# MedicalDemo2

VTKExamples/Python/Medical/MedicalDemo2

### Description

Skin and bone isosurfaces.

Note

This original source code for this example is here.

Other Languages

See (Cxx)

### Code

MedicalDemo2.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)

        # 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)

        # 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 many systems.
        skinExtractor = vtk.vtkMarchingCubes()
        skinExtractor.SetInputConnection(reader.GetOutputPort())
        skinExtractor.SetValue(0, 500)

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

        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)
        skin.GetProperty().SetOpacity(.5)

        # 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())

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

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

        # 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. An initial camera view is created.
        # The Dolly() method moves the camera towards the FocalPoint,
        # thereby enlarging the image.
        aRenderer.AddActor(outline)
        aRenderer.AddActor(skin)
        aRenderer.AddActor(bone)
        aRenderer.SetActiveCamera(aCamera)
        aRenderer.ResetCamera()
        aCamera.Dolly(1.5)

        # 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)

        # 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()

        # Initialize the event loop and then start it.
        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/Medical2.cxx
        This example reads a volume dataset, extracts two isosurfaces that
         represent the skin and bone, and then displays it.
        '''
        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()