# IdentifyHoles

VTKExamples/Cxx/Meshes/IdentifyHoles

### Description

This example fills the holes in a mesh and then extracts the filled holes as seprate regions.

The example proceeds as follow:

1. Read the polydata.
2. Fill the holes with vtkFillHolesFilter.
3. Create a new polydata that contains the filled holes. To do this we rely on the fact that the fill holes filter stores the original cells first and then adds the new cells that fill the holes. Using vtkCellIterator, we skip the original cells and then continue iterating to obtain the new cells.
4. Use vtkConnectivityFilter on the filled polydata to identify the individual holes.

Note

We have to use vtkConnectivtyFilter and not vtkPolyDataConnectivityFilter since the later does not create RegionIds cell data.

### Code

IdentifyHoles.cxx

    #include <vtkSmartPointer.h>
    #include <vtkFillHolesFilter.h>
    #include <vtkXMLPolyDataReader.h>
    #include <vtkPolyDataNormals.h>
    #include <vtkConnectivityFilter.h>

    #include <vtkRenderWindow.h>
    #include <vtkRenderWindowInteractor.h>
    #include <vtkRenderer.h>
    #include <vtkDataSetMapper.h>
    #include <vtkPolyDataMapper.h>
    #include <vtkActor.h>
    #include <vtkCamera.h>
    #include <vtkProperty.h>

    #include <vtkUnstructuredGrid.h>
    #include <vtkPolyData.h>
    #include <vtkPointData.h>
    #include <vtkCellData.h>

    #include <vtkCellIterator.h>
    #include <vtkGenericCell.h>

    #include <vtkNamedColors.h>

    int main(int argc, char *argv[])
    {
      if (argc < 2)
      {
        std::cout << "Usgae: " << argv[0] << " file.vtp" << std::endl;
        return EXIT_FAILURE;
      }
      vtkSmartPointer<vtkNamedColors> colors =
        vtkSmartPointer<vtkNamedColors>::New();

      vtkSmartPointer<vtkXMLPolyDataReader> reader =
        vtkSmartPointer<vtkXMLPolyDataReader>::New();
      reader->SetFileName(argv[1]);
      reader->Update();

      // Fill the holes
      vtkSmartPointer<vtkFillHolesFilter> fillHoles =
        vtkSmartPointer<vtkFillHolesFilter>::New();
      fillHoles->SetInputConnection(reader->GetOutputPort());
      fillHoles->SetHoleSize(1000.0);

      // Make the triangle winding order consistent
      vtkSmartPointer<vtkPolyDataNormals> normals =
        vtkSmartPointer<vtkPolyDataNormals>::New();
      normals->SetInputConnection(fillHoles->GetOutputPort());
      normals->ConsistencyOn();
      normals->SplittingOff();
      normals->Update();
      normals->GetOutput()->GetPointData()->
        SetNormals(reader->GetOutput()->GetPointData()->GetNormals());

      // How many added cells
      vtkIdType numOriginalCells = reader->GetOutput()->GetNumberOfCells();
      vtkIdType numNewCells = normals->GetOutput()->GetNumberOfCells();

      // Iterate over the original cells
      vtkSmartPointer<vtkCellIterator> it = normals->GetOutput()->NewCellIterator();
      vtkIdType numCells = 0;
      for (it->InitTraversal();
           !it->IsDoneWithTraversal() && numCells < numOriginalCells;
           it->GoToNextCell(), ++numCells)
      {
      }
      std::cout << "Num original: " << numOriginalCells
                << ", Num new: " << numNewCells
                << ", Num added: " << numNewCells - numOriginalCells << std::endl;
      vtkSmartPointer<vtkPolyData> holePolyData =
        vtkSmartPointer<vtkPolyData>::New();
      holePolyData->Allocate(normals->GetOutput(), numNewCells - numOriginalCells);
      holePolyData->SetPoints(normals->GetOutput()->GetPoints());

      vtkSmartPointer<vtkGenericCell> cell =
        vtkSmartPointer<vtkGenericCell>::New();

      // The remaining cells are the new ones from the hole filler
      for (;
           !it->IsDoneWithTraversal();
           it->GoToNextCell(), numCells)
      {
        it->GetCell(cell);
        holePolyData->InsertNextCell(it->GetCellType(), cell->GetPointIds());
      }

      // We have to use ConnectivtyFilter and not
      // PolyDataConnectivityFilter since the later does not create
      // RegionIds cell data.
      vtkSmartPointer<vtkConnectivityFilter> connectivity =
        vtkSmartPointer<vtkConnectivityFilter>::New();
      connectivity->SetInputData(holePolyData);
      connectivity->SetExtractionModeToAllRegions();
      connectivity->ColorRegionsOn();
      connectivity->Update();
      std::cout << "Found "
                << connectivity->GetNumberOfExtractedRegions()
                << " holes" << std::endl;

      // Visualize

      // Create a mapper and actor for the fill polydata
      vtkSmartPointer<vtkDataSetMapper> filledMapper =
        vtkSmartPointer<vtkDataSetMapper>::New();
      filledMapper->SetInputConnection(connectivity->GetOutputPort());
      filledMapper->SetScalarModeToUseCellData();
      filledMapper->SetScalarRange(
        connectivity->GetOutput()->GetCellData()->GetArray("RegionId")->GetRange());
      vtkSmartPointer<vtkActor> filledActor =
        vtkSmartPointer<vtkActor>::New();
      filledActor->SetMapper(filledMapper);
      filledActor->GetProperty()->SetDiffuseColor(
        colors->GetColor3d("Peacock").GetData());

      // Create a mapper and actor for the original polydata
      vtkSmartPointer<vtkPolyDataMapper> originalMapper =
        vtkSmartPointer<vtkPolyDataMapper>::New();
      originalMapper->SetInputConnection(reader->GetOutputPort());

      vtkSmartPointer<vtkProperty> backfaceProp =
        vtkSmartPointer<vtkProperty>::New();
      backfaceProp->SetDiffuseColor(colors->GetColor3d("Banana").GetData());

      vtkSmartPointer<vtkActor> originalActor =
        vtkSmartPointer<vtkActor>::New();
      originalActor->SetMapper(originalMapper);
      originalActor->SetBackfaceProperty(backfaceProp);
      originalActor->GetProperty()->SetDiffuseColor(
        colors->GetColor3d("Flesh").GetData());
      originalActor->GetProperty()->SetRepresentationToWireframe();

      // Create a renderer, render window, and interactor
      vtkSmartPointer<vtkRenderer> renderer =
        vtkSmartPointer<vtkRenderer>::New();

      vtkSmartPointer<vtkRenderWindow> renderWindow =
        vtkSmartPointer<vtkRenderWindow>::New();
      renderWindow->SetSize(512, 512);

      renderWindow->AddRenderer(renderer);

      vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor =
        vtkSmartPointer<vtkRenderWindowInteractor>::New();
      renderWindowInteractor->SetRenderWindow(renderWindow);

      // Add the actor to the scene
      renderer->AddActor(originalActor);
      renderer->AddActor(filledActor);
      renderer->SetBackground(colors->GetColor3d("Burlywood").GetData());

      renderer->GetActiveCamera()->SetPosition(0, -1, 0);
      renderer->GetActiveCamera()->SetFocalPoint(0, 0, 0);
      renderer->GetActiveCamera()->SetViewUp(0, 0, 1);
      renderer->GetActiveCamera()->Azimuth(60);
      renderer->GetActiveCamera()->Elevation(30);

      renderer->ResetCamera();
      // Render and interact
      renderWindow->Render();

      renderWindowInteractor->Start();

      return EXIT_SUCCESS;
    }

### CMakeLists.txt

    cmake_minimum_required(VERSION 3.3 FATAL_ERROR)

    project(IdentifyHoles)

    find_package(VTK COMPONENTS
      vtkCommonColor
      vtkCommonCore
      vtkCommonDataModel
      vtkFiltersCore
      vtkFiltersModeling
      vtkIOXML
      vtkInteractionStyle
      vtkRenderingCore
      vtkRenderingFreeType
      vtkRenderingOpenGL2 QUIET)
    if (NOT VTK_FOUND)
      message("Skipping IdentifyHoles: ${VTK_NOT_FOUND_MESSAGE}")
      return ()
    endif()
    message (STATUS "VTK_VERSION: ${VTK_VERSION}")
    if (VTK_VERSION VERSION_LESS "8.90.0")
      # old system
      include(${VTK_USE_FILE})
      add_executable(IdentifyHoles MACOSX_BUNDLE IdentifyHoles.cxx )
      target_link_libraries(IdentifyHoles PRIVATE ${VTK_LIBRARIES})
    else ()
      # include all components
      add_executable(IdentifyHoles MACOSX_BUNDLE IdentifyHoles.cxx )
      target_link_libraries(IdentifyHoles PRIVATE ${VTK_LIBRARIES})
      # vtk_module_autoinit is needed
      vtk_module_autoinit(
        TARGETS IdentifyHoles
        MODULES ${VTK_LIBRARIES}
        )
    endif ()

### Download and Build IdentifyHoles

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

    cd IdentifyHoles/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:

    ./IdentifyHoles

WINDOWS USERS

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