def initialize(self):
self.layoutManager = slicer.app.layoutManager()
self.threeDWidget = self.layoutManager.threeDWidget(0)
self.threeDView = self.threeDWidget.threeDView()
self.renderWindow = self.threeDView.renderWindow()
self.renderers = self.renderWindow.GetRenderers()
self.renderer = self.renderers.GetFirstRenderer()
self.polydata = vtk.vtkPolyData()
self.points = vtk.vtkPoints()
self.planeSource = vtk.vtkPlaneSource()
self.mapper = vtk.vtkPolyDataMapper()
self.actor = vtk.vtkActor()
self.renderer.AddViewProp(self.actor)
self.renderWindow.AddRenderer(self.renderer)
def initialize(self):
self.layoutManager=slicer.app.layoutManager()
self.threeDWidget=self.layoutManager.threeDWidget(0)
self.threeDView=self.threeDWidget.threeDView()
self.renderWindow=self.threeDView.renderWindow()
self.renderers=self.renderWindow.GetRenderers()
self.renderer=self.renderers.GetFirstRenderer()
self.polydata = vtk.vtkPolyData()
self.points = vtk.vtkPoints()
self.planeSource = vtk.vtkPlaneSource()
self.mapper = vtk.vtkPolyDataMapper()
self.actor = vtk.vtkActor()
self.renderer.AddViewProp(self.actor)
self.renderWindow.AddRenderer(self.renderer)
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 PointsToPlanePolyData( self, inPoints, reverse ):
# Create the oriented bounding box
# This gives us one plane on the bounding box, not the plane of best fit
corner = [ 0, 0, 0 ]
maxVector = [ 0, 0, 0 ]
midVector = [ 0, 0, 0 ]
minVector = [ 0, 0, 0 ]
size = [ 0, 0, 0 ]
obb = vtk.vtkOBBTree()
obb.ComputeOBB( inPoints, corner, maxVector, midVector, minVector, size )
# Calculate the mean of the points on the plane
base = self.CalculateMean( inPoints )
relBase = [ 0, 0, 0 ]
# Find the projection of the mean point in the minVector direction
vtk.vtkMath().Subtract( base, corner, relBase )
normal = minVector[:]
vtk.vtkMath().Normalize( normal )
dot = vtk.vtkMath().Dot( relBase, normal )
dot = 0
proj = normal[:]
vtk.vtkMath().MultiplyScalar( proj, dot )
print dot
# Find the points on the plane
origin = [ 0, 0, 0 ]
point1 = [ 0, 0, 0 ]
point2 = [ 0, 0, 0 ]
vtk.vtkMath().Add( corner, proj, origin )
vtk.vtkMath().Add( origin, maxVector, point1 )
vtk.vtkMath().Add( origin, midVector, point2 )
# Construct the plane
plane = vtk.vtkPlaneSource()
plane.SetOrigin( origin )
plane.SetPoint1( point1 )
plane.SetPoint2( point2 )
plane.Update()
return plane.GetOutput()
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 takeUSSnapshot2(self):
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)
name="Snapshot" + str(self.numberOfUltrasoundSnapshotsTaken)
self.numberOfUltrasoundSnapshotsTaken = self.numberOfUltrasoundSnapshotsTaken + 1
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_Reference")
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)
def planeLandmarks(self, Landmark1Value, Landmark2Value, Landmark3Value, slider, sliderOpacity):
self.initialize()
# Limit the number of 3 landmarks to define a plane
# Keep the coordinates of the landmarks
listCoord = list()
fidNode = slicer.mrmlScene.GetNodeByID('vtkMRMLMarkupsFiducialNode1')
self.coord = numpy.zeros(3)
if Landmark1Value != "List of fiducials":
fidNode.GetNthFiducialPosition(int(Landmark1Value)-1, self.coord)
listCoord.append(self.coord)
print self.coord
print listCoord
r1 = self.coord[0]
a1 = self.coord[1]
s1 = self.coord[2]
# Limit the number of 3 landmarks to define a plane
# Keep the coordinates of the landmarks
listCoord = list()
fidNode = slicer.mrmlScene.GetNodeByID('vtkMRMLMarkupsFiducialNode1')
self.coord = numpy.zeros(3)
if Landmark2Value != "List of fiducials":
fidNode.GetNthFiducialPosition(int(Landmark2Value)-1, self.coord)
listCoord.append(self.coord)
print self.coord
print listCoord
r2 = self.coord[0]
a2 = self.coord[1]
s2 = self.coord[2]
# Limit the number of 3 landmarks to define a plane
# Keep the coordinates of the landmarks
listCoord = list()
fidNode = slicer.mrmlScene.GetNodeByID('vtkMRMLMarkupsFiducialNode1')
self.coord = numpy.zeros(3)
if Landmark3Value != "List of fiducials":
fidNode.GetNthFiducialPosition(int(Landmark3Value)-1, self.coord)
listCoord.append(self.coord)
print self.coord
print listCoord
r3 = self.coord[0]
a3 = self.coord[1]
s3 = self.coord[2]
A = (r1,a1,s1)
B = (r2,a2,s2)
C = (r3,a3,s3)
# Vn = Vectorial Product (AB, BC)
# Normal N = Vn/norm(Vn)
points = vtk.vtkPoints()
points.InsertNextPoint(r1,a1,s1)
points.InsertNextPoint(r2,a2,s2)
points.InsertNextPoint(r3,a3,s3)
polydata = vtk.vtkPolyData()
polydata.SetPoints(points)
centerOfMass = vtk.vtkCenterOfMass()
centerOfMass.SetInputData(polydata)
centerOfMass.SetUseScalarsAsWeights(False)
centerOfMass.Update()
G = centerOfMass.GetCenter()
print "Center of mass = ",G
# Vector GA
GA = numpy.matrix([[0],[0],[0]])
GA[0] = A[0]-G[0]
GA[1] = A[1]-G[1]
GA[2] = A[2]-G[2]
print "GA = ", GA
# Vector BG
GB = numpy.matrix([[0],[0],[0]])
GB[0] = B[0]-G[0]
GB[1] = B[1]-G[1]
GB[2] = B[2]-G[2]
print "GB = ", GB
# Vector CG
GC = numpy.matrix([[0],[0],[0]])
GC[0] = C[0]-G[0]
GC[1] = C[1]-G[1]
GC[2] = C[2]-G[2]
print "GC = ", GC
self.N = self.normalLandmarks(GA,GB)
D = numpy.matrix([[0],[0],[0]])
E = numpy.matrix([[0],[0],[0]])
F = numpy.matrix([[0],[0],[0]])
D[0] = slider*GA[0] + G[0]
D[1] = slider*GA[1] + G[1]
D[2] = slider*GA[2] + G[2]
print "Slider value : ", slider
print "D = ",D
E[0] = slider*GB[0] + G[0]
E[1] = slider*GB[1] + G[1]
E[2] = slider*GB[2] + G[2]
print "E = ",E
F[0] = slider*GC[0] + G[0]
F[1] = slider*GC[1] + G[1]
F[2] = slider*GC[2] + G[2]
print "F = ",F
self.renderWindow.AddRenderer(self.renderer)
planeSource = vtk.vtkPlaneSource()
planeSource.SetNormal(self.N[0],self.N[1],self.N[2])
planeSource.SetOrigin(D[0],D[1],D[2])
planeSource.SetPoint1(E[0],E[1],E[2])
planeSource.SetPoint2(F[0],F[1],F[2])
planeSource.Update()
plane = planeSource.GetOutput()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(plane)
self.actor.SetMapper(mapper)
self.actor.GetProperty().SetColor(0, 0.4, 0.8)
self.actor.GetProperty().SetOpacity(sliderOpacity)
self.renderer.AddActor(self.actor)
self.renderWindow.Render()
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() )
