FrogSlice

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

#include <map>
#include <string>

namespace
{
void CreateFrogLut(vtkSmartPointer<vtkLookupTable> &colorLut);
void SliceOrder(std::map<std::string,
                vtkSmartPointer<vtkTransform> > &sliceOrder);
}
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);

  vtkSmartPointer<vtkNamedColors> colors =
    vtkSmartPointer<vtkNamedColors>::New();

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  vtkSmartPointer<vtkActor> 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);

  vtkSmartPointer<vtkCamera> 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)
{
  vtkSmartPointer<vtkNamedColors> colors =
    vtkSmartPointer<vtkNamedColors>::New();
  colorLut->SetTableValue(0,
                          0, 0, 0, 0);
  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_retna 
  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 acqusition 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};
  vtkSmartPointer<vtkTransform> 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};
  vtkSmartPointer<vtkTransform> is =
    vtkSmartPointer<vtkTransform>::New();
  is->SetMatrix(isMatrix);
  sliceOrder["is"] = is;

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

  vtkSmartPointer<vtkTransform> 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};
  vtkSmartPointer<vtkTransform> 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};
  vtkSmartPointer<vtkTransform> 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};
  vtkSmartPointer<vtkTransform> hf =
    vtkSmartPointer<vtkTransform>::New();
  hf->SetMatrix(hfMatrix);
  sliceOrder["hf"] = hf;

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

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

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

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

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

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

cmake_minimum_required(VERSION 2.8)

PROJECT(FrogSlice)

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

add_executable(FrogSlice MACOSX_BUNDLE FrogSlice.cxx )

target_link_libraries(FrogSlice ${VTK_LIBRARIES})

cd FrogSlice/build 

cmake ..

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

make

./FrogSlice