MedicalDemo3

VTKExamples/Python/Medical/MedicalDemo3


Description

Composite image of three planes and translucent skin

Note

This original source code for this example is here.

Code

MedicalDemo3.py

#!/usr/bin/env python

"""
"""

import vtk


def main():
    colors = vtk.vtkNamedColors()

    fileName = get_program_parameters()

    colors.SetColor("SkinColor", [255, 125, 64, 255])
    colors.SetColor("BkgColor", [51, 77, 102, 255])

    # Create the renderer, the render window, and the interactor. The
    # renderer draws into the render window, the interactor enables
    # mouse- and keyboard-based interaction with the data within the
    # render window.
    #
    aRenderer = vtk.vtkRenderer()
    renWin = vtk.vtkRenderWindow()
    renWin.AddRenderer(aRenderer)
    iren = vtk.vtkRenderWindowInteractor()
    iren.SetRenderWindow(renWin)

    # Set a background color for the renderer and set the size of the
    # render window (expressed in pixels).
    aRenderer.SetBackground(colors.GetColor3d("BkgColor"))
    renWin.SetSize(640, 480)

    # The following reader is used to read a series of 2D slices (images)
    # that compose the volume. The slice dimensions are set, and the
    # pixel spacing. The data Endianness must also be specified. The
    # reader uses the FilePrefix in combination with the slice number to
    # construct filenames using the format FilePrefix.%d. (In this case
    # the FilePrefix is the root name of the file: quarter.)
    reader = vtk.vtkMetaImageReader()
    reader.SetFileName(fileName)
    reader.Update()

    # An isosurface, or contour value of 500 is known to correspond to
    # the skin of the patient.
    # The triangle stripper is used to create triangle
    # strips from the isosurface these render much faster on may
    # systems.
    skinExtractor = vtk.vtkMarchingCubes()
    skinExtractor.SetInputConnection(reader.GetOutputPort())
    skinExtractor.SetValue(0, 500)
    skinExtractor.Update()

    skinStripper = vtk.vtkStripper()
    skinStripper.SetInputConnection(skinExtractor.GetOutputPort())
    skinStripper.Update()

    skinMapper = vtk.vtkPolyDataMapper()
    skinMapper.SetInputConnection(skinStripper.GetOutputPort())
    skinMapper.ScalarVisibilityOff()

    skin = vtk.vtkActor()
    skin.SetMapper(skinMapper)
    skin.GetProperty().SetDiffuseColor(colors.GetColor3d("SkinColor"))
    skin.GetProperty().SetSpecular(.3)
    skin.GetProperty().SetSpecularPower(20)

    # An isosurface, or contour value of 1150 is known to correspond to
    # the bone of the patient.
    # The triangle stripper is used to create triangle
    # strips from the isosurface these render much faster on may
    # systems.
    boneExtractor = vtk.vtkMarchingCubes()
    boneExtractor.SetInputConnection(reader.GetOutputPort())
    boneExtractor.SetValue(0, 1150)

    boneStripper = vtk.vtkStripper()
    boneStripper.SetInputConnection(boneExtractor.GetOutputPort())

    boneMapper = vtk.vtkPolyDataMapper()
    boneMapper.SetInputConnection(boneStripper.GetOutputPort())
    boneMapper.ScalarVisibilityOff()

    bone = vtk.vtkActor()
    bone.SetMapper(boneMapper)
    bone.GetProperty().SetDiffuseColor(colors.GetColor3d("Ivory"))

    # An outline provides context around the data.
    #
    outlineData = vtk.vtkOutlineFilter()
    outlineData.SetInputConnection(reader.GetOutputPort())
    outlineData.Update()

    mapOutline = vtk.vtkPolyDataMapper()
    mapOutline.SetInputConnection(outlineData.GetOutputPort())

    outline = vtk.vtkActor()
    outline.SetMapper(mapOutline)
    outline.GetProperty().SetColor(colors.GetColor3d("Black"))

    # Now we are creating three orthogonal planes passing through the
    # volume. Each plane uses a different texture map and therefore has
    # different coloration.

    # Start by creating a black/white lookup table.
    bwLut = vtk.vtkLookupTable()
    bwLut.SetTableRange(0, 2000)
    bwLut.SetSaturationRange(0, 0)
    bwLut.SetHueRange(0, 0)
    bwLut.SetValueRange(0, 1)
    bwLut.Build()  # effective built

    # Now create a lookup table that consists of the full hue circle
    # (from HSV).
    hueLut = vtk.vtkLookupTable()
    hueLut.SetTableRange(0, 2000)
    hueLut.SetHueRange(0, 1)
    hueLut.SetSaturationRange(1, 1)
    hueLut.SetValueRange(1, 1)
    hueLut.Build()  # effective built

    # Finally, create a lookup table with a single hue but having a range
    # in the saturation of the hue.
    satLut = vtk.vtkLookupTable()
    satLut.SetTableRange(0, 2000)
    satLut.SetHueRange(.6, .6)
    satLut.SetSaturationRange(0, 1)
    satLut.SetValueRange(1, 1)
    satLut.Build()  # effective built

    # Create the first of the three planes. The filter vtkImageMapToColors
    # maps the data through the corresponding lookup table created above.  The
    # vtkImageActor is a type of vtkProp and conveniently displays an image on
    # a single quadrilateral plane. It does this using texture mapping and as
    # a result is quite fast. (Note: the input image has to be unsigned char
    # values, which the vtkImageMapToColors produces.) Note also that by
    # specifying the DisplayExtent, the pipeline requests data of this extent
    # and the vtkImageMapToColors only processes a slice of data.
    sagittalColors = vtk.vtkImageMapToColors()
    sagittalColors.SetInputConnection(reader.GetOutputPort())
    sagittalColors.SetLookupTable(bwLut)
    sagittalColors.Update()

    sagittal = vtk.vtkImageActor()
    sagittal.GetMapper().SetInputConnection(sagittalColors.GetOutputPort())
    sagittal.SetDisplayExtent(128, 128, 0, 255, 0, 92)

    # Create the second (axial) plane of the three planes. We use the
    # same approach as before except that the extent differs.
    axialColors = vtk.vtkImageMapToColors()
    axialColors.SetInputConnection(reader.GetOutputPort())
    axialColors.SetLookupTable(hueLut)
    axialColors.Update()

    axial = vtk.vtkImageActor()
    axial.GetMapper().SetInputConnection(axialColors.GetOutputPort())
    axial.SetDisplayExtent(0, 255, 0, 255, 46, 46)

    # Create the third (coronal) plane of the three planes. We use
    # the same approach as before except that the extent differs.
    coronalColors = vtk.vtkImageMapToColors()
    coronalColors.SetInputConnection(reader.GetOutputPort())
    coronalColors.SetLookupTable(satLut)
    coronalColors.Update()

    coronal = vtk.vtkImageActor()
    coronal.GetMapper().SetInputConnection(coronalColors.GetOutputPort())
    coronal.SetDisplayExtent(0, 255, 128, 128, 0, 92)

    # It is convenient to create an initial view of the data. The
    # FocalPoint and Position form a vector direction. Later on
    # (ResetCamera() method) this vector is used to position the camera
    # to look at the data in this direction.
    aCamera = vtk.vtkCamera()
    aCamera.SetViewUp(0, 0, -1)
    aCamera.SetPosition(0, -1, 0)
    aCamera.SetFocalPoint(0, 0, 0)
    aCamera.ComputeViewPlaneNormal()
    aCamera.Azimuth(30.0)
    aCamera.Elevation(30.0)

    # Actors are added to the renderer.
    aRenderer.AddActor(outline)
    aRenderer.AddActor(sagittal)
    aRenderer.AddActor(axial)
    aRenderer.AddActor(coronal)
    aRenderer.AddActor(skin)
    aRenderer.AddActor(bone)

    # Turn off bone for this example.
    bone.VisibilityOff()

    # Set skin to semi-transparent.
    skin.GetProperty().SetOpacity(0.5)

    # An initial camera view is created.  The Dolly() method moves
    # the camera towards the FocalPoint, thereby enlarging the image.
    aRenderer.SetActiveCamera(aCamera)

    # Calling Render() directly on a vtkRenderer is strictly forbidden.
    # Only calling Render() on the vtkRenderWindow is a valid call.
    renWin.Render()

    aRenderer.ResetCamera()
    aCamera.Dolly(1.5)

    # Note that when camera movement occurs (as it does in the Dolly()
    # method), the clipping planes often need adjusting. Clipping planes
    # consist of two planes: near and far along the view direction. The
    # near plane clips out objects in front of the plane; the far plane
    # clips out objects behind the plane. This way only what is drawn
    # between the planes is actually rendered.
    aRenderer.ResetCameraClippingRange()

    # Interact with the data.
    renWin.Render()
    iren.Initialize()
    iren.Start()


def get_program_parameters():
    import argparse
    description = 'The skin and bone is extracted from a CT dataset of the head.'
    epilogue = '''
    Derived from VTK/Examples/Cxx/Medical3.cxx
    This example reads a volume dataset, extracts two isosurfaces that
     represent the skin and bone, creates three orthogonal planes
     (sagittal, axial, coronal), and displays them.
    '''
    parser = argparse.ArgumentParser(description=description, epilog=epilogue,
                                     formatter_class=argparse.RawDescriptionHelpFormatter)
    parser.add_argument('filename', help='FullHead.mhd.')
    args = parser.parse_args()
    return args.filename


if __name__ == '__main__':
    main()