# ViewFrogSkinAndTissue

VTKExamples/Cxx/Visualization/ViewFrogSkinAndTissue

### Code

ViewFrogSkinAndTissue.cxx

    #include <vtkActor.h>
    #include <vtkCamera.h>
    #include <vtkImageGaussianSmooth.h>
    #include <vtkImageThreshold.h>
    #include <vtkLookupTable.h>
    #include <vtkMarchingCubes.h>
    #include <vtkMetaImageReader.h>
    #include <vtkNamedColors.h>
    #include <vtkPolyDataMapper.h>
    #include <vtkPolyDataNormals.h>
    #include <vtkProperty.h>
    #include <vtkRenderWindow.h>
    #include <vtkRenderWindowInteractor.h>
    #include <vtkRenderer.h>
    #include <vtkStripper.h>
    #include <vtkWindowedSincPolyDataFilter.h>

    #include <map>
    #include <vector>
    namespace
    {
    void CreateFrogLut(vtkSmartPointer<vtkLookupTable> &colorLut);
    void CreateFrogActor(std::string fileName,
                         int tissue,
                         vtkSmartPointer<vtkActor> &actor);
    void CreateFrogSkinActor(std::string fileName,
                             vtkSmartPointer<vtkActor> &actor);
    void CreateTissueMap(std::map<std::string, int> &tissueMap);
    }
    int main (int argc, char *argv[])
    {
      std::map<std::string, int> tissueMap;
      CreateTissueMap(tissueMap);

      vtkSmartPointer<vtkLookupTable> colorLut =
        vtkSmartPointer<vtkLookupTable>::New();
      colorLut->SetNumberOfColors(17);
      colorLut->SetTableRange(0, 16);
      colorLut->Build();

      CreateFrogLut(colorLut);

      vtkSmartPointer<vtkNamedColors> colors =
        vtkSmartPointer<vtkNamedColors>::New();
      // Setup render window, renderer, and interactor.
      vtkSmartPointer<vtkRenderer> renderer =
        vtkSmartPointer<vtkRenderer>::New();
      vtkSmartPointer<vtkRenderWindow> renderWindow =
        vtkSmartPointer<vtkRenderWindow>::New();
      renderWindow->AddRenderer(renderer);
      vtkSmartPointer<vtkRenderWindowInteractor> renderWindowInteractor =
        vtkSmartPointer<vtkRenderWindowInteractor>::New();
      renderWindowInteractor->SetRenderWindow(renderWindow);

      vtkSmartPointer<vtkActor> skinActor =
        vtkSmartPointer<vtkActor>::New();
      skinActor->GetProperty()->SetColor(colors->GetColor3d("LimeGreen").GetData());
      skinActor->GetProperty()->SetOpacity(.4);
      CreateFrogSkinActor(argv[1], skinActor);
      renderer->AddActor(skinActor);

      // Use this to ensure that the tissues are selected in this order.
      std::vector<std::string> tissues;
      tissues.push_back("blood");
      tissues.push_back("brain");
      tissues.push_back("duodenum");
      tissues.push_back("eyeRetina");
      tissues.push_back("eyeWhite");
      tissues.push_back("heart");
      tissues.push_back("ileum");
      tissues.push_back("kidney");
      tissues.push_back("intestine");
      tissues.push_back("liver");
      tissues.push_back("lung");
      tissues.push_back("nerve");
      tissues.push_back("skeleton");
      tissues.push_back("spleen");
      tissues.push_back("stomach");

      for (size_t i = 0; i <tissues.size(); ++i)
      {
      vtkSmartPointer<vtkActor> actor =
        vtkSmartPointer<vtkActor>::New();
      actor->GetProperty()->SetDiffuseColor(
        colorLut->GetTableValue(tissueMap[tissues[i]]));
      actor->GetProperty()->SetSpecular(.5);
      actor->GetProperty()->SetSpecularPower(10);
      CreateFrogActor(argv[2], tissueMap[tissues[i]], actor);
      renderer->AddActor(actor);
      std::cout << "Tissue: " << argv[2]
                << ", Label: " << tissueMap[tissues[i]] << std::endl;
      }

      renderer->GetActiveCamera()->SetViewUp(0, 0, -1);
      renderer->GetActiveCamera()->SetPosition(0, -1, 0);

      renderer->GetActiveCamera()->Azimuth(210);
      renderer->GetActiveCamera()->Elevation(30);
      renderer->ResetCamera();
      renderer->ResetCameraClippingRange();
      renderer->GetActiveCamera()->Dolly(1.5);
      renderer->SetBackground(colors->GetColor3d("SlateGray").GetData());

      renderWindow->SetSize(640, 480);
      renderWindow->Render();

      renderWindowInteractor->Start();

      return EXIT_SUCCESS;
    }

    namespace
    {
    void CreateTissueMap(std::map<std::string, int> &tissueMap)
    {
      tissueMap["blood"] = 1;
      tissueMap["brain"] = 2;
      tissueMap["duodenum"] = 3;
      tissueMap["eyeRetina"] = 4;
      tissueMap["eyeWhite"] = 5;
      tissueMap["heart"] = 6;
      tissueMap["ileum"] = 7;
      tissueMap["kidney"] = 8;
      tissueMap["intestine"] = 9;
      tissueMap["liver"] = 10;
      tissueMap["lung"] = 11;
      tissueMap["nerve"] = 12;
      tissueMap["skeleton"] = 13;
      tissueMap["spleen"] = 14;
      tissueMap["stomach"] = 15;
      return;
    }
    void CreateFrogSkinActor(std::string fileName,
                             vtkSmartPointer<vtkActor> &actor)
    {
      vtkSmartPointer<vtkMetaImageReader> reader =
        vtkSmartPointer<vtkMetaImageReader>::New();
      reader->SetFileName(fileName.c_str());
      reader->Update();

      double isoValue = 20.5;
      vtkSmartPointer<vtkMarchingCubes> mcubes =
        vtkSmartPointer<vtkMarchingCubes>::New();
      mcubes->SetInputConnection(reader->GetOutputPort());
      mcubes->ComputeScalarsOff();
      mcubes->ComputeGradientsOff();
      mcubes->ComputeNormalsOff();
      mcubes->SetValue(0, isoValue);

      int smoothingIterations = 5;
      double passBand = 0.001;
      double featureAngle = 60.0;
      vtkSmartPointer<vtkWindowedSincPolyDataFilter> smoother =
        vtkSmartPointer<vtkWindowedSincPolyDataFilter>::New();
      smoother->SetInputConnection(mcubes->GetOutputPort());
      smoother->SetNumberOfIterations(smoothingIterations);
      smoother->BoundarySmoothingOff();
      smoother->FeatureEdgeSmoothingOff();
      smoother->SetFeatureAngle(featureAngle);
      smoother->SetPassBand(passBand);
      smoother->NonManifoldSmoothingOn();
      smoother->NormalizeCoordinatesOn();
      smoother->Update();

      vtkSmartPointer<vtkPolyDataNormals> normals =
        vtkSmartPointer<vtkPolyDataNormals>::New();
      normals->SetInputConnection(smoother->GetOutputPort());
      normals->SetFeatureAngle(featureAngle);

      vtkSmartPointer<vtkStripper> stripper =
        vtkSmartPointer<vtkStripper>::New();
      stripper->SetInputConnection(normals->GetOutputPort());

      vtkSmartPointer<vtkPolyDataMapper> mapper =
        vtkSmartPointer<vtkPolyDataMapper>::New();
      mapper->SetInputConnection(stripper->GetOutputPort());

      actor->SetMapper(mapper);
      return;
    }

    void CreateFrogActor(std::string fileName,
                         int tissue,
                         vtkSmartPointer<vtkActor> &actor)
    {
      vtkSmartPointer<vtkMetaImageReader> reader =
        vtkSmartPointer<vtkMetaImageReader>::New();
      reader->SetFileName(fileName.c_str());
      reader->Update();

      vtkSmartPointer<vtkImageThreshold> selectTissue =
        vtkSmartPointer<vtkImageThreshold>::New();
      selectTissue->ThresholdBetween(tissue, tissue);
      selectTissue->SetInValue(255);
      selectTissue->SetOutValue(0);
      selectTissue->SetInputConnection(reader->GetOutputPort());

      int gaussianRadius = 1;
      double gaussianStandardDeviation = 2.0;
      vtkSmartPointer<vtkImageGaussianSmooth> gaussian =
        vtkSmartPointer<vtkImageGaussianSmooth>::New();
      gaussian->SetStandardDeviations (gaussianStandardDeviation,
                                       gaussianStandardDeviation,
                                       gaussianStandardDeviation);
      gaussian->SetRadiusFactors (gaussianRadius,
                                  gaussianRadius,
                                  gaussianRadius);
      gaussian->SetInputConnection(selectTissue->GetOutputPort());

      double isoValue = 127.5;
      vtkSmartPointer<vtkMarchingCubes> mcubes =
        vtkSmartPointer<vtkMarchingCubes>::New();
      mcubes->SetInputConnection(gaussian->GetOutputPort());
      mcubes->ComputeScalarsOff();
      mcubes->ComputeGradientsOff();
      mcubes->ComputeNormalsOff();
      mcubes->SetValue(0, isoValue);

      int smoothingIterations = 5;
      double passBand = 0.001;
      double featureAngle = 60.0;
      vtkSmartPointer<vtkWindowedSincPolyDataFilter> smoother =
        vtkSmartPointer<vtkWindowedSincPolyDataFilter>::New();
      smoother->SetInputConnection(mcubes->GetOutputPort());
      smoother->SetNumberOfIterations(smoothingIterations);
      smoother->BoundarySmoothingOff();
      smoother->FeatureEdgeSmoothingOff();
      smoother->SetFeatureAngle(featureAngle);
      smoother->SetPassBand(passBand);
      smoother->NonManifoldSmoothingOn();
      smoother->NormalizeCoordinatesOn();
      smoother->Update();

      vtkSmartPointer<vtkPolyDataNormals> normals =
        vtkSmartPointer<vtkPolyDataNormals>::New();
      normals->SetInputConnection(smoother->GetOutputPort());
      normals->SetFeatureAngle(featureAngle);

      vtkSmartPointer<vtkStripper> stripper =
        vtkSmartPointer<vtkStripper>::New();
      stripper->SetInputConnection(normals->GetOutputPort());

      vtkSmartPointer<vtkPolyDataMapper> mapper =
        vtkSmartPointer<vtkPolyDataMapper>::New();
      mapper->SetInputConnection(stripper->GetOutputPort());

      actor->SetMapper(mapper);
      return;
    }

    void CreateFrogLut(vtkSmartPointer<vtkLookupTable> &colorLut)
    {
      vtkSmartPointer<vtkNamedColors> colors =
        vtkSmartPointer<vtkNamedColors>::New();
      colorLut->SetTableValue(0,
                              0, 0, 0, 0);
      colorLut->SetTableValue(1,
                              colors->GetColor4d("salmon").GetData()); //blood
      colorLut->SetTableValue(2,
                              colors->GetColor4d("beige").GetData()); //brain
      colorLut->SetTableValue(3,
                              colors->GetColor4d("orange").GetData()); //duodenum
      colorLut->SetTableValue(4,
                              colors->GetColor4d("misty_rose").GetData()); //eye_retina
      colorLut->SetTableValue(5,
                              colors->GetColor4d("white").GetData()); //eye_white
      colorLut->SetTableValue(6,
                              colors->GetColor4d("tomato").GetData()); //heart
      colorLut->SetTableValue(7,
                              colors->GetColor4d("raspberry").GetData()); //ileum
      colorLut->SetTableValue(8,
                              colors->GetColor4d("banana").GetData()); //kidney
      colorLut->SetTableValue(9,
                              colors->GetColor4d("peru").GetData()); //l_intestine
      colorLut->SetTableValue(10,
                              colors->GetColor4d("pink").GetData()); //liver
      colorLut->SetTableValue(11,
                              colors->GetColor4d("powder_blue").GetData()); //lung
      colorLut->SetTableValue(12,
                              colors->GetColor4d("carrot").GetData()); //nerve
      colorLut->SetTableValue(13,
                              colors->GetColor4d("wheat").GetData()); //skeleton
      colorLut->SetTableValue(14,
                              colors->GetColor4d("violet").GetData()); //spleen
      colorLut->SetTableValue(15,
                              colors->GetColor4d("plum").GetData()); //stomach
    }
    }

### CMakeLists.txt

    cmake_minimum_required(VERSION 2.8)

    PROJECT(ViewFrogSkinAndTissue)

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

    add_executable(ViewFrogSkinAndTissue MACOSX_BUNDLE ViewFrogSkinAndTissue.cxx )

    target_link_libraries(ViewFrogSkinAndTissue ${VTK_LIBRARIES})

### Download and Build ViewFrogSkinAndTissue

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

    cd ViewFrogSkinAndTissue/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:

    ./ViewFrogSkinAndTissue

WINDOWS USERS

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