# IsoSubsample

VTKExamples/Python/ImageProcessing/IsoSubsample

### Description

An artifact called aliasing occurs when sub-sampling and is often associated with stair-stepping edges. Sampling theory proves that discrete sampled signals with spacing S, completely describe continuous functions composed of frequencies less than S/2. When a signal is sub-sampled, its capacity to hold high frequency information is reduced. However, the high frequency energy does not disappear. It wraps around the frequency spectrum appearing as a low frequency alias artifact. The solution, which eliminates this artifact, is to low-pass filter before sub-sampling.

Low-pass smoothing reduces the high frequency range of an image that would cause aliasing. The same aliasing phenomena occurs when acquiring data. If a signal from an analog source contains high frequencies, saving the analog data in a discrete form requires sub-sampling that will introduce alias artifacts. For this reason, it is common practice to acquire data at high resolutions,then smooth and subsample to reduce the image to a manageable size.

This example demonstrates aliasing that occurs when a high-frequency signal is sub-sampled. High frequencies appear as low frequency artifacts. The left image is an isosurface of a skull after sub-sampling. The right image used a low-pass filter before sub-sampling to reduce aliasing.

Note

This example uses the FullHead.mhd, FullHead.raw.gz dataset.

### Code

IsoSubsample.py

    #!/usr/bin/env python

    """
    """

    import vtk

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

        colors.SetColor("ActorColor", [235, 235, 235, 255])

        fileName = get_program_parameters()

        # Read the image.
        readerFactory = vtk.vtkImageReader2Factory()
        reader = readerFactory.CreateImageReader2(fileName)
        reader.SetFileName(fileName)
        reader.Update()

        # Smoothed pipeline.
        smooth = vtk.vtkImageGaussianSmooth()
        smooth.SetDimensionality(3)
        smooth.SetInputConnection(reader.GetOutputPort())
        smooth.SetStandardDeviations(1.75, 1.75, 0.0)
        smooth.SetRadiusFactor(2)

        subsampleSmoothed = vtk.vtkImageShrink3D()
        subsampleSmoothed.SetInputConnection(smooth.GetOutputPort())
        subsampleSmoothed.SetShrinkFactors(4, 4, 1)

        isoSmoothed = vtk.vtkImageMarchingCubes()
        isoSmoothed.SetInputConnection(smooth.GetOutputPort())
        isoSmoothed.SetValue(0, 1150)

        isoSmoothedMapper = vtk.vtkPolyDataMapper()
        isoSmoothedMapper.SetInputConnection(isoSmoothed.GetOutputPort())
        isoSmoothedMapper.ScalarVisibilityOff()

        isoSmoothedActor = vtk.vtkActor()
        isoSmoothedActor.SetMapper(isoSmoothedMapper)
        isoSmoothedActor.GetProperty().SetColor(colors.GetColor3d("ActorColor"))

        # Unsmoothed pipeline.
        # Sub sample the data.
        subsample = vtk.vtkImageShrink3D()
        subsample.SetInputConnection(reader.GetOutputPort())
        subsample.SetShrinkFactors(4, 4, 1)

        iso = vtk.vtkImageMarchingCubes()
        iso.SetInputConnection(subsample.GetOutputPort())
        iso.SetValue(0, 1150)

        isoMapper = vtk.vtkPolyDataMapper()
        isoMapper.SetInputConnection(iso.GetOutputPort())
        isoMapper.ScalarVisibilityOff()

        isoActor = vtk.vtkActor()
        isoActor.SetMapper(isoMapper)
        isoActor.GetProperty().SetColor(colors.GetColor3d("ActorColor"))

        # The rendering Pipeline.

        # Setup the render window, renderer, and interactor.
        leftViewport = [0.0, 0.0, 0.5, 1.0]
        rightViewport = [0.5, 0.0, 1.0, 1.0]

        rendererLeft = vtk.vtkRenderer()
        rendererLeft.SetViewport(leftViewport)

        rendererRight = vtk.vtkRenderer()
        rendererRight.SetViewport(rightViewport)

        renderWindow = vtk.vtkRenderWindow()
        renderWindow.AddRenderer(rendererLeft)
        renderWindow.AddRenderer(rendererRight)

        renderWindowInteractor = vtk.vtkRenderWindowInteractor()
        renderWindowInteractor.SetRenderWindow(renderWindow)

        rendererLeft.AddActor(isoActor)
        rendererRight.AddActor(isoSmoothedActor)

        rendererLeft.GetActiveCamera().SetFocalPoint(0.0, 0.0, 0.0)
        rendererLeft.GetActiveCamera().SetPosition(0.0, -1.0, 0.0)
        rendererLeft.GetActiveCamera().SetViewUp(0.0, 0.0, -1.0)
        rendererLeft.ResetCamera()
        rendererLeft.GetActiveCamera().Azimuth(-20.0)
        rendererLeft.GetActiveCamera().Elevation(20.0)
        rendererLeft.ResetCameraClippingRange()

        rendererLeft.SetBackground(colors.GetColor3d("SlateGray"))
        rendererRight.SetBackground(colors.GetColor3d("LightSlateGray"))
        rendererRight.SetActiveCamera(rendererLeft.GetActiveCamera())

        renderWindow.SetSize(640, 480)
        renderWindow.Render()

        renderWindowInteractor.Start()

    def get_program_parameters():
        import argparse
        description = 'This figure demonstrates aliasing that occurs when a high-frequency signal is subsampled.'
        epilogue = '''
        High frequencies appear as low frequency artifacts.
        The left image is an isosurface of a skull after subsampling.
        The right image used a low-pass filter before subsampling to reduce aliasing.
        '''
        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()