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Attenuation

vtk-examples/Python/ImageProcessing/Attenuation


Description

This MRI image illustrates attenuation that can occur due to sensor position. The artifact is removed by dividing by the attenuation profile determined manually. This histograms shows how the artifact hides information in the form of scalar value clusters.

Other languages

See (Cxx)

Question

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Code

Attenuation.py

#!/usr/bin/env python

"""
"""

import vtk


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

    fileName = get_program_parameters()

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

    cast = vtk.vtkImageCast()
    cast.SetInputConnection(reader.GetOutputPort())
    cast.SetOutputScalarTypeToDouble()

    # Get rid of the discrete scalars.
    smooth = vtk.vtkImageGaussianSmooth()
    smooth.SetInputConnection(cast.GetOutputPort())
    smooth.SetStandardDeviations(0.8, 0.8, 0)

    m1 = vtk.vtkSphere()
    m1.SetCenter(310, 130, 0)
    m1.SetRadius(0)

    m2 = vtk.vtkSampleFunction()
    m2.SetImplicitFunction(m1)
    m2.SetModelBounds(0, 264, 0, 264, 0, 1)
    m2.SetSampleDimensions(264, 264, 1)

    m3 = vtk.vtkImageShiftScale()
    m3.SetInputConnection(m2.GetOutputPort())
    m3.SetScale(0.000095)

    div = vtk.vtkImageMathematics()
    div.SetInputConnection(0, smooth.GetOutputPort())
    div.SetInputConnection(1, m3.GetOutputPort())
    div.SetOperationToMultiply()

    # Create the actors.
    colorWindow = 256.0
    colorLevel = 127.5
    originalActor = vtk.vtkImageActor()
    originalActor.GetMapper().SetInputConnection(cast.GetOutputPort())
    originalActor.GetProperty().SetColorWindow(colorWindow)
    originalActor.GetProperty().SetColorLevel(colorLevel)

    filteredActor = vtk.vtkImageActor()
    filteredActor.GetMapper().SetInputConnection(div.GetOutputPort())

    # Define the viewport ranges.
    # (xmin, ymin, xmax, ymax)
    originalViewport = [0.0, 0.0, 0.5, 1.0]
    filteredViewport = [0.5, 0.0, 1.0, 1.0]

    # Setup the renderers.
    originalRenderer = vtk.vtkRenderer()
    originalRenderer.SetViewport(originalViewport)
    originalRenderer.AddActor(originalActor)
    originalRenderer.ResetCamera()
    originalRenderer.SetBackground(colors.GetColor3d("SlateGray"))

    filteredRenderer = vtk.vtkRenderer()
    filteredRenderer.SetViewport(filteredViewport)
    filteredRenderer.AddActor(filteredActor)
    filteredRenderer.ResetCamera()
    filteredRenderer.SetBackground(colors.GetColor3d("LightSlateGray"))

    renderWindow = vtk.vtkRenderWindow()
    renderWindow.SetSize(600, 300)
    renderWindow.AddRenderer(originalRenderer)
    renderWindow.AddRenderer(filteredRenderer)
    renderWindow.SetWindowName('Attenuation')

    renderWindowInteractor = vtk.vtkRenderWindowInteractor()
    style = vtk.vtkInteractorStyleImage()

    renderWindowInteractor.SetInteractorStyle(style)

    renderWindowInteractor.SetRenderWindow(renderWindow)
    renderWindowInteractor.Initialize()

    renderWindowInteractor.Start()


def get_program_parameters():
    import argparse
    description = 'This MRI image illustrates attenuation that can occur due to sensor position.'
    epilogue = '''
    The artifact is removed by dividing by the attenuation profile determined manually.
    '''
    parser = argparse.ArgumentParser(description=description, epilog=epilogue,
                                     formatter_class=argparse.RawDescriptionHelpFormatter)
    parser.add_argument('filename', help='AttenuationArtifact.pgm.')
    args = parser.parse_args()
    return args.filename


if __name__ == '__main__':
    main()