiducial)
self.targetFiducial.SetDisplayVisibility(True)
self.targetFiducial.GetDisplayNode().SetGlyphType(1) # Vertex2D
self.targetFiducial.GetDisplayNode().SetTextScale(1.3)
self.targetFiducial.GetDisplayNode().SetSelectedColor(1,1,1)
self.line = slicer.util.getNode('Line')
if not self.line:
self.line = slicer.vtkMRMLModelNode()
self.line.SetName('Line')
linePolyData = vtk.vtkPolyData()
self.line.SetAndObservePolyData(linePolyData)
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetSliceIntersectionVisibility(True)
modelDisplay.SetColor(0,1,0)
slicer.mrmlScene.AddNode(modelDisplay)
self.line.SetAndObserveDisplayNodeID(modelDisplay.GetID())
slicer.mrmlScene.AddNode(self.line)
# VTK objects
self.transformPolyDataFilter = vtk.vtkTransformPolyDataFilter()
self.cellLocator = vtk.vtkCellLocator()
# 3D View
threeDWidget = slicer.app.layoutManager().threeDWidget(0)
self.threeDView = threeDWidget.threeDView()
self.callbackObserverTag = -1
self.observerTag=None
# Output Distance Label
self.outputDistanceLabel=None
import Viewpoint # Viewpoint Module must have been added to Slicer
self.viewpointLogic = Viewpoint.ViewpointLogic()
# Camera transformations
self.needleCameraToNeedle = slicer.util.getNode('needleCameraToNeedle')
if not self.needleCameraToNeedle:
self.needleCameraToNeedle=slicer.vtkMRMLLinearTransformNode()
self.needleCameraToNeedle.SetName("needleCameraToNeedle")
matrixNeedleCamera = vtk.vtkMatrix4x4()
matrixNeedleCamera.SetElement( 0, 0, -0.05 ) # Row 1
matrixNeedleCamera.SetElement( 0, 1, 0.09 )
matrixNeedleCamera.SetElement( 0, 2, -0.99 )
matrixNeedleCamera.SetElement( 0, 3, 60.72 )
matrixNeedleCamera.SetElement( 1, 0, -0.01 ) # Row 2
matrixNeedleCamera.SetElement( 1, 1, 1 )
matrixNeedleCamera.SetElement( 1, 2, 0.09 )
matrixNeedleCamera.SetElement( 1, 3, 12.17 )
matrixNeedleCamera.SetElement( 2, 0, 1 ) # Row 3
matrixNeedleCamera.SetElement( 2, 1, 0.01 )
matrixNeedleCamera.SetElement( 2, 2, -0.05 )
matrixNeedleCamera.SetElement( 2, 3, -7.26 )
self.needleCameraToNeedle.SetMatrixTransformToParent(matrixNeedleCamera)
slicer.mrmlScene.AddNode(self.needleCameraToNeedle)
self.pointerCameraToPointer = slicer.util.getNode('pointerCameraToPointer')
if not self.pointerCameraToPointer:
self.pointerCameraToPointer=slicer.vtkMRMLLinearTransformNode()
self.pointerCameraToPointer.SetName("pointerCameraToPointer")
matrixPointerCamera = vtk.vtkMatrix4x4()
matrixPointerCamera.SetElement( 0, 0, -0.05 ) # Row 1
matrixPointerCamera.SetElement( 0, 1, 0.09 )
matrixPointerCamera.SetElement( 0, 2, -0.99 )
matrixPointerCamera.SetElement( 0, 3, 121.72 )
matrixPointerCamera.SetElement( 1, 0, -0.01 ) # Row 2
matrixPointerCamera.SetElement( 1, 1, 1 )
matrixPointerCamera.SetElement( 1, 2, 0.09 )
matrixPointerCamera.SetElement( 1, 3, 17.17 )
matrixPointerCamera.SetElement( 2, 0, 1 ) # Row 3
matrixPointerCamera.SetElement( 2, 1, 0.01 )
matrixPointerCamera.SetElement( 2, 2, -0.05 )
matrixPointerCamera.SetElement( 2, 3, -7.26 )
self.pointerCameraToPointer.SetMatrixTransformToParent(matrixPointerCamera)
slicer.mrmlScene.AddNode(self.pointerCameraToPointer)
def new_electrode(self):
"""
Create new electrode model and paired,hidden transform.
"""
if self.curr_electrode:
# Get Current Electrode
self.curr_electrode = self.input_selector.currentNode()
self.save_electrode_properties(self.curr_electrode)
# Harden transform
# logic=slicer.vtkSlicerTransformLogic()
# logic.hardenTransform(self.curr_electrode)
electrode_transform = slicer.util.getNode(
"Transform_" + self.curr_electrode.GetName())
self.curr_electrode.SetAndObserveTransformNodeID(
electrode_transform.GetID())
# Set up new electrode
origin = [0, 0, 0]
terminus = [0, 0, 200]
# This section takes care of the "Electrode"
line = vtk.vtkLineSource()
line.SetPoint1(origin)
line.SetPoint2(terminus)
line.Update()
tube_filter = vtk.vtkTubeFilter()
tube_filter.SetCapping(True)
tube_filter.SetRadius(1.1)
tube_filter.SetNumberOfSides(20)
tube_filter.SetInputDataObject(line.GetOutput())
tube_filter.Update()
electrode = tube_filter.GetOutput()
new_electrode = slicer.vtkMRMLModelNode()
new_electrode.SetAndObservePolyData(electrode)
slicer.mrmlScene.AddNode(new_electrode)
electrode_display_node = slicer.vtkMRMLModelDisplayNode()
slicer.mrmlScene.AddNode(electrode_display_node)
electrode_display_node.SetName("NeedleModelDisplay")
electrode_display_node.SetColor(0.0, 1.0, 1.0)
new_electrode.SetAndObserveDisplayNodeID(
electrode_display_node.GetID())
electrode_display_node.SetAmbient(0.2)
electrode_display_node.SetSliceIntersectionVisibility(True)
new_electrode.SetAndObserveTransformNodeID(
slicer.util.getNode("Arc").GetID())
self.curr_electrode = new_electrode
electrode_transform = slicer.vtkMRMLLinearTransformNode()
electrode_transform.SetName("Transform_" +
self.curr_electrode.GetName())
electrode_transform.SetHideFromEditors(True)
slicer.mrmlScene.AddNode(electrode_transform)
self.save_electrode_properties(new_electrode)
self.input_selector.setCurrentNodeID(new_electrode.GetID())
def createModels(self):
# Reset previous model and labels
self.deleteModels()
for sr in self.summary_reports:
self.labelScores[sr] = []
self.selectedLabelList = []
if self.calcificationType == 0 and self.volumeNode and self.roiNode:
slicer.vtkSlicerCropVolumeLogic().CropVoxelBased(
self.roiNode, self.volumeNode, self.croppedNode)
croppedImage = sitk.ReadImage(
sitkUtils.GetSlicerITKReadWriteAddress(
self.croppedNode.GetName()))
thresholdImage = sitk.BinaryThreshold(croppedImage,
self.ThresholdMin,
self.ThresholdMax, 1, 0)
connectedCompImage = sitk.ConnectedComponent(thresholdImage, True)
relabelImage = sitk.RelabelComponent(connectedCompImage)
labelStatFilter = sitk.LabelStatisticsImageFilter()
labelStatFilter.Execute(croppedImage, relabelImage)
if relabelImage.GetPixelID() != sitk.sitkInt16:
relabelImage = sitk.Cast(relabelImage, sitk.sitkInt16)
sitk.WriteImage(
relabelImage,
sitkUtils.GetSlicerITKReadWriteAddress(
self.labelsNode.GetName()))
prod_spacing = np.prod(croppedImage.GetSpacing())
nLabels = labelStatFilter.GetNumberOfLabels()
self.totalScore = 0
count = 0
for n in range(0, nLabels):
max = labelStatFilter.GetMaximum(n)
mean = labelStatFilter.GetMean(n)
size = labelStatFilter.GetCount(n)
volume = size * self.voxelVolume
# current label is discarted if volume not meet the maximum allowed threshold
if volume > self.MaximumLesionSize:
continue
# As ordered, we stop here if the volume of the current label is less than threshold
if volume < self.MinimumLesionSize:
nLabels = n + 1
break
score2d, volume, mass_score = self.agatston_computation(
n, relabelImage, croppedImage, prod_spacing)
# Agatston 3d:
# -----------
density_score = self.computeDensityScore(max)
score3d = size * (self.sx * self.sy) * density_score
mass_score = mean * volume
# self.labelScores["Agatston Score"].append(score)
self.labelScores["Agatston Score 3D"].append(score3d)
self.labelScores["Agatston Score 2D"].append(score2d)
self.labelScores["Mass Score"].append(mass_score)
self.labelScores["Volume"].append(volume)
self.selectedLabelList.append(0)
# generate the contour
marchingCubes = vtk.vtkDiscreteMarchingCubes()
marchingCubes.SetInputData(self.labelsNode.GetImageData())
marchingCubes.SetValue(0, count + 1)
marchingCubes.Update()
transformPolyData = vtk.vtkTransformPolyDataFilter()
transformPolyData.SetInputData(marchingCubes.GetOutput())
mat = vtk.vtkMatrix4x4()
self.labelsNode.GetIJKToRASMatrix(mat)
trans = vtk.vtkTransform()
trans.SetMatrix(mat)
transformPolyData.SetTransform(trans)
transformPolyData.Update()
poly = vtk.vtkPolyData()
poly.DeepCopy(transformPolyData.GetOutput())
modelNode = slicer.vtkMRMLModelNode()
slicer.mrmlScene.AddNode(modelNode)
dnode = slicer.vtkMRMLModelDisplayNode()
slicer.mrmlScene.AddNode(dnode)
modelNode.AddAndObserveDisplayNodeID(dnode.GetID())
modelNode.SetAndObservePolyData(poly)
ct = slicer.mrmlScene.GetNodeByID(
'vtkMRMLColorTableNodeLabels')
rgb = [0, 0, 0]
ct.GetLookupTable().GetColor(count + 1, rgb)
dnode.SetColor(rgb)
# Enable Slice intersection
dnode.SetSliceDisplayMode(0)
dnode.SetSliceIntersectionVisibility(1)
# self.addLabel(count, rgb, [score, mass_score, volume, mean, max])
self.addLabel(
count, rgb,
[score2d, score3d, mass_score, volume, mean, max])
count = count + 1
self.modelNodes.append(modelNode)
self.selectedLabels[poly] = n
for sr in self.summary_reports:
self.scoreField[sr].setText(self.totalScores[sr])
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)
import vtk.util.numpy_support as VN
pointsArray = VN.vtk_to_numpy(points.GetData())
self.planePosition, self.planeNormal = self.planeFit(pointsArray.T)
# 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
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.SetPolyDataConnection(sphere.GetOutputPort())
# 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
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 __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
if vtk.VTK_MAJOR_VERSION <= 5:
# shall not be needed.
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()))
if vtk.VTK_MAJOR_VERSION <= 5:
cursor.SetAndObservePolyData(sphere.GetOutput())
else:
cursor.SetPolyDataConnection(sphere.GetOutputPort())
# 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
if vtk.VTK_MAJOR_VERSION <= 5:
# Shall not be needed.
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 run(self, list, filepath, filename, downsample, signals, sensor,
useSensorLimits, index):
self.filename = filename
self.index = index
browser = slicer.vtkMRMLSequenceBrowserNode()
browser.SetName(filename + ' (' + index + ')')
slicer.mrmlScene.AddNode(browser)
if useSensorLimits:
colorMap = self.createColorMap(sensor["sensorMin"],
sensor["sensorMax"])
else:
colorMap = self.createColorMap(sensor["dataMin"],
sensor["dataMax"])
num_of_fiducials = min(list.GetNumberOfFiducials(),
len(sensor["indices"]))
counter = 0
points = vtk.vtkPoints()
#Get the first row data
colors = self.getRowAsArray(signals, sensor, counter, num_of_fiducials)
arr = [0, 0, 0]
for i in range(0, num_of_fiducials):
list.GetNthFiducialPosition(i, arr)
points.InsertNextPoint(arr[0], arr[1], arr[2])
self.polydata = vtk.vtkPolyData()
self.polydata.SetPoints(points)
self.polydata.GetPointData().SetScalars(colors)
sphereSource = vtk.vtkSphereSource()
sphereSource.SetRadius(3)
self.glyph3D = vtk.vtkGlyph3D()
self.glyph3D.SetColorModeToColorByScalar()
self.glyph3D.SetSourceConnection(sphereSource.GetOutputPort())
self.glyph3D.SetInputData(self.polydata)
self.glyph3D.ScalingOff()
self.glyph3D.Update()
self.display = slicer.vtkMRMLModelDisplayNode()
self.display.SetScalarVisibility(1)
self.display.SetActiveScalarName("EDF Magnitude")
self.display.SetName("EDF Magnitude (" + index + ")")
slicer.mrmlScene.AddNode(self.display)
model = slicer.vtkMRMLModelNode()
model.SetName("EDF Magnitude (" + index + ")")
slicer.mrmlScene.AddNode(model)
model.SetAndObservePolyData(self.glyph3D.GetOutput())
model.SetAndObserveDisplayNodeID(self.display.GetID())
self.display.SetScalarRangeFlag(0)
self.display.SetAndObserveColorNodeID(colorMap.GetID())
#Add the Sequence Nodes
self.addSequence(browser, model, "Model (" + index + ")")
self.addSequence(browser, self.display, "ModelDisplay (" + index + ")")
# Get the remaining rows
while counter < len(signals):
counter += 1
if counter % downsample != 0:
continue
model.SetAndObservePolyData(self.glyph3D.GetOutput())
newArr = self.getRowAsArray(signals, sensor, counter,
num_of_fiducials)
self.polydata.GetPointData().AddArray(newArr)
self.glyph3D.Modified()
self.glyph3D.Update()
self.display.SetActiveScalarName("EDF Magnitude " + str(counter))
browser.SaveProxyNodesState() #update the sequence
return True
def visualizeNewSrep(self, filename):
# 1. parse header file
tree = ET.parse(filename)
upFileName = ''
crestFileName = ''
downFileName = ''
nCols = 0
nRows = 0
for child in tree.getroot():
if child.tag == 'upSpoke':
upFileName = child.text
elif child.tag == 'downSpoke':
downFileName = child.text
elif child.tag == 'crestSpoke':
crestFileName = child.text
elif child.tag == 'nRows':
nRows = (int)(child.text)
elif child.tag == 'nCols':
nCols = (int)(child.text)
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(upFileName)
reader.Update()
upSpokes = reader.GetOutput()
upPointData = upSpokes.GetPointData()
medial_polyData = upSpokes # this is poly data for skeleton
scene = slicer.mrmlScene
# base line of medial sheet
fidDisplayNode = slicer.vtkMRMLMarkupsDisplayNode()
scene.AddNode(fidDisplayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
fidDisplayNode.SetGlyphScale(0.01)
fidDisplayNode.SetSelectedColor(1.0, 1.0, 0.0)
fidDisplayNode.SetTextScale(0.0)
scene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(fidDisplayNode.GetID())
# \TODO come up with better name later
# prepare for arrows for upspokes
upSpoke_points = vtk.vtkPoints()
upSpoke_lines = vtk.vtkCellArray()
arr_length = upPointData.GetArray('spokeLength')
arr_dirs = upPointData.GetArray('spokeDirection')
for i in range(upSpokes.GetNumberOfPoints()):
pt = [0] * 3
upSpokes.GetPoint(i, pt)
# base point of up arrows
id0 = upSpoke_points.InsertNextPoint(pt)
# head of up arrows
spoke_length = arr_length.GetValue(i)
baseIdx = i * 3
dirX = arr_dirs.GetValue(baseIdx)
dirY = arr_dirs.GetValue(baseIdx + 1)
dirZ = arr_dirs.GetValue(baseIdx + 2)
pt1 = [0] * 3
pt1[0] = pt[0] + spoke_length * dirX
pt1[1] = pt[1] + spoke_length * dirY
pt1[2] = pt[2] + spoke_length * dirZ
id1 = upSpoke_points.InsertNextPoint(pt1)
up_arrow = vtk.vtkLine()
up_arrow.GetPointIds().SetId(0, id0)
up_arrow.GetPointIds().SetId(1, id1)
upSpoke_lines.InsertNextCell(up_arrow)
fidNode.AddFiducial(pt[0], pt[1], pt[2])
boundary_point_ids = []
# model node for medial mesh
medial_model = slicer.vtkMRMLModelNode()
medial_model.SetScene(scene)
medial_model.SetName("Medial Mesh")
medial_model.SetAndObservePolyData(reader.GetOutput())
# model display node for the medial mesh
medial_model_display = slicer.vtkMRMLModelDisplayNode()
medial_model_display.SetColor(0, 0.5, 0)
medial_model_display.SetScene(scene)
medial_model_display.SetLineWidth(3.0)
medial_model_display.SetRepresentation(1)
medial_model_display.SetBackfaceCulling(0)
scene.AddNode(medial_model_display)
medial_model.SetAndObserveDisplayNodeID(medial_model_display.GetID())
scene.AddNode(medial_model)
# model node for up spoke (poly data for arrows)
upSpoke_polyData = vtk.vtkPolyData()
upSpoke_polyData.SetPoints(upSpoke_points)
upSpoke_polyData.SetLines(upSpoke_lines)
upSpoke_model = slicer.vtkMRMLModelNode()
upSpoke_model.SetScene(scene)
upSpoke_model.SetName("Top Spoke")
upSpoke_model.SetAndObservePolyData(upSpoke_polyData)
# model display node for the top spoke
# cyan for the top spoke
upSpoke_model_display = slicer.vtkMRMLModelDisplayNode()
upSpoke_model_display.SetColor(0, 1, 1)
upSpoke_model_display.SetScene(scene)
upSpoke_model_display.SetLineWidth(3.0)
upSpoke_model_display.SetBackfaceCulling(0)
scene.AddNode(upSpoke_model_display)
upSpoke_model.SetAndObserveDisplayNodeID(upSpoke_model_display.GetID())
scene.AddNode(upSpoke_model)
# prepare for down spokes
reader.SetFileName(downFileName)
reader.Update()
downSpokes = reader.GetOutput()
downSpoke_polyData = vtk.vtkPolyData()
downSpoke_lines = vtk.vtkCellArray()
downSpoke_points = vtk.vtkPoints()
downPointData = downSpokes.GetPointData()
arr_length = downPointData.GetArray('spokeLength')
arr_dirs = downPointData.GetArray('spokeDirection')
for i in range(downSpokes.GetNumberOfPoints()):
# tail of arrows
pt_tail = [0] * 3
downSpokes.GetPoint(i, pt_tail)
id0 = downSpoke_points.InsertNextPoint(pt_tail)
# head of arrows
pt_head = [0] * 3
spoke_length = arr_length.GetValue(i)
baseIdx = i * 3
dirX = arr_dirs.GetValue(baseIdx)
dirY = arr_dirs.GetValue(baseIdx + 1)
dirZ = arr_dirs.GetValue(baseIdx + 2)
pt_head[0] = pt_tail[0] + spoke_length * dirX
pt_head[1] = pt_tail[1] + spoke_length * dirY
pt_head[2] = pt_tail[2] + spoke_length * dirZ
id1 = downSpoke_points.InsertNextPoint(pt_head)
# connection between head and tail
con = vtk.vtkLine()
con.GetPointIds().SetId(0, id0)
con.GetPointIds().SetId(1, id1)
downSpoke_lines.InsertNextCell(con)
downSpoke_polyData.SetPoints(downSpoke_points)
downSpoke_polyData.SetLines(downSpoke_lines)
downSpoke_model = slicer.vtkMRMLModelNode()
downSpoke_model.SetScene(scene)
downSpoke_model.SetName("Bottom Spoke")
downSpoke_model.SetAndObservePolyData(downSpoke_polyData)
# model display node for the down spoke
downSpoke_model_display = slicer.vtkMRMLModelDisplayNode()
downSpoke_model_display.SetColor(1, 0, 1)
downSpoke_model_display.SetScene(scene)
downSpoke_model_display.SetLineWidth(3.0)
downSpoke_model_display.SetBackfaceCulling(0)
scene.AddNode(downSpoke_model_display)
downSpoke_model.SetAndObserveDisplayNodeID(
downSpoke_model_display.GetID())
scene.AddNode(downSpoke_model)
# crest spoke
new_reader = vtk.vtkXMLPolyDataReader()
new_reader.SetFileName(crestFileName)
new_reader.Update()
foldCurve_polyData = new_reader.GetOutput()
foldPointData = foldCurve_polyData.GetPointData()
arr_length = foldPointData.GetArray('spokeLength')
arr_dirs = foldPointData.GetArray('spokeDirection')
crest_arrows_polydata = vtk.vtkPolyData()
crest_arrows_points = vtk.vtkPoints()
crest_arrows_lines = vtk.vtkCellArray()
for i in range(foldCurve_polyData.GetNumberOfPoints()):
# tail of crest arrows
pt_tail = [0] * 3
foldCurve_polyData.GetPoint(i, pt_tail)
id0 = crest_arrows_points.InsertNextPoint(pt_tail)
# head of crest arrows
pt_head = [0] * 3
spoke_length = arr_length.GetValue(i)
baseIdx = i * 3
dirX = arr_dirs.GetValue(baseIdx)
dirY = arr_dirs.GetValue(baseIdx + 1)
dirZ = arr_dirs.GetValue(baseIdx + 2)
pt_head[0] = pt_tail[0] + spoke_length * dirX
pt_head[1] = pt_tail[1] + spoke_length * dirY
pt_head[2] = pt_tail[2] + spoke_length * dirZ
id1 = crest_arrows_points.InsertNextPoint(pt_head)
crest_line = vtk.vtkLine()
crest_line.GetPointIds().SetId(0, id0)
crest_line.GetPointIds().SetId(1, id1)
crest_arrows_lines.InsertNextCell(crest_line)
crest_arrows_polydata.SetPoints(crest_arrows_points)
crest_arrows_polydata.SetLines(crest_arrows_lines)
# show crest arrows
crestSpoke_model = slicer.vtkMRMLModelNode()
crestSpoke_model.SetScene(scene)
crestSpoke_model.SetName("Crest Spoke")
crestSpoke_model.SetAndObservePolyData(crest_arrows_polydata)
# model display node
crestSpoke_model_display = slicer.vtkMRMLModelDisplayNode()
crestSpoke_model_display.SetColor(1, 1, 0)
crestSpoke_model_display.SetScene(scene)
crestSpoke_model_display.SetLineWidth(3.0)
crestSpoke_model_display.SetBackfaceCulling(0)
scene.AddNode(crestSpoke_model_display)
crestSpoke_model.SetAndObserveDisplayNodeID(
crestSpoke_model_display.GetID())
scene.AddNode(crestSpoke_model)
# show fold curve
foldCurve_model = slicer.vtkMRMLModelNode()
foldCurve_model.SetScene(scene)
foldCurve_model.SetName("Fold Curve")
foldCurve_model.SetAndObservePolyData(foldCurve_polyData)
# model display node
foldCurve_model_display = slicer.vtkMRMLModelDisplayNode()
foldCurve_model_display.SetColor(1, 1, 0)
foldCurve_model_display.SetScene(scene)
foldCurve_model_display.SetLineWidth(3.0)
foldCurve_model_display.SetBackfaceCulling(0)
scene.AddNode(foldCurve_model_display)
foldCurve_model.SetAndObserveDisplayNodeID(
foldCurve_model_display.GetID())
scene.AddNode(foldCurve_model)
# show connections to fold curve point from nearby interior points
# compute the nearest interior point
connection_polydata = vtk.vtkPolyData()
connection_points = vtk.vtkPoints()
connection_lines = vtk.vtkCellArray()
for i in range(foldCurve_polyData.GetNumberOfPoints()):
min_dist = 100000.0
nearest_index = 0
pt_fold = [0] * 3
foldCurve_polyData.GetPoint(i, pt_fold)
id0 = connection_points.InsertNextPoint(pt_fold)
for j in range(upSpokes.GetNumberOfPoints()):
pt_interior = [0] * 3
upSpokes.GetPoint(j, pt_interior)
dist = math.sqrt((pt_fold[0] - pt_interior[0])**2 +
(pt_fold[1] - pt_interior[1])**2 +
(pt_fold[2] - pt_interior[2])**2)
if dist < min_dist:
min_dist = dist
nearest_index = j
pt_nearest_interior = upSpokes.GetPoint(nearest_index)
id1 = connection_points.InsertNextPoint(pt_nearest_interior)
line = vtk.vtkLine()
line.GetPointIds().SetId(0, id0)
line.GetPointIds().SetId(1, id1)
connection_lines.InsertNextCell(line)
connection_polydata.SetPoints(connection_points)
connection_polydata.SetLines(connection_lines)
connection_model = slicer.vtkMRMLModelNode()
connection_model.SetScene(scene)
connection_model.SetName("Connection to Fold Curve")
connection_model.SetAndObservePolyData(connection_polydata)
# model display node
connection_model_display = slicer.vtkMRMLModelDisplayNode()
connection_model_display.SetColor(0, 0, 0)
connection_model_display.SetScene(scene)
connection_model_display.SetLineWidth(3.0)
connection_model_display.SetBackfaceCulling(0)
scene.AddNode(connection_model_display)
connection_model.SetAndObserveDisplayNodeID(
connection_model_display.GetID())
scene.AddNode(connection_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)
import vtk.util.numpy_support as VN
pointsArray = VN.vtk_to_numpy(points.GetData())
self.planePosition, self.planeNormal = self.planeFit(pointsArray.T)
# 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
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.SetPolyDataConnection(sphere.GetOutputPort())
# 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
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 visualizeNewSrep(self, filename):
""" Parse header.xml file, create models from the data, and visualize it. """
# 1. parse header file
tree = ET.parse(filename)
upFileName = ''
crestFileName = ''
downFileName = ''
nCols = 0
nRows = 0
headerFolder = os.path.dirname(filename)
for child in tree.getroot():
if child.tag == 'upSpoke':
if os.path.isabs(child.text):
upFileName = os.path.join(headerFolder, child.text)
upFileName = os.path.join(headerFolder, child.text)
elif child.tag == 'downSpoke':
downFileName = os.path.join(headerFolder, child.text)
elif child.tag == 'crestSpoke':
crestFileName = os.path.join(headerFolder, child.text)
elif child.tag == 'nRows':
nRows = (int)(child.text)
elif child.tag == 'nCols':
nCols = (int)(child.text)
logging.info("upSpoke file: " + upFileName)
logging.info("downSpoke file: " + downFileName)
logging.info("crestSpoke file: " + crestFileName)
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(upFileName)
reader.Update()
upSpokes = reader.GetOutput()
upPointData = upSpokes.GetPointData()
numberOfArrays = upPointData.GetNumberOfArrays()
if numberOfArrays is 0:
logging.warning("File: " + upFileName + " does not contain data")
# medial_polyData = upSpokes # this is poly data for skeleton
scene = slicer.mrmlScene
# base line of medial sheet
fidDisplayNode = slicer.vtkMRMLMarkupsDisplayNode()
scene.AddNode(fidDisplayNode)
fidNode = slicer.vtkMRMLMarkupsFiducialNode()
# If we would have more than 100 fiducial points (meant for editing points) better to use a regular MRMLModelNode
# In the future, we would like the user to be able to move the nodes, and the connected structures to update accordingly.
# Meanwhile, we lock the moving.
fidNode.SetLocked(True)
fidDisplayNode.SetGlyphScale(0.01)
fidDisplayNode.SetSelectedColor(1.0, 1.0, 0.0)
fidDisplayNode.SetTextScale(0.0)
scene.AddNode(fidNode)
fidNode.SetAndObserveDisplayNodeID(fidDisplayNode.GetID())
# \TODO come up with better name later
# prepare for arrows for upspokes
upSpoke_points = vtk.vtkPoints()
upSpoke_lines = vtk.vtkCellArray()
arr_length = upPointData.GetArray('spokeLength')
arr_dirs = upPointData.GetArray('spokeDirection')
for i in range(upSpokes.GetNumberOfPoints()):
pt = [0] * 3
upSpokes.GetPoint(i, pt)
# base point of up arrows
id0 = upSpoke_points.InsertNextPoint(pt)
# head of up arrows
spoke_length = arr_length.GetValue(i)
baseIdx = i * 3
dirX = arr_dirs.GetValue(baseIdx)
dirY = arr_dirs.GetValue(baseIdx + 1)
dirZ = arr_dirs.GetValue(baseIdx + 2)
pt1 = [0] * 3
pt1[0] = pt[0] + spoke_length * dirX
pt1[1] = pt[1] + spoke_length * dirY
pt1[2] = pt[2] + spoke_length * dirZ
id1 = upSpoke_points.InsertNextPoint(pt1)
up_arrow = vtk.vtkLine()
up_arrow.GetPointIds().SetId(0, id0)
up_arrow.GetPointIds().SetId(1, id1)
upSpoke_lines.InsertNextCell(up_arrow)
fidNode.AddFiducial(pt[0], pt[1], pt[2])
# boundary_point_ids = []
# model node for medial mesh
medial_model = slicer.vtkMRMLModelNode()
medial_model.SetScene(scene)
medial_model.SetName("Medial Mesh")
medial_model.SetAndObservePolyData(reader.GetOutput())
# model display node for the medial mesh
medial_model_display = slicer.vtkMRMLModelDisplayNode()
medial_model_display.SetColor(0, 0.5, 0)
medial_model_display.SetScene(scene)
medial_model_display.SetLineWidth(3.0)
medial_model_display.SetRepresentation(1)
medial_model_display.SetBackfaceCulling(0)
scene.AddNode(medial_model_display)
medial_model.SetAndObserveDisplayNodeID(medial_model_display.GetID())
scene.AddNode(medial_model)
# model node for up spoke (poly data for arrows)
upSpoke_polyData = vtk.vtkPolyData()
upSpoke_polyData.SetPoints(upSpoke_points)
upSpoke_polyData.SetLines(upSpoke_lines)
upSpoke_model = slicer.vtkMRMLModelNode()
upSpoke_model.SetScene(scene)
upSpoke_model.SetName("Top Spoke")
upSpoke_model.SetAndObservePolyData(upSpoke_polyData)
# model display node for the top spoke
# cyan for the top spoke
upSpoke_model_display = slicer.vtkMRMLModelDisplayNode()
upSpoke_model_display.SetColor(0, 1, 1)
upSpoke_model_display.SetScene(scene)
upSpoke_model_display.SetLineWidth(3.0)
upSpoke_model_display.SetBackfaceCulling(0)
scene.AddNode(upSpoke_model_display)
upSpoke_model.SetAndObserveDisplayNodeID(upSpoke_model_display.GetID())
scene.AddNode(upSpoke_model)
# prepare for down spokes
reader.SetFileName(downFileName)
reader.Update()
downSpokes = reader.GetOutput()
downSpoke_polyData = vtk.vtkPolyData()
downSpoke_lines = vtk.vtkCellArray()
downSpoke_points = vtk.vtkPoints()
downPointData = downSpokes.GetPointData()
arr_length = downPointData.GetArray('spokeLength')
arr_dirs = downPointData.GetArray('spokeDirection')
for i in range(downSpokes.GetNumberOfPoints()):
# tail of arrows
pt_tail = [0] * 3
downSpokes.GetPoint(i, pt_tail)
id0 = downSpoke_points.InsertNextPoint(pt_tail)
# head of arrows
pt_head = [0] * 3
spoke_length = arr_length.GetValue(i)
baseIdx = i * 3
dirX = arr_dirs.GetValue(baseIdx)
dirY = arr_dirs.GetValue(baseIdx + 1)
dirZ = arr_dirs.GetValue(baseIdx + 2)
pt_head[0] = pt_tail[0] + spoke_length * dirX
pt_head[1] = pt_tail[1] + spoke_length * dirY
pt_head[2] = pt_tail[2] + spoke_length * dirZ
id1 = downSpoke_points.InsertNextPoint(pt_head)
# connection between head and tail
con = vtk.vtkLine()
con.GetPointIds().SetId(0, id0)
con.GetPointIds().SetId(1, id1)
downSpoke_lines.InsertNextCell(con)
downSpoke_polyData.SetPoints(downSpoke_points)
downSpoke_polyData.SetLines(downSpoke_lines)
downSpoke_model = slicer.vtkMRMLModelNode()
downSpoke_model.SetScene(scene)
downSpoke_model.SetName("Bottom Spoke")
downSpoke_model.SetAndObservePolyData(downSpoke_polyData)
# model display node for the down spoke
downSpoke_model_display = slicer.vtkMRMLModelDisplayNode()
downSpoke_model_display.SetColor(1, 0, 1)
downSpoke_model_display.SetScene(scene)
downSpoke_model_display.SetLineWidth(3.0)
downSpoke_model_display.SetBackfaceCulling(0)
scene.AddNode(downSpoke_model_display)
downSpoke_model.SetAndObserveDisplayNodeID(
downSpoke_model_display.GetID())
scene.AddNode(downSpoke_model)
# crest spoke
new_reader = vtk.vtkXMLPolyDataReader()
new_reader.SetFileName(crestFileName)
new_reader.Update()
foldCurve_polyData = new_reader.GetOutput()
foldPointData = foldCurve_polyData.GetPointData()
arr_length = foldPointData.GetArray('spokeLength')
arr_dirs = foldPointData.GetArray('spokeDirection')
crest_arrows_polydata = vtk.vtkPolyData()
crest_arrows_points = vtk.vtkPoints()
crest_arrows_lines = vtk.vtkCellArray()
for i in range(foldCurve_polyData.GetNumberOfPoints()):
# tail of crest arrows
pt_tail = [0] * 3
foldCurve_polyData.GetPoint(i, pt_tail)
id0 = crest_arrows_points.InsertNextPoint(pt_tail)
# head of crest arrows
pt_head = [0] * 3
spoke_length = arr_length.GetValue(i)
baseIdx = i * 3
dirX = arr_dirs.GetValue(baseIdx)
dirY = arr_dirs.GetValue(baseIdx + 1)
dirZ = arr_dirs.GetValue(baseIdx + 2)
pt_head[0] = pt_tail[0] + spoke_length * dirX
pt_head[1] = pt_tail[1] + spoke_length * dirY
pt_head[2] = pt_tail[2] + spoke_length * dirZ
id1 = crest_arrows_points.InsertNextPoint(pt_head)
crest_line = vtk.vtkLine()
crest_line.GetPointIds().SetId(0, id0)
crest_line.GetPointIds().SetId(1, id1)
crest_arrows_lines.InsertNextCell(crest_line)
crest_arrows_polydata.SetPoints(crest_arrows_points)
crest_arrows_polydata.SetLines(crest_arrows_lines)
# show crest arrows
crestSpoke_model = slicer.vtkMRMLModelNode()
crestSpoke_model.SetScene(scene)
crestSpoke_model.SetName("Crest Spoke")
crestSpoke_model.SetAndObservePolyData(crest_arrows_polydata)
# model display node
crestSpoke_model_display = slicer.vtkMRMLModelDisplayNode()
crestSpoke_model_display.SetColor(1, 1, 0)
crestSpoke_model_display.SetScene(scene)
crestSpoke_model_display.SetLineWidth(3.0)
crestSpoke_model_display.SetBackfaceCulling(0)
scene.AddNode(crestSpoke_model_display)
crestSpoke_model.SetAndObserveDisplayNodeID(
crestSpoke_model_display.GetID())
scene.AddNode(crestSpoke_model)
# show fold curve
foldCurve_model = slicer.vtkMRMLModelNode()
foldCurve_model.SetScene(scene)
foldCurve_model.SetName("Fold Curve")
foldCurve_model.SetAndObservePolyData(foldCurve_polyData)
# model display node
foldCurve_model_display = slicer.vtkMRMLModelDisplayNode()
foldCurve_model_display.SetColor(1, 1, 0)
foldCurve_model_display.SetScene(scene)
foldCurve_model_display.SetLineWidth(3.0)
foldCurve_model_display.SetBackfaceCulling(0)
scene.AddNode(foldCurve_model_display)
foldCurve_model.SetAndObserveDisplayNodeID(
foldCurve_model_display.GetID())
scene.AddNode(foldCurve_model)
# show connections to fold curve point from nearby interior points
# compute the nearest interior point
connection_polydata = vtk.vtkPolyData()
connection_points = vtk.vtkPoints()
connection_lines = vtk.vtkCellArray()
for i in range(foldCurve_polyData.GetNumberOfPoints()):
min_dist = 100000.0
nearest_index = 0
pt_fold = [0] * 3
foldCurve_polyData.GetPoint(i, pt_fold)
id0 = connection_points.InsertNextPoint(pt_fold)
for j in range(upSpokes.GetNumberOfPoints()):
pt_interior = [0] * 3
upSpokes.GetPoint(j, pt_interior)
dist = self.distance(pt_fold, pt_interior)
if dist < min_dist:
min_dist = dist
nearest_index = j
pt_nearest_interior = upSpokes.GetPoint(nearest_index)
id1 = connection_points.InsertNextPoint(pt_nearest_interior)
line = vtk.vtkLine()
line.GetPointIds().SetId(0, id0)
line.GetPointIds().SetId(1, id1)
connection_lines.InsertNextCell(line)
connection_polydata.SetPoints(connection_points)
connection_polydata.SetLines(connection_lines)
connection_model = slicer.vtkMRMLModelNode()
connection_model.SetScene(scene)
connection_model.SetName("Connection to Fold Curve")
connection_model.SetAndObservePolyData(connection_polydata)
# model display node
connection_model_display = slicer.vtkMRMLModelDisplayNode()
connection_model_display.SetColor(0, 0, 0)
connection_model_display.SetScene(scene)
connection_model_display.SetLineWidth(3.0)
connection_model_display.SetBackfaceCulling(0)
scene.AddNode(connection_model_display)
connection_model.SetAndObserveDisplayNodeID(
connection_model_display.GetID())
scene.AddNode(connection_model)
def createCone(self):
#f = slicer.util.getNode('Target')
self.pos = [0,0,0]
self.pos1 = [0,0,0]
self.targetFiducial.GetNthFiducialPosition(0,self.pos)
self.targetFiducial.GetNthFiducialPosition(1,self.pos1)
# Create a vtkPoints object and store the points in it
points = vtk.vtkPoints()
points.InsertNextPoint(self.pos)
points.InsertNextPoint(self.pos1)
# Create line
line = vtk.vtkLine()
line.GetPointIds().SetId(0,0)
line.GetPointIds().SetId(1,1)
lineCellArray = vtk.vtkCellArray()
lineCellArray.InsertNextCell(line)
self.lineNode = slicer.vtkMRMLModelNode()
self.lineNode.SetName('Line')
linePolyData = vtk.vtkPolyData()
self.lineNode.SetAndObservePolyData(linePolyData)
modelDisplay = slicer.vtkMRMLModelDisplayNode()
modelDisplay.SetSliceIntersectionVisibility(True)
modelDisplay.SetColor(0,0,1)
slicer.mrmlScene.AddNode(modelDisplay)
self.lineNode.SetAndObserveDisplayNodeID(modelDisplay.GetID())
slicer.mrmlScene.AddNode(self.lineNode)
self.lineNode.GetPolyData().SetPoints(points)
self.lineNode.GetPolyData().SetLines(lineCellArray)
self.cone = vtk.vtkConeSource()
self.cone = vtk.vtkConeSource()
self.cone.SetResolution(50)
self.cone.SetRadius(20)
vector = np.subtract(self.pos,self.pos1)
self.cone.SetDirection([vector[0],vector[1],vector[2]])
dist = np.linalg.norm(vector)
self.cone.SetHeight(dist)
self.coneModel = slicer.vtkMRMLModelNode()
self.coneModel.SetName('Cone')
self.coneModel.SetPolyDataConnection(self.cone.GetOutputPort())
slicer.mrmlScene.AddNode(self.coneModel)
modelDisplay1 = slicer.vtkMRMLModelDisplayNode()
modelDisplay1.SetSliceIntersectionVisibility(True)
modelDisplay1.SetColor(0,1,1)
modelDisplay1.SetOpacity(0.30)
slicer.mrmlScene.AddNode(modelDisplay1)
self.coneModel.SetAndObserveDisplayNodeID(modelDisplay1.GetID())
slicer.mrmlScene.AddNode(self.coneModel)
x3 = [(self.pos1[0]-self.pos[0])/2 + self.pos[0], (self.pos1[1]-self.pos[1])/2 +self.pos[1], (self.pos1[2]-self.pos[2])/2 +self.pos[2]]
self.cone.SetCenter(x3)
def setAndObserveDisplayNode(node): displayNode = slicer.vtkMRMLModelDisplayNode() slicer.mrmlScene.AddNode(displayNode) node.SetAndObserveDisplayNodeID(displayNode.GetID()) return displayNode
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)
print(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")
