# PineRootConnectivity

VTKExamples/Python/VisualizationAlgorithms/PineRootConnectivity

### Description

Demonstrates how to apply 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.

### Code

PineRootConnectivity.py

    #!/usr/bin/env python

    import vtk

    def pine_root_connectivity(fileName, noConnectivity):
        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()

        # Create the pipeline.
        reader = vtk.vtkMCubesReader()
        reader.SetFileName(fileName)
        if not noConnectivity:
            reader.Update()
            print("Before Connectivity.")
            print("There are: ", NumberOfTriangles(reader.GetOutput()), "triangles")

        connect = vtk.vtkPolyDataConnectivityFilter()
        connect.SetInputConnection(reader.GetOutputPort())
        connect.SetExtractionModeToLargestRegion()
        if not noConnectivity:
            connect.Update()
            print("After Connectivity.")
            print("There are: ", NumberOfTriangles(connect.GetOutput()), "triangles")

        isoMapper = vtk.vtkPolyDataMapper()
        if noConnectivity:
            isoMapper.SetInputConnection(reader.GetOutputPort())
        else:
            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)
        renWin.SetSize(512, 512)
        ren.SetBackground(colors.GetColor3d("SlateGray"))

        # render the image
        #
        # iren AddObserver UserEvent {wm deiconify .vtkInteract}
        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 main():
        fileName, noConnectivity = get_program_parameters()
        noConnectivity = noConnectivity != 0
        pine_root_connectivity(fileName, noConnectivity)

    def get_program_parameters():
        import argparse
        description = 'Applying connectivity filter to remove noisy isosurfaces.'
        epilogue = '''
            Applying connectivity filter to remove noisy isosurfaces.

    This example demonstrates how to use the vtkConnectivityFilter.
    If the extra parameter 'noConnectivity' is non zero, the connectivity filter will not be used.

       '''
        parser = argparse.ArgumentParser(description=description, epilog=epilogue,
                                         formatter_class=argparse.RawDescriptionHelpFormatter)
        parser.add_argument('filename', help='pine_root.tri.')
        parser.add_argument('noConnectivity', default=0, type=int, nargs='?',
                            help='If non-zero do not use the connectivity filter.')
        args = parser.parse_args()
        return args.filename, args.noConnectivity

    if __name__ == '__main__':
        main()