def createRenderer(self, **args):
background_color = args.get('background_color', VTK_BACKGROUND_COLOR)
self.renderer.SetBackground(*background_color)
self.renderWindowInteractor.AddObserver('RightButtonPressEvent',
self.onRightButtonPress)
self.textDisplayMgr = TextDisplayMgr(self.renderer)
self.pointPicker = vtk.vtkPointPicker()
self.pointPicker.PickFromListOn()
try:
self.pointPicker.SetUseCells(True)
except:
print >> sys.stderr, "Warning, vtkPointPicker patch not installed, picking will not work properly."
self.pointPicker.InitializePickList()
self.renderWindowInteractor.SetPicker(self.pointPicker)
self.addObserver(self.renderer, 'ModifiedEvent', self.activateEvent)
self.clipper = vtk.vtkBoxWidget()
self.clipper.RotationEnabledOff()
self.clipper.SetPlaceFactor(1.0)
self.clipper.KeyPressActivationOff()
self.clipper.SetInteractor(self.renderWindowInteractor)
self.clipper.SetHandleSize(0.005)
self.clipper.SetEnabled(True)
self.clipper.InsideOutOn()
self.clipper.AddObserver('StartInteractionEvent', self.startClip)
self.clipper.AddObserver('EndInteractionEvent', self.endClip)
self.clipper.AddObserver('InteractionEvent', self.executeClip)
self.clipOff()
def Execute(self):
if self.Image == None:
self.PrintError('Error: no Image.')
if self.Interactive == 1:
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
self.PlaneWidgetX = vtkvmtk.vtkvmtkImagePlaneWidget()
self.PlaneWidgetX.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidgetY = vtkvmtk.vtkvmtkImagePlaneWidget()
self.PlaneWidgetY.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidgetZ = vtkvmtk.vtkvmtkImagePlaneWidget()
self.PlaneWidgetZ.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.BoxWidget = vtk.vtkBoxWidget()
self.BoxWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.vmtkRenderer.AddKeyBinding('i','Interact.', self.InteractCallback)
self.Display()
while (self.BoxActive == 1):
self.PaintVOI()
self.Display()
else:
self.PaintVOI()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def Execute(self):
if self.Image == None:
self.PrintError('Error: no Image.')
if self.Interactive == 1:
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.PlaneWidgetX = vtk.vtkImagePlaneWidget()
self.PlaneWidgetX.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidgetY = vtk.vtkImagePlaneWidget()
self.PlaneWidgetY.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidgetZ = vtk.vtkImagePlaneWidget()
self.PlaneWidgetZ.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.BoxWidget = vtk.vtkBoxWidget()
self.BoxWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.Display()
while (self.BoxActive == 1):
self.PaintVOI()
self.Image = self.PaintedImage
self.Display()
else:
self.PaintVOI()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
self.Image = self.PaintedImage
def createRenderer(self, **args ):
background_color = args.get( 'background_color', VTK_BACKGROUND_COLOR )
self.renderer.SetBackground(*background_color)
self.textDisplayMgr = TextDisplayMgr( self.renderer )
self.renderWindowInitSize = args.get( 'window_size', None )
if self.renderWindowInitSize <> None:
self.renderWindow.SetSize( self.renderWindowInitSize )
self.pointPicker = vtk.vtkPointPicker()
self.pointPicker.PickFromListOn()
try: self.pointPicker.SetUseCells(True)
except: print>>sys.stderr, "Warning, vtkPointPicker patch not installed, picking will not work properly."
self.pointPicker.InitializePickList()
self.renderWindowInteractor.SetPicker(self.pointPicker)
self.addObserver( self.renderer, 'ModifiedEvent', self.activateEvent )
self.clipper = vtk.vtkBoxWidget()
self.clipper.RotationEnabledOff()
self.clipper.SetPlaceFactor( 1.0 )
self.clipper.KeyPressActivationOff()
self.clipper.SetInteractor( self.renderWindowInteractor )
self.clipper.SetHandleSize( 0.005 )
self.clipper.SetEnabled( True )
self.clipper.InsideOutOn()
self.clipper.AddObserver( 'StartInteractionEvent', self.startClip )
self.clipper.AddObserver( 'EndInteractionEvent', self.endClip )
self.clipper.AddObserver( 'InteractionEvent', self.executeClip )
self.clipOff()
def Execute(self):
if self.Image == None:
self.PrintError('Error: no Image.')
self.CroppedImage.DeepCopy(self.Image)
if self.Interactive == 1:
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.PlaneWidgetX = vtk.vtkImagePlaneWidget()
self.PlaneWidgetX.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidgetY = vtk.vtkImagePlaneWidget()
self.PlaneWidgetY.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidgetZ = vtk.vtkImagePlaneWidget()
self.PlaneWidgetZ.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.BoxWidget = vtk.vtkBoxWidget()
self.BoxWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.Display()
while (self.BoxActive == 1):
self.ExtractVOI()
self.Image = self.CroppedImage
self.Display()
else:
self.ExtractVOI()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
self.Image = self.CroppedImage
def Execute(self):
if self.Surface == None:
self.PrintError('Error: no Surface.')
if self.WidgetType == "box":
self.ClipFunction = vtk.vtkPlanes()
elif self.WidgetType == "sphere":
self.ClipFunction = vtk.vtkSphere()
self.Clipper = vtk.vtkClipPolyData()
self.Clipper.SetInput(self.Surface)
self.Clipper.SetClipFunction(self.ClipFunction)
self.Clipper.GenerateClippedOutputOn()
self.Clipper.InsideOutOn()
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(self.Surface)
mapper.ScalarVisibilityOff()
self.Actor = vtk.vtkActor()
self.Actor.SetMapper(mapper)
self.vmtkRenderer.Renderer.AddActor(self.Actor)
if self.WidgetType == "box":
self.ClipWidget = vtk.vtkBoxWidget()
self.ClipWidget.GetFaceProperty().SetColor(0.6,0.6,0.2)
self.ClipWidget.GetFaceProperty().SetOpacity(0.25)
elif self.WidgetType == "sphere":
self.ClipWidget = vtk.vtkSphereWidget()
self.ClipWidget.GetSphereProperty().SetColor(0.6,0.6,0.2)
self.ClipWidget.GetSphereProperty().SetOpacity(0.25)
self.ClipWidget.GetSelectedSphereProperty().SetColor(0.6,0.0,0.0)
self.ClipWidget.GetSelectedSphereProperty().SetOpacity(0.75)
self.ClipWidget.SetRepresentationToSurface()
self.ClipWidget.SetPhiResolution(20)
self.ClipWidget.SetThetaResolution(20)
self.ClipWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.Display()
self.Transform = vtk.vtkTransform()
self.ClipWidget.GetTransform(self.Transform)
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
if self.CleanOutput == 1:
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInput(self.Surface)
cleaner.Update()
self.Surface = cleaner.GetOutput()
if self.Surface.GetSource():
self.Surface.GetSource().UnRegisterAllOutputs()
def Execute(Surface, cl):
if Surface == None:
print 'Error: no Surface.'
sys.exit(0)
# Initialize
Clipper = vtk.vtkClipPolyData()
Clipper.SetInput(Surface)
Clipper.GenerateClippedOutputOn()
Clipper.SetInsideOut(0)
ClipFunction = vtk.vtkPlanes()
Clipper.SetClipFunction(ClipFunction)
Cutter = vtk.vtkCutter()
Cutter.SetInput(Surface)
Cutter.SetCutFunction(ClipFunction)
ClippedSurface = vtk.vtkPolyData()
CutLines = vtk.vtkPolyData()
ClipWidget = vtk.vtkBoxWidget()
ClipWidget.GetFaceProperty().SetColor(0.6,0.6,0.2)
ClipWidget.GetFaceProperty().SetOpacity(0.25)
Transform = vtk.vtkTransform()
ClipWidget.GetTransform(Transform)
for i in range(cl.GetNumberOfLines()):
# TODO: Implement thing here.
# Clean surface
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInput(Surface)
cleaner.Update()
Surface = cleaner.GetOutput()
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInput(ClippedSurface)
cleaner.Update()
ClippedSurface = cleaner.GetOutput()
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInput(CutLines)
cleaner.Update()
stripper = vtk.vtkStripper()
stripper.SetInput(cleaner.GetOutput())
stripper.Update()
CutLines = stripper.GetOutput()
if Surface.GetSource():
Surface.GetSource().UnRegisterAllOutputs()
if __name__=='__main__':
surface = read_command_line()
Execute()
def processVerticalScalingCommand(self, args, config_function):
# print "processVerticalScalingCommand: ", str(args)
verticalScale = config_function.value
if args and args[0] == "StartConfig":
ispec = self.inputSpecs[0]
wbounds = ispec.getDataBounds()
self.zscaleBoxWidget = vtk.vtkBoxWidget()
self.zscaleBoxWidget.SetInteractor(self.renderWindowInteractor)
self.zscaleBoxWidget.SetPlaceFactor(1.0)
self.zscaleBoxWidget.HandlesOff()
self.zscaleBoxWidget.SetEnabled(1)
oprop = self.zscaleBoxWidget.GetOutlineProperty()
oprop.SetColor(0.0, 0.0, 0.0)
oprop.SetLineWidth(2.0)
self.zscaleBoxWidget.On()
self.zscaleBoxWidget.PlaceWidget(wbounds)
# print " >>>>>>>>>>>>>>>>>>>>> Place box widget: ", str( wbounds )
elif args and args[0] == "Init":
self.parameter_initializing = True
ispec = self.inputSpecs[0]
zsval = config_function.initial_value
# plotType = ispec.getMetadata('plotType')
# if plotType == 'xyt':
# tval = ispec.getMetadata('time')
# if tval: zsval = 10.0 / len( tval )
# else:
# lval = ispec.getMetadata('lev')
# if tval: zsval = 10.0 / len( lval )
# verticalScale.setValues( [ zsval ] )
self.setZScale(zsval)
verticalScale.setValue('count', 1)
self.parameter_initializing = False
elif args and args[0] == "EndConfig":
vscale = verticalScale.getValues()
self.setZScale(vscale)
self.zscaleBoxWidget.Off()
self.zscaleBoxWidget.SetEnabled(0)
self.zscaleBoxWidget = None
self.processConfigParameterChange(verticalScale)
elif args and args[0] == "InitConfig":
self.updateTextDisplay(config_function.label)
bbar = self.getInteractionButtons()
self.skipIndex = 2
for islider in range(4):
bbar.setSliderVisibility(
islider, islider < len(config_function.sliderLabels))
elif args and args[0] == "Open":
pass
elif args and args[0] == "Close":
pass
elif args and args[0] == "UpdateConfig":
ispec = self.inputSpecs[0]
vscale = args[2].GetValue()
verticalScale.setValues([vscale])
wbounds = ispec.getDataBounds(zscale=vscale)
self.zscaleBoxWidget.PlaceWidget(wbounds)
def Execute(self):
if (self.Surface == None):
self.PrintError('Error: no Surface.')
if self.WidgetType == "box":
self.ClipFunction = vtk.vtkPlanes()
elif self.WidgetType == "sphere":
self.ClipFunction = vtk.vtkSphere()
self.Clipper = vtk.vtkClipPolyData()
self.Clipper.SetInput(self.Surface)
self.Clipper.SetClipFunction(self.ClipFunction)
self.Clipper.GenerateClippedOutputOn()
self.Clipper.InsideOutOn()
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(self.Surface)
mapper.ScalarVisibilityOff()
self.Actor = vtk.vtkActor()
self.Actor.SetMapper(mapper)
self.vmtkRenderer.Renderer.AddActor(self.Actor)
if self.WidgetType == "box":
self.ClipWidget = vtk.vtkBoxWidget()
self.ClipWidget.GetFaceProperty().SetColor(0.6, 0.6, 0.2)
self.ClipWidget.GetFaceProperty().SetOpacity(0.25)
elif self.WidgetType == "sphere":
self.ClipWidget = vtk.vtkSphereWidget()
self.ClipWidget.GetSphereProperty().SetColor(0.6, 0.6, 0.2)
self.ClipWidget.GetSphereProperty().SetOpacity(0.25)
self.ClipWidget.GetSelectedSphereProperty().SetColor(0.6, 0.0, 0.0)
self.ClipWidget.GetSelectedSphereProperty().SetOpacity(0.75)
self.ClipWidget.SetRepresentationToSurface()
self.ClipWidget.SetPhiResolution(20)
self.ClipWidget.SetThetaResolution(20)
self.ClipWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.Display()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
if self.CleanOutput == 1:
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInput(self.Surface)
cleaner.Update()
self.Surface = cleaner.GetOutput()
if self.Surface.GetSource():
self.Surface.GetSource().UnRegisterAllOutputs()
def createContent( self ):
input = self.module.inputModule.getOutput()
self.boxWidget = vtk.vtkBoxWidget()
self.boxWidget.SetRotationEnabled(0)
self.boxWidget.SetPlaceFactor(1.0)
self.boxWidget.SetInput( input )
self.planes = vtk.vtkPlanes()
self.boxWidget.AddObserver("StartInteractionEvent", self.startConfiguration )
self.boxWidget.AddObserver("InteractionEvent", self.updateConfiguration )
self.boxWidget.AddObserver("EndInteractionEvent", self.endConfiguration )
def __init__(self): super(ClippingBox, self).__init__() self.widget = None self.clippingBox = vtkBoxWidget() self.planes = [vtkImagePlaneWidget() for _ in range(6)] self.transform = vtkTransform() # For future functionality self._clippingBoxState = False self._clippingPlanesState = False
def __init__( self, parent, imode_callback, rmode_callback, ppos_callback, ao, **kwargs ):
# initialize Panel
if 'id' not in kwargs:
kwargs['id'] = wx.ID_ANY
wx.Panel.__init__( self, parent, **kwargs )
self.setInteractionMode = imode_callback
self.setInteractionMode(True)
self.recordingMode = False
self.setRecordingMode = rmode_callback
self.setRecordingMode(False)
self.setPickerPos = ppos_callback
self.ao = ao
self.aa = False
self.firstRender = True
self.vtkWidget = wxVTKRenderWindowInteractor(self, wx.ID_ANY)
self.iren = self.vtkWidget._Iren
self.iren.SetInteractorStyle(vtk.vtkInteractorStyleTrackballCamera())
self.renderer = vtk.vtkRenderer()
self.renderer.SetBackground(0,0,0)
self.imageLayer = {}
self.CISID = -1 # Current Image Set ID
self.imageLayer[self.CISID] = IBCRenderer(self.renderer, self.iren.Render)
self.bacteriaLayer = BacteriaLayer(self.renderer, self.iren.Render)
self.viewCamActive = True
# for interactive clipping
self.planes = vtk.vtkPlanes()
self.ellipsoid = None
self.ellipsoidTextActor = None
# The SetInteractor method is how 3D widgets are associated with the
# render window interactor. Internally, SetInteractor sets up a bunch
# of callbacks using the Command/Observer mechanism (AddObserver()).
self.boxWidget = vtk.vtkBoxWidget()
self.boxWidget.SetInteractor(self.iren)
self.boxWidget.SetPlaceFactor(1.0)
# init vtk window
self.vtkWidget.Enable(1)
self.vtkWidget.AddObserver("ExitEvent", lambda o,e,f=parent: f.Close())
self.vtkWidget.GetRenderWindow().AddRenderer(self.renderer)
# Bind VTK events
self.iren.AddObserver("KeyPressEvent", self.OnKeyDown)
self.Sizer = wx.BoxSizer()
self.Sizer.Add(self.vtkWidget, 1, wx.EXPAND)
def processVerticalScalingCommand( self, args, config_function ):
# print "processVerticalScalingCommand: ", str(args)
verticalScale = config_function.value
if args and args[0] == "StartConfig":
ispec = self.inputSpecs[ 0 ]
wbounds = ispec.getDataBounds()
self.zscaleBoxWidget = vtk.vtkBoxWidget()
self.zscaleBoxWidget.SetInteractor( self.renderWindowInteractor )
self.zscaleBoxWidget.SetPlaceFactor(1.0)
self.zscaleBoxWidget.HandlesOff()
self.zscaleBoxWidget.SetEnabled(1)
oprop = self.zscaleBoxWidget.GetOutlineProperty()
oprop.SetColor( 0.0, 0.0, 0.0 )
oprop.SetLineWidth( 2.0 )
self.zscaleBoxWidget.On()
self.zscaleBoxWidget.PlaceWidget(wbounds)
# print " >>>>>>>>>>>>>>>>>>>>> Place box widget: ", str( wbounds )
elif args and args[0] == "Init":
self.parameter_initializing = True
ispec = self.inputSpecs[ 0 ]
zsval = config_function.initial_value
# plotType = ispec.getMetadata('plotType')
# if plotType == 'xyt':
# tval = ispec.getMetadata('time')
# if tval: zsval = 10.0 / len( tval )
# else:
# lval = ispec.getMetadata('lev')
# if tval: zsval = 10.0 / len( lval )
# verticalScale.setValues( [ zsval ] )
self.setZScale( zsval )
verticalScale.setValue( 'count', 1 )
self.parameter_initializing = False
elif args and args[0] == "EndConfig":
vscale = verticalScale.getValues()
self.setZScale( vscale )
self.zscaleBoxWidget.Off()
self.zscaleBoxWidget.SetEnabled(0)
self.zscaleBoxWidget = None
self.processConfigParameterChange( verticalScale )
elif args and args[0] == "InitConfig":
self.updateTextDisplay( config_function.label )
bbar = self.getInteractionButtons()
self.skipIndex = 2
for islider in range(4): bbar.setSliderVisibility( islider, islider < len(config_function.sliderLabels) )
elif args and args[0] == "Open":
pass
elif args and args[0] == "Close":
pass
elif args and args[0] == "UpdateConfig":
ispec = self.inputSpecs[ 0 ]
vscale = args[2].GetValue()
verticalScale.setValues( [ vscale ] )
wbounds = ispec.getDataBounds( zscale=vscale )
self.zscaleBoxWidget.PlaceWidget( wbounds )
def vtkCreateBoxWidget(self, interactor):
"""
:param interactor:
:return:
"""
boxWidget = vtk.vtkBoxWidget()
boxWidget.SetInteractor(interactor)
boxWidget.SetProp3D(self.vtk_actor)
boxWidget.SetPlaceFactor(1.) # Make the box 1.25x larger than the actor
boxWidget.PlaceWidget()
boxWidget.On()
def setImageData(self, imageData): self.transformBox = vtkBoxWidget() self.transformBox.SetInteractor(self.widget.rwi) self.transformBox.SetPlaceFactor(1.01) self.transformBox.SetInputData(imageData) self.transformBox.SetDefaultRenderer(self.widget.rendererOverlay) self.transformBox.InsideOutOn() self.transformBox.PlaceWidget() self.AddObserver(self.transformBox, "InteractionEvent", self.transformCallback) self.transformBox.GetSelectedFaceProperty().SetOpacity(0.3) self.transformBox.EnabledOn()
def __init__(self, data_dir, reader):
tfun = vtk.vtkPiecewiseFunction()
tfun.AddPoint(2440.0, 0.0)
tfun.AddPoint(2800.0, 0.85)
ctfun = vtk.vtkColorTransferFunction()
ctfun.AddRGBPoint(0.0, 0.5, 0.0, 0.0)
ctfun.AddRGBPoint(600.0, 1.0, 0.5, 0.5)
ctfun.AddRGBPoint(1280.0, 0.9, 0.2, 0.3)
ctfun.AddRGBPoint(1960.0, 0.81, 0.27, 0.1)
ctfun.AddRGBPoint(4095.0, 0.5, 0.5, 0.5)
volumeMapper = vtk.vtkGPUVolumeRayCastMapper()
volumeMapper.SetInputConnection(reader.GetOutputPort())
volumeMapper.SetBlendModeToComposite()
volumeProperty = vtk.vtkVolumeProperty()
#volumeProperty.SetColor(ctfun)
volumeProperty.SetScalarOpacity(tfun)
volumeProperty.SetInterpolationTypeToLinear()
#volumeProperty.ShadeOn()
newvol = vtk.vtkVolume()
newvol.SetMapper(volumeMapper)
newvol.SetProperty(volumeProperty)
# The SetInteractor method is how 3D widgets are associated with the
# render window interactor. Internally, SetInteractor sets up a bunch
# of callbacks using the Command/Observer mechanism (AddObserver()).
boxWidget = vtk.vtkBoxWidget()
#boxWidget.SetInteractor(iren)
boxWidget.SetPlaceFactor(1.0)
# The implicit function vtkPlanes is used in conjunction with the
# volume ray cast mapper to limit which portion of the volume is
# volume rendered.
planes = vtk.vtkPlanes()
self.planes = planes
def ClipVolumeRender(obj, event):
#global self.planes, volumeMapper
obj.GetPlanes(self.planes)
volumeMapper.SetClippingPlanes(self.planes)
# Place the interactor initially. The output of the reader is used to
# place the box widget.
boxWidget.SetInputConnection(reader.GetOutputPort())
boxWidget.PlaceWidget()
boxWidget.InsideOutOn()
boxWidget.AddObserver("InteractionEvent", ClipVolumeRender)
self.boxWidget = boxWidget
def move_stl2(self):
if self.move_button.isChecked():
self.state_moving()
# self.interactor.SetInteractorStyle(self.actor_interactor_style)
self.axesWidget.SetEnabled(False)
if self.boxWidget is None:
self.boxWidget = vtk.vtkBoxWidget()
self.boxWidget.SetInteractor(self.interactor)
# self.boxWidget.SetProp3D(self.stlActor)
self.boxWidget.SetPlaceFactor(1.25)
self.boxWidget.SetHandleSize(0.005)
self.boxWidget.SetEnabled(True)
self.boxWidget.SetScalingEnabled(False)
# hack for boxWidget - 1. reset actor transform
# 2. place boxWidget
# 3. apply transform to actor and boxWidget
tf = self.stlActor.GetUserTransform()
self.stlActor.SetUserTransform(vtk.vtkTransform())
self.boxWidget.SetProp3D(self.stlActor)
self.boxWidget.PlaceWidget()
self.boxWidget.SetTransform(tf)
self.stlActor.SetUserTransform(tf)
def TransformActor(obj, event):
tf = vtk.vtkTransform()
obj.GetTransform(tf)
# print(tf.GetScale())
self.stlActor.SetUserTransform(tf)
self.updateTransform()
self.boxWidget.AddObserver("InteractionEvent", TransformActor)
else:
self.boxWidget.SetEnabled(True)
# self.interactor.GetInteractorStyle().SetCurrentStyleToTrackballActor()
else:
self.state_stl() # TODO: might be not stl but both or gcode
# self.interactor.SetInteractorStyle(self.camera_interactor_style)
self.boxWidget.SetEnabled(False)
self.axesWidget.SetEnabled(True)
xc, yc, zmin = gui_utils.findStlOrigin(self.stlActor)
tf = self.stlActor.GetUserTransform()
tf.PostMultiply()
tf.Translate(0, 0, -zmin)
self.stlActor.SetUserTransform(tf)
self.boxWidget.SetTransform(tf)
self.updateTransform()
# self.interactor.GetInteractorStyle().SetCurrentStyleToTrackballCamera()
self.reload_scene()
def __init__(self, actorlist, volumelist):
self.render = vtk.vtkRenderer()
self.renWindow = vtk.vtkRenderWindow()
self.renWindow.AddRenderer(self.render)
self.interactor = vtk.vtkRenderWindowInteractor()
self.interactor.SetRenderWindow(self.renWindow)
self.actorstoadd = actorlist
self.volumestoadd = volumelist
self.t = vtk.vtkTransform()
self.box = vtk.vtkBoxWidget()
self.planes = vtk.vtkPlanes()
self.clipper = vtk.vtkClipPolyData()
self.selectMapper = vtk.vtkPolyDataMapper()
self.selectActor = vtk.vtkLODActor()
def __init__(self):
'''
Constructor
'''
vtkPythonViewImage.__init__(self)
# texture mapper in 3D: vtkVolumeMapper
self.__VolumeMapper = None
# texture mapper in 3D: vtkVolumeTextureMapper3D
self.__VolumeTextureMapper = vtk.vtkVolumeTextureMapper3D()
# volume ray cast mapper vtkFixedPointVolumeRayCastMapper
self.__VolumeRayCastMapper = vtk.vtkFixedPointVolumeRayCastMapper()
# volume property: vtkVolumeProperty
self.__VolumeProperty = vtk.vtkVolumeProperty()
# volume actor: vtkVolume
self.__VolumeActor = vtk.vtkVolume()
# opacity transfer function: vtkPiecewiseFunction
self.__OpacityFunction = vtk.vtkPiecewiseFunction()
# color transfer function: vtkColorTransferFunction
self.__ColorFunction = vtk.vtkColorTransferFunction()
# vtkProp3DCollection
self.__PhantomCollection = vtk.vtkProp3DCollection()
# blender: vtkImageBlend
self.__Blender = None
# image 3D cropping box callback: vtkImage3DCroppingBoxCallback
self.__Callback = vtkPythonImage3DCroppingBoxCallback()
# box widget: vtkOrientedBoxWidget
# self.__BoxWidget = vtkOrientedBoxWidget() # Now I could not wrap vtkOrientedBoxWidget
self.__BoxWidget = vtk.vtkBoxWidget()
# vtkPlane widget: vtkPlaneWidget
self.__PlaneWidget = vtk.vtkPlaneWidget()
# annotated cube actor: vtkAnnotatedCubeActor, vtkOrientationMarkerWidget
self.__Cube = vtk.vtkAnnotatedCubeActor()
self.__Marker = vtk.vtkOrientationMarkerWidget()
self.SetupVolumeRendering()
self.SetupWidgets()
self.ShowAnnotationsOn()
self.getTextProperty().SetColor(0, 0, 0)
self.SetBackground(0.9, 0.9, 0.9) # white
self.__FirstRender = 1
self.__RenderingMode = self.PLANAR_RENDERING
self.__VRQuality = 1
self.__InteractorStyleSwitcher = None
def initBoxWidget(self):
self.boxWidget = vtk.vtkBoxWidget()
self.boxWidget.SetInteractor(self.iren)
self.boxWidget.SetProp3D(self.volume)
self.boxWidget.SetPlaceFactor(1.25)
self.boxWidget.PlaceWidget(self.boxWidget.GetProp3D().GetBounds())
self.boxWidget.SetRotationEnabled(0)
self.boxWidget.AddObserver("InteractionEvent", self.sliceCubevolum)
self.boxWidget.GetOutlineProperty().SetOpacity(0.1)
self.boxWidget.GetOutlineProperty().SetColor(0, 0, 0.3)
self.boxWidget.On()
self.volumMapper.SetCropping(1) # 开启3D剪切模式
self.volumMapper.SetCroppingRegionPlanes(
self.boxWidget.GetProp3D().GetBounds())
pass
def box():
colors = vtk.vtkNamedColors()
# Create a Cone
cone = vtk.vtkConeSource()
cone.SetResolution(20)
coneMapper = vtk.vtkPolyDataMapper()
coneMapper.SetInputConnection(cone.GetOutputPort())
coneActor = vtk.vtkActor()
coneActor.SetMapper(coneMapper)
coneActor.GetProperty().SetColor(colors.GetColor3d('BurlyWood'))
# A renderer and render window
renderer = vtk.vtkRenderer()
renderer.SetBackground(colors.GetColor3d('Blue'))
renderer.AddActor(coneActor)
renwin = vtk.vtkRenderWindow()
renwin.AddRenderer(renderer)
# An interactor
interactor = vtk.vtkRenderWindowInteractor()
#interactor = vtk.vtkGenericRenderWindowInteractor()
interactor.SetRenderWindow(renwin)
# A Box widget
boxWidget = vtk.vtkBoxWidget()
boxWidget.SetInteractor(interactor)
boxWidget.SetProp3D(coneActor)
boxWidget.SetPlaceFactor(1.25) # Make the box 1.25x larger than the actor
boxWidget.PlaceWidget()
boxWidget.On()
# Connect the event to a function
# This call makes cone move and stretch with the box.
# See complete list of event at
# https://vtk.org/doc/nightly/html/vtkCommand_8h_source.html
boxWidget.AddObserver('InteractionEvent', boxCallback)
# Start
interactor.Initialize()
renwin.SetWindowName('BoxWidget')
renwin.Render()
interactor.Start()
def createBoxWidget(image, iren):
boxWidget = vtk.vtkBoxWidget()
boxWidget.SetInteractor(iren)
boxWidget.SetPlaceFactor(1.0)
boxWidget.SetInput(image)
boxWidget.PlaceWidget()
boxWidget.InsideOutOn()
outlineProperty = boxWidget.GetOutlineProperty()
outlineProperty.SetRepresentationToWireframe()
outlineProperty.SetAmbient(1.0)
outlineProperty.SetAmbientColor(0, 0, 0)
outlineProperty.SetLineWidth(2)
selectedOutlineProperty = boxWidget.GetSelectedOutlineProperty()
selectedOutlineProperty.SetRepresentationToWireframe()
selectedOutlineProperty.SetAmbient(1.0)
selectedOutlineProperty.SetAmbientColor(1, 0, 0)
selectedOutlineProperty.SetLineWidth(3)
return boxWidget
def Execute(self):
if self.Image == None:
self.PrintError('Error: no Image.')
self.CroppedImage.DeepCopy(self.Image)
if self.Interactive == 1:
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
self.PlaneWidgetX = vtkvmtk.vtkvmtkImagePlaneWidget()
self.PlaneWidgetX.SetInteractor(
self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidgetY = vtkvmtk.vtkvmtkImagePlaneWidget()
self.PlaneWidgetY.SetInteractor(
self.vmtkRenderer.RenderWindowInteractor)
self.PlaneWidgetZ = vtkvmtk.vtkvmtkImagePlaneWidget()
self.PlaneWidgetZ.SetInteractor(
self.vmtkRenderer.RenderWindowInteractor)
self.BoxWidget = vtk.vtkBoxWidget()
self.BoxWidget.SetInteractor(
self.vmtkRenderer.RenderWindowInteractor)
self.vmtkRenderer.AddKeyBinding('i', 'Interact.',
self.InteractCallback)
self.InputInfo("Press 'i' to activate interactor")
self.Display()
while (self.BoxActive == 1):
self.ExtractVOI()
self.Image = self.CroppedImage
self.Display()
else:
self.ExtractVOI()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
self.Image = self.CroppedImage
def Execute(self):
if (self.Mesh == None):
self.PrintError('Error: no Mesh.')
self.Planes = vtk.vtkPlanes()
self.Clipper = vtk.vtkClipDataSet()
self.Clipper.SetInput(self.Mesh)
self.Clipper.SetClipFunction(self.Planes)
self.Clipper.GenerateClippedOutputOn()
self.Clipper.InsideOutOn()
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
mapper = vtk.vtkDataSetMapper()
mapper.SetInput(self.Mesh)
mapper.ScalarVisibilityOff()
self.Actor = vtk.vtkActor()
self.Actor.SetMapper(mapper)
self.vmtkRenderer.Renderer.AddActor(self.Actor)
self.BoxWidget = vtk.vtkBoxWidget()
self.BoxWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.BoxWidget.GetFaceProperty().SetColor(0.6, 0.6, 0.2)
self.BoxWidget.GetFaceProperty().SetOpacity(0.25)
self.vmtkRenderer.AddKeyBinding('i', 'Interact.',
self.InteractCallback)
self.vmtkRenderer.AddKeyBinding('space', 'Clip.', self.ClipCallback)
self.Display()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
if self.Mesh.GetSource():
self.Mesh.GetSource().UnRegisterAllOutputs()
def Execute(self):
if (self.Mesh == None):
self.PrintError('Error: no Mesh.')
self.Planes = vtk.vtkPlanes()
self.Clipper = vtk.vtkClipDataSet()
self.Clipper.SetInput(self.Mesh)
self.Clipper.SetClipFunction(self.Planes)
self.Clipper.GenerateClippedOutputOn()
self.Clipper.InsideOutOn()
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
mapper = vtk.vtkDataSetMapper()
mapper.SetInput(self.Mesh)
mapper.ScalarVisibilityOff()
self.Actor = vtk.vtkActor()
self.Actor.SetMapper(mapper)
self.vmtkRenderer.Renderer.AddActor(self.Actor)
self.BoxWidget = vtk.vtkBoxWidget()
self.BoxWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.BoxWidget.GetFaceProperty().SetColor(0.6,0.6,0.2)
self.BoxWidget.GetFaceProperty().SetOpacity(0.25)
self.vmtkRenderer.AddKeyBinding('i','Interact.', self.InteractCallback)
self.vmtkRenderer.AddKeyBinding('space','Clip.', self.ClipCallback)
self.Display()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
if self.Mesh.GetSource():
self.Mesh.GetSource().UnRegisterAllOutputs()
def OnBox(self, event):
boxWidget = vtk.vtkBoxWidget()
# change handle properties
boxWidget.SetHandleSize(0.005) # default is 0.01
boxWidget.SetInteractor(self.widget)
boxWidget.SetPlaceFactor(1.25)
boxWidget.SetInput(self.normals.GetOutput())
boxWidget.PlaceWidget()
boxCallback = self.BoxSelectPolygons()
boxWidget.AddObserver("EndInteractionEvent", boxCallback)
boxWidget.KeyPressActivationOff()
plane = vtk.vtkPlanes()
self.boxes.append(boxWidget)
self.planes[boxWidget.GetAddressAsString('')] = plane
self.region.AddFunction(plane)
newId = self.GateMenu.AppendCheckItem(-1, "Box #" + str(self.boxCount))
self.boxCount = self.boxCount + 1
self.boxIds[newId.GetId()] = boxWidget.GetAddressAsString('')
newId.Check(True)
self.Bind(wx.EVT_MENU, self.OnBoxSelect, newId)
boxWidget.On()
def main():
colors = vtk.vtkNamedColors()
# Create a Cone
cone = vtk.vtkConeSource()
cone.SetResolution(20)
coneMapper = vtk.vtkPolyDataMapper()
coneMapper.SetInputConnection(cone.GetOutputPort())
coneActor = vtk.vtkActor()
coneActor.SetMapper(coneMapper)
coneActor.GetProperty().SetColor(colors.GetColor3d('BurlyWood'))
# A renderer and render window
renderer = vtk.vtkRenderer()
renderer.SetBackground(colors.GetColor3d('Blue'))
renderer.AddActor(coneActor)
renwin = vtk.vtkRenderWindow()
renwin.AddRenderer(renderer)
renwin.SetWindowName('BoxWidget')
# An interactor
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(renwin)
# A Box widget
boxWidget = vtk.vtkBoxWidget()
boxWidget.SetInteractor(interactor)
boxWidget.SetProp3D(coneActor)
boxWidget.SetPlaceFactor(1.25) # Make the box 1.25x larger than the actor
boxWidget.PlaceWidget()
boxWidget.On()
# Connect the event to a function
boxWidget.AddObserver('InteractionEvent', boxCallback)
# Start
interactor.Initialize()
renwin.Render()
interactor.Start()
def _addVolumeCutterTool(vol):
vp = settings.plotter_instance
if not vp.renderer:
save_int = vp.interactive
vp.show(interactive=0)
vp.interactive = save_int
boxWidget = vtk.vtkBoxWidget()
boxWidget.SetInteractor(vp.interactor)
boxWidget.SetPlaceFactor(1.0)
vp.cutterWidget = boxWidget
planes = vtk.vtkPlanes()
def ClipVolumeRender(obj, event):
obj.GetPlanes(planes)
vol.mapper.SetClippingPlanes(planes)
boxWidget.SetInputData(vol.image)
boxWidget.OutlineCursorWiresOn()
boxWidget.GetSelectedOutlineProperty().SetColor(1, 0, 1)
boxWidget.GetOutlineProperty().SetColor(0.1, 0.1, 0.1)
boxWidget.GetOutlineProperty().SetOpacity(0.7)
boxWidget.SetPlaceFactor(1.05)
boxWidget.PlaceWidget()
boxWidget.InsideOutOn()
boxWidget.AddObserver("InteractionEvent", ClipVolumeRender)
colors.printc("Mesh Cutter Tool:", c="m", invert=1)
colors.printc(" Move gray handles to cut away parts of the mesh", c="m")
colors.printc(" Press X to save file to: clipped.vtk", c="m")
vp.renderer.ResetCamera()
boxWidget.On()
vp.interactor.Start()
boxWidget.Off()
vp.widgets.append(boxWidget)
def __init__(self, parent, visualizer, **kws):
"""
Initialization
"""
self.boxWidget = None
VisualizationModule.__init__(self, parent, visualizer, **kws)
self.descs = {
"ShowControls": "Show controls",
"ClippedModule": "Module to clip",
"AllModules": "Clip all modules",
"InsideOut": "Clip from outside"
}
boxWidget = self.boxWidget = vtk.vtkBoxWidget()
self.cut = 0
self.clippedMappers = []
self.renderer = self.parent.getRenderer()
iactor = parent.wxrenwin.GetRenderWindow().GetInteractor()
self.boxWidget.SetInteractor(iactor)
self.boxWidget.SetPlaceFactor(1.0)
outlineProperty = boxWidget.GetOutlineProperty()
outlineProperty.SetRepresentationToWireframe()
outlineProperty.SetAmbient(1.0)
outlineProperty.SetAmbientColor(1, 1, 1)
outlineProperty.SetLineWidth(3)
selectedOutlineProperty = boxWidget.GetSelectedOutlineProperty()
selectedOutlineProperty.SetRepresentationToWireframe()
selectedOutlineProperty.SetAmbient(1.0)
selectedOutlineProperty.SetAmbientColor(1, 0, 0)
selectedOutlineProperty.SetLineWidth(3)
# iactor = self.wxrenwin.GetRenderWindow().GetInteractor()
boxWidget.AddObserver("InteractionEvent", self.clipVolumeRender)
self.renew = 0
self.filterDesc = "Clip rendering using a box"
def __init__(self, parent, visualizer, **kws):
"""
Initialization
"""
self.boxWidget = None
VisualizationModule.__init__(self, parent, visualizer, **kws)
self.descs = {"ShowControls": "Show controls",
"ClippedModule": "Module to clip",
"AllModules": "Clip all modules",
"InsideOut": "Clip from outside"}
boxWidget = self.boxWidget = vtk.vtkBoxWidget()
self.cut = 0
self.clippedMappers = []
self.renderer = self.parent.getRenderer()
iactor = parent.wxrenwin.GetRenderWindow().GetInteractor()
self.boxWidget.SetInteractor(iactor)
self.boxWidget.SetPlaceFactor(1.0)
outlineProperty = boxWidget.GetOutlineProperty()
outlineProperty.SetRepresentationToWireframe()
outlineProperty.SetAmbient(1.0)
outlineProperty.SetAmbientColor(1, 1, 1)
outlineProperty.SetLineWidth(3)
selectedOutlineProperty = boxWidget.GetSelectedOutlineProperty()
selectedOutlineProperty.SetRepresentationToWireframe()
selectedOutlineProperty.SetAmbient(1.0)
selectedOutlineProperty.SetAmbientColor(1, 0, 0)
selectedOutlineProperty.SetLineWidth(3)
# iactor = self.wxrenwin.GetRenderWindow().GetInteractor()
boxWidget.AddObserver("InteractionEvent", self.clipVolumeRender)
self.renew = 0
self.filterDesc = "Clip rendering using a box"
def Execute(self):
if self.Mesh == None:
self.PrintError("Error: no Mesh.")
self.Clipper = vtk.vtkClipDataSet()
self.Clipper.SetInput(self.Mesh)
self.Clipper.GenerateClippedOutputOn()
self.Clipper.SetInsideOut(self.InsideOut)
if self.Interactive:
self.Planes = vtk.vtkPlanes()
self.Clipper.SetClipFunction(self.Planes)
self.Cutter = vtk.vtkCutter()
self.Cutter.SetInput(self.Mesh)
self.Cutter.SetCutFunction(self.Planes)
self.ClippedMesh = vtk.vtkUnstructuredGrid()
self.Surface = vtk.vtkPolyData()
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
mapper = vtk.vtkDataSetMapper()
mapper.SetInput(self.Mesh)
mapper.ScalarVisibilityOff()
self.Actor = vtk.vtkActor()
self.Actor.SetMapper(mapper)
self.vmtkRenderer.Renderer.AddActor(self.Actor)
self.BoxWidget = vtk.vtkBoxWidget()
self.BoxWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.BoxWidget.GetFaceProperty().SetColor(0.6, 0.6, 0.2)
self.BoxWidget.GetFaceProperty().SetOpacity(0.25)
self.vmtkRenderer.AddKeyBinding("i", "Interact.", self.InteractCallback)
self.vmtkRenderer.AddKeyBinding("space", "Clip.", self.ClipCallback)
self.Display()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
else:
self.Mesh.GetPointData().SetActiveScalars(self.ClipArrayName)
self.Clipper.GenerateClipScalarsOff()
self.Clipper.SetValue(self.ClipValue)
self.Clipper.Update()
self.Cutter = vtk.vtkContourFilter()
self.Cutter.SetInput(self.Mesh)
self.Cutter.SetValue(0, self.ClipValue)
self.Cutter.Update()
self.Mesh = self.Clipper.GetOutput()
self.Surface = self.Cutter.GetOutput()
self.ClippedMesh = self.Clipper.GetClippedOutput()
if self.Mesh.GetSource():
self.Mesh.GetSource().UnRegisterAllOutputs()
def __init__(self, file_list,spacing_list,feature_type,irad = 1.2, h_th=-200,
glyph_type='sphere', glyph_scale_factor=1,use_field_data=True, opacity_list=[],
color_list=[], lung=[]):
assert feature_type == "ridge_line" or feature_type == "valley_line" \
or feature_type == "ridge_surface" or feature_type == "valley_surface" \
or feature_type == "vessel" or feature_type == "airway" \
or feature_type == "fissure", "Invalid feature type"
if feature_type == "airway":
feature_type = "valley_line"
elif feature_type == "vessel":
feature_type = "ridge_line"
elif feature_type == "fissure":
feature_type = "ridge_surface"
self.mapper_list = list()
self.actor_list = list()
self.glyph_list = list()
self.glyph_type = glyph_type
self.file_list = file_list
self.spacing_list = spacing_list
self.opacity_list = opacity_list
self.irad = irad
self.h_th = h_th
self.color_list = color_list
self.lung = lung
self.use_field_data = use_field_data
self.feature_type = feature_type
self.normal_map=dict()
self.normal_map['ridge_line'] = "hevec0"
self.normal_map['valley_line'] = "hevec2"
self.normal_map['ridge_surface'] = "hevec2"
self.normal_map['valley_surface'] = "hevec0"
self.strength_map=dict()
self.strength_map['ridge_line'] = "h1"
self.strength_map['valley_line'] = "h1"
self.strength_map['ridge_surface'] = "h2"
self.strength_map['valley_surface'] = "h0"
if feature_type == 'ridge_line' or feature_type == 'valley_line':
self.height = irad
self.radius = 0.5
elif feature_type == 'ridge_surface' or feature_type == 'valley_surface':
self.height = 0.5
self.radius = irad
self.min_rad = 0.5
self.max_rad = 6
self.glyph_scale_factor = glyph_scale_factor
self.capture_prefix = ""
self.capture_count = 1
self.image_count = 1
# VTK Objects
self.ren = vtk.vtkOpenGLRenderer()
self.renWin = vtk.vtkRenderWindow()
self.iren = vtk.vtkRenderWindowInteractor()
# Volume rendering objects
self.volumeActor = vtk.vtkVolume()
self.volumeMapper = vtk.vtkVolumeRayCastMapper()
#self.volumeMapper = vtk.vtkGPUVolumeRayCastMapper()
# Variables for the interaction
self.volume_loaded = False
self.volume_added_to_renderer = False
self.volume_size = [0,0,0]
self.particles_loaded = False
self.particles_added_to_renderer = False
self.planeWidgetX = vtk.vtkImagePlaneWidget()
self.planeWidgetY = vtk.vtkImagePlaneWidget()
self.planeWidgetZ = vtk.vtkImagePlaneWidget()
self.lastPlaneWidget = self.planeWidgetX
self.lastPlaneWidgetIndex = 0
self.planeWidgetLayer = [0,0,0]
self.boxWidgetVolume = vtk.vtkBoxWidget()
self.boxWidgetParticles = vtk.vtkBoxWidget()
self.planesParticles = vtk.vtkPlanes()
self.planesParticles.SetBounds(-10000,10000,-10000,10000,-10000,10000); # For some reason planes needs initializaiton
self.planesVolume = vtk.vtkPlanes()
self.planesVolume.SetBounds(-10000,10000,-10000,10000,-10000,10000); # For some reason planes needs initializaiton
def load_muscleSI(self, t_T2image, m_bounds, iren, ren, picker, xplane, yplane, zplane):
""" load_muscleSI: Place automatically a widget over muscle location from file
INPUTS:
=======
images: (vtkImageData) list of Input image to Transform
OUTPUTS:
=======
muscleSI (float) Signal intensity from muscle
muscleSIcoords (float[3]) cords where Signal intensity from muscle is measured
"""
## Transform T2 img
# loadDisplay = Display()
#
# # Proceed to build reference frame for display objects based on DICOM coords
# [t_T2image, transform_cube] = loadDisplay.dicomTransform(T2image, image_pos_pat, image_ori_pat)
#
# # Calculate the center of the volume
# t_T2image.UpdateInformation()
print "\nBoxwidget placed..."
#################################################################
# The box widget observes the events invoked by the render window
# interactor. These events come from user interaction in the render
# window.
# Place the interactor initially. The output of the reader is used to
# place the box widget.
self.boxWidget = vtk.vtkBoxWidget()
self.boxWidget.SetInteractor(iren)
self.boxWidget.SetPlaceFactor(1)
self.boxWidget.SetInput(t_T2image)
self.boxWidget.ScalingEnabledOff()
self.boxWidget.OutlineCursorWiresOn()
# Construct a bounding box
bwidg = [0,0,0,0,0,0]
bwidg[0] = m_bounds[0]; bwidg[1] = m_bounds[1];
bwidg[2] = m_bounds[2]; bwidg[3] = m_bounds[3];
bwidg[4] = m_bounds[4]; bwidg[5] = m_bounds[5];
self.bounds_muscleSI = bwidg
print "\nbounds_muscleSI "
print self.bounds_muscleSI
# add to visualize
self.boxWidget.PlaceWidget( self.bounds_muscleSI )
self.boxWidget.On()
#iren.Start()
############################# Do extract_muscleSI
print "\n Re-extract muscle VOI? "
rexorNot=0
rexorNot = int(raw_input('type 1 to Re-extract or anykey: '))
if rexorNot == 1:
# custom interaction
self.picker = picker
self.textMapper = vtk.vtkTextMapper()
tprop = self.textMapper.GetTextProperty()
tprop.SetFontFamilyToArial()
tprop.SetFontSize(10)
tprop.BoldOn()
tprop.ShadowOn()
tprop.SetColor(1, 0, 0)
self.textActor = vtk.vtkActor2D()
self.textActor.VisibilityOff()
self.textActor.SetMapper(self.textMapper)
ren.AddActor2D(self.textActor)
picker.AddObserver("EndPickEvent", self.annotatePick)
iren.Start()
# Construct a bounding box
bwidg = [0,0,0,0,0,0]
bwidg[0] = self.pickPos[0]; bwidg[1] = self.pickPos[0]+5;
bwidg[2] = self.pickPos[1]; bwidg[3] = self.pickPos[1]+5;
bwidg[4] = self.pickPos[2]; bwidg[5] = self.pickPos[2]+5;
self.bounds_muscleSI = bwidg
print "\nbounds_muscleSI "
print self.bounds_muscleSI
self.boxWidget.PlaceWidget( self.bounds_muscleSI )
# turn off planes
xplane.Off()
yplane.Off()
self.boxWidget.On()
##########
### Set image stencil for muscle
# create a simple box VOI mask shape using previously found boundsPlane_preselected
VOIStencil = vtk.vtkROIStencilSource()
VOIStencil.SetShapeToBox()
VOIStencil.SetBounds( self.bounds_muscleSI )
VOIStencil.SetInformationInput(t_T2image)
VOIStencil.Update()
# cut the corresponding VOI region and set the background:
extractVOI_imgstenc = vtk.vtkImageStencil()
extractVOI_imgstenc.SetInput(t_T2image)
extractVOI_imgstenc.SetStencil(VOIStencil.GetOutput())
extractVOI_imgstenc.ReverseStencilOff()
extractVOI_imgstenc.SetBackgroundValue(5000)
extractVOI_imgstenc.Update()
# take out average image
finalmuscleSIIm = vtk.vtkImageData()
finalmuscleSIIm = extractVOI_imgstenc.GetOutput()
finalmuscleSIIm.Update()
## Display histogram
dims = finalmuscleSIIm .GetDimensions()
scalars = finalmuscleSIIm.GetPointData().GetScalars()
np_scalars = vtk_to_numpy(scalars)
np_scalars = np_scalars.reshape(dims[2], dims[1], dims[0])
np_scalars = np_scalars.transpose(2,1,0)
muscleSI = np_scalars[np_scalars<5000]
print "ave. T2_muscleSI: %d" % mean(muscleSI)
muscle_scalar_range = [muscleSI.min(), muscleSI.max()]
print "\nMuscle scalar Range:"
print muscle_scalar_range[0], muscle_scalar_range[1]
return muscleSI, muscle_scalar_range, self.bounds_muscleSI
coneMapper.SetInputConnection(cone.GetOutputPort())
coneActor = vtk.vtkActor()
coneActor.SetMapper(coneMapper)
# A renderer and render window
renderer = vtk.vtkRenderer()
renderer.SetBackground(0, 0, 1)
renderer.AddActor(coneActor)
renwin = vtk.vtkRenderWindow()
renwin.AddRenderer(renderer)
# An interactor
interactor = vtk.vtkRenderWindowInteractor()
interactor.SetRenderWindow(renwin)
# A Box widget
boxWidget = vtk.vtkBoxWidget()
boxWidget.SetInteractor(interactor)
boxWidget.SetProp3D(coneActor)
boxWidget.SetPlaceFactor( 1.25 ) # Make the box 1.25x larger than the actor
boxWidget.PlaceWidget()
boxWidget.On()
# Connect the event to a function
boxWidget.AddObserver("InteractionEvent", boxCallback)
# Start
interactor.Initialize()
interactor.Start()
def buildPipeline(self):
""" execute() -> None
Dispatch the vtkRenderer to the actual rendering widget
"""
extent = self.input().GetExtent()
rangeBounds = self.getRangeBounds()
self.sliceCenter = [(extent[2 * i + 1] - extent[2 * i]) / 2
for i in range(3)]
spacing = self.input().GetSpacing()
sx, sy, sz = spacing
origin = self.input().GetOrigin()
ox, oy, oz = origin
self._range = [rangeBounds[0], rangeBounds[1], rangeBounds[0], 0]
dataType = self.input().GetScalarTypeAsString()
self.setMaxScalarValue(self.input().GetScalarType())
self.pos = [spacing[i] * extent[2 * i] for i in range(3)]
# if ( (origin[0] + self.pos[0]) < 0.0): self.pos[0] = self.pos[0] + 360.0
bounds = [(origin[i / 2] + spacing[i / 2] * extent[i])
for i in range(6)]
print " @@@VolumeRenderer@@@ Data Type = %s, range = (%f,%f), max_scalar = %s" % (
dataType, rangeBounds[0], rangeBounds[1], self._max_scalar_value)
print "Extent: %s " % str(self.input().GetExtent())
print "Spacing: %s " % str(spacing)
print "Origin: %s " % str(origin)
print "Dimensions: %s " % str(self.input().GetDimensions())
print "Bounds: %s " % str(bounds)
print "Input Bounds: %s " % str(self.input().GetBounds())
print "VolumePosition: %s " % str(self.pos)
# self.inputInfo = self.inputPort.GetInformation()
# translation = inputInfo.Get( ResampleTranslationKey )
# Create transfer mapping scalar value to color
self.colorTransferFunction = vtk.vtkColorTransferFunction()
# Create transfer mapping scalar value to opacity
self.opacityTransferFunction = vtk.vtkPiecewiseFunction()
# The property describes how the data will look
self.volumeProperty = vtk.vtkVolumeProperty()
self.volumeProperty.SetInterpolationType(vtk.VTK_LINEAR_INTERPOLATION)
self.volumeProperty.SetColor(self.colorTransferFunction)
self.volumeProperty.SetScalarOpacity(self.opacityTransferFunction)
# self.volumeProperty.SetGradientOpacity(self.opacityTransferFunction)
# The mapper knows how to render the data
# self.volumeMapperTexture2D = vtk.vtkVolumeTextureMapper2D()
self.volumeMapper = vtk.vtkSmartVolumeMapper()
self.volumeMapper.SetBlendModeToComposite()
self.volumeMapper.CroppingOff()
self.clipper = vtk.vtkBoxWidget()
self.clipper.RotationEnabledOff()
self.clipper.SetPlaceFactor(1.0)
self.clipper.AddObserver('StartInteractionEvent', self.startClip)
self.clipper.AddObserver('EndInteractionEvent', self.endClip)
self.clipper.AddObserver('InteractionEvent', self.executeClip)
# self.clipper.AddObserver( 'AnyEvent', self.clipObserver )
# self.volumeMapper.SetScalarModeToUsePointFieldData()
# self.inputModule.inputToAlgorithm( self.volumeMapper )
# The volume holds the mapper and the property and can be used to
# position/orient the volume
self.volume = vtk.vtkVolume()
self.volume.SetScale(1.0, 1.0, 1.0)
self.volume.SetMapper(self.volumeMapper)
# self.volume.SetScale( spacing[0], spacing[1], spacing[2] )
self.setVolRenderCfg(None, False)
self.volume.SetProperty(self.volumeProperty)
# self.clipper.AddObserver( 'AnyEvent', self.EventWatcher )
# self.input().AddObserver( 'AnyEvent', self.EventWatcher )
self.volume.SetPosition(self.pos)
self.renderer.AddVolume(self.volume)
self.renderer.SetBackground(VTK_BACKGROUND_COLOR[0],
VTK_BACKGROUND_COLOR[1],
VTK_BACKGROUND_COLOR[2])
def add_box_widget(self,
callback,
bounds=None,
factor=1.25,
rotation_enabled=True,
color=None,
use_planes=False,
outline_translation=True,
pass_widget=False):
"""Add a box widget to the scene.
This is useless without a callback function. You can pass a callable
function that takes a single argument, the PolyData box output from
this widget, and performs a task with that box.
Parameters
----------
callback : callable
The method called every time the box is updated. This has two
options: Take a single argument, the ``PolyData`` box (default) or
if ``use_planes=True``, then it takes a single argument of the
plane collection as a ``vtkPlanes`` object.
bounds : tuple(float)
Length 6 tuple of the bounding box where the widget is placed.
factor : float, optional
An inflation factor to expand on the bounds when placing
rotation_enabled : bool
If ``False``, the box widget cannot be rotated and is strictly
orthogonal to the cartesian axes.
color : string or 3 item list, optional, defaults to white
Either a string, rgb list, or hex color string.
use_planes : bool, optional
Changes the arguments passed to the callback to the planes that
make up the box.
outline_translation : bool
If ``False``, the box widget cannot be translated and is strictly
placed at the given bounds.
pass_widget : bool
If true, the widget will be passed as the last argument of the
callback
"""
if hasattr(self, 'notebook') and self.notebook:
raise AssertionError(
'Box widget not available in notebook plotting')
if not hasattr(self, 'iren'):
raise AttributeError(
'Widgets must be used with an intereactive renderer. No off screen plotting.'
)
if not hasattr(self, "box_widgets"):
self.box_widgets = []
if bounds is None:
bounds = self.bounds
if color is None:
color = rcParams['font']['color']
def _the_callback(box_widget, event_id):
the_box = pyvista.PolyData()
box_widget.GetPolyData(the_box)
planes = vtk.vtkPlanes()
box_widget.GetPlanes(planes)
if hasattr(callback, '__call__'):
if use_planes:
args = [planes]
else:
args = [the_box]
if pass_widget:
args.append(box_widget)
try_callback(callback, *args)
return
box_widget = vtk.vtkBoxWidget()
box_widget.GetOutlineProperty().SetColor(parse_color(color))
box_widget.SetInteractor(self.iren)
box_widget.SetCurrentRenderer(self.renderer)
box_widget.SetPlaceFactor(factor)
box_widget.SetRotationEnabled(rotation_enabled)
box_widget.SetTranslationEnabled(outline_translation)
box_widget.PlaceWidget(bounds)
box_widget.On()
box_widget.AddObserver(vtk.vtkCommand.EndInteractionEvent,
_the_callback)
_the_callback(box_widget, None)
self.box_widgets.append(box_widget)
return box_widget
def buildPipeline(self):
""" execute() -> None
Dispatch the vtkRenderer to the actual rendering widget
"""
extent = self.input().GetExtent()
rangeBounds = self.getRangeBounds()
self.sliceCenter = [ (extent[2*i+1]-extent[2*i])/2 for i in range(3) ]
spacing = self.input().GetSpacing()
sx, sy, sz = spacing
origin = self.input().GetOrigin()
ox, oy, oz = origin
self._range = [ rangeBounds[0], rangeBounds[1], rangeBounds[0], 0 ]
dataType = self.input().GetScalarTypeAsString()
self.setMaxScalarValue( self.input().GetScalarType() )
self.pos = [ spacing[i]*extent[2*i] for i in range(3) ]
# if ( (origin[0] + self.pos[0]) < 0.0): self.pos[0] = self.pos[0] + 360.0
bounds = [0]*6
for i in range(6):
io2 = int(i/2)
bounds[i] = origin[io2] + spacing[io2]*extent[i]
print " --VolumeRenderer-- Data Type = %s, range = (%f,%f), max_scalar = %s" % ( dataType, rangeBounds[0], rangeBounds[1], self._max_scalar_value )
print "Extent: %s " % str( self.input().GetWholeExtent() )
print "Spacing: %s " % str( spacing )
print "Origin: %s " % str( origin )
print "Dimensions: %s " % str( self.input().GetDimensions() )
print "Bounds: %s " % str( bounds )
print "Input Bounds: %s " % str( self.input().GetBounds() )
print "VolumePosition: %s " % str( self.pos )
# self.inputInfo = self.inputPort.GetInformation()
# translation = inputInfo.Get( ResampleTranslationKey )
# Create transfer mapping scalar value to color
self.colorTransferFunction = vtk.vtkColorTransferFunction()
# Create transfer mapping scalar value to opacity
self.opacityTransferFunction = vtk.vtkPiecewiseFunction()
# The property describes how the data will look
self.volumeProperty = vtk.vtkVolumeProperty()
self.volumeProperty.SetInterpolationType( vtk.VTK_LINEAR_INTERPOLATION )
self.volumeProperty.SetColor(self.colorTransferFunction)
self.volumeProperty.SetScalarOpacity(self.opacityTransferFunction)
# self.volumeProperty.SetGradientOpacity(self.opacityTransferFunction)
# The mapper knows how to render the data
# self.volumeMapperTexture2D = vtk.vtkVolumeTextureMapper2D()
self.volumeMapper = vtk.vtkSmartVolumeMapper()
self.volumeMapper.SetBlendModeToComposite()
self.volumeMapper.CroppingOff()
self.clipper = vtk.vtkBoxWidget()
self.clipper.RotationEnabledOff()
self.clipper.SetPlaceFactor( 1.0 )
self.clipper.AddObserver( 'StartInteractionEvent', self.startClip )
self.clipper.AddObserver( 'EndInteractionEvent', self.endClip )
self.clipper.AddObserver( 'InteractionEvent', self.executeClip )
# self.clipper.AddObserver( 'AnyEvent', self.clipObserver )
# self.volumeMapper.SetScalarModeToUsePointFieldData()
# if vtk.VTK_MAJOR_VERSION <= 5: self.volumeMapper.SetInput(self.input())
# else: self.volumeMapper.SetInputData(self.input())
# The volume holds the mapper and the property and can be used to
# position/orient the volume
self.volume = vtk.vtkVolume()
self.volume.SetScale( 1.0, 1.0, 1.0 )
self.volume.SetMapper( self.volumeMapper )
# self.volume.SetScale( spacing[0], spacing[1], spacing[2] )
self.setVolRenderCfg( None, False )
self.volume.SetProperty(self.volumeProperty)
# self.clipper.AddObserver( 'AnyEvent', self.EventWatcher )
# self.input().AddObserver( 'AnyEvent', self.EventWatcher )
self.volume.SetPosition( self.pos )
self.renderer.AddVolume( self.volume )
self.renderer.SetBackground( VTK_BACKGROUND_COLOR[0], VTK_BACKGROUND_COLOR[1], VTK_BACKGROUND_COLOR[2] )
self.setColormap( [ 'jet', 1, 0, 0 ] )
def Execute(self):
if (self.Surface == None):
self.PrintError('Error: no Surface.')
#if (self.ReferenceSurface == None):
# self.PrintError('Error: no Reference Surface.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
if self.Transform == None:
self.Transform = vtk.vtkTransform()
if self.TransformFilter == None:
self.TransformFilter= vtk.vtkTransformPolyDataFilter()
self.TransformFilter.SetInput(self.Surface)
self.TransformFilter.SetTransform(self.Transform)
self.TransformFilter.Update()
self.TransformFilter.GetOutput().Update()
self.TransformedSurface.ShallowCopy(self.TransformFilter.GetOutput())
self.TransformedSurface.Update()
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(self.TransformedSurface)
mapper.ScalarVisibilityOff()
self.Actor = vtk.vtkActor()
self.Actor.SetMapper(mapper)
self.Actor.GetProperty().SetColor(1.0, 0.1, 0.1)
#self.Actor.GetProperty().SetOpacity(0.5)
self.vmtkRenderer.Renderer.AddActor(self.Actor)
if self.ReferenceSurface:
mapper2 = vtk.vtkPolyDataMapper()
mapper2.SetInput(self.ReferenceSurface)
mapper2.ScalarVisibilityOff()
self.Actor2 = vtk.vtkActor()
self.Actor2.SetMapper(mapper2)
self.Actor2.GetProperty().SetColor(1.0, 1.0, 1.0)
self.Actor2.GetProperty().SetOpacity(0.5)
self.vmtkRenderer.Renderer.AddActor(self.Actor2)
self.BoxWidget = vtk.vtkBoxWidget()
self.BoxWidget.SetPlaceFactor(1.0)
self.BoxWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.BoxWidget.GetFaceProperty().SetColor(0.6,0.6,0.2)
self.BoxWidget.GetFaceProperty().SetOpacity(0.25)
self.BoxWidget.ScalingEnabledOff()
self.BoxWidget.HandlesOff()
if self.Scaling:
self.BoxWidget.ScalingEnabledOn()
self.BoxWidget.HandlesOn()
self.vmtkRenderer.RegisterScript(self)
self.InputInfo('Use the left-mousebutton to rotate the box \nUse the middle-mouse-button to move the box \nPress space to move the surface to its new postion')
#self.OutputText('Press \'i\' to activate the box widget interactor \n')
#self.OutputText('Use the left-mousebutton to rotate the box \n')
#self.OutputText('Use the middle-mouse-button to move the box \n')
#self.OutputText('Press space to move the surface to its new postion \n')
#self.OutputText('Press \'q\' to quit and apply the transform \n')
self.vmtkRenderer.AddKeyBinding('space','Move the surface.',self.MoveCallback)
self.vmtkRenderer.AddKeyBinding('i','Interact.',self.InteractCallback)
self.Display()
self.Surface = self.TransformedSurface
self.Matrix4x4 = self.Transform.GetMatrix()
matrix = self.Matrix4x4
self.MatrixCoefficients = [
matrix.GetElement(0,0), matrix.GetElement(0,1), matrix.GetElement(0,2), matrix.GetElement(0,3),
matrix.GetElement(1,0), matrix.GetElement(1,1), matrix.GetElement(1,2), matrix.GetElement(1,3),
matrix.GetElement(2,0), matrix.GetElement(2,1), matrix.GetElement(2,2), matrix.GetElement(2,3),
matrix.GetElement(3,0), matrix.GetElement(3,1), matrix.GetElement(3,2), matrix.GetElement(3,3)]
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def __init__(self, module_manager):
# call base constructor
ModuleBase.__init__(self, module_manager)
ColourDialogMixin.__init__(
self, module_manager.get_module_view_parent_window())
self._numDataInputs = self.NUM_INPUTS
# use list comprehension to create list keeping track of inputs
self._inputs = [{'Connected' : None, 'inputData' : None,
'vtkActor' : None, 'ipw' : None}
for i in range(self._numDataInputs)]
# then the window containing the renderwindows
self.threedFrame = None
# the renderers corresponding to the render windows
self._threedRenderer = None
self._outline_source = vtk.vtkOutlineSource()
om = vtk.vtkPolyDataMapper()
om.SetInputConnection(self._outline_source.GetOutputPort())
self._outline_actor = vtk.vtkActor()
self._outline_actor.SetMapper(om)
self._cube_axes_actor2d = vtk.vtkCubeAxesActor2D()
self._cube_axes_actor2d.SetFlyModeToOuterEdges()
#self._cube_axes_actor2d.SetFlyModeToClosestTriad()
# use box widget for VOI selection
self._voi_widget = vtk.vtkBoxWidget()
# we want to keep it aligned with the cubic volume, thanks
self._voi_widget.SetRotationEnabled(0)
self._voi_widget.AddObserver('InteractionEvent',
self.voiWidgetInteractionCallback)
self._voi_widget.AddObserver('EndInteractionEvent',
self.voiWidgetEndInteractionCallback)
self._voi_widget.NeedsPlacement = True
# also create the VTK construct for actually extracting VOI from data
#self._extractVOI = vtk.vtkExtractVOI()
self._currentVOI = 6 * [0]
# set the whole UI up!
self._create_window()
# our interactor styles (we could add joystick or something too)
self._cInteractorStyle = vtk.vtkInteractorStyleTrackballCamera()
# set the default
self.threedFrame.threedRWI.SetInteractorStyle(self._cInteractorStyle)
rwi = self.threedFrame.threedRWI
rwi.Unbind(wx.EVT_MOUSEWHEEL)
rwi.Bind(wx.EVT_MOUSEWHEEL, self._handler_mousewheel)
# initialise our sliceDirections, this will also setup the grid and
# bind all slice UI events
self.sliceDirections = sliceDirections(
self, self.controlFrame.sliceGrid)
self.selectedPoints = selectedPoints(
self, self.controlFrame.pointsGrid)
# we now have a wx.ListCtrl, let's abuse it
self._tdObjects = tdObjects(self,
self.controlFrame.objectsListGrid)
self._implicits = implicits(self,
self.controlFrame.implicitsGrid)
# setup orientation widget stuff
# NB NB NB: we switch interaction with this off later
# (InteractiveOff()), thus disabling direct translation and
# scaling. If we DON'T do this, interaction with software
# raycasters are greatly slowed down.
self._orientation_widget = vtk.vtkOrientationMarkerWidget()
self._annotated_cube_actor = aca = vtk.vtkAnnotatedCubeActor()
#aca.TextEdgesOff()
aca.GetXMinusFaceProperty().SetColor(1,0,0)
aca.GetXPlusFaceProperty().SetColor(1,0,0)
aca.GetYMinusFaceProperty().SetColor(0,1,0)
aca.GetYPlusFaceProperty().SetColor(0,1,0)
aca.GetZMinusFaceProperty().SetColor(0,0,1)
aca.GetZPlusFaceProperty().SetColor(0,0,1)
self._axes_actor = vtk.vtkAxesActor()
self._orientation_widget.SetInteractor(
self.threedFrame.threedRWI)
self._orientation_widget.SetOrientationMarker(
self._axes_actor)
self._orientation_widget.On()
# make sure interaction is off; when on, interaction with
# software raycasters is greatly slowed down!
self._orientation_widget.InteractiveOff()
def testBoxWidget(self):
# Demonstrate how to use the vtkBoxWidget.
# This script uses a 3D box widget to define a "clipping box" to clip some
# simple geometry (a mace). Make sure that you hit the "W" key to activate the widget.
# create a sphere source
#
sphere = vtk.vtkSphereSource()
cone = vtk.vtkConeSource()
glyph = vtk.vtkGlyph3D()
glyph.SetInputConnection(sphere.GetOutputPort())
glyph.SetSourceConnection(cone.GetOutputPort())
glyph.SetVectorModeToUseNormal()
glyph.SetScaleModeToScaleByVector()
glyph.SetScaleFactor(0.25)
apd = vtk.vtkAppendPolyData()
apd.AddInputConnection(glyph.GetOutputPort())
apd.AddInputConnection(sphere.GetOutputPort())
maceMapper = vtk.vtkPolyDataMapper()
maceMapper.SetInputConnection(apd.GetOutputPort())
maceActor = vtk.vtkLODActor()
maceActor.SetMapper(maceMapper)
maceActor.VisibilityOn()
planes = vtk.vtkPlanes()
clipper = vtk.vtkClipPolyData()
clipper.SetInputConnection(apd.GetOutputPort())
clipper.SetClipFunction(planes)
clipper.InsideOutOn()
selectMapper = vtk.vtkPolyDataMapper()
selectMapper.SetInputConnection(clipper.GetOutputPort())
selectActor = vtk.vtkLODActor()
selectActor.SetMapper(selectMapper)
selectActor.GetProperty().SetColor(0, 1, 0)
selectActor.VisibilityOff()
selectActor.SetScale(1.01, 1.01, 1.01)
# Create the RenderWindow, Renderer and both Actors
#
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iRen = vtk.vtkRenderWindowInteractor()
iRen.SetRenderWindow(renWin);
boxWidget = vtk.vtkBoxWidget()
boxWidget.SetInteractor(iRen)
ren.AddActor(maceActor)
ren.AddActor(selectActor)
# Add the actors to the renderer, set the background and size
#
ren.SetBackground(0.1, 0.2, 0.4)
renWin.SetSize(300, 300)
def SelectPolygons(widget, event_string):
'''
The callback takes two parameters.
Parameters:
widget - the object that generates the event.
event_string - the event name (which is a string).
'''
boxWidget, selectActor
boxWidget.GetPlanes(planes)
selectActor.VisibilityOn()
# place the interactor initially
boxWidget.SetInputConnection(glyph.GetOutputPort())
boxWidget.PlaceWidget()
boxWidget.AddObserver("EndInteractionEvent", SelectPolygons)
# render and interact with data
renWin.Render()
img_file = "TestBoxWidget.png"
vtk.test.Testing.compareImage(iRen.GetRenderWindow(), vtk.test.Testing.getAbsImagePath(img_file), threshold=25)
vtk.test.Testing.interact()
def addVol(self, data, header=None):
pix_diag = 5.0 / 10.0
img = vtkImageImportFromArray()
img.SetArray(data)
img.ConvertIntToUnsignedShortOn()
'''
Origin and Data spacing setting are essential for a normalized volume rendering of
the DWI image volumes
------- dawdling for a long time for addressing the problem that the volume is too thin
and even resorted to pre-resampling of the DWI volumes
'''
#img.GetImport().SetDataSpacing(0.9375, 0.9375, 4.5200)
img.GetImport().SetDataSpacing(header['pixdim'][1:4])
#img.GetImport().SetDataOrigin(128.0, 128.0, 68.50)
img.GetImport().SetDataOrigin(header['dim'][0] * header['pixdim'][0],
header['dim'][1] * header['pixdim'][1],
header['dim'][2] * header['pixdim'][2])
print img.GetDataExtent()
volMapper = vtk.vtkVolumeRayCastMapper()
compositeFunction = vtk.vtkVolumeRayCastCompositeFunction()
compositeFunction.SetCompositeMethodToInterpolateFirst()
#compositeFunction.SetCompositeMethodToClassifyFirst()
volMapper.SetVolumeRayCastFunction(compositeFunction)
volMapper.SetSampleDistance(pix_diag / 5.0)
volMapper.SetImageSampleDistance(1.0)
volMapper.SetInputConnection(img.GetOutputPort())
# The property describes how the data will look
self.volProperty = volProperty = vtk.vtkVolumeProperty()
volProperty.SetColor(self.color_tf)
volProperty.SetScalarOpacity(self.opacity_tf)
volProperty.SetGradientOpacity(self.opacity_tf)
if self.parent.lighting:
volProperty.ShadeOn()
#volProperty.SetInterpolationTypeToLinear()
volProperty.SetInterpolationTypeToNearest()
volProperty.SetScalarOpacityUnitDistance(pix_diag / 5.0)
vol = vtk.vtkVolume()
vol.SetMapper(volMapper)
vol.SetProperty(volProperty)
self.ren.AddVolume(vol)
boxWidget = vtk.vtkBoxWidget()
boxWidget.SetInteractor(self.parent.m_ui.renderView)
boxWidget.SetPlaceFactor(1.0)
planes = vtk.vtkPlanes()
def ClipVolumeRender(obj, event):
obj.GetPlanes(planes)
volMapper.SetClippingPlanes(planes)
boxWidget.SetInput(img.GetOutput())
boxWidget.PlaceWidget(img.GetOutput().GetBounds())
boxWidget.InsideOutOn()
boxWidget.AddObserver("InteractionEvent", ClipVolumeRender)
outlineProperty = boxWidget.GetOutlineProperty()
outlineProperty.SetRepresentationToWireframe()
outlineProperty.SetAmbient(1.0)
outlineProperty.SetAmbientColor(1, 1, 1)
outlineProperty.SetLineWidth(3)
selectedOutlineProperty = boxWidget.GetSelectedOutlineProperty()
selectedOutlineProperty.SetRepresentationToWireframe()
selectedOutlineProperty.SetAmbient(1.0)
selectedOutlineProperty.SetAmbientColor(1, 0, 0)
selectedOutlineProperty.SetLineWidth(1)
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(img.GetOutputPort())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
self.ren.AddActor(outlineActor)
self.volnum += 1
def segmentFromSeeds(self, images, image_pos_pat, image_ori_pat, seeds, iren, xplane, yplane, zplane):
""" segmentFromSeeds: Extracts VOI from seeds
INPUTS:
=======
images: (vtkImageData) list of Input image to Transform
seeds: vtkPoints list of seeded coordinates from picker
OUTPUTS:
=======
transformed_image (vtkImageData) Transformed imaged mapped to dicom coords frame
transform (vtkTransform) Transform used
"""
for postS in range(1,len(images)):
print "\n Segmenting image post no : %s " % str(postS)
subimage = self.loadDisplay.subImage(images, postS)
# Proceed to build reference frame for display objects based on DICOM coords
[transformed_image, transform_cube] = self.loadDisplay.dicomTransform(subimage, image_pos_pat, image_ori_pat)
# Calculate the center of the volume
transformed_image.UpdateInformation()
print "\nBoxwidget placed..."
#################################################################
# The box widget observes the events invoked by the render window
# interactor. These events come from user interaction in the render
# window.
# Place the interactor initially. The output of the reader is used to
# place the box widget.
self.boxWidget = vtk.vtkBoxWidget()
self.boxWidget.SetInteractor(iren)
self.boxWidget.SetPlaceFactor(1)
self.boxWidget.SetInput(transformed_image)
if( self.boundsPlane_presel != []):
self.boxWidget.PlaceWidget( self.boundsPlane_presel )
# Construct a bounding box around the seeds
init_seedsBounds = [0,0,0,0,0,0]
seeds.GetBounds( init_seedsBounds )
if postS == 1:
# polygonal data --> image stencil:
# create a simple box VOI mask shape using previously found boundsPlane_preselected
VOIStencil = vtk.vtkROIStencilSource()
VOIStencil.SetShapeToBox()
VOIStencil.SetBounds( init_seedsBounds )
VOIStencil.SetInformationInput(transformed_image)
VOIStencil.Update()
# cut the corresponding VOI region and set the background:
extractVOI_imgstenc = vtk.vtkImageStencil()
extractVOI_imgstenc.SetInput(transformed_image)
extractVOI_imgstenc.SetStencil(VOIStencil.GetOutput())
extractVOI_imgstenc.ReverseStencilOff()
extractVOI_imgstenc.SetBackgroundValue(0.0)
extractVOI_imgstenc.Update()
allSeededIm = vtk.vtkImageData()
allSeededIm.DeepCopy( extractVOI_imgstenc.GetOutput() )
# Add some bounding box radius
self.boxWidget.PlaceWidget( init_seedsBounds )
self.boundsPlane_presel = init_seedsBounds
print "seeds.GetBounds"
print init_seedsBounds
self.boxWidget.AddObserver("InteractionEvent", self.SelectPolygons)
self.boxWidget.On()
# turn off planes
xplane.Off()
yplane.Off()
iren.Start()
self.boxWidget.Off()
# polygonal data --> image stencil:
print "\n Create vtkPolyDataToImageStencil with bounds:"
print self.boundsPlane_presel
# create a simple box VOI mask shape using previously found boundsPlane_preselected
VOIStencil = vtk.vtkROIStencilSource()
VOIStencil.SetShapeToBox()
VOIStencil.SetBounds( self.boundsPlane_presel )
VOIStencil.SetInformationInput(transformed_image)
VOIStencil.Update()
# cut the corresponding VOI region and set the background:
extractVOI_imgstenc = vtk.vtkImageStencil()
extractVOI_imgstenc.SetInput(transformed_image)
extractVOI_imgstenc.SetStencil(VOIStencil.GetOutput())
extractVOI_imgstenc.ReverseStencilOff()
extractVOI_imgstenc.SetBackgroundValue(0.0)
extractVOI_imgstenc.Update()
# add subsecuent VOI stencils
addsegROI = vtk.vtkImageMathematics()
addsegROI.SetInput(0, allSeededIm)
addsegROI.SetInput(1, extractVOI_imgstenc.GetOutput())
addsegROI.SetOperationToAdd()
addsegROI.Update()
# turn off the box
allSeededIm = addsegROI.GetOutput()
avegSeededIm = vtk.vtkImageMathematics()
avegSeededIm.SetInput(0, allSeededIm)
avegSeededIm.SetOperationToMultiplyByK()
avegSeededIm.SetConstantK( 0.2 )
avegSeededIm.Update()
# take out average image
finalSeedIm = avegSeededIm.GetOutput()
xplane.SetInput( finalSeedIm )
yplane.SetInput( finalSeedIm )
zplane.SetInput( finalSeedIm )
image_scalar_range = finalSeedIm.GetScalarRange()
lThre = image_scalar_range[0]
uThre = image_scalar_range[1]
print "\n Image Scalar Range:"
print image_scalar_range[0], image_scalar_range[1]
print "Uper thresholding by"
print uThre*0.25
## Display histogram
scalars = finalSeedIm.GetPointData().GetScalars()
np_scalars = vtk_to_numpy(scalars)
pylab.figure()
pylab.hist(np_scalars.flatten(), histtype='bar')
pylab.show()
# Now performed threshold on initialized VOI
# vtkImageThresholdConnectivity will perform a flood fill on an image, given upper and lower pixel intensity
# thresholds. It works similarly to vtkImageThreshold, but also allows the user to set seed points to limit
# the threshold operation to contiguous regions of the image. The filled region, or the "inside", will be passed
# through to the output by default, while the "outside" will be replaced with zeros. The scalar type of the output is the same as the input.
thresh_sub = vtk.vtkImageThresholdConnectivity()
thresh_sub.SetSeedPoints(seeds)
thresh_sub.SetNeighborhoodRadius(3, 3, 2) #The radius of the neighborhood that must be within the threshold values in order for the voxel to be included in the mask. The default radius is zero (one single voxel). The radius is measured in voxels
thresh_sub.SetNeighborhoodFraction(0.10) #The fraction of the neighborhood that must be within the thresholds. The default value is 0.5.
thresh_sub.ThresholdBetween(0.25*uThre, uThre);
thresh_sub.SetInput( finalSeedIm )
thresh_sub.Update()
xplane.SetInput( thresh_sub.GetOutput() )
yplane.SetInput( thresh_sub.GetOutput() )
zplane.SetInput( thresh_sub.GetOutput() )
iren.Start()
# Convert VOIlesion into polygonal struct
VOIlesion_poly = vtk.vtkMarchingCubes()
VOIlesion_poly.SetValue(0,255)
VOIlesion_poly.SetInput(thresh_sub.GetOutput())
VOIlesion_poly.ComputeNormalsOff()
VOIlesion_poly.Update()
# Recalculate num_voxels and vol_lesion on VOI
nvoxels = VOIlesion_poly.GetOutput().GetNumberOfCells()
print "\n Number of Voxels: %d" % nvoxels # After the filter has executed, use GetNumberOfVoxels() to find out how many voxels were filled.
return VOIlesion_poly.GetOutput()
def clip_polydata_by_box(polydata,
point,
tangent,
normal,
binormal,
size=[10, 10, 1]):
"""Clip the input polydata with given box shape and direction
Parameters:
polydata (polydata): Input polydata
point (array): Coordinate of clipping box center
normal (array): Direction tangent of the clipping box (major axis)
normal (array): Direction normal of the clipping box
normal (array): Direction binormal of the clipping box
size (array): Size of the clipping box (default: [10,10,1])
Returns:
vtkPolyData: Clipped polydata
vtkPolyData: Clipping box
vtkPolyData: Clipping plane
"""
# create a clipping box widget
clipWidget = vtk.vtkBoxWidget()
transform = vtk.vtkTransform()
transform.Translate(point)
w = math.atan(
math.sqrt(tangent[0]**2 + tangent[1]**2) / tangent[2]) * 180 / 3.14
transform.RotateWXYZ(w, -tangent[1], tangent[0], 0)
transform.Scale(size)
# print(transform.GetMatrix())
clipBox = vtk.vtkCubeSource()
transformFilter = vtk.vtkTransformPolyDataFilter()
transformFilter.SetInputConnection(clipBox.GetOutputPort())
transformFilter.SetTransform(transform)
transformFilter.Update()
clipBoxPolyData = vtk.vtkPolyData()
clipBoxPolyData.DeepCopy(transformFilter.GetOutput())
clipWidget.SetTransform(transform)
clipFunction = vtk.vtkPlanes()
clipWidget.GetPlanes(clipFunction)
clipper = vtk.vtkClipPolyData()
clipper.SetClipFunction(clipFunction)
clipper.SetInputData(polydata)
clipper.GenerateClippedOutputOn()
clipper.SetValue(0.0)
clipper.Update()
polydata.DeepCopy(clipper.GetOutput())
# clipping plane
point1 = []
point2 = []
origin = []
for i in range(3):
point1.append(point[i] - normal[i] * math.sqrt(2) / 2 * size[0])
point2.append(point[i] + normal[i] * math.sqrt(2) / 2 * size[0])
origin.append(point[i] + binormal[i] * math.sqrt(2) / 2 * size[0])
planeSource = vtk.vtkPlaneSource()
planeSource.SetResolution(10, 10)
planeSource.SetOrigin(origin)
planeSource.SetPoint1(point1)
planeSource.SetPoint2(point2)
planeSource.Update()
clipPlanePolyData = vtk.vtkPolyData()
clipPlanePolyData.DeepCopy(planeSource.GetOutput())
return polydata, clipBoxPolyData, clipPlanePolyData
def addVolumeToRenderer(self,img):
pix_diag = 5.0
self.compositeFunction = vtk.vtkVolumeRayCastCompositeFunction()
self.compositeFunction.SetCompositeMethodToInterpolateFirst()
self.vtkWidget.Render()
self.volMapper = vtk.vtkVolumeRayCastMapper()
self.window.Render()
self.extensions = vtk.vtkOpenGLExtensionManager()
self.extensions.SetRenderWindow(self.window)
self.extensions.Update()
string = self.extensions.GetExtensionsString()
print(self.extensions.GetExtensionsString())
self.volMapper.SetVolumeRayCastFunction(self.compositeFunction)
self.volMapper.SetSampleDistance(pix_diag / 5.0)
self.volMapper.SetInputConnection(img.GetOutputPort())
self.updateColourTransferFunction()
self.updateOpacityTransferFunction()
self.plane = vtk.vtkPlanes()
def ClipVolumeRender(obj, event):
obj.GetPlanes(self.plane)
self.volMapper.SetClippingPlanes(self.plane)
self.boxWidget = vtk.vtkBoxWidget()
self.boxWidget.SetInteractor(self.vtkWidget)
self.boxWidget.SetPlaceFactor(1.0)
self.boxWidget.SetInput(img.GetOutput())
self.boxWidget.PlaceWidget()
self.boxWidget.InsideOutOn()
self.boxWidget.AddObserver("InteractionEvent", ClipVolumeRender)
self.outlineProperty = self.boxWidget.GetOutlineProperty()
self.outlineProperty.SetRepresentationToWireframe()
self.outlineProperty.SetAmbient(1.0)
self.outlineProperty.SetAmbientColor(0, 0, 0)
self.outlineProperty.SetLineWidth(3)
self.selectedOutlineProperty = self.boxWidget.GetSelectedOutlineProperty()
self.selectedOutlineProperty.SetRepresentationToWireframe()
self.selectedOutlineProperty.SetAmbient(1.0)
self.selectedOutlineProperty.SetAmbientColor(1, 0, 0)
self.selectedOutlineProperty.SetLineWidth(3)
self.outline = vtk.vtkOutlineFilter()
self.outline.SetInputConnection(img.GetOutputPort())
self.outlineMapper = vtk.vtkPolyDataMapper()
self.outlineMapper.SetInputConnection(self.outline.GetOutputPort())
self.outlineActor = vtk.vtkActor()
self.outlineActor.SetMapper(self.outlineMapper)
self.vol = vtk.vtkVolume()
self.vol.SetMapper(self.volMapper)
self.vol.SetProperty(self.vtkWidget.volProperty)
self.ren.AddVolume(self.vol)
self.ren.AddActor(self.outlineActor)
self.window.Render()
def buildPipeline(self):
""" execute() -> None
Dispatch the vtkRenderer to the actual rendering widget
"""
texture_ispec = self.getInputSpec( 1 )
xMin, xMax, yMin, yMax, zMin, zMax = self.input().GetWholeExtent()
self.sliceCenter = [ (xMax-xMin)/2, (yMax-yMin)/2, (zMax-zMin)/2 ]
spacing = self.input().GetSpacing()
sx, sy, sz = spacing
# self.input().SetSpacing( sx, sy, 5*sz )
origin = self.input().GetOrigin()
ox, oy, oz = origin
dataType = self.input().GetScalarTypeAsString()
self.setMaxScalarValue( self.input().GetScalarType() )
self.colorByMappedScalars = False
rangeBounds = self.getRangeBounds()
dr = rangeBounds[1] - rangeBounds[0]
range_offset = .2*dr
self.range = [ rangeBounds[0] + range_offset, rangeBounds[1] - range_offset ]
print "Data Type = %s, range = (%f,%f), range bounds = (%f,%f), max_scalar = %s" % ( dataType, self.range[0], self.range[1], rangeBounds[0], rangeBounds[1], self._max_scalar_value )
self.probeFilter = None
textureRange = self.range
if texture_ispec and texture_ispec.input():
self.probeFilter = vtk.vtkProbeFilter()
textureRange = texture_ispec.input().GetScalarRange()
self.probeFilter.SetSource( texture_ispec.input() )
self.generateTexture = True
if (self.surfacePicker == None):
self.surfacePicker = vtk.vtkPointPicker()
self.levelSetFilter = vtk.vtkContourFilter()
self.inputModule().inputToAlgorithm( self.levelSetFilter )
self.clipPlanes = vtk.vtkPlanes()
self.polyClipper = vtk.vtkClipPolyData()
self.polyClipper.SetInputConnection( self.levelSetFilter.GetOutputPort() )
self.polyClipper.SetClipFunction( self.clipPlanes )
self.polyClipper.InsideOutOn()
self.levelSetMapper = vtk.vtkPolyDataMapper()
self.levelSetMapper.SetColorModeToMapScalars()
if ( self.probeFilter == None ):
imageRange = self.getImageValues( self.range )
self.levelSetMapper.SetInputConnection( self.polyClipper.GetOutputPort() )
self.levelSetMapper.SetScalarRange( imageRange[0], imageRange[1] )
else:
self.probeFilter.SetInputConnection( self.polyClipper.GetOutputPort() )
self.levelSetMapper.SetInputConnection( self.probeFilter.GetOutputPort() )
self.levelSetMapper.SetScalarRange( textureRange )
colormapManager = self.getColormapManager( index=1 ) if texture_ispec and texture_ispec.input() else self.getColormapManager()
colormapManager.setAlphaRange ( self.opacityRange )
self.levelSetMapper.SetLookupTable( colormapManager.lut )
self.levelSetMapper.UseLookupTableScalarRangeOn()
self.updateLevels()
# levelSetMapper.SetColorModeToMapScalars()
# levelSetActor = vtk.vtkLODActor()
self.levelSetActor = vtk.vtkLODActor()
# levelSetMapper.ScalarVisibilityOff()
# levelSetActor.SetProperty( self.levelSetProperty )
self.levelSetActor.SetMapper( self.levelSetMapper )
self.cursorActor = vtk.vtkActor()
self.cursorProperty = None
self.cursor = vtk.vtkSphereSource()
self.cursor.SetRadius(2.0)
self.cursor.SetThetaResolution(8)
self.cursor.SetPhiResolution(8)
self.clipper = vtk.vtkBoxWidget()
self.clipper.RotationEnabledOff()
self.clipper.SetPlaceFactor( 1.0 )
self.clipper.AddObserver( 'StartInteractionEvent', self.startClip )
self.clipper.AddObserver( 'EndInteractionEvent', self.executeClip )
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(self.cursor.GetOutput())
self.cursorActor.SetMapper(mapper)
self.createDefaultProperties()
# pointData = self.levelSetFilter.GetOutput().GetPointData()
# pointData.SetScalars( colorLevelData )
# if pd <> None:
# na = pd.GetNumberOfArrays()
# print " ** Dataset has %d arrays. ** " % ( pd.GetNumberOfArrays() )
# for i in range( na ): print " --- Array %d: %s " % ( i, str( pd.GetArrayName(i) ) )
# else: print " ** No point data. "
self.renderer.AddActor( self.levelSetActor )
self.surfacePicker.AddPickList( self.levelSetActor )
self.surfacePicker.PickFromListOn()
self.renderer.AddViewProp(self.cursorActor)
self.cursorActor.SetProperty(self.cursorProperty)
self.renderer.SetBackground( VTK_BACKGROUND_COLOR[0], VTK_BACKGROUND_COLOR[1], VTK_BACKGROUND_COLOR[2] )
self.set3DOutput()
def Execute(self):
if (self.Surface == None):
self.PrintError('Error: no Surface.')
#if (self.ReferenceSurface == None):
# self.PrintError('Error: no Reference Surface.')
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
if self.Transform == None:
self.Transform = vtk.vtkTransform()
if self.TransformFilter == None:
self.TransformFilter= vtk.vtkTransformPolyDataFilter()
self.TransformFilter.SetInputData(self.Surface)
self.TransformFilter.SetTransform(self.Transform)
self.TransformFilter.Update()
self.TransformedSurface.ShallowCopy(self.TransformFilter.GetOutput())
mapper = vtk.vtkPolyDataMapper()
mapper.SetInputData(self.TransformedSurface)
mapper.ScalarVisibilityOff()
self.Actor = vtk.vtkActor()
self.Actor.SetMapper(mapper)
self.Actor.GetProperty().SetColor(1.0, 0.1, 0.1)
#self.Actor.GetProperty().SetOpacity(0.5)
self.vmtkRenderer.Renderer.AddActor(self.Actor)
if self.ReferenceSurface:
mapper2 = vtk.vtkPolyDataMapper()
mapper2.SetInputData(self.ReferenceSurface)
mapper2.ScalarVisibilityOff()
self.Actor2 = vtk.vtkActor()
self.Actor2.SetMapper(mapper2)
self.Actor2.GetProperty().SetColor(1.0, 1.0, 1.0)
self.Actor2.GetProperty().SetOpacity(0.5)
self.vmtkRenderer.Renderer.AddActor(self.Actor2)
self.BoxWidget = vtk.vtkBoxWidget()
self.BoxWidget.SetPlaceFactor(1.0)
self.BoxWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.BoxWidget.GetFaceProperty().SetColor(0.6,0.6,0.2)
self.BoxWidget.GetFaceProperty().SetOpacity(0.25)
self.BoxWidget.ScalingEnabledOff()
self.BoxWidget.HandlesOff()
if self.Scaling:
self.BoxWidget.ScalingEnabledOn()
self.BoxWidget.HandlesOn()
self.vmtkRenderer.RegisterScript(self)
self.InputInfo('Use the left-mousebutton to rotate the box \nUse the middle-mouse-button to move the box \nPress space to move the surface to its new postion')
#self.OutputText('Press \'i\' to activate the box widget interactor \n')
#self.OutputText('Use the left-mousebutton to rotate the box \n')
#self.OutputText('Use the middle-mouse-button to move the box \n')
#self.OutputText('Press space to move the surface to its new postion \n')
#self.OutputText('Press \'q\' to quit and apply the transform \n')
self.vmtkRenderer.AddKeyBinding('space','Move the surface.',self.MoveCallback)
self.vmtkRenderer.AddKeyBinding('i','Interact.',self.InteractCallback)
self.Display()
self.Surface = self.TransformedSurface
self.Matrix4x4 = self.Transform.GetMatrix()
matrix = self.Matrix4x4
self.MatrixCoefficients = [
matrix.GetElement(0,0), matrix.GetElement(0,1), matrix.GetElement(0,2), matrix.GetElement(0,3),
matrix.GetElement(1,0), matrix.GetElement(1,1), matrix.GetElement(1,2), matrix.GetElement(1,3),
matrix.GetElement(2,0), matrix.GetElement(2,1), matrix.GetElement(2,2), matrix.GetElement(2,3),
matrix.GetElement(3,0), matrix.GetElement(3,1), matrix.GetElement(3,2), matrix.GetElement(3,3)]
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def addVol(self, data, header=None):
pix_diag = 5.0/10.0
img = vtkImageImportFromArray()
img.SetArray(data)
img.ConvertIntToUnsignedShortOn()
'''
Origin and Data spacing setting are essential for a normalized volume rendering of
the DWI image volumes
------- dawdling for a long time for addressing the problem that the volume is too thin
and even resorted to pre-resampling of the DWI volumes
'''
#img.GetImport().SetDataSpacing(0.9375, 0.9375, 4.5200)
img.GetImport().SetDataSpacing(header['pixdim'][1:4])
#img.GetImport().SetDataOrigin(128.0, 128.0, 68.50)
img.GetImport().SetDataOrigin(
header['dim'][0]*header['pixdim'][0],
header['dim'][1]*header['pixdim'][1],
header['dim'][2]*header['pixdim'][2])
print img.GetDataExtent()
volMapper = vtk.vtkGPUVolumeRayCastMapper()
compositeFunction = vtk.vtkVolumeRayCastCompositeFunction()
compositeFunction.SetCompositeMethodToInterpolateFirst()
#compositeFunction.SetCompositeMethodToClassifyFirst()
#volMapper.SetVolumeRayCastFunction(compositeFunction)
#volMapper.SetSampleDistance(pix_diag / 5.0)
volMapper.SetImageSampleDistance( .5 )
volMapper.SetSampleDistance(1.0)
volMapper.SetInputConnection( img.GetOutputPort() )
volMapper.SetBlendModeToComposite()
# The property describes how the data will look
self.volProperty = volProperty = vtk.vtkVolumeProperty()
volProperty.SetColor(self.color_tf)
volProperty.SetScalarOpacity(self.opacity_tf)
volProperty.SetGradientOpacity(self.opacity_tf)
if self.parent.lighting:
volProperty.ShadeOn()
#volProperty.SetInterpolationTypeToLinear()
volProperty.SetInterpolationTypeToNearest()
volProperty.SetScalarOpacityUnitDistance(pix_diag/5.0)
vol = vtk.vtkVolume()
vol.SetMapper(volMapper)
vol.SetProperty(volProperty)
self.ren.AddVolume(vol)
boxWidget = vtk.vtkBoxWidget()
boxWidget.SetInteractor(self.parent.m_ui.renderView)
boxWidget.SetPlaceFactor(1.0)
planes = vtk.vtkPlanes()
def ClipVolumeRender(obj, event):
obj.GetPlanes(planes)
volMapper.SetClippingPlanes(planes)
boxWidget.SetInput(img.GetOutput())
boxWidget.PlaceWidget(img.GetOutput().GetBounds())
boxWidget.InsideOutOn()
boxWidget.AddObserver("InteractionEvent", ClipVolumeRender)
outlineProperty = boxWidget.GetOutlineProperty()
outlineProperty.SetRepresentationToWireframe()
outlineProperty.SetAmbient(1.0)
outlineProperty.SetAmbientColor(1, 1, 1)
outlineProperty.SetLineWidth(3)
selectedOutlineProperty = boxWidget.GetSelectedOutlineProperty()
selectedOutlineProperty.SetRepresentationToWireframe()
selectedOutlineProperty.SetAmbient(1.0)
selectedOutlineProperty.SetAmbientColor(1, 0, 0)
selectedOutlineProperty.SetLineWidth(1)
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(img.GetOutputPort())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
self.ren.AddActor(outlineActor)
self.volnum += 1
def __init__(self, parent, data_set):
wxVTKRenderWindowInteractor.__init__(self, parent, -1, size=parent.GetSize())
ren = vtk.vtkRenderer()
self.GetRenderWindow().AddRenderer(ren)
# prob should allow a string as data_set also, but for now assume it's a python or numpy array
#img = self.LoadVolumeData(data_set) # load from filename
img = vtkImageImportFromArray()
img.SetArray(data_set)
pix_diag = 5.0
# volMapper = vtk.vtkVolumeTextureMapper3D()
volMapper = vtk.vtkVolumeRayCastMapper()
compositeFunction = vtk.vtkVolumeRayCastCompositeFunction()
compositeFunction.SetCompositeMethodToInterpolateFirst()
volMapper.SetVolumeRayCastFunction(compositeFunction)
volMapper.SetSampleDistance(pix_diag / 5.0)
volMapper.SetInputConnection(img.GetOutputPort())
# Transfer Functions
self.opacity_tf = vtk.vtkPiecewiseFunction()
self.color_tf = vtk.vtkColorTransferFunction()
# The property describes how the data will look
self.volProperty = volProperty = vtk.vtkVolumeProperty()
volProperty.SetColor(self.color_tf)
volProperty.SetScalarOpacity(self.opacity_tf)
volProperty.ShadeOn()
volProperty.SetInterpolationTypeToLinear()
volProperty.SetScalarOpacityUnitDistance(pix_diag)
vol = vtk.vtkVolume()
vol.SetMapper(volMapper)
vol.SetProperty(volProperty)
ren.AddVolume(vol)
boxWidget = vtk.vtkBoxWidget()
boxWidget.SetInteractor(self)
boxWidget.SetPlaceFactor(1.0)
# The implicit function vtkPlanes is used in conjunction with the
# volume ray cast mapper to limit which portion of the volume is
# volume rendered.
planes = vtk.vtkPlanes()
def ClipVolumeRender(obj, event):
obj.GetPlanes(planes)
volMapper.SetClippingPlanes(planes)
# Place the interactor initially. The output of the reader is used to
# place the box widget.
boxWidget.SetInput(img.GetOutput())
boxWidget.PlaceWidget()
boxWidget.InsideOutOn()
boxWidget.AddObserver("InteractionEvent", ClipVolumeRender)
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(img.GetOutputPort())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
outlineProperty = boxWidget.GetOutlineProperty()
outlineProperty.SetRepresentationToWireframe()
outlineProperty.SetAmbient(1.0)
outlineProperty.SetAmbientColor(1, 1, 1)
outlineProperty.SetLineWidth(3)
selectedOutlineProperty = boxWidget.GetSelectedOutlineProperty()
selectedOutlineProperty.SetRepresentationToWireframe()
selectedOutlineProperty.SetAmbient(1.0)
selectedOutlineProperty.SetAmbientColor(1, 0, 0)
selectedOutlineProperty.SetLineWidth(3)
ren.AddActor(outlineActor)
style = vtk.vtkInteractorStyleTrackballCamera()
self.SetInteractorStyle(style)
self.t_graph = TransferGraph(self)
self.SetFocus()
# So we know when new values are added / changed on the tgraph
self.t_graph.Connect(-1, -1, wx.wxEVT_COMMAND_SLIDER_UPDATED,
self.OnTGraphUpdate)
self.OnTGraphUpdate(None)
self.lighting = True
# This is the transfer graph
self.t_graph.Show()
def load_muscleSI_mha(self, T2image, image_pos_pat, image_ori_pat, m_bounds, iren):
""" load_muscleSI: Place automatically a widget over muscle location from file
INPUTS:
=======
images: (vtkImageData) list of Input image to Transform
OUTPUTS:
=======
muscleSI (float) Signal intensity from muscle
muscleSIcoords (float[3]) cords where Signal intensity from muscle is measured
"""
## Transform T2 img
loadDisplay = Display()
# Proceed to build reference frame for display objects based on DICOM coords
t_T2image = loadDisplay.mhaTransform(T2image, image_pos_pat, image_ori_pat)
# Calculate the center of the volume
t_T2image.UpdateInformation()
print "\nBoxwidget placed..."
#################################################################
# The box widget observes the events invoked by the render window
# interactor. These events come from user interaction in the render
# window.
# Place the interactor initially. The output of the reader is used to
# place the box widget.
self.boxWidget = vtk.vtkBoxWidget()
self.boxWidget.SetInteractor(iren)
self.boxWidget.SetPlaceFactor(1)
self.boxWidget.SetInput(t_T2image)
self.boxWidget.ScalingEnabledOff()
self.boxWidget.OutlineCursorWiresOn()
# Construct a bounding box
bwidg = [0,0,0,0,0,0]
bwidg[0] = m_bounds[0]; bwidg[1] = m_bounds[1];
bwidg[2] = m_bounds[2]; bwidg[3] = m_bounds[3];
bwidg[4] = m_bounds[4]; bwidg[5] = m_bounds[5];
self.bounds_muscleSI = bwidg
print "\nbounds_muscleSI "
print self.bounds_muscleSI
# add to visualize
self.boxWidget.PlaceWidget( self.bounds_muscleSI )
self.boxWidget.On()
##########
### Set image stencil for muscle
# create a simple box VOI mask shape using previously found boundsPlane_preselected
VOIStencil = vtk.vtkROIStencilSource()
VOIStencil.SetShapeToBox()
VOIStencil.SetBounds( self.bounds_muscleSI )
VOIStencil.SetInformationInput(t_T2image)
VOIStencil.Update()
# cut the corresponding VOI region and set the background:
extractVOI_imgstenc = vtk.vtkImageStencil()
extractVOI_imgstenc.SetInput(t_T2image)
extractVOI_imgstenc.SetStencil(VOIStencil.GetOutput())
extractVOI_imgstenc.ReverseStencilOff()
extractVOI_imgstenc.SetBackgroundValue(5000)
extractVOI_imgstenc.Update()
# take out average image
finalmuscleSIIm = vtk.vtkImageData()
finalmuscleSIIm = extractVOI_imgstenc.GetOutput()
finalmuscleSIIm.Update()
## Display histogram
dims = finalmuscleSIIm .GetDimensions()
scalars = finalmuscleSIIm.GetPointData().GetScalars()
np_scalars = vtk_to_numpy(scalars)
np_scalars = np_scalars.reshape(dims[2], dims[1], dims[0])
np_scalars = np_scalars.transpose(2,1,0)
muscleSI = np_scalars[np_scalars<5000]
muscle_scalar_range = [muscleSI.min(), muscleSI.max()]
print "\nMuscle scalar Range:"
print muscle_scalar_range[0], muscle_scalar_range[1]
return muscleSI, muscle_scalar_range, self.bounds_muscleSI
def BuildView(self):
# ensure python 2-3 compatibility for checking string type (difference with unicode str handeling)
PY3 = sys.version_info[0] == 3
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
if (self.ArrayName != ''):
self.Image.GetPointData().SetActiveScalars(self.ArrayName)
if PY3:
string_types = str,
else:
string_types = basestring,
if not isinstance(self.VolumeRenderingMethod, string_types):
self.PrintError(
'Specified Rendering Method is not of required "string" type')
# create volume mapper and apply requested volume rendering method
volumeMapper = vtk.vtkSmartVolumeMapper()
if self.VolumeRenderingMethod.lower() == 'default':
volumeMapper.SetRequestedRenderModeToDefault()
elif self.VolumeRenderingMethod.lower() == 'gpu':
volumeMapper.SetRequestedRenderModeToGPU()
elif self.VolumeRenderingMethod.lower() == 'ospray':
volumeMapper.SetRequestedRenderModeToOSPRay()
elif self.VolumeRenderingMethod.lower() == 'raycast':
volumeMapper.SetRequestedRenderModeToRayCast()
else:
self.PrintError(
'Specified Rendering Method: ' + self.VolumeRenderingMethod +
' not supported. Please choose from ["default", "gpu", "ospray", "raycast"]'
)
volumeMapper.SetInputData(self.Image)
volumeMapper.SetBlendModeToComposite()
# parse the xml file which is loaded in the same path as the vmtkimagevolumeviewer.py file at runtime
presetElementTree = ET.parse(
os.path.join(os.path.dirname(__file__), 'share',
'vmtkimagevolumeviewerpresets.xml'))
presetRoot = presetElementTree.getroot()
volProperties = presetRoot.findall(
'VolumeProperty[@name="' + self.Preset +
'"]') # should return a list with only one element
volPropertiesDict = volProperties[0].attrib
def chunks(l, n):
"""Yield successive n-sized chunks from l."""
if PY3:
range_func = range
else:
range_func = xrange
for i in range_func(0, len(l), n):
yield l[i:i + n]
# need to convert the space seperated string displaying values into a list of floats
colorList = [
float(i) for i in volPropertiesDict['colorTransfer'].split()
]
gradientOpacityList = [
float(i) for i in volPropertiesDict['gradientOpacity'].split()
]
opacityList = [
float(i) for i in volPropertiesDict['scalarOpacity'].split()
]
# create an array of arrays with each list split into subarrays of desired size
colorMapList = chunks(colorList, 4)
gradientOpacityMapList = chunks(gradientOpacityList, 2)
opacityMapList = chunks(opacityList, 2)
# create vtk objects from the mapped lists (now arrays of arrays)
self.ColorTransferFunction = self.BuildVTKColorTransferFunction(
colorMapList)
self.GradientOpacityTransferFunction = self.BuildVTKPiecewiseFunction(
gradientOpacityMapList)
self.OpacityTransferFunction = self.BuildVTKPiecewiseFunction(
opacityMapList)
# assign other properties from the element tree to variables with the appropriate type
self.InterpolationType = int(volPropertiesDict['interpolation'])
self.Shade = int(volPropertiesDict['shade'])
self.SpecularPower = float(volPropertiesDict['specularPower'])
self.Specular = float(volPropertiesDict['specular'])
self.Diffuse = float(volPropertiesDict['diffuse'])
self.Ambient = float(volPropertiesDict['ambient'])
# set transfer function and lighting properties of the vtk volume object
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetScalarOpacity(self.OpacityTransferFunction)
volumeProperty.SetGradientOpacity(self.GradientOpacityTransferFunction)
volumeProperty.SetColor(self.ColorTransferFunction)
volumeProperty.SetInterpolationType(self.InterpolationType)
volumeProperty.SetShade(self.Shade)
volumeProperty.SetSpecularPower(self.SpecularPower)
volumeProperty.SetSpecular(self.Specular)
volumeProperty.SetDiffuse(self.Diffuse)
volumeProperty.SetAmbient(self.Ambient)
# create the volume from the mapper (defining image data and render mode) with the defined properties
# this is the last pipeline step applied. self.Volume just needs to now be added to the Renderer
self.Volume = vtk.vtkVolume()
self.Volume.SetMapper(volumeMapper)
self.Volume.SetProperty(volumeProperty)
# add the actors to the renderer
self.vmtkRenderer.Renderer.AddVolume(self.Volume)
# This next section is responsible for creating the box outline around the volume's data extent.
if self.BoxOutline:
outline = vtk.vtkOutlineFilter()
outline.SetInputData(self.Image)
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
# The SetInteractor method is how 3D widgets are associated with the
# render window interactor. Internally, SetInteractor sets up a bunch
# of callbacks using the Command/Observer mechanism (AddObserver()).
boxWidget = vtk.vtkBoxWidget()
boxWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
boxWidget.SetPlaceFactor(1.0)
# Place the interactor initially. The output of the reader is used to
# place the box widget.
boxWidget.SetInputData(self.Image)
boxWidget.PlaceWidget()
boxWidget.InsideOutOn()
# Add the actors to the renderer
self.vmtkRenderer.Renderer.AddActor(outlineActor)
if (self.Display == 1):
self.vmtkRenderer.Render()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
def cutterWidget(obj,
outputname='clipped.vtk',
c=(0.2, 0.2, 1),
alpha=1,
bc=(0.7, 0.8, 1),
legend=None):
'''Pop up a box widget to cut parts of actor. Return largest part.'''
apd = polydata(obj)
planes = vtk.vtkPlanes()
planes.SetBounds(apd.GetBounds())
clipper = vtk.vtkClipPolyData()
setInput(clipper, apd)
clipper.SetClipFunction(planes)
clipper.InsideOutOn()
clipper.GenerateClippedOutputOn()
# check if color string contains a float, in this case ignore alpha
al = colors.getAlpha(c)
if al: alpha = al
act0Mapper = vtk.vtkPolyDataMapper() # the part which stays
act0Mapper.SetInputConnection(clipper.GetOutputPort())
act0 = vtk.vtkActor()
act0.SetMapper(act0Mapper)
act0.GetProperty().SetColor(colors.getColor(c))
act0.GetProperty().SetOpacity(alpha)
backProp = vtk.vtkProperty()
backProp.SetDiffuseColor(colors.getColor(bc))
backProp.SetOpacity(alpha)
act0.SetBackfaceProperty(backProp)
act0.GetProperty().SetInterpolationToFlat()
assignPhysicsMethods(act0)
assignConvenienceMethods(act0, legend)
act1Mapper = vtk.vtkPolyDataMapper() # the part which is cut away
act1Mapper.SetInputConnection(clipper.GetClippedOutputPort())
act1 = vtk.vtkActor()
act1.SetMapper(act1Mapper)
act1.GetProperty().SetColor(colors.getColor(c))
act1.GetProperty().SetOpacity(alpha / 10.)
act1.GetProperty().SetRepresentationToWireframe()
act1.VisibilityOn()
ren = vtk.vtkRenderer()
ren.SetBackground(1, 1, 1)
ren.AddActor(act0)
ren.AddActor(act1)
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
renWin.SetSize(600, 700)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
istyl = vtk.vtkInteractorStyleSwitch()
istyl.SetCurrentStyleToTrackballCamera()
iren.SetInteractorStyle(istyl)
def SelectPolygons(vobj, event):
vobj.GetPlanes(planes)
boxWidget = vtk.vtkBoxWidget()
boxWidget.OutlineCursorWiresOn()
boxWidget.GetSelectedOutlineProperty().SetColor(1, 0, 1)
boxWidget.GetOutlineProperty().SetColor(0.1, 0.1, 0.1)
boxWidget.GetOutlineProperty().SetOpacity(0.8)
boxWidget.SetPlaceFactor(1.05)
boxWidget.SetInteractor(iren)
setInput(boxWidget, apd)
boxWidget.PlaceWidget()
boxWidget.AddObserver("InteractionEvent", SelectPolygons)
boxWidget.On()
colors.printc('\nCutterWidget:\n Move handles to cut parts of the actor',
'm')
colors.printc(' Press q to continue, Escape to exit', 'm')
colors.printc((" Press X to save file to", outputname), 'm')
def cwkeypress(obj, event):
key = obj.GetKeySym()
if key == "q" or key == "space" or key == "Return":
iren.ExitCallback()
elif key == "X":
confilter = vtk.vtkPolyDataConnectivityFilter()
setInput(confilter, clipper.GetOutput())
confilter.SetExtractionModeToLargestRegion()
confilter.Update()
cpd = vtk.vtkCleanPolyData()
setInput(cpd, confilter.GetOutput())
cpd.Update()
w = vtk.vtkPolyDataWriter()
setInput(w, cpd.GetOutput())
w.SetFileName(outputname)
w.Write()
colors.printc("Saved file: " + outputname, 'g')
elif key == "Escape":
exit(0)
iren.Initialize()
iren.AddObserver("KeyPressEvent", cwkeypress)
iren.Start()
boxWidget.Off()
return act0
selectActor.GetProperty().SetColor(0, 1, 0)
selectActor.VisibilityOff()
selectActor.SetScale(1.01, 1.01, 1.01)
# Create the RenderWindow, Renderer and both Actors
ren = vtk.vtkRenderer()
renWin = vtk.vtkRenderWindow()
renWin.AddRenderer(ren)
iren = vtk.vtkRenderWindowInteractor()
iren.SetRenderWindow(renWin)
# The SetInteractor method is how 3D widgets are associated with the
# render window interactor. Internally, SetInteractor sets up a bunch
# of callbacks using the Command/Observer mechanism (AddObserver()).
boxWidget = vtk.vtkBoxWidget()
boxWidget.SetInteractor(iren)
boxWidget.SetPlaceFactor(1.25)
ren.AddActor(maceActor)
ren.AddActor(selectActor)
# Add the actors to the renderer, set the background and size
ren.SetBackground(0.1, 0.2, 0.4)
renWin.SetSize(300, 300)
# This callback funciton does the actual work: updates the vtkPlanes
# implicit function. This in turn causes the pipeline to update.
def SelectPolygons(object, event):
# object will be the boxWidget
def Execute(self):
if self.Surface == None:
self.PrintError('Error: no Surface.')
self.Clipper = vtk.vtkClipPolyData()
self.Clipper.SetInput(self.Surface)
self.Clipper.GenerateClippedOutputOn()
self.Clipper.SetInsideOut(self.InsideOut)
if self.Interactive:
if self.WidgetType == "box":
self.ClipFunction = vtk.vtkPlanes()
elif self.WidgetType == "sphere":
self.ClipFunction = vtk.vtkSphere()
self.Clipper.SetClipFunction(self.ClipFunction)
self.Cutter = vtk.vtkCutter()
self.Cutter.SetInput(self.Surface)
self.Cutter.SetCutFunction(self.ClipFunction)
self.ClippedSurface = vtk.vtkPolyData()
self.CutLines = vtk.vtkPolyData()
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
mapper = vtk.vtkPolyDataMapper()
mapper.SetInput(self.Surface)
mapper.ScalarVisibilityOff()
self.Actor = vtk.vtkActor()
self.Actor.SetMapper(mapper)
self.vmtkRenderer.Renderer.AddActor(self.Actor)
if self.WidgetType == "box":
self.ClipWidget = vtk.vtkBoxWidget()
self.ClipWidget.GetFaceProperty().SetColor(0.6,0.6,0.2)
self.ClipWidget.GetFaceProperty().SetOpacity(0.25)
elif self.WidgetType == "sphere":
self.ClipWidget = vtk.vtkSphereWidget()
self.ClipWidget.GetSphereProperty().SetColor(0.6,0.6,0.2)
self.ClipWidget.GetSphereProperty().SetOpacity(0.25)
self.ClipWidget.GetSelectedSphereProperty().SetColor(0.6,0.0,0.0)
self.ClipWidget.GetSelectedSphereProperty().SetOpacity(0.75)
self.ClipWidget.SetRepresentationToSurface()
self.ClipWidget.SetPhiResolution(20)
self.ClipWidget.SetThetaResolution(20)
self.ClipWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
self.vmtkRenderer.AddKeyBinding('space','Clip.',self.ClipCallback)
self.vmtkRenderer.AddKeyBinding('i','Interact.',self.InteractCallback)
self.Display()
self.Transform = vtk.vtkTransform()
self.ClipWidget.GetTransform(self.Transform)
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
else:
self.Surface.GetPointData().SetActiveScalars(self.ClipArrayName)
self.Clipper.GenerateClipScalarsOff()
self.Clipper.SetValue(self.ClipValue)
self.Clipper.Update()
self.Cutter = vtk.vtkContourFilter()
self.Cutter.SetInput(self.Surface)
self.Cutter.SetValue(0,self.ClipValue)
self.Cutter.Update()
self.Surface = self.Clipper.GetOutput()
self.ClippedSurface = self.Clipper.GetClippedOutput()
self.CutLines = self.Cutter.GetOutput()
if self.CleanOutput == 1:
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInput(self.Surface)
cleaner.Update()
self.Surface = cleaner.GetOutput()
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInput(self.ClippedSurface)
cleaner.Update()
self.ClippedSurface = cleaner.GetOutput()
cleaner = vtk.vtkCleanPolyData()
cleaner.SetInput(self.CutLines)
cleaner.Update()
stripper = vtk.vtkStripper()
stripper.SetInput(cleaner.GetOutput())
stripper.Update()
self.CutLines = stripper.GetOutput()
if self.Surface.GetSource():
self.Surface.GetSource().UnRegisterAllOutputs()
def __init__(self, parent=None):
QtWidgets.QMainWindow.__init__(self, parent)
self.frame = QtWidgets.QFrame()
self.vl = QtWidgets.QVBoxLayout()
self.vtkWidget = QVTKRenderWindowInteractor(self.frame)
self.vl.addWidget(self.vtkWidget)
self.ren = vtk.vtkRenderer()
self.renWin= self.vtkWidget.GetRenderWindow()
self.renWin.AddRenderer(self.ren)
self.iren = self.renWin.GetInteractor()
self.iren.SetRenderWindow(self.renWin)
dicomReader = vtk.vtk.vtkDICOMImageReader()
dicomReader.SetDirectoryName(r'G:\PythonTrainFaile\SE2')#G:\PythonTrainFaile\SE2 F:\sliver_07\segmentation-0.nii
dicomReader.Update()
srange = dicomReader.GetOutput().GetScalarRange()
print(dicomReader.GetOutput().GetDimensions())
min = srange[0]
max = srange[1]
diff = max - min
slope = 4000 / diff
inter = -slope * min
shift = inter / slope
shifter = vtk.vtkImageShiftScale() # 对偏移和比例参数来对图像数据进行操作 数据转换
shifter.SetShift(shift)
shifter.SetScale(slope)
shifter.SetOutputScalarTypeToUnsignedShort()
shifter.SetInputData(dicomReader.GetOutput())
shifter.ReleaseDataFlagOff()
shifter.Update()
print(min, max, slope, inter, shift)
tfun = vtk.vtkPiecewiseFunction() # 梯度不透明度函数
tfun.AddPoint(2000, 0)
tfun.AddPoint(2300.0, 0.3)
tfun.AddPoint(2501.0, 1)
tfun.AddPoint(2600.0, 1)
tfun.AddPoint(2700.0, 1)
tfun.AddPoint(2900.0, 1)
tfun.AddPoint(3024.0, 1)
ctfun = vtk.vtkColorTransferFunction() # 颜色传输函数
ctfun.AddRGBPoint(0.0, 0.5, 0.0, 0.0)
ctfun.AddRGBPoint(600.0, 1.0, 0.5, 0.5)
ctfun.AddRGBPoint(1280.0, 0.9, 0.2, 0.3)
ctfun.AddRGBPoint(1960.0, 0.81, 0.27, 0.1)
ctfun.AddRGBPoint(2200.0, 0.9, 0.2, 0.3)
ctfun.AddRGBPoint(2500.0, 1, 0.5, 0.5)
ctfun.AddRGBPoint(3024.0, 0.5, 0.5, 0.5)
self.volumeMapper = vtk.vtkGPUVolumeRayCastMapper()
self.volumeMapper.SetInputConnection(shifter.GetOutputPort())
volumeProperty = vtk.vtkVolumeProperty()
volumeProperty.SetColor(ctfun)
volumeProperty.SetScalarOpacity(tfun)
volumeProperty.SetInterpolationTypeToLinear()
volumeProperty.ShadeOn()
newvol = vtk.vtkVolume()
newvol.SetMapper(self.volumeMapper)
newvol.SetProperty(volumeProperty)
outline = vtk.vtkOutlineFilter()
outline.SetInputConnection(shifter.GetOutputPort())
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
# Create an actor
boxWidget = vtk.vtkBoxWidget()
boxWidget.SetInteractor(self.iren)
boxWidget.SetPlaceFactor(1.0)
# Add the actors to the renderer, set the background and size
self.ren.AddActor(outlineActor)
self.ren.AddVolume(newvol)
self.ren.SetBackground(0, 0, 0)
self.renWin.SetSize(600, 600)
self.planes = vtk.vtkPlanes()
boxWidget.PlaceWidget()
boxWidget.InsideOutOn()
boxWidget.AddObserver("StartInteractionEvent", self.StartInteraction)
boxWidget.AddObserver("InteractionEvent", self.ClipVolumeRender)
boxWidget.AddObserver("EndInteractionEvent", self.EndInteraction)
outlineProperty = boxWidget.GetOutlineProperty()
outlineProperty.SetRepresentationToWireframe()
outlineProperty.SetAmbient(1.0)
outlineProperty.SetAmbientColor(1, 1, 1)
outlineProperty.SetLineWidth(9)
selectedOutlineProperty = boxWidget.GetSelectedOutlineProperty()
selectedOutlineProperty.SetRepresentationToWireframe()
selectedOutlineProperty.SetAmbient(1.0)
selectedOutlineProperty.SetAmbientColor(1, 0, 0)
selectedOutlineProperty.SetLineWidth(3)
self.ren.ResetCamera()
self.frame.setLayout(self.vl)
self.setCentralWidget(self.frame)
self.show()
self.iren.Initialize()
self.renWin.Render()
self.iren.Start()
def BuildView(self):
# ensure python 2-3 compatibility for checking string type (difference with unicode str handeling)
PY3 = sys.version_info[0] == 3
if not self.vmtkRenderer:
self.vmtkRenderer = vmtkrenderer.vmtkRenderer()
self.vmtkRenderer.Initialize()
self.OwnRenderer = 1
self.vmtkRenderer.RegisterScript(self)
if (self.ArrayName != ''):
self.Image.GetPointData().SetActiveScalars(self.ArrayName)
if PY3:
string_types = str,
else:
string_types = basestring,
if not isinstance(self.VolumeRenderingMethod, string_types):
self.PrintError('Specified Rendering Method is not of required "string" type')
# create volume mapper and apply requested volume rendering method
volumeMapper = vtk.vtkSmartVolumeMapper()
if self.VolumeRenderingMethod.lower() == 'default':
volumeMapper.SetRequestedRenderModeToDefault()
elif self.VolumeRenderingMethod.lower() == 'gpu':
volumeMapper.SetRequestedRenderModeToGPU()
elif self.VolumeRenderingMethod.lower() == 'ospray':
volumeMapper.SetRequestedRenderModeToOSPRay()
elif self.VolumeRenderingMethod.lower() == 'raycast':
volumeMapper.SetRequestedRenderModeToRayCast()
else:
self.PrintError('Specified Rendering Method: ' + self.VolumeRenderingMethod + ' not supported. Please choose from ["default", "gpu", "ospray", "raycast"]')
volumeMapper.SetInputData(self.Image)
volumeMapper.SetBlendModeToComposite()
# create the volume from the mapper (defining image data and render mode) with the defined properties
# this is the last pipeline step applied. self.Volume just needs to now be added to the Renderer
self.SetPresetVolumeProperty()
self.Volume = vtk.vtkVolume()
self.Volume.SetMapper(volumeMapper)
self.Volume.SetProperty(self.VolumeProperty)
# add the actors to the renderer
self.vmtkRenderer.Renderer.AddVolume(self.Volume)
# This next section is responsible for creating the box outline around the volume's data extent.
if self.BoxOutline:
outline = vtk.vtkOutlineFilter()
outline.SetInputData(self.Image)
outlineMapper = vtk.vtkPolyDataMapper()
outlineMapper.SetInputConnection(outline.GetOutputPort())
outlineActor = vtk.vtkActor()
outlineActor.SetMapper(outlineMapper)
# The SetInteractor method is how 3D widgets are associated with the
# render window interactor. Internally, SetInteractor sets up a bunch
# of callbacks using the Command/Observer mechanism (AddObserver()).
boxWidget = vtk.vtkBoxWidget()
boxWidget.SetInteractor(self.vmtkRenderer.RenderWindowInteractor)
boxWidget.SetPlaceFactor(1.0)
# Place the interactor initially. The output of the reader is used to
# place the box widget.
boxWidget.SetInputData(self.Image)
boxWidget.PlaceWidget()
boxWidget.InsideOutOn()
# Add the actors to the renderer
self.vmtkRenderer.Renderer.AddActor(outlineActor)
# add preset callback
self.vmtkRenderer.AddKeyBinding('w','Change volume render property.',self.PresetCallback)
if (self.Display == 1):
self.vmtkRenderer.Render()
if self.OwnRenderer:
self.vmtkRenderer.Deallocate()
