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FroggieView

web-test/Cxx/Visualization/FroggieView

Description

View surfaces of a segmented frog dataset using preprocessed *.vtk tissue files. This means that loading and processing is much faster when comapred with FroggieSurface.

FroggieView provides the ability to turn on and off surfaces, control their opacity through the use of sliders and control the camera position.

By default the frog is oriented so that we look down on the dorsal (posterior) surface and the superior surface faces the top of the screen. The frog is rendered with the skin being translucent so that you can see the internal organs.

In the lower left of the image there is a prop assembly with labelled XYZ axes and a cube labelled with anatomical orientations:

  • Sagittal plane
  • L - left
  • R - right
  • Coronal plane
  • A - anterior
  • P - posterior
  • Transverse plane
  • S - superior
  • I - inferior

This prop assembly can be moved and resized.

The opacity of each tissue is controlled by a slider, additionally you can turn all the sliders on or off by pressing the "n" key.

If the option "-n" is selected, no sliders will displayed.

Individual tissues can be specified by using the "-t" option e.g. "-t skin skeleton".

The parameters used to generate the example image are loaded from a JSON file containing the data needed to access and generate the actors for each tissue along with other supplementary data such as the data file names. This means that the user need only load this one file in order to generate the data for rendering. This file is called:

<DATA>/Frog_vtk.json

Where <DATA> is the path to vtk-examples/src/Testing/Data.

For information about the parameters in the JSON file, please see Frog_vtk_format.

The code uses a general way of specifying transformations that can permute image and other geometric data in order to maintain proper orientation regardless of the acquisition order. See the class SliceOrder.

The dataset was prepared at the Lawrence Berkeley National Laboratories. It is included with their permission. The data was acquired by physically slicing the frog and photographing the slices. The original segmented data is in the form of tissue masks with one file per tissue. There are 136 slices per tissue and 15 different tissues. Each slice is 470 by 500 pixels.

Further information:

Info

Mutually exclusive options "-a -b -c -d" are provided to let you generate approximations to the following figures: Figure 12-9a, Figure 12-9b, Figure 12-9c, and Figure 12-9d in Chapter 12 of the VTK Textbook.

Other languages

See (Python)

Question

If you have a question about this example, please use the VTK Discourse Forum

Code

FroggieView.cxx

#include <vtkActor.h>
#include <vtkAnnotatedCubeActor.h>
#include <vtkAxesActor.h>
#include <vtkCallbackCommand.h>
#include <vtkCamera.h>
#include <vtkCameraOrientationWidget.h>
#include <vtkCaptionActor2D.h>
#include <vtkInteractorStyleTrackballCamera.h>
#include <vtkLookupTable.h>
#include <vtkMatrix4x4.h>
#include <vtkNamedColors.h>
#include <vtkNew.h>
#include <vtkOrientationMarkerWidget.h>
#include <vtkPolyDataMapper.h>
#include <vtkPolyDataNormals.h>
#include <vtkPolyDataReader.h>
#include <vtkProp3D.h>
#include <vtkPropAssembly.h>
#include <vtkProperty.h>
#include <vtkProperty2D.h>
#include <vtkRenderWindow.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkRenderer.h>
#include <vtkSliderRepresentation2D.h>
#include <vtkSliderWidget.h>
#include <vtkSmartPointer.h>
#include <vtkTextProperty.h>
#include <vtkTransform.h>
#include <vtkTransformPolyDataFilter.h>

#include <vtk_cli11.h>
#include <vtk_jsoncpp.h>

#include <array>
#include <cstdlib>
#include <filesystem>
#include <fstream>
#include <iomanip>
#include <iostream>
#include <sstream>
#include <string>

namespace fs = std::filesystem;

namespace {
struct Parameters
{
  std::vector<std::string> names;
  std::map<std::string, std::string> colors;
  std::map<std::string, int> indices;
  std::map<std::string, std::string> orientation;
  std::map<std::string, double> opacity;
  std::map<std::string, std::string> vtkFiles;
  std::vector<std::string> fig_129b;
  std::vector<std::string> fig_129cd;

  bool parsedOk{false};
};

/**
 * Take a string and convert it to lowercase.
 *
 * See: https://en.cppreference.com/w/cpp/string/byte/tolower
 * Only works with ASCII characters.
 *
 * @param s: The string to be converted to lowercase.
 *
 * @return The lowercase version of the string.
 */
std::string ToLowerCase(std::string s);

/**
 * Read the parameters from a json file and check that the file paths exist.
 *
 * @param fnPath: The path to the json file.
 * @param parameters:  The parameters.
 */
void ParseJSON(const fs::path fnPath, Parameters& parameters);

/**
 * Create the lookup table for the frog tissues.
 *
 * Each table value corresponds the color of one of the frog tissues.
 *
 * @param indices: The tissue name and index.
 * @param colors: The tissue name and color.
 * @return: The lookup table.
 */
vtkNew<vtkLookupTable>
CreateTissueLUT(std::map<std::string, int> const& indices,
                std::map<std::string, std::string>& colors);

class SliceOrder
{
  // clang-format off
  /*
    These transformations permute image and other geometric data to maintain
      proper orientation regardless of the acquisition order. After applying
      these transforms with vtkTransformFilter, a view up of 0, -1, 0 will
      result in the body part facing the viewer.

    NOTE: Some transformations have a -1 scale factor for one of the components.
          To ensure proper polygon orientation and normal direction,
            you must apply the vtkPolyDataNormals filter.

    Naming (the nomenclature is medical):
      si - superior to inferior (top to bottom)
      is - inferior to superior (bottom to top)
      ap - anterior to posterior (front to back)
      pa - posterior to anterior (back to front)
      lr - left to right
      rl - right to left

    */
  // clang-format on

public:
  /**
   * Generate the transforms corresponding to the slice order.
   */
  SliceOrder();

  virtual ~SliceOrder() = default;

public:
  /**
   * Returns the vtkTransform corresponding to the slice order.
   *
   * @param sliceOrder: The slice order.
   * @return The vtkTransform corresponding to the slice order.
   */
  vtkSmartPointer<vtkTransform> Get(std::string const& sliceOrder);

  /**
   * Print the homogenous matrix corresponding to the slice order.
   *
   * @param order: The slice order.
   */
  void PrintTransform(std::string const& order);

  /**
   * Print all the homogenous matrices corresponding to the slice orders.
   *
   */
  void PrintAlltransforms();

private:
  std::map<std::string, vtkSmartPointer<vtkTransform>> transform;
};

/**
 * @param scale: Sets the scale and direction of the axes.
 * @param xyzLabels: Labels for the axes.
 * @return The axes actor.
 */
vtkNew<vtkAxesActor> MakeAxesActor(std::array<double, 3>& scale,
                                   std::array<std::string, 3> const& xyzLabels);

/**
 * @param cubeLabels: The labels for the cube faces.
 * @param colors: Used to set the colors of the cube faces.
 * @return The annotated cube actor.
 */
vtkNew<vtkAnnotatedCubeActor>
MakeAnnotatedCubeActor(std::array<std::string, 6> const& cubeLabels,
                       vtkNamedColors* colors);

/**
 * @param labelSelector: The selector used to define labels for the axes and
 * cube.
 * @param colors: Used to set the colors of the cube faces.
 * @return The combined axes and annotated cube prop.
 */
vtkNew<vtkPropAssembly> MakeCubeActor(std::string const& labelSelector,
                                      vtkNamedColors* colors);

class SliderCallbackOpacity : public vtkCallbackCommand
{
public:
  static SliderCallbackOpacity* New()
  {
    return new SliderCallbackOpacity;
  }
  virtual void Execute(vtkObject* caller, unsigned long, void*)
  {
    vtkSliderWidget* sliderWidget = reinterpret_cast<vtkSliderWidget*>(caller);
    double value = static_cast<vtkSliderRepresentation2D*>(
                       sliderWidget->GetRepresentation())
                       ->GetValue();
    this->property->SetOpacity(value);
  }
  SliderCallbackOpacity() : property(nullptr)
  {
  }
  vtkProperty* property;
};
struct SliderProperties
{
  double tubeWidth{0.004};
  double sliderLength{0.015};
  double sliderWidth{0.008};
  double endCapLength{0.008};
  double endCapWidth{0.02};
  double titleHeight{0.02};
  double labelHeight{0.02};

  double valueMinimum{0.0};
  double valueMaximum{1.0};
  double valueInitial{1.0};

  std::array<double, 2> p1{0.02, 0.1};
  std::array<double, 2> p2{0.18, 0.1};

  std::string title;

  std::string titleColor{"Black"};
  std::string labelColor{"Black"};
  std::string valueColor{"DarkSlateGray"};
  std::string sliderColor{"BurlyWood"};
  std::string selectedColor{"Lime"};
  std::string barColor{"Black"};
  std::string barEndsColor{"Indigo"};
};

/**
 * @param properties: The slider properties.
 * @param lut: The color lookup table.
 * @param idx: The tissue index.
 * @return The slider widget.
 */
vtkNew<vtkSliderWidget> MakeSliderWidget(SliderProperties const& sp,
                                         vtkLookupTable* lut, int const& idx);

class SliderToggleCallback : public vtkCallbackCommand
{
public:
  SliderToggleCallback() = default;

  static SliderToggleCallback* New()
  {
    return new SliderToggleCallback;
  }

  /*
   * Create a vtkCallbackCommand and reimplement it.
   *
   */
  void Execute(vtkObject* caller, unsigned long /*evId*/, void*) override
  {
    // Note the use of reinterpret_cast to cast the caller to the expected type.
    auto rwi = reinterpret_cast<vtkRenderWindowInteractor*>(caller);

    // Get the keypress
    std::string key = rwi->GetKeySym();
    if (key == "n")
    {
      for (auto const& p : *this->sliders)
      {
        if (p.second->GetEnabled())
        {
          p.second->Off();
        }
        else
        {
          p.second->On();
        }
      }
    }
  }

  /**
   * For handling the sliders.
   *
   * @param sliders The sliders.
   *
   */
  void SetParameters(
      std::map<std::string, vtkSmartPointer<vtkSliderWidget>>* sliders)
  {
    this->sliders = sliders;
  }

private:
  SliderToggleCallback(const SliderToggleCallback&) = delete;
  void operator=(const SliderToggleCallback&) = delete;

  std::map<std::string, vtkSmartPointer<vtkSliderWidget>>* sliders{nullptr};
};

} // namespace

int main(int argc, char* argv[])
{
  CLI::App app{"View surfaces of a segmented frog dataset using preprocessed "
               "VTK tissue files."};

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

  std::vector<std::string> chosenTissues;
  app.add_option("-t", chosenTissues, "Select one or more tissues.");
  auto noSliders = false;
  app.add_flag("-n", noSliders, "No sliders");

  std::array<bool, 6> view{false, false, false, false};
  auto* ogroup = app.add_option_group(
      "view",
      "Select a view corresponding to Fig 12-9 in the VTK Textbook. Only one "
      "or none of these can be selected.");
  ogroup->add_flag("-a", view[0],
                   "The view corresponds to Fig 12-9a in the VTK Textbook");
  ogroup->add_flag("-b", view[1],
                   "The view corresponds to Fig 12-9b in the VTK Textbook");
  ogroup->add_flag("-c", view[2],
                   "The view corresponds to Fig 12-9c in the VTK Textbook");
  ogroup->add_flag("-d", view[3],
                   "The view corresponds to Fig 12-9d in the VTK Textbook");
  ogroup->add_flag(
      "-l", view[4],
      "The view corresponds to looking down on the anterior surface");
  ogroup->add_flag("-p", view[5],
                   "The view corresponds to looking down on the posterior "
                   "surface (the default)");

  CLI11_PARSE(app, argc, argv);

  auto selectCount = std::count_if(view.begin(), view.end(),
                                   [=](const bool& e) { return e == true; });
  if (selectCount > 1)
  {
    std::cerr << "Only one or none of the options -a, -b, -c, -d, -l, -p can "
                 "be selected;"
              << std::endl;
    return EXIT_FAILURE;
  }

  auto fnPath = fs::path(fileName);
  if (!fnPath.has_extension())
  {
    fnPath.replace_extension(".json");
  }
  if (!fs::is_regular_file(fnPath))
  {
    std::cerr << "Unable to find: " << fnPath << std::endl;
    return EXIT_FAILURE;
  }

  Parameters parameters;
  ParseJSON(fnPath, parameters);
  if (!parameters.parsedOk)
  {
    return EXIT_FAILURE;
  }

  auto tissues = parameters.names;
  auto indices = parameters.indices;

  auto lut = CreateTissueLUT(parameters.indices, parameters.colors);

  char selectFigure{'\0'};
  if (selectCount == 1)
  {
    if (view[0])
    {
      selectFigure = 'a';
    }
    else if (view[1])
    {
      // No skin.
      tissues = parameters.fig_129b;
      selectFigure = 'b';
    }
    else if (view[2])
    {
      // No skin, blood and skeleton.
      tissues = parameters.fig_129cd;
      selectFigure = 'c';
    }
    else if (view[3])
    {
      // No skin, blood and skeleton.
      tissues = parameters.fig_129cd;
      selectFigure = 'd';
    }
    else if (view[4])
    {
      // Looking down on the anterior surface.
      selectFigure = 'l';
    }
    else // The default
    {
      // Looking down on the posterior surface.
      selectFigure = 'p';
    }
  }

  if (!chosenTissues.empty())
  {
    for (auto i = 0; i < chosenTissues.size(); ++i)
    {
      chosenTissues[i] = ToLowerCase(chosenTissues[i]);
    }
    std::vector<std::string> res;
    auto has_brainbin{false};
    if (std::find(chosenTissues.begin(), chosenTissues.end(), "brainbin") !=
        chosenTissues.end())
    {
      std::cout << "Using brainbin instead of brain." << std::endl;
      res.push_back("brainbin");
      indices.erase("brain");
      indices["brainbin"] = 2;
      parameters.colors.erase("brain");
      parameters.colors["brainbin"] = "beige";
      has_brainbin = true;
    }
    for (auto const& ct : chosenTissues)
    {
      if (has_brainbin && (ct == "brain" || ct == "brainbin"))
      {
        continue;
      }
      if (std::find(tissues.begin(), tissues.end(), ct) != tissues.end())
      {
        res.push_back(ct);
      }
      else
      {
        std::cout << "Tissue: " << ct << " is not available." << std::endl;
        return EXIT_FAILURE;
      }
    }
    if (res.size() == 1 && res[0] == "skin")
    {
      parameters.opacity["skin"] = 1.0;
    }
    tissues = res;
  }

  vtkNew<vtkNamedColors> colors;
  colors->SetColor("ParaViewBkg",
                   std::array<unsigned char, 4>{82, 87, 110, 255}.data());

  // Setup render window, renderer, and interactor.
  vtkNew<vtkRenderer> ren;
  vtkNew<vtkRenderWindow> renWin;
  renWin->AddRenderer(ren);
  vtkNew<vtkRenderWindowInteractor> iRen;
  iRen->SetRenderWindow(renWin);
  vtkNew<vtkInteractorStyleTrackballCamera> style;
  iRen->SetInteractorStyle(style);

  SliceOrder so;
  // so.PrintAlltransforms();

  size_t colorSize{0};
  for (auto const& p : parameters.colors)
  {
    colorSize = std::max(colorSize, p.second.size());
  }
  size_t nameSize{0};
  for (auto const& p : parameters.names)
  {
    nameSize = std::max(nameSize, p.size());
  }

  std::map<std::string, vtkSmartPointer<vtkSliderWidget>> sliders;
  auto leftStepSize = 1.0 / 9;
  auto leftPosY = 0.275;
  auto leftPosX0 = 0.02;
  auto leftPosX1 = 0.18;
  auto rightStepSize = 1.0 / 9;
  auto rightPosY = 0.05;
  auto rightPosX0 = 0.8 + 0.02;
  auto rightPosX1 = 0.8 + 0.18;

  auto sliderCount = 0;

  std::string line(7 + nameSize + colorSize, '-');

  std::cout << line << '\n'
            << std::setw(nameSize) << std::left << "Tissue"
            << " Label "
            << "Color" << '\n'
            << line << std::endl;
  auto intSize = 2;

  for (auto const& tissue : tissues)
  {
    vtkNew<vtkPolyDataReader> reader;
    reader->SetFileName(parameters.vtkFiles[tissue].c_str());
    reader->Update();

    auto trans = so.Get(parameters.orientation[tissue]);
    trans->Scale(1, -1, -1);

    vtkNew<vtkTransformPolyDataFilter> tf;
    tf->SetInputConnection(reader->GetOutputPort());
    tf->SetTransform(trans);
    tf->SetInputConnection(reader->GetOutputPort());

    vtkNew<vtkPolyDataNormals> normals;
    normals->SetInputConnection(tf->GetOutputPort());
    normals->SetFeatureAngle(60.0);

    vtkNew<vtkPolyDataMapper> mapper;
    mapper->SetInputConnection(normals->GetOutputPort());

    vtkNew<vtkActor> actor;
    actor->SetMapper(mapper);
    actor->GetProperty()->SetOpacity(parameters.opacity[tissue]);
    actor->GetProperty()->SetDiffuseColor(lut->GetTableValue(indices[tissue]));
    actor->GetProperty()->SetSpecular(0.2);
    actor->GetProperty()->SetSpecularPower(10);

    ren->AddActor(actor);

    if (!noSliders)
    {
      auto sp = SliderProperties();

      sp.valueInitial = parameters.opacity[tissue];
      sp.title = tissue;

      // Screen coordinates.
      if (sliderCount < 7)
      {
        sp.p1[0] = leftPosX0;
        sp.p1[1] = leftPosY;
        sp.p2[0] = leftPosX1;
        sp.p2[1] = leftPosY;
        leftPosY += leftStepSize;
      }
      else
      {
        sp.p1[0] = rightPosX0;
        sp.p1[1] = rightPosY;
        sp.p2[0] = rightPosX1;
        sp.p2[1] = rightPosY;
        rightPosY += rightStepSize;
      }

      auto sliderWidget = MakeSliderWidget(sp, lut, parameters.indices[tissue]);

      sliderWidget->SetInteractor(iRen);
      sliderWidget->SetAnimationModeToAnimate();
      sliderWidget->EnabledOn();

      vtkNew<SliderCallbackOpacity> cb;
      cb->property = actor->GetProperty();
      sliderWidget->AddObserver(vtkCommand::InteractionEvent, cb);
      sliders[tissue] = sliderWidget;
      sliderCount += 1;
    }
    std::cout << std::setw(nameSize) << std::left << tissue << " "
              << std::setw(intSize + 3) << std::right << indices[tissue] << " "
              << std::setw(colorSize) << std::left << parameters.colors[tissue]
              << std::endl;
  }
  std::cout << line << std::endl;

  if (noSliders)
  {
    renWin->SetSize(1024, 1024);
  }
  else
  {
    renWin->SetSize(1024 + 400, 1024);
  }
  renWin->SetWindowName("FroggieView");

  ren->SetBackground(colors->GetColor3d("ParaViewBkg").GetData());

  auto camera = ren->GetActiveCamera();
  // Superior Anterior Left
  auto labels{"sal"};
  if (selectFigure == 'a')
  {
    // Fig 12-9a in the VTK Textbook
    camera->SetPosition(495.722368, -447.474954, -646.308030);
    camera->SetFocalPoint(137.612066, -40.962376, -195.171023);
    camera->SetViewUp(-0.323882, -0.816232, 0.478398);
    camera->SetDistance(704.996499);
    camera->SetClippingRange(319.797039, 1809.449285);
  }
  else if (selectFigure == 'b')
  {
    // Fig 12-9b in the VTK Textbook
    camera->SetPosition(478.683494, -420.477744, -643.112038);
    camera->SetFocalPoint(135.624874, -36.478435, -210.614440);
    camera->SetViewUp(-0.320495, -0.820148, 0.473962);
    camera->SetDistance(672.457328);
    camera->SetClippingRange(307.326771, 1765.990822);
  }
  else if (selectFigure == 'c')
  {
    // Fig 12-9c in the VTK Textbook
    camera->SetPosition(201.363313, -147.260834, -229.885066);
    camera->SetFocalPoint(140.626206, -75.857216, -162.352531);
    camera->SetViewUp(-0.425438, -0.786048, 0.448477);
    camera->SetDistance(115.534047);
    camera->SetClippingRange(7.109870, 854.091718);
  }
  else if (selectFigure == 'd')
  {
    // Fig 12-9d in the VTK Textbook
    camera->SetPosition(115.361727, -484.656410, -6.193827);
    camera->SetFocalPoint(49.126343, 98.501094, 1.323317);
    camera->SetViewUp(-0.649127, -0.083475, 0.756086);
    camera->SetDistance(586.955116);
    camera->SetClippingRange(360.549218, 866.876230);
  }
  else if (selectFigure == 'l')
  {
    // Orient so that we look down on the anterior surface and
    //  the superior surface faces the top of the screen.
    // Left Superior Anterior
    labels = "lsa";
    vtkNew<vtkTransform> transform;
    transform->SetMatrix(camera->GetModelTransformMatrix());
    transform->RotateY(90);
    transform->RotateZ(90);
    camera->SetModelTransformMatrix(transform->GetMatrix());
    ren->ResetCamera();
  }
  else
  {
    // Orient so that we look down on the posterior surface and
    //  the superior surface faces the top of the screen.
    // Right Superior Posterior
    labels = "rsp";
    vtkNew<vtkTransform> transform;
    transform->SetMatrix(camera->GetModelTransformMatrix());
    transform->RotateY(-90);
    transform->RotateZ(90);
    camera->SetModelTransformMatrix(transform->GetMatrix());
    ren->ResetCamera();
  }

  vtkNew<vtkCameraOrientationWidget> cow;
  cow->SetParentRenderer(ren);
  if (noSliders)
  {
    // Turn off if you do not want it.
    cow->On();
    cow->EnabledOn();
  }
  else
  {
    cow->Off();
    cow->EnabledOff();
  }

  auto axes = MakeCubeActor(labels, colors);
  vtkNew<vtkOrientationMarkerWidget> om;
  om->SetOrientationMarker(axes);
  // Position upper left in the viewport.
  // om->SetViewport(0.0, 0.8, 0.2, 1.0);
  // Position lower left in the viewport.
  om->SetViewport(0, 0, 0.2, 0.2);
  om->SetInteractor(iRen);
  om->EnabledOn();
  om->InteractiveOn();

  renWin->Render();

  vtkNew<SliderToggleCallback> sliderToggle;
  sliderToggle->SetParameters(&sliders);
  iRen->AddObserver(vtkCommand::KeyPressEvent, sliderToggle);

  iRen->Start();

  return EXIT_SUCCESS;
}

namespace {

std::string ToLowerCase(std::string s)
{
  std::transform(s.begin(), s.end(), s.begin(),
                 [](unsigned char c) { return std::tolower(c); } // correct
  );
  return s;
}

void ParseJSON(const fs::path fnPath, Parameters& parameters)
{
  std::ifstream ifs(fnPath);
  Json::Value root;

  if (ifs)
  {
    std::string str;
    std::string errors;
    Json::CharReaderBuilder builder{};
    auto reader = std::unique_ptr<Json::CharReader>(builder.newCharReader());

    std::ostringstream ss;
    ss << ifs.rdbuf(); // Read in the file comtents
    str = ss.str();
    auto parsingSuccessful =
        reader->parse(str.c_str(), str.c_str() + str.size(), &root, &errors);
    ifs.close();
    if (!parsingSuccessful)
    {
      std::cout << errors << std::endl;
      parameters.parsedOk = false;
      return;
    }
    parameters.parsedOk = true;
  }
  else
  {
    std::cerr << "Unable to open: " << fnPath << std::endl;
    parameters.parsedOk = false;
  }

  // Get the parameters that we need.
  fs::path vtkPath;
  std::vector<std::string> fileNames;
  for (Json::Value::const_iterator outer = root.begin(); outer != root.end();
       ++outer)
  {
    if (outer.name() == "files")
    {
      std::string path;
      for (Json::Value::const_iterator pth = root["files"].begin();
           pth != root["files"].end(); ++pth)
      {
        if (pth.name() == "root")
        {
          vtkPath = fs::path(pth->asString());
        }
        if (pth.name() == "vtk_files")
        {
          for (Json::Value::const_iterator fls =
                   root["files"]["vtk_files"].begin();
               fls != root["files"]["vtk_files"].end(); ++fls)
          {
            fileNames.push_back(fls->asString());
          }
        }
      }
    }
    if (outer.name() == "tissues")
    {
      for (Json::Value::const_iterator tc = root["tissues"]["names"].begin();
           tc != root["tissues"]["names"].end(); ++tc)
      {
        parameters.names.push_back(tc->asString());
      }
      for (Json::Value::const_iterator tc = root["tissues"]["indices"].begin();
           tc != root["tissues"]["indices"].end(); ++tc)
      {
        parameters.indices[tc.name()] = tc->asInt();
      }
      for (Json::Value::const_iterator tc = root["tissues"]["colors"].begin();
           tc != root["tissues"]["colors"].end(); ++tc)
      {
        parameters.colors[tc.name()] = tc->asString();
      }
      for (Json::Value::const_iterator tc = root["tissues"]["indices"].begin();
           tc != root["tissues"]["indices"].end(); ++tc)
      {
        parameters.indices[tc.name()] = tc->asInt();
      }
      for (Json::Value::const_iterator tc =
               root["tissues"]["orientation"].begin();
           tc != root["tissues"]["orientation"].end(); ++tc)
      {
        parameters.orientation[tc.name()] = tc->asString();
      }
      for (Json::Value::const_iterator tc = root["tissues"]["opacity"].begin();
           tc != root["tissues"]["opacity"].end(); ++tc)
      {
        parameters.opacity[tc.name()] = tc->asDouble();
      }
    }
    if (outer.name() == "figures")
    {
      for (Json::Value::const_iterator c = root["figures"]["fig12-9b"].begin();
           c != root["figures"]["fig12-9b"].end(); ++c)
      {
        parameters.fig_129b.push_back(c->asString());
      }
      for (Json::Value::const_iterator c = root["figures"]["fig12-9cd"].begin();
           c != root["figures"]["fig12-9cd"].end(); ++c)
      {
        parameters.fig_129cd.push_back(c->asString());
      }
    }
  }

  //  Build and check the paths.
  if (!fileNames.empty())
  {
    if (fileNames.size() != 17)
    {
      std::cerr << "Expected seventeen file names.";
      parameters.parsedOk = false;
    }
    else
    {
      for (size_t i = 0; i < fileNames.size(); i++)
      {
        auto pth = fnPath.parent_path() / vtkPath / fs::path(fileNames[i]);
        fileNames[i] = pth.make_preferred().string();
        if (!(fs::is_regular_file(pth) && fs::exists(pth)))
        {
          std::cerr << "Not a file or path does not exist: " << fileNames[i]
                    << std::endl;
          parameters.parsedOk = false;
        }
        else
        {
          parameters.vtkFiles[pth.stem().string()] =
              pth.make_preferred().string();
        }
      }
    }
  }
  else
  {
    std::cerr << "Expected .vtk file names in the JSON file.";
    parameters.parsedOk = false;
  }
}

vtkNew<vtkLookupTable>
CreateTissueLUT(std::map<std::string, int> const& indices,
                std::map<std::string, std::string>& colors)
{
  vtkNew<vtkLookupTable> lut;
  lut->SetNumberOfColors(colors.size());
  lut->SetTableRange(0, colors.size() - 1);
  lut->Build();

  vtkNew<vtkNamedColors> nc;

  for (auto const& p : indices)
  {
    lut->SetTableValue(p.second, nc->GetColor4d(colors[p.first]).GetData());
  }

  return lut;
}

SliceOrder::SliceOrder()
{
  vtkNew<vtkMatrix4x4> si_mat;
  si_mat->Zero();
  si_mat->SetElement(0, 0, 1);
  si_mat->SetElement(1, 2, 1);
  si_mat->SetElement(2, 1, -1);
  si_mat->SetElement(3, 3, 1);

  vtkNew<vtkMatrix4x4> is_mat;
  is_mat->Zero();
  is_mat->SetElement(0, 0, 1);
  is_mat->SetElement(1, 2, -1);
  is_mat->SetElement(2, 1, -1);
  is_mat->SetElement(3, 3, 1);

  vtkNew<vtkMatrix4x4> lr_mat;
  lr_mat->Zero();
  lr_mat->SetElement(0, 2, -1);
  lr_mat->SetElement(1, 1, -1);
  lr_mat->SetElement(2, 0, 1);
  lr_mat->SetElement(3, 3, 1);

  vtkNew<vtkMatrix4x4> rl_mat;
  rl_mat->Zero();
  rl_mat->SetElement(0, 2, 1);
  rl_mat->SetElement(1, 1, -1);
  rl_mat->SetElement(2, 0, 1);
  rl_mat->SetElement(3, 3, 1);

  // The previous transforms assume radiological views of the slices
  //  (viewed from the feet).
  // Other modalities such as physical sectioning may view from the head.
  // The following transforms modify the original with a 180° rotation about y

  vtkNew<vtkMatrix4x4> hf_mat;
  hf_mat->Zero();
  hf_mat->SetElement(0, 0, -1);
  hf_mat->SetElement(1, 1, 1);
  hf_mat->SetElement(2, 2, -1);
  hf_mat->SetElement(3, 3, 1);

  vtkNew<vtkTransform> si_trans;
  si_trans->SetMatrix(si_mat);
  this->transform["si"] = si_trans;

  vtkNew<vtkTransform> is_trans;
  is_trans->SetMatrix(is_mat);
  this->transform["is"] = is_trans;

  vtkNew<vtkTransform> ap_trans;
  ap_trans->Scale(1, -1, 1);
  this->transform["ap"] = ap_trans;

  vtkNew<vtkTransform> pa_trans;
  pa_trans->Scale(1, -1, -1);
  this->transform["pa"] = pa_trans;

  vtkNew<vtkTransform> lr_trans;
  lr_trans->SetMatrix(lr_mat);
  this->transform["lr"] = lr_trans;

  vtkNew<vtkTransform> rl_trans;
  lr_trans->SetMatrix(rl_mat);
  this->transform["rl"] = rl_trans;

  vtkNew<vtkTransform> hf_trans;
  hf_trans->SetMatrix(hf_mat);
  this->transform["hf"] = hf_trans;

  vtkNew<vtkTransform> hf_si_trans;
  hf_si_trans->SetMatrix(hf_mat);
  hf_si_trans->Concatenate(si_mat);
  this->transform["hfsi"] = hf_si_trans;

  vtkNew<vtkTransform> hf_is_trans;
  hf_is_trans->SetMatrix(hf_mat);
  hf_is_trans->Concatenate(is_mat);
  this->transform["hfis"] = hf_is_trans;

  vtkNew<vtkTransform> hf_ap_trans;
  hf_ap_trans->SetMatrix(hf_mat);
  hf_ap_trans->Scale(1, -1, 1);
  this->transform["hfap"] = hf_ap_trans;

  vtkNew<vtkTransform> hf_pa_trans;
  hf_pa_trans->SetMatrix(hf_mat);
  hf_pa_trans->Scale(1, -1, -1);
  this->transform["hfpa"] = hf_pa_trans;

  vtkNew<vtkTransform> hf_lr_trans;
  hf_lr_trans->SetMatrix(hf_mat);
  hf_lr_trans->Concatenate(lr_mat);
  this->transform["hflr"] = hf_lr_trans;

  vtkNew<vtkTransform> hf_rl_trans;
  hf_rl_trans->SetMatrix(hf_mat);
  hf_rl_trans->Concatenate(rl_mat);
  this->transform["hfrl"] = hf_rl_trans;

  // Identity
  this->transform["I"] = vtkNew<vtkTransform>();

  // Zero
  vtkNew<vtkTransform> z_trans;
  z_trans->Scale(0, 0, 0);
  this->transform["Z"] = z_trans;
}

void SliceOrder::PrintTransform(std::string const& order)
{
  auto m = this->transform[order]->GetMatrix();
  std::ostringstream os;
  os.setf(std::ios_base::fmtflags(), std::ios_base::floatfield);
  os << order << '\n';
  for (int i = 0; i < 4; ++i)
  {
    for (int j = 0; j < 4; ++j)
    {
      if (j < 3)
      {
        os << std::setw(6) << std::right << std::setprecision(2)
           << m->GetElement(i, j) << " ";
      }
      else
      {
        os << std::setw(6) << std::right << m->GetElement(i, j) << '\n';
      }
    }
  }
  std::cout << os.str() << '\n';
  os.str("");
}

void SliceOrder::PrintAlltransforms()
{
  for (auto const& p : this->transform)
  {
    PrintTransform(p.first);
  }
}

vtkSmartPointer<vtkTransform> SliceOrder::Get(std::string const& sliceOrder)
{
  return this->transform[sliceOrder];
}

vtkNew<vtkAxesActor> MakeAxesActor(std::array<double, 3>& scale,
                                   std::array<std::string, 3> const& xyzLabels)
{
  vtkNew<vtkAxesActor> axes;
  axes->SetScale(scale.data());
  axes->SetShaftTypeToCylinder();
  axes->SetXAxisLabelText(xyzLabels[0].c_str());
  axes->SetYAxisLabelText(xyzLabels[1].c_str());
  axes->SetZAxisLabelText(xyzLabels[2].c_str());
  axes->SetCylinderRadius(0.5 * axes->GetCylinderRadius());
  axes->SetConeRadius(1.025 * axes->GetConeRadius());
  axes->SetSphereRadius(1.5 * axes->GetSphereRadius());
  auto tprop = axes->GetXAxisCaptionActor2D()->GetCaptionTextProperty();
  tprop->ItalicOn();
  tprop->ShadowOn();
  tprop->SetFontFamilyToTimes();
  // Use the same text properties on the other two axes.
  axes->GetYAxisCaptionActor2D()->GetCaptionTextProperty()->ShallowCopy(tprop);
  axes->GetZAxisCaptionActor2D()->GetCaptionTextProperty()->ShallowCopy(tprop);
  return axes;
}

vtkNew<vtkAnnotatedCubeActor>
MakeAnnotatedCubeActor(std::array<std::string, 6> const& cubeLabels,
                       vtkNamedColors* colors)
{
  // A cube with labeled faces.
  vtkNew<vtkAnnotatedCubeActor> cube;
  cube->SetXPlusFaceText(cubeLabels[0].c_str());
  cube->SetXMinusFaceText(cubeLabels[1].c_str());
  cube->SetYPlusFaceText(cubeLabels[2].c_str());
  cube->SetYMinusFaceText(cubeLabels[3].c_str());
  cube->SetZPlusFaceText(cubeLabels[4].c_str());
  cube->SetZMinusFaceText(cubeLabels[5].c_str());
  cube->SetFaceTextScale(0.5);
  cube->GetCubeProperty()->SetColor(colors->GetColor3d("Gainsboro").GetData());

  cube->GetTextEdgesProperty()->SetColor(
      colors->GetColor3d("LightSlateGray").GetData());

  // Change the vector text colors.
  cube->GetXPlusFaceProperty()->SetColor(
      colors->GetColor3d("Tomato").GetData());
  cube->GetXMinusFaceProperty()->SetColor(
      colors->GetColor3d("Tomato").GetData());
  cube->GetYPlusFaceProperty()->SetColor(
      colors->GetColor3d("DeepSkyBlue").GetData());
  cube->GetYMinusFaceProperty()->SetColor(
      colors->GetColor3d("DeepSkyBlue").GetData());
  cube->GetZPlusFaceProperty()->SetColor(
      colors->GetColor3d("SeaGreen").GetData());
  cube->GetZMinusFaceProperty()->SetColor(
      colors->GetColor3d("SeaGreen").GetData());
  return cube;
}

vtkNew<vtkPropAssembly> MakeCubeActor(std::string const& labelSelector,
                                      vtkNamedColors* colors)
{
  std::array<std::string, 3> xyzLabels;
  std::array<std::string, 6> cubeLabels;
  std::array<double, 3> scale;
  if (labelSelector == "sal")
  {
    // xyzLabels = std::array<std::string,3>{"S", "A", "L"};
    xyzLabels = std::array<std::string, 3>{"+X", "+Y", "+Z"};
    cubeLabels = std::array<std::string, 6>{"S", "I", "A", "P", "L", "R"};
    scale = std::array<double, 3>{1.5, 1.5, 1.5};
  }
  else if (labelSelector == "rsp")
  {
    // xyzLabels = std::array<std::string, 3>{"R", "S", "P"};
    xyzLabels = std::array<std::string, 3>{"+X", "+Y", "+Z"};
    cubeLabels = std::array<std::string, 6>{"R", "L", "S", "I", "P", "A"};
    scale = std::array<double, 3>{1.5, 1.5, 1.5};
  }
  else if (labelSelector == "lsa")
  {
    // xyzLabels = std::array<std::string, 3>{"L", "S", "A"};
    xyzLabels = std::array<std::string, 3>{"+X", "+Y", "+Z"};
    cubeLabels = std::array<std::string, 6>{"L", "R", "S", "I", "A", "P"};
    scale = std::array<double, 3>{1.5, 1.5, 1.5};
  }
  else
  {
    xyzLabels = std::array<std::string, 3>{"+X", "+Y", "+Z"};
    cubeLabels = std::array<std::string, 6>{"+X", "-X", "+Y", "-Y", "+Z", "-Z"};
    scale = std::array<double, 3>{1.5, 1.5, 1.5};
  }

  // We are combining a vtkAxesActor and a vtkAnnotatedCubeActor
  // into a vtkPropAssembly
  auto cube = MakeAnnotatedCubeActor(cubeLabels, colors);
  auto axes = MakeAxesActor(scale, xyzLabels);

  // Combine orientation markers into one with an assembly.
  vtkNew<vtkPropAssembly> assembly;
  assembly->AddPart(axes);
  assembly->AddPart(cube);
  return assembly;
}

vtkNew<vtkSliderWidget> MakeSliderWidget(SliderProperties const& sp,
                                         vtkLookupTable* lut, int const& idx)
{
  vtkNew<vtkSliderRepresentation2D> slider;

  slider->SetMinimumValue(sp.valueMinimum);
  slider->SetMaximumValue(sp.valueMaximum);
  slider->SetValue(sp.valueInitial);
  slider->SetTitleText(sp.title.c_str());

  slider->GetPoint1Coordinate()->SetCoordinateSystemToNormalizedDisplay();
  slider->GetPoint1Coordinate()->SetValue(sp.p1[0], sp.p1[1]);
  slider->GetPoint2Coordinate()->SetCoordinateSystemToNormalizedDisplay();
  slider->GetPoint2Coordinate()->SetValue(sp.p2[0], sp.p2[1]);

  slider->SetTubeWidth(sp.tubeWidth);
  slider->SetSliderLength(sp.sliderLength);
  slider->SetSliderWidth(sp.sliderWidth);
  slider->SetEndCapLength(sp.endCapLength);
  slider->SetEndCapWidth(sp.endCapWidth);
  slider->SetTitleHeight(sp.titleHeight);
  slider->SetLabelHeight(sp.labelHeight);

  vtkNew<vtkNamedColors> colors;
  // Set the colors of the slider components.
  // Change the color of the bar.
  slider->GetTubeProperty()->SetColor(
      colors->GetColor3d(sp.barColor).GetData());
  // Change the color of the ends of the bar.
  slider->GetCapProperty()->SetColor(
      colors->GetColor3d(sp.barEndsColor).GetData());
  // Change the color of the knob that slides.
  slider->GetSliderProperty()->SetColor(
      colors->GetColor3d(sp.sliderColor).GetData());
  // Change the color of the knob when the mouse is held on it.
  slider->GetSelectedProperty()->SetColor(
      colors->GetColor3d(sp.selectedColor).GetData());
  // Change the color of the text displaying the value.
  slider->GetLabelProperty()->SetColor(
      colors->GetColor3d(sp.valueColor).GetData());
  //  Use the one color for the labels.
  // slider->GetTitleProperty()->SetColor(colors->GetColor3d(sp.labelColor));
  // Change the color of the text indicating what the slider controls.
  if (idx >= 0 && idx < 16)
  {
    slider->GetTitleProperty()->SetColor(lut->GetTableValue(idx));
    slider->GetTitleProperty()->ShadowOff();
  }
  else
  {
    slider->GetTitleProperty()->SetColor(
        colors->GetColor3d(sp.titleColor).GetData());
  }

  vtkNew<vtkSliderWidget> sliderWidget;
  sliderWidget->SetRepresentation(slider);

  return sliderWidget;
}

} // namespace

CMakeLists.txt

cmake_minimum_required(VERSION 3.12 FATAL_ERROR)

project(FroggieView)

find_package(VTK COMPONENTS 
  CommonColor
  CommonCore
  CommonMath
  CommonTransforms
  FiltersCore
  FiltersGeneral
  IOLegacy
  InteractionStyle
  InteractionWidgets
  RenderingAnnotation
  RenderingContextOpenGL2
  RenderingCore
  RenderingFreeType
  RenderingGL2PSOpenGL2
  RenderingOpenGL2
  cli11
  jsoncpp
)

if (NOT VTK_FOUND)
  message(FATAL_ERROR "FroggieView: 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(FroggieView MACOSX_BUNDLE FroggieView.cxx )
  target_link_libraries(FroggieView PRIVATE ${VTK_LIBRARIES}
)
# vtk_module_autoinit is needed
vtk_module_autoinit(
  TARGETS FroggieView
  MODULES ${VTK_LIBRARIES}
)

Download and Build FroggieView

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

cd FroggieView/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:

./FroggieView

WINDOWS USERS

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