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# PineRootDecimation

VTKEx/Python/VisualizationAlgorithms/PineRootDecimation

### Description

Demonstrates how to apply the decimation filter to get a reduced data size and then the connectivity filter to remove noisy isosurfaces. The data is from the root system of a pine tree.

To count the number of triangles in the polydata we do the following:

#### C++

We use a lambda function

    auto NumberofTriangles = [](auto *pd)

#### Python

We just implement:

    def NumberOfTriangles(pd):

within the scope of the calling function.

Other languages

See (Cxx)

Question

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### Code

PineRootDecimation.py

    #!/usr/bin/env python

    import vtk

    def main():
        def NumberOfTriangles(pd):
            """
            Count the number of triangles.
            :param pd: vtkPolyData.
            :return: The number of triangles.
            """
            cells = pd.GetPolys()
            numOfTriangles = 0
            idList = vtk.vtkIdList()
            for i in range(0, cells.GetNumberOfCells()):
                cells.GetNextCell(idList)
                # If a cell has three points it is a triangle.
                if idList.GetNumberOfIds() == 3:
                    numOfTriangles += 1
            return numOfTriangles

        colors = vtk.vtkNamedColors()

        fileName = get_program_parameters()

        # Create the pipeline.
        reader = vtk.vtkMCubesReader()
        reader.SetFileName(fileName)
        reader.FlipNormalsOff()
        reader.Update()
        print("Before Decimation.")
        print("There are: ", NumberOfTriangles(reader.GetOutput()), "triangles")

        deci = vtk.vtkDecimatePro()
        deci.SetInputConnection(reader.GetOutputPort())
        deci.SetTargetReduction(0.9)
        deci.SetAbsoluteError(0.0005)
        deci.MaximumIterations = 6
        deci.SetFeatureAngle(30)
        deci.SetErrorIsAbsolute(1)
        deci.AccumulateErrorOn()
        # deci.SplittingOff()
        deci.Update()
        print("After Decimation.")
        print("There are: ", NumberOfTriangles(deci.GetOutput()), "triangles")

        connect = vtk.vtkConnectivityFilter()
        connect.SetInputConnection(deci.GetOutputPort())
        connect.SetExtractionModeToLargestRegion()
        connect.Update()
        print("After Connectivity.")
        print("There are: ", NumberOfTriangles(connect.GetOutput()), "triangles")

        isoMapper = vtk.vtkDataSetMapper()
        isoMapper.SetInputConnection(connect.GetOutputPort())
        isoMapper.ScalarVisibilityOff()
        isoActor = vtk.vtkActor()
        isoActor.SetMapper(isoMapper)
        isoActor.GetProperty().SetColor(colors.GetColor3d("raw_sienna"))

        #  Get an outline of the data set for context.
        outline = vtk.vtkOutlineFilter()
        outline.SetInputConnection(reader.GetOutputPort())
        outlineMapper = vtk.vtkPolyDataMapper()
        outlineMapper.SetInputConnection(outline.GetOutputPort())
        outlineActor = vtk.vtkActor()
        outlineActor.SetMapper(outlineMapper)
        outlineActor.GetProperty().SetColor(colors.GetColor3d("Black"))

        #  Create the Renderer, RenderWindow and RenderWindowInteractor.
        ren = vtk.vtkRenderer()
        renWin = vtk.vtkRenderWindow()
        renWin.AddRenderer(ren)
        iren = vtk.vtkRenderWindowInteractor()
        iren.SetRenderWindow(renWin)

        # Add the actors to the renderer, set the background and size.
        ren.AddActor(outlineActor)
        ren.AddActor(isoActor)
        ren.SetBackground(1, 1, 1)
        # renWin.SetSize(750, 750)
        renWin.SetSize(512, 512)
        ren.SetBackground(colors.GetColor3d("SlateGray"))

        # render the image

        cam = ren.GetActiveCamera()
        cam.SetFocalPoint(40.6018, 37.2813, 50.1953)
        cam.SetPosition(40.6018, -280.533, 47.0172)
        cam.ComputeViewPlaneNormal()
        cam.SetClippingRange(26.1073, 1305.36)
        cam.SetViewAngle(20.9219)
        cam.SetViewUp(0.0, 0.0, 1.0)

        iren.Initialize()
        renWin.Render()
        iren.Start()

    def get_program_parameters():
        import argparse
        description = 'Applying connectivity and decimation filters to remove noisy isosurfaces and reduce data size.'
        epilogue = '''
            Applying connectivity and decimation filters to remove noisy isosurfaces and reduce data size..

    This example demonstrates how to use the vtkConnectivityFilter and vtkDecimate.

       '''
        parser = argparse.ArgumentParser(description=description, epilog=epilogue,
                                         formatter_class=argparse.RawDescriptionHelpFormatter)
        parser.add_argument('filename', help='pine_root.tri.')
        args = parser.parse_args()
        return args.filename

    if __name__ == '__main__':
        main()