class QMeshViewer(QtWidgets.QFrame):
def __init__(self, parent):
super(QMeshViewer, self).__init__(parent)
self.platformModel: vtk.vtkCubeSource = None
self.platformGrid: vtk.vtkPolyData = None
self.platformModelActor: vtk.vtkActor = None
self.platformGridActor: vtk.vtkActor = None
self.platformWidth: float = 200.0
self.platformDepth: float = 200.0
self.platformThickness: float = 2.0
self.gridBottomHeight: float = 0.15
self.gridSize: np.uint16 = 10
# Make the actual QtWidget a child so that it can be re_parented
self.interactor = QVTKRenderWindowInteractor(self)
self.layout = QtWidgets.QHBoxLayout()
self.layout.addWidget(self.interactor)
self.layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(self.layout)
self.initScene()
self.initPlatform()
self.initAxes()
self.resetCamera()
self.style = vtk.vtkInteractorStyleTrackballCamera()
self.style.SetDefaultRenderer(self.renderer)
self.interactor.SetInteractorStyle(self.style)
def resetCamera(self):
m_camPositionX = -237.885
m_camPositionY = -392.348
m_camPositionZ = 369.477
self.renderer.GetActiveCamera().SetPosition(m_camPositionX,
m_camPositionY,
m_camPositionZ)
self.renderer.GetActiveCamera().SetFocalPoint(0.0, 0.0, 0.0)
self.renderer.GetActiveCamera().SetViewUp(0.0, 0.0, 1.0)
self.renderer.ResetCameraClippingRange()
def initScene(self):
qDebug('initScene()')
self.renderer = vtk.vtkOpenGLRenderer()
self.render_window = self.interactor.GetRenderWindow()
self.render_window.AddRenderer(self.renderer)
self.cellPicker = vtk.vtkCellPicker()
self.cellPicker.SetTolerance(30.0)
self.interactor.SetPicker(self.cellPicker)
#* Top background color
bg_t = np.ones(3) * 245.0 / 255.0
#* Bottom background color
bg_b = np.ones(3) * 170.0 / 255.0
self.renderer.SetBackground(bg_t)
self.renderer.SetBackground2(bg_b)
self.renderer.GradientBackgroundOn()
def createNewActor(self):
axes = vtk.vtkAxesActor()
axes_length = 50.0
axes_label_font_size = np.int16(20)
axes.SetTotalLength(axes_length, axes_length, axes_length)
axes.SetCylinderRadius(0.01)
axes.SetShaftTypeToCylinder()
axes.GetXAxisCaptionActor2D().GetTextActor().SetTextScaleModeToNone()
axes.GetYAxisCaptionActor2D().GetTextActor().SetTextScaleModeToNone()
axes.GetZAxisCaptionActor2D().GetTextActor().SetTextScaleModeToNone()
axes.GetXAxisCaptionActor2D().GetCaptionTextProperty().SetFontSize(
axes_label_font_size)
axes.GetYAxisCaptionActor2D().GetCaptionTextProperty().SetFontSize(
axes_label_font_size)
axes.GetZAxisCaptionActor2D().GetCaptionTextProperty().SetFontSize(
axes_label_font_size)
axes.PickableOn()
return axes
def initAxes(self):
# #* Axes
axes = self.createNewActor()
self.axes = axes
self.renderer.AddActor(self.axes)
def initPlatform(self):
qDebug('initPlatform()')
#* Platform Model
platformModelMapper = vtk.vtkPolyDataMapper()
self.platformModel = vtk.vtkCubeSource()
platformModelMapper.SetInputConnection(
self.platformModel.GetOutputPort())
self.platformModelActor = vtk.vtkActor()
self.platformModelActor.SetMapper(platformModelMapper)
self.platformModelActor.GetProperty().SetColor(1, 1, 1)
self.platformModelActor.GetProperty().LightingOn()
self.platformModelActor.GetProperty().SetOpacity(1)
self.platformModelActor.GetProperty().SetAmbient(0.45)
self.platformModelActor.GetProperty().SetDiffuse(0.4)
self.platformModelActor.PickableOff()
self.renderer.AddActor(self.platformModelActor)
#* Platform Grid
self.platformGrid = vtk.vtkPolyData()
platformGridMapper = vtk.vtkPolyDataMapper()
platformGridMapper.SetInputData(self.platformGrid)
self.platformGridActor = vtk.vtkActor()
self.platformGridActor.SetMapper(platformGridMapper)
self.platformGridActor.GetProperty().LightingOff()
self.platformGridActor.GetProperty().SetColor(0.45, 0.45, 0.45)
self.platformGridActor.GetProperty().SetOpacity(1)
self.platformGridActor.PickableOff()
self.renderer.AddActor(self.platformGridActor)
self.updatePlatform()
def updatePlatform(self):
qDebug('updatePlatform()')
#* Platform Model
if self.platformModel:
self.platformModel.SetXLength(self.platformWidth)
self.platformModel.SetYLength(self.platformDepth)
self.platformModel.SetZLength(self.platformThickness)
self.platformModel.SetCenter(0.0, 0.0, -self.platformThickness / 2)
#* Platform Grid
gridPoints = vtk.vtkPoints()
gridCells = vtk.vtkCellArray()
i = -self.platformWidth / 2
while i <= self.platformWidth / 2:
self.createLine(i, -self.platformDepth / 2, self.gridBottomHeight,
i, self.platformDepth / 2, self.gridBottomHeight,
gridPoints, gridCells)
i += self.gridSize
i = -self.platformDepth / 2
while i <= self.platformDepth / 2:
self.createLine(-self.platformWidth / 2, i, self.gridBottomHeight,
self.platformWidth / 2, i, self.gridBottomHeight,
gridPoints, gridCells)
i += self.gridSize
self.platformGrid.SetPoints(gridPoints)
self.platformGrid.SetLines(gridCells)
def createLine(self, x1: float, y1: float, z1: float, x2: float, y2: float,
z2: float, points: vtk.vtkPoints, cells: vtk.vtkCellArray):
line = vtk.vtkPolyLine()
line.GetPointIds().SetNumberOfIds(2)
id_1 = points.InsertNextPoint(x1, y1, z1) # vtkIdType
id_2 = points.InsertNextPoint(x2, y2, z2) # vtkIdType
line.GetPointIds().SetId(0, id_1)
line.GetPointIds().SetId(1, id_2)
cells.InsertNextCell(line)
def start(self):
self.interactor.Initialize()
# If a big Qt application, call app.exec instead of having two GUI threads
self.interactor.Start()
def moveAxes(self, axes, aff):
self.interactor.Disable()
# Axes
transform = vtk.vtkTransform()
mat = vtk.vtkMatrix4x4()
for i in range(4):
for j in range(4):
mat.SetElement(i, j, aff[i, j])
transform.SetMatrix(mat)
axes.SetUserTransform(transform)
self.interactor.Enable()
self.render_window.Render()
def removeActor(self, actor):
self.interactor.Disable()
self.renderer.RemoveActor(actor)
self.interactor.Enable()
self.render_window.Render()
def addActor(self, actor):
self.interactor.Disable()
self.renderer.AddActor(actor)
self.interactor.Enable()
self.render_window.Render()
class QLiverViewer(QtWidgets.QFrame):
colors = vtk.vtkNamedColors()
widgetMoved = Signal(object, object, object) #float)
widgetRegistered = Signal(object, object, object)
def __init__(self, parent):
super(QLiverViewer, self).__init__(parent)
# Make the actual QtWidget a child so that it can be re_parented
self.interactor = QVTKRenderWindowInteractor(self)
self.layout = QtWidgets.QHBoxLayout()
self.layout.addWidget(self.interactor)
self.layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(self.layout)
self.imgWidth: float = 50.0 # mm
self.worldScale: float = 0.05
self.worldScale: float = 1.0
self.brighter25: bool = True
self.opacity: float = 0.35
self.showReferencePlane = False
self.nReferences = 2
self.refplanes = [] # Displayed reference planes
self.planeWidgets = [] # Widgets for manipulation
self.contours = [] # Contours clipped to reference plane
self.fullcontours = [] # Full contour data
self.planeSources = []
self.userAttempts = []
self.contourResults = self.nReferences * [None]
self.vessels = None
self.liver = None
self.initScene()
self.initLiver()
self.initVessels() # Must be before planeWidgets
self.lastPositions = dict({
'origin': self.nReferences * [None],
'normal': self.nReferences * [None],
'axis1': self.nReferences * [None],
'reset': self.nReferences * [None]
})
self.lastIndex = None
self.initPlaneWidgets(0)
if not IOUSFAN:
self.initPlaneWidgets(1)
self.resetCamera()
self.style = vtk.vtkInteractorStyleTrackballCamera()
self.style.SetDefaultRenderer(self.renderer)
self.interactor.SetInteractorStyle(self.style)
self.interactor.AddObserver('KeyPressEvent', self.KeyPress, 1.0)
def KeyPress(self, obj, ev):
key = obj.GetKeySym()
index = self.lastIndex
if self.lastIndex is None:
return
userAttempt = self.userAttempts[index]
planeWidget = self.planeWidgets[index]
refActor = self.refplanes[index]
resetPositions = self.lastPositions['reset'][index]
planeSource = self.planeSources[index]
contourActor = self.contours[index]
if key == 'c':
print('Reset')
userAttempt.SetUserTransform(None)
userAttempt.Modified()
# Reset planeWidget
planeWidget.SetEnabled(0)
planeWidget.SetOrigin(resetPositions[0])
planeWidget.SetPoint1(resetPositions[1])
planeWidget.SetPoint2(resetPositions[2])
planeWidget.Modified()
planeWidget.SetEnabled(1)
lastNormal = planeWidget.GetNormal()
lastAxis1 = vtk.vtkVector3d()
vtk.vtkMath.Subtract(planeWidget.GetPoint1(),
planeWidget.GetOrigin(), lastAxis1)
lastOrigin = planeWidget.GetCenter()
self.lastPositions['origin'][index] = lastOrigin
self.lastPositions['normal'][index] = lastNormal
self.lastPositions['axis1'][index] = lastAxis1
if self.contourResults[index] is not None:
self.renderer.RemoveActor(self.contourResults[index])
self.contourResults[index] = None
self.render_window.Render()
elif key == 's':
print('Registration')
# ============ run ICP ==============
icp = vtk.vtkIterativeClosestPointTransform()
# Transform contours
tfpdf0 = vtk.vtkTransformPolyDataFilter()
tfpdf0.SetInputData(self.fullcontours[index])
tfpdf0.SetTransform(userAttempt.GetUserTransform())
tfpdf0.Update()
wrongContours = tfpdf0.GetOutput()
icp.SetSource(wrongContours)
icp.SetTarget(self.vesselPolyData)
icp.GetLandmarkTransform().SetModeToRigidBody()
icp.DebugOn()
icp.SetMaximumNumberOfIterations(10)
icp.StartByMatchingCentroidsOff()
icp.SetCheckMeanDistance(1) # Experiment
#icp.SetMeanDistanceModeToAbsoluteValue() # Original
icp.SetMeanDistanceModeToRMS() # Default
#print(icp.GetLandmarkTransform())
#sys.stdout.write("Before: ")
#print(icp.GetMeanDistance())
from vtkUtils import CloudMeanDist
dist0 = CloudMeanDist(wrongContours, self.vesselPolyData)
print(dist0)
icp.Modified()
icp.Update()
#print(icp) # Shows mean distance
#print(icp.GetLandmarkTransform())
icpTransformFilter = vtk.vtkTransformPolyDataFilter()
icpTransformFilter.SetInputData(wrongContours)
icpTransformFilter.SetTransform(icp)
icpTransformFilter.Update()
correctedContours = icpTransformFilter.GetOutput()
dist1 = CloudMeanDist(correctedContours, self.vesselPolyData)
print(dist1)
#sys.stdout.write("After: ")
#print(icp.GetMeanDistance())
tubes = vtk.vtkTubeFilter()
tubes.SetInputData(correctedContours)
tubes.CappingOn()
tubes.SidesShareVerticesOff()
tubes.SetNumberOfSides(12)
tubes.SetRadius(1.0)
edgeMapper = vtk.vtkPolyDataMapper()
edgeMapper.ScalarVisibilityOff()
edgeMapper.SetInputConnection(tubes.GetOutputPort())
if self.contourResults[index] is not None:
self.renderer.RemoveActor(self.contourResults[index])
testActor = vtk.vtkActor()
testActor.SetMapper(edgeMapper)
prop = testActor.GetProperty()
prop.SetColor(yellow)
prop.SetLineWidth(3)
self.renderer.AddActor(testActor)
self.contourResults[index] = testActor
# Concatenate and get transform (w,x,y,z)
userAttempt.GetUserTransform().Concatenate(icp.GetMatrix())
userAttempt.GetUserTransform().Update()
(deg, x, y,
z) = userAttempt.GetUserTransform().GetOrientationWXYZ()
resetPositions = self.lastPositions['reset'][index]
# Not correct!!!
positionError = np.array(
userAttempt.GetUserTransform().GetPosition())
positionError = np.array(
userAttempt.GetUserTransform().TransformPoint(
resetPositions[3])) - np.array(resetPositions[3])
# Reset afterwards
userAttempt.SetUserTransform(None)
userAttempt.Modified()
# Reset planeWidget.
planeWidget.SetEnabled(0)
planeWidget.SetOrigin(resetPositions[0])
planeWidget.SetPoint1(resetPositions[1])
planeWidget.SetPoint2(resetPositions[2])
planeWidget.Modified()
planeWidget.SetEnabled(1)
lastNormal = planeWidget.GetNormal()
lastAxis1 = vtk.vtkVector3d()
vtk.vtkMath.Subtract(planeWidget.GetPoint1(),
planeWidget.GetOrigin(), lastAxis1)
lastOrigin = planeWidget.GetCenter()
self.lastPositions['origin'][index] = lastOrigin
self.lastPositions['normal'][index] = lastNormal
self.lastPositions['axis1'][index] = lastAxis1
self.render_window.Render()
originalNormal = resetPositions[4]
originalNormal = originalNormal / np.sqrt(np.sum(originalNormal**
2))
self.widgetRegistered.emit((deg, np.r_[x, y, z]), originalNormal,
positionError)
elif key == 'm':
# Move a reference
print('Moving reference')
showReferencePlane = False
# Remove old reference plane
if refActor is not None:
self.removeActor(refActor)
refActor = None
showReferencePlane = True
# Move reference plane
planeSource.SetOrigin(planeWidget.GetOrigin())
planeSource.SetPoint1(planeWidget.GetPoint1())
planeSource.SetPoint2(planeWidget.GetPoint2())
# mapper
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(planeSource.GetOutputPort())
# New reference actor
if showReferencePlane:
refActor = vtk.vtkActor()
refActor.SetMapper(mapper)
prop = refActor.GetProperty()
prop.SetColor(blue)
prop.SetOpacity(self.opacity)
self.refplanes[index] = refActor
self.renderer.AddActor(refActor)
self.removeActor(contourActor)
tubes, oldContours = self.computeContoursAndTubes(planeSource)
edgeMapper = vtk.vtkPolyDataMapper()
edgeMapper.ScalarVisibilityOff()
edgeMapper.SetInputConnection(tubes.GetOutputPort())
planes = self.computeClippingPlanes(planeSource)
edgeMapper.SetClippingPlanes(planes)
actor = vtk.vtkActor()
actor.SetMapper(edgeMapper)
prop = actor.GetProperty()
prop.SetColor(green)
prop.SetLineWidth(3)
self.contours[index] = actor
self.renderer.AddActor(actor)
# User attempt
self.removeActor(userAttempt)
attempt = vtk.vtkActor()
transform = vtk.vtkTransform()
trans = vtk.vtkMatrix4x4()
trans.Identity()
transform.SetMatrix(trans)
transform.PostMultiply()
attempt.SetUserTransform(transform)
self.fullcontours[index] = oldContours
mapper = vtk.vtkPolyDataMapper()
mapper.ScalarVisibilityOff()
mapper.SetInputData(oldContours)
attempt.SetMapper(mapper)
attempt.GetProperty().SetColor(red)
self.userAttempts[index] = attempt
self.renderer.AddActor(attempt)
# Update reset positions of plane widget
self.lastPositions['reset'][index] = [
planeWidget.GetOrigin(),
planeWidget.GetPoint1(),
planeWidget.GetPoint2(),
planeWidget.GetCenter(),
np.array(planeWidget.GetNormal())
] # Redundant
sys.stdout.write('Plane origin: ')
print(planeWidget.GetOrigin())
sys.stdout.write('Plane point1: ')
print(planeWidget.GetPoint1())
sys.stdout.write('Plane point2: ')
print(planeWidget.GetPoint2())
print(
"To make the app start at this location, insert these points near the tag\n 'FIXED PLANE POSITION AND ORIENTATION' in LiverView.py"
)
self.render_window.Render()
def removeActor(self, actor):
self.interactor.Disable()
self.renderer.RemoveActor(actor)
self.interactor.Enable()
# self.render_window.Render()
def scale(self, polyData):
if self.worldScale == 1.0:
return polyData
else:
transform = vtk.vtkTransform()
transform.Scale(self.worldScale, self.worldScale, self.worldScale)
transformFilter = vtk.vtkTransformPolyDataFilter()
transformFilter.SetInputData(polyData)
transformFilter.SetTransform(transform)
transformFilter.Update()
return transformFilter.GetOutput()
def getReferencePosition(self, index):
"""
Dumped from slicer program
"""
refplanes = []
centers = []
if IOUSFAN:
refplanes.append(
np.array([[1, 0, 0, -191.357], [0, 0, -1, 17.9393],
[0, 1, 0, 192.499], [0, 0, 0, 1]]))
centers.append(np.r_[117.54695990115218, 103.95861040356766,
127.81653778974703])
else:
refplanes.append(
np.array([[
0.99722, -0.00658366270883304, 0.0741938205770847, -321.64
], [0.07419, 0.17584, -0.98162, -227.46],
[-0.0065837, 0.98440, 0.17584, -563.67],
[0, 0, 0, 1.0]]))
centers.append(np.r_[-75.696, -149.42, -231.76])
refplanes.append(
np.array([[
0.9824507428729312, -0.028608856565971154,
0.1843151408713164, -221.425151769367
],
[
0.18431514087131629, 0.3004711475787132,
-0.935812491003576, -325.6553959586223
],
[
-0.028608856565971223, 0.9533617481306448,
0.3004711475787133, -547.1574253306663
], [0, 0, 0, 1]]))
centers.append(np.r_[-31.317285034663634, -174.62449255285645,
-193.39018826551072])
return centers[index], refplanes[index]
def resetCamera(self):
qDebug('resetCamera')
self.renderer.ResetCamera()
def initScene(self):
qDebug('initScene()')
self.renderer = vtk.vtkOpenGLRenderer()
self.render_window = self.interactor.GetRenderWindow()
self.render_window.AddRenderer(self.renderer)
self.cellPicker = vtk.vtkCellPicker()
self.cellPicker.SetTolerance(30.0)
self.interactor.SetPicker(self.cellPicker)
#* Top background color
bg_t = np.ones(3) * 245.0 / 255.0
#* Bottom background color
bg_b = np.ones(3) * 170.0 / 255.0
self.renderer.SetBackground(bg_t)
self.renderer.SetBackground2(bg_b)
self.renderer.GradientBackgroundOn()
def computeClippingPlanes(self, source):
# Clipping planes
planes = vtk.vtkPlaneCollection()
axis1 = np.array(source.GetPoint1()) - np.array(source.GetOrigin())
axis2 = np.array(source.GetPoint2()) - np.array(source.GetOrigin())
# Okay
plane1 = vtk.vtkPlane()
plane1.SetOrigin(source.GetOrigin())
plane1.SetNormal(axis2)
plane2 = vtk.vtkPlane()
plane2.SetOrigin(source.GetOrigin())
plane2.SetNormal(axis1)
tmp = axis2 + np.array(source.GetPoint1())
plane3 = vtk.vtkPlane()
plane3.SetOrigin(tmp)
plane3.SetNormal(-axis2)
plane4 = vtk.vtkPlane()
plane4.SetOrigin(tmp)
plane4.SetNormal(-axis1)
planes.AddItem(plane1)
planes.AddItem(plane2)
planes.AddItem(plane3)
planes.AddItem(plane4)
return planes
def computeContoursAndTubes(self, source):
# Plane for intersection
plane = vtk.vtkPlane()
plane.SetOrigin(source.GetOrigin())
plane.SetNormal(source.GetNormal())
cutEdges = vtk.vtkCutter()
cutEdges.SetInputConnection(self.vesselNormals.GetOutputPort())
cutEdges.SetCutFunction(plane)
cutEdges.GenerateCutScalarsOff() # Was on
cutEdges.SetValue(0, 0.5)
cutEdges.Update()
cutStrips = vtk.vtkStripper()
cutStrips.SetInputConnection(cutEdges.GetOutputPort())
cutStrips.Update()
oldContours = cutStrips.GetOutput()
tubes = vtk.vtkTubeFilter()
tubes.SetInputConnection(cutStrips.GetOutputPort())
tubes.CappingOn()
tubes.SidesShareVerticesOff()
tubes.SetNumberOfSides(12)
tubes.SetRadius(self.worldScale * 1.0)
return tubes, oldContours
def initPlaneWidgets(self, index):
qDebug('initPlaneWidgets()')
center, htrans = self.getReferencePosition(index)
hw = self.imgWidth
shw = self.worldScale * hw
source = vtk.vtkPlaneSource()
source.SetOrigin(0, 0, 0)
source.SetPoint1(shw, 0, 0)
source.SetPoint2(0, shw, 0)
transform = vtk.vtkTransform()
mat = vtk.vtkMatrix4x4()
for i in range(4):
for j in range(4):
mat.SetElement(i, j, htrans[i, j])
# Should transformation also be scaled??
for i in range(3):
mat.SetElement(i, 3, self.worldScale * mat.GetElement(i, 3))
transform.SetMatrix(mat)
transform.Update()
origin = source.GetOrigin()
origin = transform.TransformPoint(origin)
source.SetOrigin(origin)
p1 = source.GetPoint1()
p1 = transform.TransformPoint(p1)
source.SetPoint1(p1)
p2 = source.GetPoint2()
p2 = transform.TransformPoint(p2)
source.SetPoint2(p2)
source.Update()
source.SetCenter(self.worldScale * center)
source.Update()
# Test position good for slice 17 (HACK)
if (IOUSFAN):
source.SetOrigin(-36.00039424299387, 58.447421532729656,
116.93018531955384)
source.SetPoint1(13.731795848152041, 54.203001711976306,
119.87877296847647)
source.SetPoint2(-40.18599847580337, 8.635225461941415,
115.82300881527104)
source.Update()
self.planeSources.append(source)
#####################################
# Blue reference plane
#####################################
# mapper
if self.showReferencePlane:
mapper0 = vtk.vtkPolyDataMapper()
mapper0.SetInputConnection(source.GetOutputPort())
# actor
refActor = vtk.vtkActor()
refActor.SetMapper(mapper0)
prop = refActor.GetProperty()
prop.SetColor(blue)
prop.SetOpacity(self.opacity)
self.refplanes.append(refActor)
self.renderer.AddActor(refActor)
else:
self.refplanes.append(None)
#####################################
# Compute contours, tubes and clipping
#####################################
tubes, oldContours = self.computeContoursAndTubes(source)
edgeMapper = vtk.vtkPolyDataMapper()
edgeMapper.ScalarVisibilityOff()
edgeMapper.SetInputConnection(tubes.GetOutputPort())
planes = self.computeClippingPlanes(source)
edgeMapper.SetClippingPlanes(planes)
actor = vtk.vtkActor()
actor.SetMapper(edgeMapper)
prop = actor.GetProperty()
prop.SetColor(green)
prop.SetLineWidth(3)
self.contours.append(actor)
self.renderer.AddActor(actor)
###################################################
# Plane widget for interaction
###################################################
planeWidget = vtk.vtkPlaneWidget()
planeWidget.SetInteractor(self.interactor)
planeWidget.SetOrigin(source.GetOrigin())
planeWidget.SetPoint1(source.GetPoint1())
planeWidget.SetPoint2(source.GetPoint2())
prop = planeWidget.GetHandleProperty()
prop.SetColor(QLiverViewer.colors.GetColor3d("Red"))
prop = planeWidget.GetPlaneProperty()
prop.SetColor(QLiverViewer.colors.GetColor3d("Red"))
# Original position and orientation of reference plane
self.lastPositions['reset'][index] = [
planeWidget.GetOrigin(),
planeWidget.GetPoint1(),
planeWidget.GetPoint2(),
planeWidget.GetCenter(),
np.array(planeWidget.GetNormal())
] # Redundant
print('normal')
print(planeWidget.GetNormal())
planeWidget.SetEnabled(1)
planeWidget.AddObserver(vtk.vtkCommand.EndInteractionEvent,
self.onWidgetMoved, 1.0)
attempt = vtk.vtkActor()
self.fullcontours.append(oldContours)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(oldContours)
attempt.SetMapper(mapper)
attempt.GetProperty().SetColor(red)
self.userAttempts.append(attempt)
self.renderer.AddActor(attempt)
lastNormal = planeWidget.GetNormal()
lastAxis1 = vtk.vtkVector3d()
vtk.vtkMath.Subtract(planeWidget.GetPoint1(), planeWidget.GetOrigin(),
lastAxis1)
lastOrigin = planeWidget.GetCenter()
self.lastPositions['origin'][index] = lastOrigin
self.lastPositions['normal'][index] = lastNormal
self.lastPositions['axis1'][index] = lastAxis1
self.planeWidgets.append(planeWidget)
self.render_window.Render()
def onWidgetMoved(self, obj, ev):
if (obj in self.planeWidgets):
index = self.planeWidgets.index(obj)
self.lastIndex = index
normal0 = self.lastPositions['normal'][index]
first0 = self.lastPositions['axis1'][index]
origin0 = self.lastPositions['origin'][index]
normal1 = np.array(obj.GetNormal())
first1 = np.array(obj.GetPoint1()) - np.array(obj.GetOrigin())
origin1 = obj.GetCenter()
trans = AxesToTransform(normal0, first0, origin0, normal1, first1,
origin1)
if self.userAttempts[index].GetUserTransform() is not None:
self.userAttempts[index].GetUserTransform().Concatenate(trans)
else:
transform = vtk.vtkTransform()
transform.SetMatrix(trans)
transform.PostMultiply()
self.userAttempts[index].SetUserTransform(transform)
(deg, x, y, z) = self.userAttempts[index].GetUserTransform(
).GetOrientationWXYZ()
self.lastPositions['origin'][index] = obj.GetCenter()
lastAxis1 = [first1[0], first1[1], first1[2]]
lastNormal = (normal1[0], normal1[1], normal1[2])
self.lastPositions['axis1'][index] = lastAxis1
self.lastPositions['normal'][index] = lastNormal
self.userAttempts[index].Modified()
self.render_window.Render()
print("center")
print('wtf')
originalNormal = self.lastPositions['reset'][index][4]
originalNormal = originalNormal / np.sqrt(np.sum(originalNormal**
2))
self.widgetMoved.emit(
(deg, np.r_[x, y, z]), originalNormal,
np.array(obj.GetCenter()) -
np.array(self.lastPositions['reset'][index][3]))
#print(ev)
def initVessels(self):
qDebug('initVessels()')
if os.name == 'nt':
filename = os.path.join(filedir,
'../../data/Abdomen/Connected.vtp')
if IOUSFAN:
#filename = 'e:/analogic/TrialVTK/data/VesselMeshData.vtk'
filename = 'e:/analogic/TrialVTK/data/LiverVesselMeshData.vtk'
else:
filename = '/home/jmh/bkmedical/data/CT/Connected.vtp'
# read data
if IOUSFAN:
reader = vtk.vtkGenericDataObjectReader()
else:
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(filename)
reader.Update()
connectFilter = vtk.vtkPolyDataConnectivityFilter()
connectFilter.SetInputConnection(reader.GetOutputPort())
connectFilter.SetExtractionModeToLargestRegion()
connectFilter.Update()
self.vesselPolyData = self.scale(connectFilter.GetOutput())
# compute normals
self.vesselNormals = vtk.vtkPolyDataNormals()
self.vesselNormals.SetInputData(self.vesselPolyData)
# mapper
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(self.vesselNormals.GetOutputPort())
# actor for vessels
self.vessels = vtk.vtkActor()
self.vessels.SetMapper(mapper)
prop = self.vessels.GetProperty()
if self.brighter25:
prop.SetColor(vtk.vtkColor3d(hexCol("#517487"))) # 25% lighter
else:
prop.SetColor(vtk.vtkColor3d(hexCol("#415d6c")))
# assign actor to the renderer
self.renderer.AddActor(self.vessels)
def initLiver(self):
qDebug('initLiver()')
if os.name == 'nt':
filename = os.path.join(
filedir, '../../data/Abdomen/Liver_3D-interpolation.vtp')
if IOUSFAN:
filename = 'e:/analogic/TrialVTK/data/segmented_liver_ITK_snap.vtk'
else:
filename = '/home/jmh/bkmedical/data/CT/Liver_3D-interpolation.vtp'
if IOUSFAN:
reader = vtk.vtkGenericDataObjectReader()
else:
reader = vtk.vtkXMLPolyDataReader()
reader.SetFileName(filename)
reader.Update()
connectFilter = vtk.vtkPolyDataConnectivityFilter()
connectFilter.SetInputConnection(reader.GetOutputPort())
connectFilter.SetExtractionModeToLargestRegion()
connectFilter.Update()
surfNormals = vtk.vtkPolyDataNormals()
surfNormals.SetInputData(self.scale(connectFilter.GetOutput()))
#Create a mapper and actor
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputConnection(surfNormals.GetOutputPort()) # was reader
self.liver = vtk.vtkActor()
self.liver.SetMapper(mapper)
prop = self.liver.GetProperty()
if self.brighter25:
prop.SetColor(vtk.vtkColor3d(hexCol("#873927")))
else:
prop.SetColor(vtk.vtkColor3d(hexCol("#6c2e1f")))
prop.SetOpacity(self.opacity)
self.renderer.AddActor(self.liver)
def start(self):
self.interactor.Initialize()
