# GenerateCubesFromLabels

VTKExamples/Cxx/Medical/GenerateCubesFromLabels

### Description

Sometimes it is helpful to view the results of a segmentation without any post processing. This example converts the point data from a labeled volume into cell data. The surfaces are displayed as polydata. If you want to created smoothed polydata models from your segmented volumes, see the example [models from labeled volume data (Discrete MarchingCubes)]]. The input volume must be in [ MetaIO/Documentation| META format].

### Code

GenerateCubesFromLabels.cxx

    //
    // GenerateCubesFromLabels
    //   Usage: GenerateCubesFromLabels InputVolume Startlabel Endlabel
    //          where
    //          InputVolume is a meta file containing a 3 volume of
    //            discrete labels.
    //          StartLabel is the first label to be processed
    //          EndLabel is the last label to be processed
    //          NOTE: There can be gaps in the labeling. If a label does
    //          not exist in the volume, it will be skipped.
    //
    //
    #include <vtkMetaImageReader.h>
    #include <vtkImageAccumulate.h>
    #include <vtkImageWrapPad.h>
    #include <vtkMaskFields.h>
    #include <vtkThreshold.h>
    #include <vtkTransformFilter.h>
    #include <vtkGeometryFilter.h>
    #include <vtkSmartPointer.h>
    #include <vtkTransform.h>
    #include <vtkImageData.h>
    #include <vtkPointData.h>
    #include <vtkCellData.h>
    #include <vtkUnstructuredGrid.h>
    #include <vtkRenderer.h>
    #include <vtkRenderWindow.h>
    #include <vtkRenderWindowInteractor.h>
    #include <vtkPolyDataMapper.h>

    int main (int argc, char *argv[])
    {
      if(argc < 4)
      {
        std::cout << "Usage: " << argv[0] << " InputVolume StartLabel EndLabel" << std::endl;
        return EXIT_FAILURE;
      }

      // Define all of the variables
      unsigned int startLabel = atoi(argv[2]);
      unsigned int endLabel = atoi(argv[3]);

      // Generate cubes from labels
      // 1) Read the meta file
      // 2) Convert point data to cell data
      // 3) Convert to geometry and display

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

      // Pad the volume so that we can change the point data into cell
      // data.
      int *extent = reader->GetOutput()->GetExtent();
      vtkSmartPointer<vtkImageWrapPad> pad =
        vtkSmartPointer<vtkImageWrapPad>::New();
      pad->SetInputConnection(reader->GetOutputPort());
      pad->SetOutputWholeExtent(extent[0], extent[1] + 1,
                                extent[2], extent[3] + 1,
                                extent[4], extent[5] + 1);
      pad->Update();

      // Copy the scalar point data of the volume into the scalar cell data
      pad->GetOutput()->GetCellData()->SetScalars(
        reader->GetOutput()->GetPointData()->GetScalars());

      vtkSmartPointer<vtkThreshold> selector =
        vtkSmartPointer<vtkThreshold>::New();
      selector->SetInputArrayToProcess(0, 0, 0,
                                       vtkDataObject::FIELD_ASSOCIATION_CELLS,
                                       vtkDataSetAttributes::SCALARS);
      selector->SetInputConnection(pad->GetOutputPort());
      selector->ThresholdBetween(startLabel, endLabel);
      selector->Update();

      // Shift the geometry by 1/2
      vtkSmartPointer<vtkTransform> transform =
        vtkSmartPointer<vtkTransform>::New();
      transform->Translate (-.5, -.5, -.5);

      vtkSmartPointer<vtkTransformFilter> transformModel =
        vtkSmartPointer<vtkTransformFilter>::New();
      transformModel->SetTransform(transform);
      transformModel->SetInputConnection(selector->GetOutputPort());

      vtkSmartPointer<vtkGeometryFilter> geometry =
        vtkSmartPointer<vtkGeometryFilter>::New();
      geometry->SetInputConnection(transformModel->GetOutputPort());

      vtkSmartPointer<vtkPolyDataMapper> mapper =
        vtkSmartPointer<vtkPolyDataMapper>::New();
      mapper->SetInputConnection(geometry->GetOutputPort());
      mapper->SetScalarRange(startLabel, endLabel);
      mapper->SetScalarModeToUseCellData();
      mapper->SetColorModeToMapScalars();

      vtkSmartPointer<vtkActor> actor =
        vtkSmartPointer<vtkActor>::New();
      actor->SetMapper(mapper);

      vtkSmartPointer<vtkRenderer> renderer =
        vtkSmartPointer<vtkRenderer>::New();
      vtkSmartPointer<vtkRenderWindow> renderWindow =
        vtkSmartPointer<vtkRenderWindow>::New();
      renderWindow->AddRenderer(renderer);
      vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor =
        vtkSmartPointer<vtkRenderWindowInteractor>::New();
      renderWindowInteractor->SetRenderWindow(renderWindow);

      renderer->AddActor(actor);
      renderer->SetBackground(.1, .2, .3);

      renderWindow->Render();
      renderWindowInteractor->Start();
      return EXIT_SUCCESS;
    }

### CMakeLists.txt

    cmake_minimum_required(VERSION 2.8)

    PROJECT(GenerateCubesFromLabels)

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

    add_executable(GenerateCubesFromLabels MACOSX_BUNDLE GenerateCubesFromLabels.cxx)

    target_link_libraries(GenerateCubesFromLabels ${VTK_LIBRARIES})

### Download and Build GenerateCubesFromLabels

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

    cd GenerateCubesFromLabels/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:

    ./GenerateCubesFromLabels

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