MedicalDemo4

// Derived from VTK/Examples/Cxx/Medical4.cxx
// This example reads a volume dataset and displays it via volume rendering.
//

#include <vtkCamera.h>
#include <vtkCameraOrientationRepresentation.h>
#include <vtkCameraOrientationWidget.h>
#include <vtkColorTransferFunction.h>
#include <vtkFixedPointVolumeRayCastMapper.h>
#include <vtkImageChangeInformation.h>
#include <vtkImageData.h>
#include <vtkInteractorStyleSwitch.h>
#include <vtkMapper.h>
#include <vtkMetaImageReader.h>
#include <vtkNamedColors.h>
#include <vtkNew.h>
#include <vtkOutlineFilter.h>
#include <vtkPiecewiseFunction.h>
#include <vtkPolyDataMapper.h>
#include <vtkProperty.h>
#include <vtkRenderWindow.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkRenderer.h>
#include <vtkTransform.h>
#include <vtkTransformFilter.h>
#include <vtkVolume.h>
#include <vtkVolumeProperty.h>

#include <vtk_cli11.h>
#include <vtk_fmt.h>
// clang-format off
#include VTK_FMT(fmt/format.h)
// clang-format on

#include <array>
#include <filesystem>

namespace fs = std::filesystem;

namespace {

typedef std::map<std::string, std::string> TAxisParams;
typedef std::map<std::string, TAxisParams> TAxesParams;

/**
 * @brief Define the axes labels.
 *
 * @return The axes labels.
 */
TAxesParams DefineAxesLabels();

/**
 * @brief Define the axes colors.
 *
 * @return The axes colors.
 */
TAxesParams DefineAxesColors();

/**
 * @brief Gather the defined axes labels and colors into a map.
 *
 * @return The map of axes labels and colors.
 */
std::map<std::string, std::pair<TAxisParams, TAxisParams>> GetAxesParams();

/**
 * @brief Make a camera orientation widget for a given renderer.
 *
 * position has these values 0: LowerLeft, 1: UpperLeft, 2: LowerRight, 3:
 * UpperRight
 *
 * @param ren The renderer.
 * @param alc The key specifying the desired labels and colors for the axes.
 * @param colors A reference to the vtkNamedColors object.
 * @param position Move the camera orientation widget to upper left.
 *
 * @return The camera orientation widget.
 */
vtkNew<vtkCameraOrientationWidget>
MakeCameraOrientationWidget(vtkRenderer* ren, std::string alcKey = "xyz",
                            int const& position = 3);
} // namespace

int main(int argc, char* argv[])
{
  CLI::App app{"Read a volume dataset and display it via volume rendering."};

  // Define options
  std::string fileName;
  app.add_option("fileName", fileName,
                 "The path to the data file e.g. FullHead.mhd.")
      ->required()
      ->check(CLI::ExistingFile);

  CLI11_PARSE(app, argc, argv);

  vtkNew<vtkNamedColors> colors;

  std::array<unsigned char, 4> bkg{{51, 77, 102, 255}};
  colors->SetColor("BkgColor", bkg.data());

  // 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 scene.
  vtkNew<vtkRenderer> ren;
  ren->SetBackground(colors->GetColor3d("BkgColor").GetData());
  vtkNew<vtkRenderWindow> renWin;
  renWin->SetSize(640, 480);
  auto appFn = fs::path((app.get_name())).stem().string();
  renWin->SetWindowName(appFn.c_str());
  renWin->AddRenderer(ren);
  vtkNew<vtkRenderWindowInteractor> iren;
  iren->SetRenderWindow(renWin);
  auto is = vtkInteractorStyleSwitch::SafeDownCast(iren->GetInteractorStyle());
  if (is)
  {
    is->SetCurrentStyleToTrackballCamera();
  }

  // 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.)
  vtkNew<vtkMetaImageReader> reader;
  reader->SetFileName(fileName.c_str());
  reader->SetDataByteOrderToLittleEndian();
  reader->Update();

  // Get the current physical center of the volume
  // Bounds returns: [xmin, xmax, ymin, ymax, zmin, zmax]
  auto bounds = reader->GetOutput()->GetBounds();
  std::vector<double> centroid;
  for (auto i = 0; i < 6; i += 2)
  {
    centroid.push_back(bounds[i] + (bounds[i + 1] - bounds[i]) / 2.0);
  }
  // Apply the shift using vtkImageChangeInformation.
  vtkNew<vtkImageChangeInformation> changeInformation;
  changeInformation->SetInputConnection(reader->GetOutputPort());
  // Center the image by shifting it by the negative center coordinates.
  changeInformation->SetOriginTranslation(-centroid[0], -centroid[1],
                                          -centroid[2]);

  // An outline provides context around the data.
  vtkNew<vtkOutlineFilter> outlineFilter;
  outlineFilter->SetInputConnection(changeInformation->GetOutputPort());
  // We need to transform the outline so that it outlines the head.
  auto transform = vtkSmartPointer<vtkTransform>::New();
  //  Move the outline from the origin to the new center inside the head.
  transform->Translate(-centroid[0] * 2.0, -centroid[1] / 32.0,
                       -centroid[2] * 2.0);
  // Apply the transform to the geometry
  auto transformFilter = vtkSmartPointer<vtkTransformFilter>::New();
  transformFilter->SetInputConnection(outlineFilter->GetOutputPort());
  transformFilter->SetTransform(transform);
  transformFilter->Update();

  vtkNew<vtkPolyDataMapper> outlineMapper;
  outlineMapper->SetInputConnection(transformFilter->GetOutputPort());
  vtkNew<vtkProperty> outlineProperty;
  outlineProperty->SetDiffuseColor(colors->GetColor3d("Black").GetData());
  vtkNew<vtkActor> outline;
  outline->SetMapper(outlineMapper);
  outline->SetProperty(outlineProperty);
  ren->AddActor(outline);

  // The volume will be displayed by ray-cast alpha compositing.
  // A ray-cast mapper is needed to do the ray-casting.
  vtkNew<vtkFixedPointVolumeRayCastMapper> volumeMapper;
  volumeMapper->SetInputConnection(changeInformation->GetOutputPort());

  // The color transfer function maps voxel intensities to colors.
  // It is modality-specific, and often anatomy-specific as well.
  // The goal is to one color for flesh (between 500 and 1000)
  // and another color for bone (1150 and over).
  vtkNew<vtkColorTransferFunction> volumeColor;
  volumeColor->AddRGBPoint(0, 0.0, 0.0, 0.0);
  volumeColor->AddRGBPoint(500, 240.0 / 255.0, 184.0 / 255.0, 160.0 / 255.0);
  volumeColor->AddRGBPoint(1000, 240.0 / 255.0, 184.0 / 255.0, 160.0 / 255.0);
  volumeColor->AddRGBPoint(1150, 1.0, 1.0, 240.0 / 255.0); // Ivory

  // The opacity transfer function is used to control the opacity
  // of different tissue types.
  vtkNew<vtkPiecewiseFunction> volumeScalarOpacity;
  volumeScalarOpacity->AddPoint(0, 0.00);
  volumeScalarOpacity->AddPoint(500, 0.15);
  volumeScalarOpacity->AddPoint(1000, 0.15);
  volumeScalarOpacity->AddPoint(1150, 0.85);

  // The gradient opacity function is used to decrease the opacity
  // in the "flat" regions of the volume while maintaining the opacity
  // at the boundaries between tissue types. The gradient is measured
  // as the amount by which the intensity changes over unit distance.
  // For most medical data, the unit distance is 1mm.
  vtkNew<vtkPiecewiseFunction> volumeGradientOpacity;
  volumeGradientOpacity->AddPoint(0, 0.0);
  volumeGradientOpacity->AddPoint(90, 0.5);
  volumeGradientOpacity->AddPoint(100, 1.0);

  // The VolumeProperty attaches the color and opacity functions to the
  // volume, and sets other volume properties. The interpolation should
  // be set to linear to do a high-quality rendering. The ShadeOn option
  // turns on directional lighting, which will usually enhance the
  // appearance of the volume and make it look more "3D". However,
  // the quality of the shading depends on how accurately the gradient
  // of the volume can be calculated, and for noisy data the gradient
  // estimation will be very poor. The impact of the shading can be
  // decreased by increasing the Ambient coefficient while decreasing
  // the Diffuse and Specular coefficient. To increase the impact
  // of shading, decrease the Ambient and increase the Diffuse and Specular.
  vtkNew<vtkVolumeProperty> volumeProperty;
  volumeProperty->SetColor(volumeColor);
  volumeProperty->SetScalarOpacity(volumeScalarOpacity);
  volumeProperty->SetGradientOpacity(volumeGradientOpacity);
  volumeProperty->SetInterpolationTypeToLinear();
  volumeProperty->ShadeOn();
  volumeProperty->SetAmbient(0.4);
  volumeProperty->SetDiffuse(0.6);
  volumeProperty->SetSpecular(0.2);

  // The vtkVolume is a vtkProp3D (like a vtkActor) and controls the position
  // and orientation of the volume in world coordinates.
  vtkNew<vtkVolume> volume;
  volume->SetMapper(volumeMapper);
  volume->SetProperty(volumeProperty);

  // Finally, add the volume to the renderer
  ren->AddViewProp(volume);

  // Set up an initial view of the volume. The focal point will be the
  // center of the volume, and the camera position will be 400mm to the
  // patient's left (which is our right).
  vtkCamera* camera = ren->GetActiveCamera();
  camera->SetViewUp(0, 0, -1);
  camera->SetPosition(-400, 0, 0);
  camera->SetFocalPoint(0, 0, 0);
  camera->ComputeViewPlaneNormal();
  camera->Elevation(30);
  camera->Dolly(1.5);
  ren->ResetCameraClippingRange();

  // Interact with the data.
  renWin->Render();

  // Important: The interactor must be set prior to enabling the widget.
  auto category = "rlpais";
  auto cow = MakeCameraOrientationWidget(ren, category, 1);
  cow->On();

  iren->Initialize();
  iren->Start();

  return EXIT_SUCCESS;
}

namespace {
TAxesParams DefineAxesLabels()
{
  // clang-format off
  return {
          // Labels are: Anterior, Posterior, Dorsal, Ventral, Left, Right
          {"apdvlr", {{"+X", "A"},{"-X", "P"},{"+Y", "D"},{"-Y", "V"},{"+Z", "L"},{"-Z", "R"}}},
          {"apdvrl",{{"+X", "A"},{"-X", "P"},{"+Y", "D"},{"-Y", "V"},{"+Z", "R"},{"-Z", "L"}}},
          {"aprlvd",{{"+X", "A"},{"-X", "P"},{"+Y", "R"},{"-Y", "L"},{"+Z", "V"},{"-Z", "D"}}},
          {"padvlr", {{"+X", "P"},{"-X", "A"},{"+Y", "D"},{"-Y", "V"},{"+Z", "L"},{"-Z", "R"}}},
          // Labels are: Left, Right, Superior, Inferior, Anterior, Posterior
          {"lrsiap",{{"+X", "L"},{"-X", "R"},{"+Y", "S"},{"-Y", "I"},{"+Z", "A"},{"-Z", "P"}}},
          {"lrpasi",{{"+X", "L"},{"-X", "R"},{"+Y", "P"},{"-Y", "A"},{"+Z", "S"},{"-Z", "I"}}},
          {"rlpais",{{"+X", "R"},{"-X", "L"},{"+Y", "P"},{"-Y", "A"},{"+Z", "I"},{"-Z", "S"}}},
          // Default labels.
          {"xyz", {}},
          };
  // clang-format on
}

TAxesParams DefineAxesColors()
{
  // clang-format off
  TAxisParams color1{{"+X", "IndianRed"},{"-X", "FireBrick"},
                     {"+Y", "LimeGreen"},{"-Y", "DarkGreen"},
                     {"+Z", "Blue"}, {"-Z", "SteelBlue"}};
  return {
          {"apdvlr",color1},
          {"apdvrl",color1},
          {"aprlvd",color1},
          {"padvlr",color1},
          {"lrsiap",color1},
          // Default colors.
          {"lrpasi", {}},
          {"rlpais", {}},
          {"xyz", {}},
          };
  // clang-format on
}

std::map<std::string, std::pair<TAxisParams, TAxisParams>> GetAxesParams()
{
  vtkNew<vtkNamedColors> colors;

  // The keys must be the same.
  auto axesLabels = DefineAxesLabels();
  auto axesColors = DefineAxesColors();
  // Get the keys.
  std::set<std::string> labelKeys;
  for (auto&& label : axesLabels)
  {
    labelKeys.insert(label.first);
  }
  std::set<std::string> colorKeys;
  for (auto&& label : axesLabels)
  {
    colorKeys.insert(label.first);
  }
  std::vector<std::string> commonKeys;
  std::set_intersection(labelKeys.begin(), labelKeys.end(), colorKeys.begin(),
                        colorKeys.end(), std::back_inserter(commonKeys));
  std::map<std::string, std::pair<TAxisParams, TAxisParams>> alc;
  for (auto&& k : commonKeys)
  {
    alc[k] = std::pair<TAxisParams, TAxisParams>{axesLabels[k], axesColors[k]};
  }

  return alc;
};

vtkNew<vtkCameraOrientationWidget>
MakeCameraOrientationWidget(vtkRenderer* ren, std::string alcKey,
                            int const& position)
{

  vtkNew<vtkCameraOrientationWidget> cow;
  cow->SetParentRenderer(ren);
  cow->EnabledOn();

  auto axesParameters = GetAxesParams();

  std::set<std::string> keys;
  for (auto&& label : axesParameters)
  {
    keys.insert(label.first);
  }
  auto it = keys.find(alcKey);
  if (it == keys.end())
  {
    std::string res =
        "Invalid key for axes labels and colors.\nValid keys are: ";
    for (const auto& [key, value] : axesParameters)
    {
      res += fmt::format("{:s}, ", key);
    }
    if (res.length() >= 2)
    {
      auto pos = res.length() - 2;
      res.replace(pos, 2, "");
    }
    res += "\nUsing the key: xyz";
    std::cout << res << std::endl;
    alcKey = "xyz";
  }
  auto alc = axesParameters[alcKey];

  vtkNew<vtkCameraOrientationRepresentation> rep;

  switch (position)
  {
  case 0:
    rep->AnchorToLowerLeft();
    break;
  case 1:
    rep->AnchorToUpperLeft();
    break;
  case 2:
    rep->AnchorToLowerRight();
    break;
  default:
    rep->AnchorToUpperRight();
  }

  if (!alc.first.empty())
  {
    rep->SetXPlusLabelText(alc.first["+X"]);
    rep->SetXMinusLabelText(alc.first["-X"]);
    rep->SetYPlusLabelText(alc.first["+Y"]);
    rep->SetYMinusLabelText(alc.first["-Y"]);
    rep->SetZPlusLabelText(alc.first["+Z"]);
    rep->SetZMinusLabelText(alc.first["-Z"]);
  }

  if (!alc.second.empty())
  {
    vtkNew<vtkNamedColors> colors;

    rep->SetXAxisColor(colors->GetColor3d(alc.second["+X"]).GetData());
    rep->SetYAxisColor(colors->GetColor3d(alc.second["+Y"]).GetData());
    rep->SetZAxisColor(colors->GetColor3d(alc.second["+Z"]).GetData());
  }

  cow->SetRepresentation(rep);

  cow->Off();

  return cow;
}

} // namespace

cmake_minimum_required(VERSION 3.12 FATAL_ERROR)

project(MedicalDemo4)

find_package(VTK COMPONENTS 
  CommonColor
  CommonCore
  CommonDataModel
  IOImage
  InteractionStyle
  RenderingContextOpenGL2
  RenderingCore
  RenderingFreeType
  RenderingGL2PSOpenGL2
  RenderingOpenGL2
  RenderingVolume
  RenderingVolumeOpenGL2
)

if (NOT VTK_FOUND)
  message(FATAL_ERROR "MedicalDemo4: Unable to find the VTK build folder.")
endif()

# Prevent a "command line is too long" failure in Windows.
set(CMAKE_NINJA_FORCE_RESPONSE_FILE "ON" CACHE BOOL "Force Ninja to use response files.")
add_executable(MedicalDemo4 MACOSX_BUNDLE MedicalDemo4.cxx )
  target_link_libraries(MedicalDemo4 PRIVATE ${VTK_LIBRARIES}
)
# vtk_module_autoinit is needed
vtk_module_autoinit(
  TARGETS MedicalDemo4
  MODULES ${VTK_LIBRARIES}
)

cd MedicalDemo4/build

cmake ..

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

make

./MedicalDemo4