ViewFrogBoth

#!/usr/bin/env python

"""
"""

import vtk


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

    fileName, tissue = get_program_parameters()

    tissueMap = CreateTissueMap()
    colorLut = CreateFrogLut()

    # Setup render window, renderer, and interactor.
    rendererLeft = vtk.vtkRenderer()
    rendererLeft.SetViewport(0, 0, .5, 1)
    rendererRight = vtk.vtkRenderer()
    rendererRight.SetViewport(.5, 0, 1, 1)
    renderWindow = vtk.vtkRenderWindow()
    renderWindow.AddRenderer(rendererLeft)
    renderWindow.AddRenderer(rendererRight)
    renderWindowInteractor = vtk.vtkRenderWindowInteractor()
    renderWindowInteractor.SetRenderWindow(renderWindow)

    actor = CreateFrogActor(fileName, tissueMap[tissue])
    actor.GetProperty().SetDiffuseColor(colorLut.GetTableValue(tissueMap[tissue])[:3])
    rendererLeft.AddActor(actor)

    actorSmooth = CreateSmoothFrogActor(fileName, tissueMap[tissue])
    actorSmooth.GetProperty().SetDiffuseColor(colorLut.GetTableValue(tissueMap[tissue])[:3])
    actorSmooth.GetProperty().SetDiffuse(1.0)
    actorSmooth.GetProperty().SetSpecular(.5)
    actorSmooth.GetProperty().SetSpecularPower(100)

    rendererRight.AddActor(actorSmooth)

    rendererLeft.ResetCamera()
    rendererLeft.GetActiveCamera().SetViewUp(-1, 0, 0)
    rendererLeft.GetActiveCamera().Azimuth(180)
    rendererLeft.ResetCameraClippingRange()

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

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


def get_program_parameters():
    import argparse
    description = 'The frog’s brain.'
    epilogue = '''
    Model extracted without smoothing (left) and with smoothing (right).
    '''
    parser = argparse.ArgumentParser(description=description, epilog=epilogue,
                                     formatter_class=argparse.RawDescriptionHelpFormatter)
    parser.add_argument('filename', help='frog.mhd.')
    parser.add_argument('tissue', default='brain', nargs='?', help='The tissue to use.')
    args = parser.parse_args()
    return args.filename, args.tissue


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

    colorLut = vtk.vtkLookupTable()
    colorLut.SetNumberOfColors(17)
    colorLut.SetTableRange(0, 16)
    colorLut.Build()

    colorLut.SetTableValue(0, 0, 0, 0, 0)
    colorLut.SetTableValue(1, colors.GetColor4d("salmon"))  # blood
    colorLut.SetTableValue(2, colors.GetColor4d("beige"))  # brain
    colorLut.SetTableValue(3, colors.GetColor4d("orange"))  # duodenum
    colorLut.SetTableValue(4, colors.GetColor4d("misty_rose"))  # eye_retina
    colorLut.SetTableValue(5, colors.GetColor4d("white"))  # eye_white
    colorLut.SetTableValue(6, colors.GetColor4d("tomato"))  # heart
    colorLut.SetTableValue(7, colors.GetColor4d("raspberry"))  # ileum
    colorLut.SetTableValue(8, colors.GetColor4d("banana"))  # kidney
    colorLut.SetTableValue(9, colors.GetColor4d("peru"))  # l_intestine
    colorLut.SetTableValue(10, colors.GetColor4d("pink"))  # liver
    colorLut.SetTableValue(11, colors.GetColor4d("powder_blue"))  # lung
    colorLut.SetTableValue(12, colors.GetColor4d("carrot"))  # nerve
    colorLut.SetTableValue(13, colors.GetColor4d("wheat"))  # skeleton
    colorLut.SetTableValue(14, colors.GetColor4d("violet"))  # spleen
    colorLut.SetTableValue(15, colors.GetColor4d("plum"))  # stomach

    return colorLut


def CreateTissueMap():
    tissueMap = dict()
    tissueMap["blood"] = 1
    tissueMap["brain"] = 2
    tissueMap["duodenum"] = 3
    tissueMap["eyeRetina"] = 4
    tissueMap["eyeWhite"] = 5
    tissueMap["heart"] = 6
    tissueMap["ileum"] = 7
    tissueMap["kidney"] = 8
    tissueMap["intestine"] = 9
    tissueMap["liver"] = 10
    tissueMap["lung"] = 11
    tissueMap["nerve"] = 12
    tissueMap["skeleton"] = 13
    tissueMap["spleen"] = 14
    tissueMap["stomach"] = 15

    return tissueMap


def CreateSmoothFrogActor(fileName, tissue):
    reader = vtk.vtkMetaImageReader()
    reader.SetFileName(fileName)
    reader.Update()

    selectTissue = vtk.vtkImageThreshold()
    selectTissue.ThresholdBetween(tissue, tissue)
    selectTissue.SetInValue(255)
    selectTissue.SetOutValue(0)
    selectTissue.SetInputConnection(reader.GetOutputPort())

    gaussianRadius = 1
    gaussianStandardDeviation = 2.0
    gaussian = vtk.vtkImageGaussianSmooth()
    gaussian.SetStandardDeviations(gaussianStandardDeviation, gaussianStandardDeviation, gaussianStandardDeviation)
    gaussian.SetRadiusFactors(gaussianRadius, gaussianRadius, gaussianRadius)
    gaussian.SetInputConnection(selectTissue.GetOutputPort())

    isoValue = 127.5
    mcubes = vtk.vtkMarchingCubes()
    mcubes.SetInputConnection(gaussian.GetOutputPort())
    mcubes.ComputeScalarsOff()
    mcubes.ComputeGradientsOff()
    mcubes.ComputeNormalsOff()
    mcubes.SetValue(0, isoValue)

    smoothingIterations = 0
    passBand = 0.001
    featureAngle = 60.0
    smoother = vtk.vtkWindowedSincPolyDataFilter()
    smoother.SetInputConnection(mcubes.GetOutputPort())
    smoother.SetNumberOfIterations(smoothingIterations)
    smoother.BoundarySmoothingOff()
    smoother.FeatureEdgeSmoothingOff()
    smoother.SetFeatureAngle(featureAngle)
    smoother.SetPassBand(passBand)
    smoother.NonManifoldSmoothingOn()
    smoother.NormalizeCoordinatesOn()
    smoother.Update()

    normals = vtk.vtkPolyDataNormals()
    normals.SetInputConnection(smoother.GetOutputPort())
    normals.SetFeatureAngle(featureAngle)

    stripper = vtk.vtkStripper()
    stripper.SetInputConnection(normals.GetOutputPort())

    mapper = vtk.vtkPolyDataMapper()
    mapper.SetInputConnection(stripper.GetOutputPort())

    actor = vtk.vtkActor()
    actor.SetMapper(mapper)

    return actor


def CreateFrogActor(fileName, tissue):
    reader = vtk.vtkMetaImageReader()
    reader.SetFileName(fileName)
    reader.Update()

    selectTissue = vtk.vtkImageThreshold()
    selectTissue.ThresholdBetween(tissue, tissue)
    selectTissue.SetInValue(255)
    selectTissue.SetOutValue(0)
    selectTissue.SetInputConnection(reader.GetOutputPort())

    isoValue = 63.5
    mcubes = vtk.vtkMarchingCubes()
    mcubes.SetInputConnection(selectTissue.GetOutputPort())
    mcubes.ComputeScalarsOff()
    mcubes.ComputeGradientsOff()
    mcubes.ComputeNormalsOn()
    mcubes.SetValue(0, isoValue)

    stripper = vtk.vtkStripper()
    stripper.SetInputConnection(mcubes.GetOutputPort())

    mapper = vtk.vtkPolyDataMapper()
    mapper.SetInputConnection(stripper.GetOutputPort())

    actor = vtk.vtkActor()
    actor.SetMapper(mapper)

    return actor


if __name__ == '__main__':
    main()