# MedicalDemo3

VTKExamples/Cxx/Medical/MedicalDemo3

### Code

MedicalDemo3.cxx

    // Derived from VTK/Examples/Cxx/Medical3.cxx
    // This example reads a volume dataset, extracts two isosurfaces that
    // represent the skin and bone, creates three orthogonal planes
    // (sagittal, axial, coronal), and displays them.
    //
    #include <vtkRenderer.h>
    #include <vtkRenderWindow.h>
    #include <vtkRenderWindowInteractor.h>
    #include <vtkMetaImageReader.h>
    #include <vtkPolyDataMapper.h>
    #include <vtkActor.h>
    #include <vtkOutlineFilter.h>
    #include <vtkCamera.h>
    #include <vtkStripper.h>
    #include <vtkLookupTable.h>
    #include <vtkImageDataGeometryFilter.h>
    #include <vtkProperty.h>
    #include <vtkMarchingCubes.h>
    #include <vtkImageData.h>
    #include <vtkImageMapToColors.h>
    #include <vtkImageActor.h>
    #include <vtkSmartPointer.h>
    #include <vtkImageMapper3D.h>

    int main (int argc, char *argv[])
    {
      if (argc < 2)
      {
        cout << "Usage: " << argv[0] << " file.mhd" << endl;
        return EXIT_FAILURE;
      }

      // Create the renderer, the render window, and the interactor. The
      // renderer draws into the render window, the interactor enables
      // mouse- and keyboard-based interaction with the data within the
      // render window.
      //
      vtkSmartPointer<vtkRenderer> aRenderer = vtkSmartPointer<vtkRenderer>::New();
      vtkSmartPointer<vtkRenderWindow> renWin =
        vtkSmartPointer<vtkRenderWindow>::New();
      renWin->AddRenderer(aRenderer);
      vtkSmartPointer<vtkRenderWindowInteractor> iren =
        vtkSmartPointer<vtkRenderWindowInteractor>::New();
      iren->SetRenderWindow(renWin);

      // Set a background color for the renderer and set the size of the
      // render window (expressed in pixels).
      aRenderer->SetBackground(.2, .3, .4);
      renWin->SetSize(640, 480);

      // The following reader is used to read a series of 2D slices (images)
      // that compose the volume. The slice dimensions are set, and the
      // pixel spacing. The data Endianness must also be specified. The
      // reader uses the FilePrefix in combination with the slice number to
      // construct filenames using the format FilePrefix.%d. (In this case
      // the FilePrefix is the root name of the file: quarter.)
      vtkSmartPointer<vtkMetaImageReader> reader =
        vtkSmartPointer<vtkMetaImageReader>::New();
      reader->SetFileName (argv[1]);
      reader->Update();

      // An isosurface, or contour value of 500 is known to correspond to
      // the skin of the patient.
      // The triangle stripper is used to create triangle
      // strips from the isosurface; these render much faster on may
      // systems.
      vtkSmartPointer<vtkMarchingCubes> skinExtractor =
        vtkSmartPointer<vtkMarchingCubes>::New();
      skinExtractor->SetInputConnection( reader->GetOutputPort());
      skinExtractor->SetValue(0, 500);
      skinExtractor->Update();

      vtkSmartPointer<vtkStripper> skinStripper =
        vtkSmartPointer<vtkStripper>::New();
      skinStripper->SetInputConnection(skinExtractor->GetOutputPort());
      skinStripper->Update();

      vtkSmartPointer<vtkPolyDataMapper> skinMapper =
        vtkSmartPointer<vtkPolyDataMapper>::New();
      skinMapper->SetInputConnection(skinStripper->GetOutputPort());
      skinMapper->ScalarVisibilityOff();

      vtkSmartPointer<vtkActor> skin =
        vtkSmartPointer<vtkActor>::New();
      skin->SetMapper(skinMapper);
      skin->GetProperty()->SetDiffuseColor(1, .49, .25);
      skin->GetProperty()->SetSpecular(.3);
      skin->GetProperty()->SetSpecularPower(20);

      // An isosurface, or contour value of 1150 is known to correspond to
      // the skin of the patient.
      // The triangle stripper is used to create triangle
      // strips from the isosurface; these render much faster on may
      // systems.
      vtkSmartPointer<vtkMarchingCubes> boneExtractor =
        vtkSmartPointer<vtkMarchingCubes>::New();
      boneExtractor->SetInputConnection(reader->GetOutputPort());
      boneExtractor->SetValue(0, 1150);

      vtkSmartPointer<vtkStripper> boneStripper =
        vtkSmartPointer<vtkStripper>::New();
      boneStripper->SetInputConnection(boneExtractor->GetOutputPort());

      vtkSmartPointer<vtkPolyDataMapper> boneMapper =
        vtkSmartPointer<vtkPolyDataMapper>::New();
      boneMapper->SetInputConnection(boneStripper->GetOutputPort());
      boneMapper->ScalarVisibilityOff();

      vtkSmartPointer<vtkActor> bone =
        vtkSmartPointer<vtkActor>::New();
      bone->SetMapper(boneMapper);
      bone->GetProperty()->SetDiffuseColor(1, 1, .9412);

      // An outline provides context around the data.
      //
      vtkSmartPointer<vtkOutlineFilter> outlineData =
        vtkSmartPointer<vtkOutlineFilter>::New();
      outlineData->SetInputConnection(reader->GetOutputPort());
      outlineData->Update();

      vtkSmartPointer<vtkPolyDataMapper> mapOutline =
        vtkSmartPointer<vtkPolyDataMapper>::New();
      mapOutline->SetInputConnection(outlineData->GetOutputPort());

      vtkSmartPointer<vtkActor> outline =
        vtkSmartPointer<vtkActor>::New();
      outline->SetMapper(mapOutline);
      outline->GetProperty()->SetColor(0,0,0);

      // Now we are creating three orthogonal planes passing through the
      // volume. Each plane uses a different texture map and therefore has
      // different coloration.

      // Start by creating a black/white lookup table.
      vtkSmartPointer<vtkLookupTable> bwLut =
        vtkSmartPointer<vtkLookupTable>::New();
      bwLut->SetTableRange (0, 2000);
      bwLut->SetSaturationRange (0, 0);
      bwLut->SetHueRange (0, 0);
      bwLut->SetValueRange (0, 1);
      bwLut->Build(); //effective built

      // Now create a lookup table that consists of the full hue circle
      // (from HSV).
      vtkSmartPointer<vtkLookupTable> hueLut =
        vtkSmartPointer<vtkLookupTable>::New();
      hueLut->SetTableRange (0, 2000);
      hueLut->SetHueRange (0, 1);
      hueLut->SetSaturationRange (1, 1);
      hueLut->SetValueRange (1, 1);
      hueLut->Build(); //effective built

      // Finally, create a lookup table with a single hue but having a range
      // in the saturation of the hue.
      vtkSmartPointer<vtkLookupTable> satLut =
        vtkSmartPointer<vtkLookupTable>::New();
      satLut->SetTableRange (0, 2000);
      satLut->SetHueRange (.6, .6);
      satLut->SetSaturationRange (0, 1);
      satLut->SetValueRange (1, 1);
      satLut->Build(); //effective built

      // Create the first of the three planes. The filter vtkImageMapToColors
      // maps the data through the corresponding lookup table created above.  The
      // vtkImageActor is a type of vtkProp and conveniently displays an image on
      // a single quadrilateral plane. It does this using texture mapping and as
      // a result is quite fast. (Note: the input image has to be unsigned char
      // values, which the vtkImageMapToColors produces.) Note also that by
      // specifying the DisplayExtent, the pipeline requests data of this extent
      // and the vtkImageMapToColors only processes a slice of data.
      vtkSmartPointer<vtkImageMapToColors> sagittalColors =
        vtkSmartPointer<vtkImageMapToColors>::New();
      sagittalColors->SetInputConnection(reader->GetOutputPort());
      sagittalColors->SetLookupTable(bwLut);
      sagittalColors->Update();

      vtkSmartPointer<vtkImageActor> sagittal =
        vtkSmartPointer<vtkImageActor>::New();
      sagittal->GetMapper()->SetInputConnection(sagittalColors->GetOutputPort());
      sagittal->SetDisplayExtent(128, 128, 0,255, 0,92);

      // Create the second (axial) plane of the three planes. We use the
      // same approach as before except that the extent differs.
      vtkSmartPointer<vtkImageMapToColors> axialColors =
        vtkSmartPointer<vtkImageMapToColors>::New();
      axialColors->SetInputConnection(reader->GetOutputPort());
      axialColors->SetLookupTable(hueLut);
      axialColors->Update();

      vtkSmartPointer<vtkImageActor> axial =
        vtkSmartPointer<vtkImageActor>::New();
      axial->GetMapper()->SetInputConnection(axialColors->GetOutputPort());
      axial->SetDisplayExtent(0,255, 0,255, 46,46);

      // Create the third (coronal) plane of the three planes. We use
      // the same approach as before except that the extent differs.
      vtkSmartPointer<vtkImageMapToColors> coronalColors =
        vtkSmartPointer<vtkImageMapToColors>::New();
      coronalColors->SetInputConnection(reader->GetOutputPort());
      coronalColors->SetLookupTable(satLut);
      coronalColors->Update();

      vtkSmartPointer<vtkImageActor> coronal =
        vtkSmartPointer<vtkImageActor>::New();
      coronal->GetMapper()->SetInputConnection(coronalColors->GetOutputPort());
      coronal->SetDisplayExtent(0,255, 128,128, 0,92);

      // It is convenient to create an initial view of the data. The
      // FocalPoint and Position form a vector direction. Later on
      // (ResetCamera() method) this vector is used to position the camera
      // to look at the data in this direction.
      vtkSmartPointer<vtkCamera> aCamera =
        vtkSmartPointer<vtkCamera>::New();
      aCamera->SetViewUp (0, 0, -1);
      aCamera->SetPosition (0, -1, 0);
      aCamera->SetFocalPoint (0, 0, 0);
      aCamera->ComputeViewPlaneNormal();
      aCamera->Azimuth(30.0);
      aCamera->Elevation(30.0);

      // Actors are added to the renderer.
      aRenderer->AddActor(outline);
      aRenderer->AddActor(sagittal);
      aRenderer->AddActor(axial);
      aRenderer->AddActor(coronal);
      aRenderer->AddActor(skin);
      aRenderer->AddActor(bone);

      // Turn off bone for this example.
      bone->VisibilityOff();

      // Set skin to semi-transparent.
      skin->GetProperty()->SetOpacity(0.5);

      // An initial camera view is created.  The Dolly() method moves
      // the camera towards the FocalPoint, thereby enlarging the image.
      aRenderer->SetActiveCamera(aCamera);

      // Calling Render() directly on a vtkRenderer is strictly forbidden.
      // Only calling Render() on the vtkRenderWindow is a valid call.
      renWin->Render();

      aRenderer->ResetCamera ();
      aCamera->Dolly(1.5);

      // Note that when camera movement occurs (as it does in the Dolly()
      // method), the clipping planes often need adjusting. Clipping planes
      // consist of two planes: near and far along the view direction. The
      // near plane clips out objects in front of the plane; the far plane
      // clips out objects behind the plane. This way only what is drawn
      // between the planes is actually rendered.
      aRenderer->ResetCameraClippingRange ();

      // interact with data
      iren->Initialize();
      iren->Start();

      return EXIT_SUCCESS;
    }

### CMakeLists.txt

    cmake_minimum_required(VERSION 2.8)

    PROJECT(MedicalDemo3)

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

    add_executable(MedicalDemo3 MACOSX_BUNDLE MedicalDemo3.cxx)

    target_link_libraries(MedicalDemo3 ${VTK_LIBRARIES})

### Download and Build MedicalDemo3

Danger

The generation of tar files has not been ported to the new VTKExamples. Some tarballs may be missing or out-of-date.

Click here to download MedicalDemo3 and its CMakeLists.txt file. Once the tarball MedicalDemo3.tar has been downloaded and extracted,

    cd MedicalDemo3/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:

    ./MedicalDemo3

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.