# MedicalDemo4

VTKExamples/Python/Medical/MedicalDemo4

### Code

MedicalDemo4.py

    #!/usr/bin/env python

    """
    """

    import vtk

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

        fileName = get_program_parameters()

        bkgColor = map(lambda x: x / 255.0, [51, 77, 102])
        colors.SetColor('BkgColor', *bkgColor)

        # 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 scene.
        ren = vtk.vtkRenderer()
        renWin = vtk.vtkRenderWindow()
        renWin.AddRenderer(ren)
        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)

        # The volume will be displayed by ray-cast alpha compositing.
        # A ray-cast mapper is needed to do the ray-casting.
        volumeMapper = vtk.vtkFixedPointVolumeRayCastMapper()
        volumeMapper.SetInputConnection(reader.GetOutputPort())

        # The color transfer function maps voxel intensities to colors.
        # It is modality-specific, and often anatomy-specific as well.
        # The goal is to one color for flesh (between 500 and 1000)
        # and another color for bone (1150 and over).
        volumeColor = vtk.vtkColorTransferFunction()
        volumeColor.AddRGBPoint(0, 0.0, 0.0, 0.0)
        volumeColor.AddRGBPoint(500, 1.0, 0.5, 0.3)
        volumeColor.AddRGBPoint(1000, 1.0, 0.5, 0.3)
        volumeColor.AddRGBPoint(1150, 1.0, 1.0, 0.9)

        # The opacity transfer function is used to control the opacity
        # of different tissue types.
        volumeScalarOpacity = vtk.vtkPiecewiseFunction()
        volumeScalarOpacity.AddPoint(0, 0.00)
        volumeScalarOpacity.AddPoint(500, 0.15)
        volumeScalarOpacity.AddPoint(1000, 0.15)
        volumeScalarOpacity.AddPoint(1150, 0.85)

        # The gradient opacity function is used to decrease the opacity
        # in the "flat" regions of the volume while maintaining the opacity
        # at the boundaries between tissue types.  The gradient is measured
        # as the amount by which the intensity changes over unit distance.
        # For most medical data, the unit distance is 1mm.
        volumeGradientOpacity = vtk.vtkPiecewiseFunction()
        volumeGradientOpacity.AddPoint(0, 0.0)
        volumeGradientOpacity.AddPoint(90, 0.5)
        volumeGradientOpacity.AddPoint(100, 1.0)

        # The VolumeProperty attaches the color and opacity functions to the
        # volume, and sets other volume properties.  The interpolation should
        # be set to linear to do a high-quality rendering.  The ShadeOn option
        # turns on directional lighting, which will usually enhance the
        # appearance of the volume and make it look more "3D".  However,
        # the quality of the shading depends on how accurately the gradient
        # of the volume can be calculated, and for noisy data the gradient
        # estimation will be very poor.  The impact of the shading can be
        # decreased by increasing the Ambient coefficient while decreasing
        # the Diffuse and Specular coefficient.  To increase the impact
        # of shading, decrease the Ambient and increase the Diffuse and Specular.
        volumeProperty = vtk.vtkVolumeProperty()
        volumeProperty.SetColor(volumeColor)
        volumeProperty.SetScalarOpacity(volumeScalarOpacity)
        volumeProperty.SetGradientOpacity(volumeGradientOpacity)
        volumeProperty.SetInterpolationTypeToLinear()
        volumeProperty.ShadeOn()
        volumeProperty.SetAmbient(0.4)
        volumeProperty.SetDiffuse(0.6)
        volumeProperty.SetSpecular(0.2)

        # The vtkVolume is a vtkProp3D (like a vtkActor) and controls the position
        # and orientation of the volume in world coordinates.
        volume = vtk.vtkVolume()
        volume.SetMapper(volumeMapper)
        volume.SetProperty(volumeProperty)

        # Finally, add the volume to the renderer
        ren.AddViewProp(volume)

        # Set up an initial view of the volume.  The focal point will be the
        # center of the volume, and the camera position will be 400mm to the
        # patient's left (which is our right).
        camera = ren.GetActiveCamera()
        c = volume.GetCenter()
        camera.SetViewUp(0, 0, -1)
        camera.SetPosition(c[0], c[1] - 400, c[2])
        camera.SetFocalPoint(c[0], c[1], c[2])
        camera.Azimuth(30.0)
        camera.Elevation(30.0)

        # Set a background color for the renderer
        ren.SetBackground(colors.GetColor3d("BkgColor"))

        # Increase the size of the render window
        renWin.SetSize(640, 480)

        # Interact with the data.
        iren.Start()

    def get_program_parameters():
        import argparse
        description = 'Read a volume dataset and displays it via volume rendering.'
        epilogue = '''
        Derived from VTK/Examples/Cxx/Medical4.cxx
        '''
        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()