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FrogSlice

Repository source: 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.

Info

See Figure 12-6 in Chapter 12 the VTK Textbook.

Other languages

See (Python)

Question

If you have a question about this example, 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 <vtkNew.h>
#include <vtkPlaneSource.h>
#include <vtkPolyDataMapper.h>
#include <vtkPolyDataNormals.h>
#include <vtkProperty.h>
#include <vtkRenderWindow.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkRenderer.h>
#include <vtkSmartPointer.h>
#include <vtkTexture.h>
#include <vtkTransform.h>
#include <vtkTransformPolyDataFilter.h>
#include <vtkWindowLevelLookupTable.h>

#include <map>
#include <string>

namespace {
void CreateFrogLut(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);

  vtkNew<vtkNamedColors> colors;

  // Now create the RenderWindow, Renderer and Interactor
  //
  vtkNew<vtkRenderer> ren1;
  vtkNew<vtkRenderer> ren2;
  vtkNew<vtkRenderer> ren3;
  vtkNew<vtkRenderWindow> renWin;
  renWin->AddRenderer(ren1);
  renWin->AddRenderer(ren2);
  renWin->AddRenderer(ren3);
  renWin->SetWindowName("FrogSlice");

  vtkNew<vtkRenderWindowInteractor> iren;
  iren->SetRenderWindow(renWin);

  vtkNew<vtkMetaImageReader> greyReader;
  greyReader->SetFileName(argv[1]);
  greyReader->Update();

  vtkNew<vtkImageConstantPad> greyPadder;
  greyPadder->SetInputConnection(greyReader->GetOutputPort());
  greyPadder->SetOutputWholeExtent(0, 511, 0, 511, sliceNumber, sliceNumber);
  greyPadder->SetConstant(0);

  vtkNew<vtkPlaneSource> greyPlane;

  vtkNew<vtkTransformPolyDataFilter> greyTransform;
  greyTransform->SetTransform(sliceOrder["hfsi"]);
  greyTransform->SetInputConnection(greyPlane->GetOutputPort());

  vtkNew<vtkPolyDataNormals> greyNormals;
  greyNormals->SetInputConnection(greyTransform->GetOutputPort());
  greyNormals->FlipNormalsOff();

  vtkNew<vtkWindowLevelLookupTable> wllut;
  wllut->SetWindow(255);
  wllut->SetLevel(128);
  wllut->SetTableRange(0, 255);
  wllut->Build();

  vtkNew<vtkPolyDataMapper> greyMapper;
  greyMapper->SetInputConnection(greyPlane->GetOutputPort());

  vtkNew<vtkTexture> greyTexture;
  greyTexture->SetInputConnection(greyPadder->GetOutputPort());
  greyTexture->SetLookupTable(wllut);
  greyTexture->SetColorModeToMapScalars();
  greyTexture->InterpolateOn();

  vtkNew<vtkActor> greyActor;
  greyActor->SetMapper(greyMapper);
  greyActor->SetTexture(greyTexture);

  vtkNew<vtkMetaImageReader> segmentReader;
  segmentReader->SetFileName(argv[2]);
  segmentReader->Update();

  vtkNew<vtkImageConstantPad> segmentPadder;
  segmentPadder->SetInputConnection(segmentReader->GetOutputPort());
  segmentPadder->SetOutputWholeExtent(0, 511, 0, 511, sliceNumber, sliceNumber);
  segmentPadder->SetConstant(0);

  vtkNew<vtkPlaneSource> segmentPlane;

  vtkNew<vtkTransformPolyDataFilter> segmentTransform;
  segmentTransform->SetTransform(sliceOrder["hfsi"]);
  segmentTransform->SetInputConnection(segmentPlane->GetOutputPort());

  vtkNew<vtkPolyDataNormals> segmentNormals;
  segmentNormals->SetInputConnection(segmentTransform->GetOutputPort());
  segmentNormals->FlipNormalsOn();

  vtkNew<vtkLookupTable> colorLut;
  colorLut->SetNumberOfColors(17);
  colorLut->SetTableRange(0, 16);
  colorLut->Build();
  CreateFrogLut(colorLut);

  vtkNew<vtkPolyDataMapper> segmentMapper;
  segmentMapper->SetInputConnection(segmentPlane->GetOutputPort());

  vtkNew<vtkTexture> segmentTexture;
  segmentTexture->SetInputConnection(segmentPadder->GetOutputPort());
  segmentTexture->SetLookupTable(colorLut);
  segmentTexture->SetColorModeToMapScalars();
  segmentTexture->InterpolateOff();

  vtkNew<vtkActor> segmentActor;
  segmentActor->SetMapper(segmentMapper);
  segmentActor->SetTexture(segmentTexture);

  vtkNew<vtkActor> segmentOverlayActor;
  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);

  vtkNew<vtkCamera> cam1;
  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, -0.01);

  ren1->SetBackground(colors->GetColor3d("SlateGray").GetData());
  ren2->SetBackground(colors->GetColor3d("SlateGray").GetData());
  ren3->SetBackground(colors->GetColor3d("SlateGray").GetData());

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

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

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

  return EXIT_SUCCESS;
}

namespace {
void CreateFrogLut(vtkLookupTable* colorLut)
{
  vtkNew<vtkNamedColors> colors;
  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};
  vtkNew<vtkTransform> si;
  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};
  vtkNew<vtkTransform> is;
  is->SetMatrix(isMatrix);
  sliceOrder["is"] = is;

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

  vtkNew<vtkTransform> pa;
  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};
  vtkNew<vtkTransform> lr;
  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};
  vtkNew<vtkTransform> rl;
  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};
  vtkNew<vtkTransform> hf;
  hf->SetMatrix(hfMatrix);
  sliceOrder["hf"] = hf;

  vtkNew<vtkTransform> hfsi;
  hfsi->Concatenate(hf->GetMatrix());
  hfsi->Concatenate(si->GetMatrix());
  sliceOrder["hfsi"] = hfsi;

  vtkNew<vtkTransform> hfis;
  hfis->Concatenate(hf->GetMatrix());
  hfis->Concatenate(is->GetMatrix());
  sliceOrder["hfis"] = hfis;

  vtkNew<vtkTransform> hfap;
  hfap->Concatenate(hf->GetMatrix());
  hfap->Concatenate(ap->GetMatrix());
  sliceOrder["hfap"] = hfap;

  vtkNew<vtkTransform> hfpa;
  hfpa->Concatenate(hf->GetMatrix());
  hfpa->Concatenate(pa->GetMatrix());
  sliceOrder["hfpa"] = hfpa;

  vtkNew<vtkTransform> hflr;
  hflr->Concatenate(hf->GetMatrix());
  hflr->Concatenate(lr->GetMatrix());
  sliceOrder[""] = hflr;

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

CMakeLists.txt

cmake_minimum_required(VERSION 3.12 FATAL_ERROR)

project(FrogSlice)

find_package(VTK COMPONENTS 
  CommonColor
  CommonCore
  CommonTransforms
  FiltersCore
  FiltersGeneral
  FiltersSources
  IOImage
  ImagingCore
  InteractionStyle
  RenderingContextOpenGL2
  RenderingCore
  RenderingFreeType
  RenderingGL2PSOpenGL2
  RenderingOpenGL2
)

if (NOT VTK_FOUND)
  message(FATAL_ERROR "FrogSlice: 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(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}
)

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.