[Insight-users] Problem with volume rendering using ITK, VTK and DICOM files

[Phrenology for Bipolarity]

Hi all,

I'm trying to visualize a DICOM series of files with VTK but when the volume is rendered everything is wrapped within a big black box.

This is what I get: http://img64.imageshack.us/img64/3506/visualize.png

And the volume I should be getting is inside it.

Can someone tell me what I'm doing wrong please? Or give some advice to fix this problem?


Below is my code, which is a combination of "InsightToolkit\Examples\IO\DicomSeriesReadImageWrite2.cxx" and "InsightApplications\Auxiliary\vtk\itkReadITKImageShowVTK.cxx" with some adjustments.

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#include "itkOrientedImage.h"
#include "itkGDCMImageIO.h"
#include "itkGDCMSeriesFileNames.h"
#include "itkImageSeriesReader.h"
#include "itkImageFileWriter.h"

#include "itkCommand.h"
#include "itkImage.h"
#include "itkVTKImageExport.h"
#include "itkVTKImageImport.h"
#include "itkCurvatureFlowImageFilter.h"
#include "itkCastImageFilter.h"
#include "itkRGBPixel.h"
#include "itkImageFileReader.h"
#include "itkImageFileWriter.h"
#include "vtkImageData.h"

#include "vtkImageImport.h"
#include "vtkImageExport.h"
#include "vtkImageActor.h"
#include "vtkRenderer.h"
#include "vtkRenderWindow.h"
#include "vtkRenderWindowInteractor.h"
#include "vtkInteractorStyleImage.h" 
#include "vtkPiecewiseFunction.h"
#include "vtkColorTransferFunction.h"
#include "vtkVolumeProperty.h"
#include "vtkVolumeTextureMapper3D.h"
#include "vtkFixedPointVolumeRayCastMapper.h"
#include "vtkSmartPointer.h"

template <typename ITK_Exporter, typename VTK_Importer>
void ConnectPipelines(ITK_Exporter exporter, VTK_Importer* importer)
{
  importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback());
  importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback());
  importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());
  importer->SetSpacingCallback(exporter->GetSpacingCallback());
  importer->SetOriginCallback(exporter->GetOriginCallback());
  importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());
  importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback());
  importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback());
  importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
  importer->SetDataExtentCallback(exporter->GetDataExtentCallback());
  importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback());
  importer->SetCallbackUserData(exporter->GetCallbackUserData());
}

template <typename VTK_Exporter, typename ITK_Importer>
void ConnectPipelines(VTK_Exporter* exporter, ITK_Importer importer)
{
  importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback());
  importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback());
  importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback());
  importer->SetSpacingCallback(exporter->GetSpacingCallback());
  importer->SetOriginCallback(exporter->GetOriginCallback());
  importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback());
  importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback());
  importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback());
  importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback());
  importer->SetDataExtentCallback(exporter->GetDataExtentCallback());
  importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback());
  importer->SetCallbackUserData(exporter->GetCallbackUserData());
}

void visualize(std::string dcm)
{ 

 typedef itk::RGBPixel< signed short > PixelType;
 const unsigned int      Dimension = 3;

 typedef itk::OrientedImage< PixelType, 3 > ImageType;

 typedef itk::ImageSeriesReader< ImageType > ReaderType;
 ReaderType::Pointer reader = ReaderType::New();

 typedef itk::GDCMImageIO       ImageIOType;
 ImageIOType::Pointer dicomIO = ImageIOType::New();

 reader->SetImageIO( dicomIO );

 typedef itk::GDCMSeriesFileNames NamesGeneratorType;
 NamesGeneratorType::Pointer nameGenerator = NamesGeneratorType::New();

 nameGenerator->SetUseSeriesDetails( true );
 nameGenerator->AddSeriesRestriction("0008|0021" );

 nameGenerator->SetDirectory(directoryPath);
 
 try{
     std::cout << std::endl << "The directory: " << std::endl;
     std::cout << std::endl << directoryPath << std::endl << std::endl;
     std::cout << "Contains the following DICOM Series: ";
     std::cout << std::endl << std::endl;

     typedef std::vector< std::string >    SeriesIdContainer;

     const SeriesIdContainer & seriesUID = nameGenerator->GetSeriesUIDs();
 
     SeriesIdContainer::const_iterator seriesItr = seriesUID.begin();
     SeriesIdContainer::const_iterator seriesEnd = seriesUID.end();
     while( seriesItr != seriesEnd ) {
          std::cout << seriesItr->c_str() << std::endl;
          seriesItr++;
     }

    std::string seriesIdentifier;
    seriesIdentifier = seriesUID.begin()->c_str();
 
    std::cout << std::endl << std::endl;
    std::cout << "Now reading series: " << std::endl << std::endl;
    std::cout << seriesIdentifier << std::endl;
    std::cout << std::endl << std::endl;

    typedef std::vector< std::string >   FileNamesContainer;
    FileNamesContainer fileNames;

    fileNames = nameGenerator->GetFileNames( seriesIdentifier );

    FileNamesContainer::const_iterator iterator = fileNames.begin();
    FileNamesContainer::const_iterator final = fileNames.end();
    while( iterator != final )
      {
      std::cout << iterator->c_str() << std::endl;
      iterator++;
      }

reader->SetFileNames( fileNames );  

 try
      {
      reader->Update();
      }
    catch (itk::ExceptionObject &ex)
      {
      std::cout << ex << std::endl;
      return EXIT_FAILURE;
      }

 }
catch (itk::ExceptionObject &ex)
    {
    std::cout << ex << std::endl;
    return EXIT_FAILURE;
    }


typedef itk::VTKImageExport< ImageType > ExportFilterType;
ExportFilterType::Pointer itkExporter = ExportFilterType::New(); 

itkExporter->SetInput( reader->GetOutput() );
 
vtkImageImport* vtkImporter = vtkImageImport::New();  
ConnectPipelines(itkExporter, vtkImporter);

typedef itk::VTKImageImport< ImageType > ImportFilterType;
ImportFilterType::Pointer itkImporter = ImportFilterType::New();

vtkImageExport* vtkExporter = vtkImageExport::New();  
ConnectPipelines(vtkExporter, itkImporter);
    
vtkExporter->SetInput( vtkImporter->GetOutput() );
    
    
vtkPiecewiseFunction* opacityTransferFunction = vtkPiecewiseFunction::New();
opacityTransferFunction->AddPoint(0,    0.00);
opacityTransferFunction->AddPoint(500,  0.15);
opacityTransferFunction->AddPoint(1000, 0.15);
opacityTransferFunction->AddPoint(1150, 0.85);

vtkColorTransferFunction* colorTransferFunction = vtkColorTransferFunction::New(); 
colorTransferFunction->AddRGBPoint(0,    0.0, 0.0, 0.0);
colorTransferFunction->AddRGBPoint(500,  1.0, 0.5, 0.3);
colorTransferFunction->AddRGBPoint(1000, 1.0, 0.5, 0.3);
colorTransferFunction->AddRGBPoint(1150, 1.0, 1.0, 0.9);
 
vtkVolume* volume = vtkVolume::New();
vtkVolumeProperty* volumeProperty = vtkVolumeProperty::New(); 
    vtkFixedPointVolumeRayCastMapper* volumeMapperSoftware = vtkFixedPointVolumeRayCastMapper::New();

volumeProperty->SetScalarOpacity(opacityTransferFunction);
volumeProperty->SetColor(colorTransferFunction);
volumeProperty->SetInterpolationTypeToLinear();
volumeProperty->ShadeOff();
volume->SetProperty(volumeProperty); 

volumeMapperSoftware->SetInput(vtkImporter->GetOutput());
volumeMapperSoftware->SetSampleDistance(1.0);
volume->SetMapper(volumeMapperSoftware);

vtkInteractorStyleTrackballCamera * interactorStyle = vtkInteractorStyleTrackballCamera::New();

vtkRenderer* renderer = vtkRenderer::New();
vtkRenderWindow* renWin = vtkRenderWindow::New();
vtkRenderWindowInteractor* iren = vtkRenderWindowInteractor::New();
    
  renWin->SetSize(500, 500);
  renWin->AddRenderer(renderer);
  iren->SetRenderWindow(renWin);
  iren->SetInteractorStyle(interactorStyle);

  renderer->AddVolume(volume);

  renderer->SetBackground(0.5, 0.5, 0.5);

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

  vtkImporter->Delete();
  vtkExporter->Delete();
  renWin->Delete();
  renderer->Delete();
  iren->Delete();
}

int main(int argc, char * argv [] )
{  
    if( argc < 2 )
    {
    std::cerr << "Usage: " << argv[0] << " path to DICOM series" << std::endl;
    return 1;
    }

    visualize(argv[1]);

    return 0;
} 		 	   		  
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