# PineRootConnectivity

VTKExamples/Cxx/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.cxx

    #include <vtkActor.h>
    #include <vtkCamera.h>
    #include <vtkDataSetMapper.h>
    #include <vtkMCubesReader.h>
    #include <vtkNamedColors.h>
    #include <vtkOutlineFilter.h>
    #include <vtkPolyData.h>
    #include <vtkPolyDataConnectivityFilter.h>
    #include <vtkPolyDataMapper.h>
    #include <vtkProperty.h>
    #include <vtkRenderWindow.h>
    #include <vtkRenderWindowInteractor.h>
    #include <vtkRenderer.h>

    int main(int argc, char* argv[])
    {
      if (argc < 2)
      {
        std::cout << "Usage: " << argv[0] << " filename [noConnectivity]"
                  << std::endl;
        std::cout << "where: filename is pine_root.tri." << std::endl;
        std::cout << "       if noConnectivity is nonzero then the connectivity "
                     "filter is ignored."
                  << std::endl;
        return EXIT_FAILURE;
      }

      /**
      * Count the triangles in the polydata.
      * @param pd: vtkPolyData.
      * @return The number of triangles.
      */
      auto NumberofTriangles = [](vtkPolyData* pd) {
        vtkCellArray* cells = pd->GetPolys();
        vtkIdType npts = 0;
        vtkIdType* pts;
        auto numOfTriangles = 0;
        for (auto i = 0; i < pd->GetNumberOfPolys(); ++i)
        {
          int c = cells->GetNextCell(npts, pts);
          if (c == 0)
          {
            break;
          }
          // If a cell has three points it is a triangle.
          if (npts == 3)
          {
            numOfTriangles++;
          }
        }
        return numOfTriangles;
      };

      std::string fileName = argv[1];
      auto noConnectivity = false;
      if (argc > 2)
      {
        noConnectivity = atoi(argv[2]) != 0;
      }

      vtkSmartPointer<vtkNamedColors> colors =
        vtkSmartPointer<vtkNamedColors>::New();

      // Create the pipeline.
      vtkSmartPointer<vtkMCubesReader> reader =
        vtkSmartPointer<vtkMCubesReader>::New();
      reader->SetFileName(fileName.c_str());
      reader->FlipNormalsOff();
      if (!noConnectivity)
      {
        reader->Update();
        std::cout << "Before Connectivity." << std::endl;
        std::cout << "There are: " << NumberofTriangles(reader->GetOutput())
                  << " triangles." << std::endl;
      }

      vtkSmartPointer<vtkPolyDataConnectivityFilter> connect =
        vtkSmartPointer<vtkPolyDataConnectivityFilter>::New();
      connect->SetInputConnection(reader->GetOutputPort());
      connect->SetExtractionModeToLargestRegion();
      if (!noConnectivity)
      {
        connect->Update();
        std::cout << "After Connectivity." << std::endl;
        // Note the use of vtkPolyData::SafeDownCast here.
        std::cout << "There are: " << NumberofTriangles(vtkPolyData::SafeDownCast(
                                        connect->GetOutput()))
                  << " triangles." << std::endl;
      }

      vtkSmartPointer<vtkDataSetMapper> isoMapper =
        vtkSmartPointer<vtkDataSetMapper>::New();
      if (noConnectivity)
      {
        isoMapper->SetInputConnection(reader->GetOutputPort());
      }
      else
      {
        isoMapper->SetInputConnection(connect->GetOutputPort());
      }
      isoMapper->ScalarVisibilityOff();
      vtkSmartPointer<vtkActor> isoActor = vtkSmartPointer<vtkActor>::New();
      isoActor->SetMapper(isoMapper);
      isoActor->GetProperty()->SetColor(colors->GetColor3d("raw_sienna").GetData());

      // Get an outline of the data set for context.
      vtkSmartPointer<vtkOutlineFilter> outline =
        vtkSmartPointer<vtkOutlineFilter>::New();
      outline->SetInputConnection(reader->GetOutputPort());
      vtkSmartPointer<vtkPolyDataMapper> outlineMapper =
        vtkSmartPointer<vtkPolyDataMapper>::New();
      outlineMapper->SetInputConnection(outline->GetOutputPort());
      vtkSmartPointer<vtkActor> outlineActor = vtkSmartPointer<vtkActor>::New();
      outlineActor->SetMapper(outlineMapper);
      outlineActor->GetProperty()->SetColor(colors->GetColor3d("Black").GetData());

      // Create the Renderer, RenderWindow and RenderWindowInteractor.
      vtkSmartPointer<vtkRenderer> ren = vtkSmartPointer<vtkRenderer>::New();
      vtkSmartPointer<vtkRenderWindow> renWin =
        vtkSmartPointer<vtkRenderWindow>::New();
      renWin->AddRenderer(ren);
      vtkSmartPointer<vtkRenderWindowInteractor> iren =
        vtkSmartPointer<vtkRenderWindowInteractor>::New();
      iren->SetRenderWindow(renWin);

      // Add the actors to the renderer, set the background and size.
      ren->AddActor(outlineActor);
      ren->AddActor(isoActor);
      // renWin->SetSize(750, 750);
      renWin->SetSize(512, 512);
      ren->SetBackground(colors->GetColor3d("SlateGray").GetData());

      vtkCamera* 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();

      return EXIT_SUCCESS;
    }

### CMakeLists.txt

    cmake_minimum_required(VERSION 2.8)

    PROJECT(PineRootConnectivity)

    find_package(VTK REQUIRED)
    include(${VTK_USE_FILE})

    add_executable(PineRootConnectivity MACOSX_BUNDLE PineRootConnectivity.cxx )

    target_link_libraries(PineRootConnectivity ${VTK_LIBRARIES})

### Download and Build PineRootConnectivity

Click here to download PineRootConnectivity and its CMakeLists.txt file. Once the tarball PineRootConnectivity.tar has been downloaded and extracted,

    cd PineRootConnectivity/build

If VTK is installed:

    cmake ..

If VTK is not installed but compiled on your system, you will need to specify the path to your VTK build:

    cmake -DVTK_DIR:PATH=/home/me/vtk_build ..

Build the project:

    make

and run it:

    ./PineRootConnectivity

WINDOWS USERS

Be sure to add the VTK bin directory to your path. This will resolve the VTK dll's at run time.