FixedPointVolumeRayCastMapperCT

#include <vtkFixedPointVolumeRayCastMapper.h>

#include <vtkBoxWidget.h>
#include <vtkCamera.h>
#include <vtkCommand.h>
#include <vtkColorTransferFunction.h>
#include <vtkDICOMImageReader.h>
#include <vtkImageData.h>
#include <vtkImageResample.h>
#include <vtkMetaImageReader.h>
#include <vtkPiecewiseFunction.h>
#include <vtkPlanes.h>
#include <vtkProperty.h>
#include <vtkRenderer.h>
#include <vtkRenderWindow.h>
#include <vtkRenderWindowInteractor.h>
#include <vtkVolume.h>
#include <vtkVolumeProperty.h>
#include <vtkXMLImageDataReader.h>
#include <vtkNamedColors.h>

#define VTI_FILETYPE 1
#define MHA_FILETYPE 2

namespace
{
void PrintUsage()
{
  cout << "Usage: " << endl;
  cout << endl;
  cout << "  FixedPointVolumeRayCastMapperCT <options>" << endl;
  cout << endl;
  cout << "where options may include: " << endl;
  cout << endl;
  cout << "  -DICOM <directory>" << endl;
  cout << "  -VTI <filename>" << endl;
  cout << "  -MHA <filename>" << endl;
  cout << "  -DependentComponents" << endl;
  cout << "  -Clip" << endl;
  cout << "  -MIP <window> <level>" << endl;
  cout << "  -CompositeRamp <window> <level>" << endl;
  cout << "  -CompositeShadeRamp <window> <level>" << endl;
  cout << "  -CT_Skin" << endl;
  cout << "  -CT_Bone" << endl;
  cout << "  -CT_Muscle" << endl;
  cout << "  -FrameRate <rate>" << endl;
  cout << "  -DataReduction <factor>" << endl;
  cout << endl;
  cout << "You must use either the -DICOM option to specify the directory where" << endl;
  cout << "the data is located or the -VTI or -MHA option to specify the path of a .vti file." << endl;
  cout << endl;
  cout << "By default, the program assumes that the file has independent components," << endl;
  cout << "use -DependentComponents to specify that the file has dependent components." << endl;
  cout << endl;
  cout << "Use the -Clip option to display a cube widget for clipping the volume." << endl;
  cout << "Use the -FrameRate option with a desired frame rate (in frames per second)" << endl;
  cout << "which will control the interactive rendering rate." << endl;
  cout << "Use the -DataReduction option with a reduction factor (greater than zero and" << endl;
  cout << "less than one) to reduce the data before rendering." << endl;
  cout << "Use one of the remaining options to specify the blend function" << endl;
  cout << "and transfer functions. The -MIP option utilizes a maximum intensity" << endl;
  cout << "projection method, while the others utilize compositing. The" << endl;
  cout << "-CompositeRamp option is unshaded compositing, while the other" << endl;
  cout << "compositing options employ shading." << endl;
  cout << endl;
  cout << "Note: MIP, CompositeRamp, CompositeShadeRamp, CT_Skin, CT_Bone," << endl;
  cout << "and CT_Muscle are appropriate for DICOM data. MIP, CompositeRamp," << endl;
  cout << "and RGB_Composite are appropriate for RGB data." << endl;
  cout << endl;
  cout << "Example: FixedPointVolumeRayCastMapperCT -DICOM CTNeck -MIP 4096 1024" << endl;
  cout << endl;
}
}
int main(int argc, char *argv[])
{
  // Parse the parameters

  int count = 1;
  char *dirname = NULL;
  double opacityWindow = 4096;
  double opacityLevel = 2048;
  int blendType = 0;
  int clip = 0;
  double reductionFactor = 1.0;
  double frameRate = 10.0;
  char *fileName=0;
  int fileType=0;

  bool independentComponents=true;

  while ( count < argc )
  {
    if ( !strcmp( argv[count], "?" ) )
    {
      PrintUsage();
      exit(EXIT_SUCCESS);
    }
    else if ( !strcmp( argv[count], "-DICOM" ) )
    {
      size_t size = strlen(argv[count+1])+1;
      dirname = new char[size];
      snprintf( dirname, size, "%s", argv[count+1] );
      count += 2;
    }
    else if ( !strcmp( argv[count], "-VTI" ) )
    {
      size_t size = strlen(argv[count+1])+1;
      fileName = new char[size];
      fileType = VTI_FILETYPE;
      snprintf( fileName, size, "%s", argv[count+1] );
      count += 2;
    }
    else if ( !strcmp( argv[count], "-MHA" ) )
    {
      size_t size = strlen(argv[count+1])+1;
      fileName = new char[size];
      fileType = MHA_FILETYPE;
      snprintf( fileName, size, "%s", argv[count+1] );
      count += 2;
    }
    else if ( !strcmp( argv[count], "-Clip") )
    {
      clip = 1;
      count++;
    }
    else if ( !strcmp( argv[count], "-MIP" ) )
    {
      opacityWindow = atof( argv[count+1] );
      opacityLevel  = atof( argv[count+2] );
      blendType = 0;
      count += 3;
    }
    else if ( !strcmp( argv[count], "-CompositeRamp" ) )
    {
      opacityWindow = atof( argv[count+1] );
      opacityLevel  = atof( argv[count+2] );
      blendType = 1;
      count += 3;
    }
    else if ( !strcmp( argv[count], "-CompositeShadeRamp" ) )
    {
      opacityWindow = atof( argv[count+1] );
      opacityLevel  = atof( argv[count+2] );
      blendType = 2;
      count += 3;
    }
    else if ( !strcmp( argv[count], "-CT_Skin" ) )
    {
      blendType = 3;
      count += 1;
    }
    else if ( !strcmp( argv[count], "-CT_Bone" ) )
    {
      blendType = 4;
      count += 1;
    }
    else if ( !strcmp( argv[count], "-CT_Muscle" ) )
    {
      blendType = 5;
      count += 1;
    }
    else if ( !strcmp( argv[count], "-RGB_Composite" ) )
    {
      blendType = 6;
      count += 1;
    }
    else if ( !strcmp( argv[count], "-FrameRate") )
    {
      frameRate = atof( argv[count+1] );
      if ( frameRate < 0.01 || frameRate > 60.0 )
      {
        cout << "Invalid frame rate - use a number between 0.01 and 60.0" << endl;
        cout << "Using default frame rate of 10 frames per second." << endl;
        frameRate = 10.0;
      }
      count += 2;
    }
    else if ( !strcmp( argv[count], "-ReductionFactor") )
    {
      reductionFactor = atof( argv[count+1] );
      if ( reductionFactor <= 0.0 || reductionFactor >= 1.0 )
      {
        cout << "Invalid reduction factor - use a number between 0 and 1 (exclusive)" << endl;
        cout << "Using the default of no reduction." << endl;
        reductionFactor = 1.0;
      }
      count += 2;
    }
     else if ( !strcmp( argv[count], "-DependentComponents") )
     {
      independentComponents=false;
      count += 1;
     }
    else
    {
      cout << "Unrecognized option: " << argv[count] << endl;
      cout << endl;
      PrintUsage();
      exit(EXIT_FAILURE);
    }
  }

  if ( !dirname && !fileName)
  {
    cout << "Error: you must specify a directory of DICOM data or a .vti file or a .mha!" << endl;
    cout << endl;
    PrintUsage();
    exit(EXIT_FAILURE);
  }

  // Create the renderer, render window and interactor
  vtkSmartPointer<vtkNamedColors> colors =
    vtkSmartPointer<vtkNamedColors>::New();
  vtkSmartPointer<vtkRenderer> renderer =
    vtkSmartPointer<vtkRenderer>::New();
  vtkSmartPointer<vtkRenderWindow> renWin =
    vtkSmartPointer<vtkRenderWindow>::New();
  renWin->AddRenderer(renderer);

  // Connect it all. Note that funny arithematic on the
  // SetDesiredUpdateRate - the vtkRenderWindow divides it
  // allocated time across all renderers, and the renderer
  // divides it time across all props. If clip is
  // true then there are two props
  vtkSmartPointer<vtkRenderWindowInteractor> iren =
    vtkSmartPointer<vtkRenderWindowInteractor>::New();
  iren->SetRenderWindow(renWin);
  iren->SetDesiredUpdateRate(frameRate / (1+clip) );

  iren->GetInteractorStyle()->SetDefaultRenderer(renderer);

  // Read the data
  vtkSmartPointer<vtkAlgorithm> reader =
    vtkSmartPointer<vtkAlgorithm>::New();
  vtkSmartPointer<vtkImageData> input =
    vtkSmartPointer<vtkImageData>::New();
  if(dirname)
  {
    vtkSmartPointer<vtkDICOMImageReader> dicomReader =
      vtkSmartPointer<vtkDICOMImageReader>::New();
    dicomReader->SetDirectoryName(dirname);
    dicomReader->Update();
    input=dicomReader->GetOutput();
    reader=dicomReader;
  }
  else if ( fileType == VTI_FILETYPE )
  {
    vtkSmartPointer<vtkXMLImageDataReader> xmlReader =
      vtkSmartPointer<vtkXMLImageDataReader>::New();
    xmlReader->SetFileName(fileName);
    xmlReader->Update();
    input=xmlReader->GetOutput();
    reader=xmlReader;
  }
  else if ( fileType == MHA_FILETYPE )
  {
    vtkSmartPointer<vtkMetaImageReader> metaReader =
      vtkSmartPointer<vtkMetaImageReader>::New();
    metaReader->SetFileName(fileName);
    metaReader->Update();
    input=metaReader->GetOutput();
    reader=metaReader;
  }
  else
  {
    cout << "Error! Not VTI or MHA!" << endl;
    exit(EXIT_FAILURE);
  }

  // Verify that we actually have a volume
  int dim[3];
  input->GetDimensions(dim);

  if ( dim[0] < 2 ||
       dim[1] < 2 ||
       dim[2] < 2 )
  {
    cout << "Error loading data!" << endl;
    exit(EXIT_FAILURE);
  }

  vtkSmartPointer<vtkImageResample> resample =
    vtkSmartPointer<vtkImageResample>::New();
  if ( reductionFactor < 1.0 )
  {
    resample->SetInputConnection( reader->GetOutputPort() );
    resample->SetAxisMagnificationFactor(0, reductionFactor);
    resample->SetAxisMagnificationFactor(1, reductionFactor);
    resample->SetAxisMagnificationFactor(2, reductionFactor);
  }

  // Create our volume and mapper
  vtkSmartPointer<vtkVolume> volume =
    vtkSmartPointer<vtkVolume>::New();
  vtkSmartPointer<vtkFixedPointVolumeRayCastMapper> mapper =
    vtkSmartPointer<vtkFixedPointVolumeRayCastMapper>::New();

  if ( reductionFactor < 1.0 )
  {
    mapper->SetInputConnection( resample->GetOutputPort() );
  }
  else
  {
    mapper->SetInputConnection( reader->GetOutputPort() );
  }


  // Set the sample distance on the ray to be 1/2 the average spacing
  double spacing[3];
  if ( reductionFactor < 1.0 )
  {
    resample->GetOutput()->GetSpacing(spacing);
  }
  else
  {
    input->GetSpacing(spacing);
  }

//  mapper->SetSampleDistance( (spacing[0]+spacing[1]+spacing[2])/6.0 );
//  mapper->SetMaximumImageSampleDistance(10.0);


  // Create our transfer function
  vtkSmartPointer<vtkColorTransferFunction> colorFun =
    vtkSmartPointer<vtkColorTransferFunction>::New();
  vtkSmartPointer<vtkPiecewiseFunction> opacityFun =
    vtkSmartPointer<vtkPiecewiseFunction>::New();
  // Create the property and attach the transfer functions
  vtkSmartPointer<vtkVolumeProperty> property =
    vtkSmartPointer<vtkVolumeProperty>::New();
  property->SetIndependentComponents(independentComponents);
  property->SetColor( colorFun );
  property->SetScalarOpacity( opacityFun );
  property->SetInterpolationTypeToLinear();

  // connect up the volume to the property and the mapper
  volume->SetProperty( property );
  volume->SetMapper( mapper );

  // Depending on the blend type selected as a command line option,
  // adjust the transfer function
  switch ( blendType )
  {
    // MIP
    // Create an opacity ramp from the window and level values.
    // Color is white. Blending is MIP.
    case 0:
      colorFun->AddRGBSegment(0.0, 1.0, 1.0, 1.0, 255.0, 1.0, 1.0, 1.0 );
      opacityFun->AddSegment( opacityLevel - 0.5*opacityWindow, 0.0,
                              opacityLevel + 0.5*opacityWindow, 1.0 );
      mapper->SetBlendModeToMaximumIntensity();
      break;

    // CompositeRamp
    // Create a ramp from the window and level values. Use compositing
    // without shading. Color is a ramp from black to white.
    case 1:
      colorFun->AddRGBSegment(opacityLevel - 0.5*opacityWindow, 0.0, 0.0, 0.0,
                              opacityLevel + 0.5*opacityWindow, 1.0, 1.0, 1.0 );
      opacityFun->AddSegment( opacityLevel - 0.5*opacityWindow, 0.0,
                              opacityLevel + 0.5*opacityWindow, 1.0 );
      mapper->SetBlendModeToComposite();
      property->ShadeOff();
      break;

    // CompositeShadeRamp
    // Create a ramp from the window and level values. Use compositing
    // with shading. Color is white.
    case 2:
      colorFun->AddRGBSegment(0.0, 1.0, 1.0, 1.0, 255.0, 1.0, 1.0, 1.0 );
      opacityFun->AddSegment( opacityLevel - 0.5*opacityWindow, 0.0,
                              opacityLevel + 0.5*opacityWindow, 1.0 );
      mapper->SetBlendModeToComposite();
      property->ShadeOn();
      break;

    // CT_Skin
    // Use compositing and functions set to highlight skin in CT data
    // Not for use on RGB data
    case 3:
      colorFun->AddRGBPoint( -3024, 0, 0, 0, 0.5, 0.0 );
      colorFun->AddRGBPoint( -1000, .62, .36, .18, 0.5, 0.0 );
      colorFun->AddRGBPoint( -500, .88, .60, .29, 0.33, 0.45 );
      colorFun->AddRGBPoint( 3071, .83, .66, 1, 0.5, 0.0 );

      opacityFun->AddPoint(-3024, 0, 0.5, 0.0 );
      opacityFun->AddPoint(-1000, 0, 0.5, 0.0 );
      opacityFun->AddPoint(-500, 1.0, 0.33, 0.45 );
      opacityFun->AddPoint(3071, 1.0, 0.5, 0.0);

      mapper->SetBlendModeToComposite();
      property->ShadeOn();
      property->SetAmbient(0.1);
      property->SetDiffuse(0.9);
      property->SetSpecular(0.2);
      property->SetSpecularPower(10.0);
      property->SetScalarOpacityUnitDistance(0.8919);
      break;

    // CT_Bone
    // Use compositing and functions set to highlight bone in CT data
    // Not for use on RGB data
    case 4:
      colorFun->AddRGBPoint( -3024, 0, 0, 0, 0.5, 0.0 );
      colorFun->AddRGBPoint( -16, 0.73, 0.25, 0.30, 0.49, .61 );
      colorFun->AddRGBPoint( 641, .90, .82, .56, .5, 0.0 );
      colorFun->AddRGBPoint( 3071, 1, 1, 1, .5, 0.0 );

      opacityFun->AddPoint(-3024, 0, 0.5, 0.0 );
      opacityFun->AddPoint(-16, 0, .49, .61 );
      opacityFun->AddPoint(641, .72, .5, 0.0 );
      opacityFun->AddPoint(3071, .71, 0.5, 0.0);

      mapper->SetBlendModeToComposite();
      property->ShadeOn();
      property->SetAmbient(0.1);
      property->SetDiffuse(0.9);
      property->SetSpecular(0.2);
      property->SetSpecularPower(10.0);
      property->SetScalarOpacityUnitDistance(0.8919);
      break;

    // CT_Muscle
    // Use compositing and functions set to highlight muscle in CT data
    // Not for use on RGB data
    case 5:
      colorFun->AddRGBPoint( -3024, 0, 0, 0, 0.5, 0.0 );
      colorFun->AddRGBPoint( -155, .55, .25, .15, 0.5, .92 );
      colorFun->AddRGBPoint( 217, .88, .60, .29, 0.33, 0.45 );
      colorFun->AddRGBPoint( 420, 1, .94, .95, 0.5, 0.0 );
      colorFun->AddRGBPoint( 3071, .83, .66, 1, 0.5, 0.0 );

      opacityFun->AddPoint(-3024, 0, 0.5, 0.0 );
      opacityFun->AddPoint(-155, 0, 0.5, 0.92 );
      opacityFun->AddPoint(217, .68, 0.33, 0.45 );
      opacityFun->AddPoint(420,.83, 0.5, 0.0);
      opacityFun->AddPoint(3071, .80, 0.5, 0.0);

      mapper->SetBlendModeToComposite();
      property->ShadeOn();
      property->SetAmbient(0.1);
      property->SetDiffuse(0.9);
      property->SetSpecular(0.2);
      property->SetSpecularPower(10.0);
      property->SetScalarOpacityUnitDistance(0.8919);
      break;

    // RGB_Composite
    // Use compositing and functions set to highlight red/green/blue regions
    // in RGB data. Not for use on single component data
    case 6:
      opacityFun->AddPoint(0, 0.0);
      opacityFun->AddPoint(5.0, 0.0);
      opacityFun->AddPoint(30.0, 0.05);
      opacityFun->AddPoint(31.0, 0.0);
      opacityFun->AddPoint(90.0, 0.0);
      opacityFun->AddPoint(100.0, 0.3);
      opacityFun->AddPoint(110.0, 0.0);
      opacityFun->AddPoint(190.0, 0.0);
      opacityFun->AddPoint(200.0, 0.4);
      opacityFun->AddPoint(210.0, 0.0);
      opacityFun->AddPoint(245.0, 0.0);
      opacityFun->AddPoint(255.0, 0.5);

      mapper->SetBlendModeToComposite();
      property->ShadeOff();
      property->SetScalarOpacityUnitDistance(1.0);
      break;
    default:
       vtkGenericWarningMacro("Unknown blend type.");
       break;
  }

  // Set the default window size
  renWin->SetSize(600,600);
  renWin->Render();

  // Add the volume to the scene
  renderer->AddVolume( volume );

  renderer->ResetCamera();
  renderer->SetBackground(colors->GetColor3d("SlateGray").GetData());

  // interact with data
  renWin->Render();

  iren->Start();

  return EXIT_SUCCESS;;
}

cmake_minimum_required(VERSION 3.3 FATAL_ERROR)

project(FixedPointVolumeRayCastMapperCT)

find_package(VTK COMPONENTS 
  vtkvtkCommonColor
  vtkvtkCommonCore
  vtkvtkCommonDataModel
  vtkvtkIOImage
  vtkvtkIOXML
  vtkvtkImagingCore
  vtkvtkInteractionStyle
  vtkvtkInteractionWidgets
  vtkvtkRenderingContextOpenGL2
  vtkvtkRenderingCore
  vtkvtkRenderingFreeType
  vtkvtkRenderingGL2PSOpenGL2
  vtkvtkRenderingOpenGL2
  vtkvtkRenderingVolume
  vtkvtkRenderingVolumeOpenGL2 QUIET)
if (NOT VTK_FOUND)
  message("Skipping FixedPointVolumeRayCastMapperCT: ${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(FixedPointVolumeRayCastMapperCT MACOSX_BUNDLE FixedPointVolumeRayCastMapperCT.cxx )
  target_link_libraries(FixedPointVolumeRayCastMapperCT PRIVATE ${VTK_LIBRARIES})
else ()
  # include all components
  add_executable(FixedPointVolumeRayCastMapperCT MACOSX_BUNDLE FixedPointVolumeRayCastMapperCT.cxx )
  target_link_libraries(FixedPointVolumeRayCastMapperCT PRIVATE ${VTK_LIBRARIES})
  # vtk_module_autoinit is needed
  vtk_module_autoinit(
    TARGETS FixedPointVolumeRayCastMapperCT
    MODULES ${VTK_LIBRARIES}
    )
endif ()

cd FixedPointVolumeRayCastMapperCT/build

cmake ..

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

make

./FixedPointVolumeRayCastMapperCT