def VisualizeSegmentation(input_filename, segmentation_filename, window, level,
nThreads, opacity):
# Python 2/3 compatible input
from six.moves import input
# Read input
for filename in [input_filename, segmentation_filename]:
if not os.path.isfile(filename):
os.sys.exit('[ERROR] Cannot find file \"{}\"'.format(filename))
# Set a minimum thread count
nThreads = max(1, nThreads)
# Max/min opacity
opacity = max(0, opacity)
opacity = min(1, opacity)
# Read the input
image_reader = get_vtk_reader(input_filename)
if image_reader is None:
os.sys.exit('[ERROR] Cannot find reader for file \"{}\"'.format(
input_filename))
print('Reading input image ' + input_filename)
image_reader.SetFileName(input_filename)
image_reader.Update()
# Read the segmentation
seg_reader = get_vtk_reader(segmentation_filename)
if seg_reader is None:
os.sys.exit('[ERROR] Cannot find reader for file \"{}\"'.format(
segmentation_filename))
print('Reading input image ' + segmentation_filename)
seg_reader.SetFileName(segmentation_filename)
seg_reader.Update()
# Get scalar range for W/L and padding
image_scalar_range = image_reader.GetOutput().GetScalarRange()
# Determine if we need to autocompute the window/level
if window <= 0:
window = image_scalar_range[1] - image_scalar_range[0]
level = (image_scalar_range[1] + image_scalar_range[0]) / 2
# Get data range
seg_scalar_range = [
int(x) for x in seg_reader.GetOutput().GetScalarRange()
]
if seg_scalar_range[0] < 0:
os.sys.exit(
"Segmentation image \"{}\" has values less than zero which cannot currently be handled. Exiting..."
.format(segmentation_filename))
nLabels = seg_scalar_range[1]
print("Segmented image has {} labels".format(nLabels))
# Setup LUT
segLUT = vtk.vtkLookupTable()
segLUT.SetRange(0, nLabels)
segLUT.SetRampToLinear()
segLUT.SetAlphaRange(1, 1) # Make it slightly transparent
segLUT.Build()
segLUT.SetTableValue(0, 0.0, 0.0, 0.0,
0.0) # Set zero to black, transparent
# Setup input Mapper + Property -> Slice
inputMapper = vtk.vtkImageResliceMapper()
inputMapper.SetInputConnection(image_reader.GetOutputPort())
inputMapper.SliceAtFocalPointOn()
inputMapper.SliceFacesCameraOn()
inputMapper.BorderOn()
inputMapper.SetNumberOfThreads(nThreads)
inputMapper.ResampleToScreenPixelsOn()
inputMapper.StreamingOn()
imageProperty = vtk.vtkImageProperty()
imageProperty.SetColorLevel(level)
imageProperty.SetColorWindow(window)
imageProperty.SetLayerNumber(1)
imageProperty.SetInterpolationTypeToNearest()
inputSlice = vtk.vtkImageSlice()
inputSlice.SetMapper(inputMapper)
inputSlice.SetProperty(imageProperty)
# Setup seg Mapper + Property -> Slice
segImageProperty = vtk.vtkImageProperty()
segImageProperty.SetLookupTable(segLUT)
segImageProperty.UseLookupTableScalarRangeOn()
segImageProperty.SetInterpolationTypeToLinear()
segImageProperty.SetOpacity(opacity)
segImageProperty.SetLayerNumber(2)
segImageProperty.SetInterpolationTypeToNearest()
segMapper = vtk.vtkImageResliceMapper()
segMapper.SetInputConnection(seg_reader.GetOutputPort())
segMapper.SliceAtFocalPointOn()
segMapper.SliceFacesCameraOn()
segMapper.BorderOn()
segMapper.SetNumberOfThreads(nThreads)
segMapper.ResampleToScreenPixelsOn()
segMapper.StreamingOn()
segSlice = vtk.vtkImageSlice()
segSlice.SetProperty(segImageProperty)
segSlice.SetMapper(segMapper)
# Add everything to a vtkImageStack
imageStack = vtk.vtkImageStack()
imageStack.AddImage(inputSlice)
imageStack.AddImage(segSlice)
imageStack.SetActiveLayer(1)
# Create Renderer -> RenderWindow -> RenderWindowInteractor -> InteractorStyle
renderer = vtk.vtkRenderer()
renderer.AddViewProp(imageStack)
renderWindow = vtk.vtkRenderWindow()
renderWindow.AddRenderer(renderer)
interactor = vtk.vtkRenderWindowInteractor()
interactorStyle = vtk.vtkInteractorStyleImage()
interactorStyle.SetInteractionModeToImageSlicing()
interactorStyle.KeyPressActivationOn()
interactor.SetInteractorStyle(interactorStyle)
interactor.SetRenderWindow(renderWindow)
# Add some functionality to switch layers for window/level
def layerSwitcher(obj, event):
if str(interactor.GetKeyCode()) == 'w':
# Print the w/l for the image
print("Image W/L: {w}/{l}".format(w=imageProperty.GetColorWindow(),
l=imageProperty.GetColorLevel()))
elif str(interactor.GetKeyCode()) == 'n':
# Set interpolation to nearest neighbour (good for voxel visualization)
imageProperty.SetInterpolationTypeToNearest()
interactor.Render()
elif str(interactor.GetKeyCode()) == 'c':
# Set interpolation to cubic (makes a better visualization)
imageProperty.SetInterpolationTypeToCubic()
interactor.Render()
elif str(interactor.GetKeyCode()) == 'r':
window = image_scalar_range[1] - image_scalar_range[0]
level = (image_scalar_range[1] + image_scalar_range[0]) / 2
imageProperty.SetColorLevel(level)
imageProperty.SetColorWindow(window)
interactor.Render()
# Add ability to switch between active layers
interactor.AddObserver('KeyPressEvent', layerSwitcher,
-1.0) # Call layerSwitcher as last observer
# Initialize and go
interactor.Initialize()
interactor.Start()
input2Mapper.StreamingOn() image2Property = vtk.vtkImageProperty() image2Property.SetColorLevel(level[1]) image2Property.SetColorWindow(window[1]) image2Property.SetInterpolationTypeToCubic() image2Property.CheckerboardOn() image2Property.SetCheckerboardSpacing(args.divisions) image2Property.SetCheckerboardOffset(0, 1) # offset from image1 checkerboard image2Property.SetLayerNumber(2) input2Slice = vtk.vtkImageSlice() input2Slice.SetMapper(input2Mapper) input2Slice.SetProperty(image2Property) imageStack = vtk.vtkImageStack() imageStack.AddImage(input1Slice) imageStack.AddImage(input2Slice) imageStack.SetActiveLayer(1) # Create Renderer -> RenderWindow -> RenderWindowInteractor -> InteractorStyle renderer = vtk.vtkRenderer() renderer.AddViewProp(imageStack) renderer.ResetCamera() renderWindow = vtk.vtkRenderWindow() renderWindow.AddRenderer(renderer) interactor = vtk.vtkRenderWindowInteractor() interactorStyle = vtk.vtkInteractorStyleImage() interactorStyle.SetInteractionModeToImageSlicing()