FrogSlice

VTKExamples/Cxx/Visualization/FrogSlice


Description

This example uses a dataset derived from a frog. This data was prepared at Lawrence Berkeley National Laboratories and 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. (To accommodate the volume readers we have in VTK, we processed the mask files and combined them all into one vtkMetaImageReader .mhd file. Integer numbers 1–15 to represent the 15 tissues.

This example shows a photographic slice of frog (upper left), segmented frog (upper right) and composite of photo and segmentation (bottom). The purple color represents the stomach and the kidneys are yellow.

Other Languages

See (Python)

Question

If you have a simple question about this example contact us at VTKExamplesProject If your question is more complex and may require extended discussion, please use the VTK Discourse Forum

Code

FrogSlice.cxx

#include <vtkActor.h>
#include <vtkCamera.h>
#include <vtkImageConstantPad.h>
#include <vtkLookupTable.h>
#include <vtkMetaImageReader.h>
#include <vtkNamedColors.h>
#include <vtkPlaneSource.h>
#include <vtkPolyDataMapper.h>
#include <vtkPolyDataNormals.h>
#include <vtkProperty.h>
#include <vtkRenderWindow.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkRenderer.h>
#include <vtkTexture.h>
#include <vtkTransform.h>
#include <vtkTransformPolyDataFilter.h>
#include <vtkWindowLevelLookupTable.h>

#include <map>
#include <string>

namespace {
void CreateFrogLut(vtkSmartPointer<vtkLookupTable>& colorLut);
void SliceOrder(
    std::map<std::string, vtkSmartPointer<vtkTransform>>& sliceOrder);
} // namespace
int main(int argc, char* argv[])
{
  if (argc < 3)
  {
    std::cout << "Usage: " << argv[0] << " frog.mhd frogtissue.mhd [slice]"
              << std::endl;
    return EXIT_FAILURE;
  }
  int sliceNumber = 39; // to match figure 12-6
  if (argc > 3)
  {
    sliceNumber = atoi(argv[3]);
  }
  std::map<std::string, vtkSmartPointer<vtkTransform>> sliceOrder;
  SliceOrder(sliceOrder);

  // Now create the RenderWindow, Renderer and Interactor
  //
  auto ren1 =
    vtkSmartPointer<vtkRenderer>::New();
  auto ren2 =
    vtkSmartPointer<vtkRenderer>::New();
  auto ren3 =
    vtkSmartPointer<vtkRenderer>::New();
  auto renWin =
    vtkSmartPointer<vtkRenderWindow>::New();
  renWin->AddRenderer(ren1);
  renWin->AddRenderer(ren2);
  renWin->AddRenderer(ren3);

  auto iren =
    vtkSmartPointer<vtkRenderWindowInteractor>::New();
  iren->SetRenderWindow(renWin);

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

  auto greyPadder =
    vtkSmartPointer<vtkImageConstantPad>::New();
  greyPadder->SetInputConnection(greyReader->GetOutputPort());
  greyPadder->SetOutputWholeExtent(0, 511, 0, 511, sliceNumber, sliceNumber);
  greyPadder->SetConstant(0);

  auto greyPlane =
    vtkSmartPointer<vtkPlaneSource>::New();

  auto greyTransform =
    vtkSmartPointer<vtkTransformPolyDataFilter>::New();
  greyTransform->SetTransform(sliceOrder["hfsi"]);
  greyTransform->SetInputConnection(greyPlane->GetOutputPort());

  auto greyNormals =
    vtkSmartPointer<vtkPolyDataNormals>::New();
  greyNormals->SetInputConnection(greyTransform->GetOutputPort());
  greyNormals->FlipNormalsOff();

  auto wllut =
    vtkSmartPointer<vtkWindowLevelLookupTable>::New();
  wllut->SetWindow(255);
  wllut->SetLevel(128);
  wllut->SetTableRange(0, 255);
  wllut->Build();

  auto greyMapper =
    vtkSmartPointer<vtkPolyDataMapper>::New();
  greyMapper->SetInputConnection(greyPlane->GetOutputPort());

  auto greyTexture =
    vtkSmartPointer<vtkTexture>::New();
  greyTexture->SetInputConnection(greyPadder->GetOutputPort());
  greyTexture->SetLookupTable(wllut);
  greyTexture->SetColorModeToMapScalars();
  greyTexture->InterpolateOn();

  auto greyActor =
    vtkSmartPointer<vtkActor>::New();
  greyActor->SetMapper(greyMapper);
  greyActor->SetTexture(greyTexture);

  auto segmentReader =
    vtkSmartPointer<vtkMetaImageReader>::New();
  segmentReader->SetFileName(argv[2]);
  segmentReader->Update();

  auto segmentPadder =
    vtkSmartPointer<vtkImageConstantPad>::New();
  segmentPadder->SetInputConnection(segmentReader->GetOutputPort());
  segmentPadder->SetOutputWholeExtent(0, 511, 0, 511, sliceNumber, sliceNumber);
  segmentPadder->SetConstant(0);

  auto segmentPlane =
    vtkSmartPointer<vtkPlaneSource>::New();

  auto segmentTransform =
    vtkSmartPointer<vtkTransformPolyDataFilter>::New();
  segmentTransform->SetTransform(sliceOrder["hfsi"]);
  segmentTransform->SetInputConnection(segmentPlane->GetOutputPort());

  auto segmentNormals =
    vtkSmartPointer<vtkPolyDataNormals>::New();
  segmentNormals->SetInputConnection(segmentTransform->GetOutputPort());
  segmentNormals->FlipNormalsOn();

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

  auto segmentMapper =
    vtkSmartPointer<vtkPolyDataMapper>::New();
  segmentMapper->SetInputConnection(segmentPlane->GetOutputPort());

  auto segmentTexture =
    vtkSmartPointer<vtkTexture>::New();
  segmentTexture->SetInputConnection(segmentPadder->GetOutputPort());
  segmentTexture->SetLookupTable(colorLut);
  segmentTexture->SetColorModeToMapScalars();
  segmentTexture->InterpolateOff();

  auto segmentActor =
    vtkSmartPointer<vtkActor>::New();
  segmentActor->SetMapper(segmentMapper);
  segmentActor->SetTexture(segmentTexture);

  auto segmentOverlayActor =
    vtkSmartPointer<vtkActor>::New();
  segmentOverlayActor->SetMapper(segmentMapper);
  segmentOverlayActor->SetTexture(segmentTexture);

  segmentOverlayActor->GetProperty()->SetOpacity(.5);
  ren1->SetBackground(0, 0, 0);
  ren1->SetViewport(0, .5, .5, 1);
  renWin->SetSize(640, 480);
  ren1->AddActor(greyActor);

  ren2->SetBackground(0, 0, 0);
  ren2->SetViewport(.5, .5, 1, 1);
  ren2->AddActor(segmentActor);

  auto cam1 =
    vtkSmartPointer<vtkCamera>::New();
  cam1->SetViewUp(0, -1, 0);
  cam1->SetPosition(0, 0, -1);
  ren1->SetActiveCamera(cam1);
  ren1->ResetCamera();
  cam1->SetViewUp(0, -1, 0);
  cam1->SetPosition(0.0554068, -0.0596001, -0.491383);
  cam1->SetFocalPoint(0.0554068, -0.0596001, 0);
  ren1->ResetCameraClippingRange();

  ren3->AddActor(greyActor);
  ren3->AddActor(segmentOverlayActor);
  segmentOverlayActor->SetPosition(0, 0, -.01);

  ren3->SetBackground(0, 0, 0);
  ren3->SetViewport(0, 0, 1, .5);

  ren2->SetActiveCamera(ren1->GetActiveCamera());
  ren3->SetActiveCamera(ren1->GetActiveCamera());

  renWin->Render();
  iren->Start();

  return EXIT_SUCCESS;
}

namespace {
void CreateFrogLut(vtkSmartPointer<vtkLookupTable>& colorLut)
{
  auto colors =
    vtkSmartPointer<vtkNamedColors>::New();
  colorLut->SetTableValue(0,
                          colors->GetColor4d("black").GetData());
  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
}

void SliceOrder(
    std::map<std::string, vtkSmartPointer<vtkTransform>>& sliceOrder)
{
  //
  // these transformations permute medical image 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:
  // 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
  //
  double siMatrix[16] = {1, 0, 0, 0, 0, 0, 1, 0, 0, -1, 0, 0, 0, 0, 0, 1};
  auto si =
    vtkSmartPointer<vtkTransform>::New();
  si->SetMatrix(siMatrix);
  sliceOrder["si"] = si;

  double isMatrix[16] = {1, 0, 0, 0, 0, 0, -1, 0, 0, -1, 0, 0, 0, 0, 0, 1};
  auto is =
    vtkSmartPointer<vtkTransform>::New();
  is->SetMatrix(isMatrix);
  sliceOrder["is"] = is;

  auto ap =
    vtkSmartPointer<vtkTransform>::New();
  ap->Scale(1, -1, 1);
  sliceOrder["ap"] = ap;

  auto pa =
    vtkSmartPointer<vtkTransform>::New();
  pa->Scale(1, -1, -1);
  sliceOrder["pa"] = pa;

  double lrMatrix[16] = {0, 0, -1, 0, 0, -1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1};
  auto lr =
    vtkSmartPointer<vtkTransform>::New();
  lr->SetMatrix(lrMatrix);
  sliceOrder["lr"] = lr;

  double rlMatrix[16] = {0, 0, 1, 0, 0, -1, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1};
  auto rl =
    vtkSmartPointer<vtkTransform>::New();
  rl->SetMatrix(rlMatrix);
  sliceOrder["rl"] = rl;

  //
  // The previous transforms assume radiological views of the slices (viewed
  // from the feet). other modalities such as physical sectioning may view from
  // the head. these transforms modify the original with a 180 rotation about y
  //
  double hfMatrix[16] = {-1, 0, 0, 0, 0, 1, 0, 0, 0, 0, -1, 0, 0, 0, 0, 1};
  auto hf =
    vtkSmartPointer<vtkTransform>::New();
  hf->SetMatrix(hfMatrix);
  sliceOrder["hf"] = hf;

  auto hfsi =
    vtkSmartPointer<vtkTransform>::New();
  hfsi->Concatenate(hf->GetMatrix());
  hfsi->Concatenate(si->GetMatrix());
  sliceOrder["hfsi"] = hfsi;

  auto hfis =
    vtkSmartPointer<vtkTransform>::New();
  hfis->Concatenate(hf->GetMatrix());
  hfis->Concatenate(is->GetMatrix());
  sliceOrder["hfis"] = hfis;

  auto hfap =
    vtkSmartPointer<vtkTransform>::New();
  hfap->Concatenate(hf->GetMatrix());
  hfap->Concatenate(ap->GetMatrix());
  sliceOrder["hfap"] = hfap;

  auto hfpa =
    vtkSmartPointer<vtkTransform>::New();
  hfpa->Concatenate(hf->GetMatrix());
  hfpa->Concatenate(pa->GetMatrix());
  sliceOrder["hfpa"] = hfpa;

  auto hflr =
    vtkSmartPointer<vtkTransform>::New();
  hflr->Concatenate(hf->GetMatrix());
  hflr->Concatenate(lr->GetMatrix());
  sliceOrder[""] = hflr;

  auto hfrl =
    vtkSmartPointer<vtkTransform>::New();
  hfrl->Concatenate(hf->GetMatrix());
  hfrl->Concatenate(rl->GetMatrix());
  sliceOrder["hfrl"] = hfrl;
}
} // namespace

CMakeLists.txt

cmake_minimum_required(VERSION 3.3 FATAL_ERROR)

project(FrogSlice)

find_package(VTK COMPONENTS 
  vtkCommonColor
  vtkCommonCore
  vtkCommonTransforms
  vtkFiltersCore
  vtkFiltersGeneral
  vtkFiltersSources
  vtkIOImage
  vtkImagingCore
  vtkInteractionStyle
  vtkRenderingContextOpenGL2
  vtkRenderingCore
  vtkRenderingFreeType
  vtkRenderingGL2PSOpenGL2
  vtkRenderingOpenGL2 QUIET)
if (NOT VTK_FOUND)
  message("Skipping FrogSlice: ${VTK_NOT_FOUND_MESSAGE}")
  return ()
endif()
message (STATUS "VTK_VERSION: ${VTK_VERSION}")
if (VTK_VERSION VERSION_LESS "8.90.0")
  # old system
  include(${VTK_USE_FILE})
  add_executable(FrogSlice MACOSX_BUNDLE FrogSlice.cxx )
  target_link_libraries(FrogSlice PRIVATE ${VTK_LIBRARIES})
else ()
  # include all components
  add_executable(FrogSlice MACOSX_BUNDLE FrogSlice.cxx )
  target_link_libraries(FrogSlice PRIVATE ${VTK_LIBRARIES})
  # vtk_module_autoinit is needed
  vtk_module_autoinit(
    TARGETS FrogSlice
    MODULES ${VTK_LIBRARIES}
    )
endif () 

Download and Build FrogSlice

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

cd FrogSlice/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:

./FrogSlice

WINDOWS USERS

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