720 lines
28 KiB
C++
720 lines
28 KiB
C++
// Released under the OSGPL license, as part of the OpenSceneGraph distribution.
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//
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// ReaderWriter for sgi's .rgb format.
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// specification can be found at http://local.wasp.uwa.edu.au/~pbourke/dataformats/sgirgb/sgiversion.html
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#include <osg/Image>
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#include <osg/Notify>
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#include <osg/Geode>
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#include <osg/GL>
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#include <osg/io_utils>
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#include <osg/ImageUtils>
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#include <osgDB/FileNameUtils>
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#include <osgDB/FileUtils>
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#include <osgDB/Registry>
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#include <osgVolume/Volume>
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#include <osgVolume/VolumeTile>
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#ifdef USE_DCMTK
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#define HAVE_CONFIG_H
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#include <dcmtk/config/osconfig.h>
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#include <dcmtk/dcmdata/dcfilefo.h>
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#include <dcmtk/dcmdata/dcdeftag.h>
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#include <dcmtk/dcmimgle/dcmimage.h>
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#endif
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#ifdef USE_ITK
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#include <itkImageFileReader.h>
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#include <itkImageFileWriter.h>
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#include <itkImage.h>
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#include <itkImageRegionConstIterator.h>
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#include <itkMetaDataDictionary.h>
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#include <itkMetaDataObject.h>
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#include <itkGDCMImageIO.h>
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#endif
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#include <stdio.h>
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#include <stdlib.h>
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#include <string.h>
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#include <memory>
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class ReaderWriterDICOM : public osgDB::ReaderWriter
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{
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public:
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ReaderWriterDICOM()
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{
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supportsExtension("mag","dicom image format");
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supportsExtension("ph","dicom image format");
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supportsExtension("ima","dicom image format");
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supportsExtension("dic","dicom image format");
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supportsExtension("dcm","dicom image format");
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supportsExtension("dicom","dicom image format");
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// supportsExtension("*","dicom image format");
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}
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std::ostream& warning() const { return osg::notify(osg::WARN); }
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std::ostream& notice() const { return osg::notify(osg::NOTICE); }
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std::ostream& info() const { return osg::notify(osg::NOTICE); }
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template<typename T>
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T* readData(std::istream& fin, unsigned int length, unsigned int& numComponents) const
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{
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numComponents = length/sizeof(T);
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T* data = new T[numComponents];
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fin.read((char*)data, numComponents*sizeof(T));
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// read over any padding
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length -= numComponents*sizeof(T);
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while(fin && length>0) { fin.get(); --length; }
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return data;
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}
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template<typename T>
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void printData(std::ostream& out, T* data, unsigned int numComponents) const
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{
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if (sizeof(T)==1)
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{
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for(unsigned int i=0; i<numComponents; ++i)
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{
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if (data[i]>32) out<<data[i];
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else out<<".";
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}
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}
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else
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{
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for(unsigned int i=0; i<numComponents; ++i)
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{
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if (i==0) out<<data[i];
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else out<<", "<<data[i];
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}
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}
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}
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virtual const char* className() const { return "DICOM Image Reader/Writer"; }
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virtual ReadResult readObject(std::istream& fin,const osgDB::ReaderWriter::Options* options =NULL) const
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{
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return readImage(fin, options);
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}
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virtual ReadResult readObject(const std::string& file, const osgDB::ReaderWriter::Options* options =NULL) const
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{
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return readImage(file, options);
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}
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virtual ReadResult readNode(std::istream& fin,const osgDB::ReaderWriter::Options* options =NULL) const
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{
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return readImage(fin, options);
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}
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virtual ReadResult readNode(const std::string& file, const osgDB::ReaderWriter::Options* options =NULL) const
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{
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ReadResult result = readImage(file, options);
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if (!result.validImage()) return result;
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osg::ref_ptr<osgVolume::Volume> volume = new osgVolume::Volume;
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osg::ref_ptr<osgVolume::VolumeTile> tile = new osgVolume::VolumeTile;
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tile->setVolume(volume.get());
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osg::ref_ptr<osgVolume::Layer> layer= new osgVolume::ImageLayer(result.getImage());
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tile->addLayer(layer.get());
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// get matrix providing size of texels (in mm)
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osg::RefMatrix* matrix = dynamic_cast<osg::RefMatrix*>(result.getImage()->getUserData());
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if (matrix)
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{
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// scale up to provide scale of complete tile
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osg::Vec3d scale(osg::Vec3(result.getImage()->s(),result.getImage()->t(), result.getImage()->r()));
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matrix->postMultScale(scale);
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tile->setLocator(new osgVolume::Locator(*matrix));
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result.getImage()->setUserData(0);
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notice()<<"Locator "<<*matrix<<std::endl;
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}
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volume->addChild(tile.get());
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return volume.release();
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}
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virtual ReadResult readImage(std::istream& fin,const osgDB::ReaderWriter::Options*) const
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{
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return 0;
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}
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#ifdef USE_ITK
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virtual ReadResult readImage(const std::string& file, const osgDB::ReaderWriter::Options* options) const
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{
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std::string ext = osgDB::getLowerCaseFileExtension(file);
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if (!acceptsExtension(ext)) return ReadResult::FILE_NOT_HANDLED;
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std::string fileName = osgDB::findDataFile( file, options );
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if (fileName.empty()) return ReadResult::FILE_NOT_FOUND;
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notice()<<"Reading DICOM file "<<fileName<<std::endl;
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typedef unsigned short PixelType;
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const unsigned int Dimension = 3;
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typedef itk::Image< PixelType, Dimension > ImageType;
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typedef itk::ImageFileReader< ImageType > ReaderType;
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ReaderType::Pointer reader = ReaderType::New();
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reader->SetFileName( fileName.c_str() );
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typedef itk::GDCMImageIO ImageIOType;
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ImageIOType::Pointer gdcmImageIO = ImageIOType::New();
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reader->SetImageIO( gdcmImageIO );
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try
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{
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reader->Update();
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}
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catch (itk::ExceptionObject & e)
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{
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std::cerr << "exception in file reader " << std::endl;
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std::cerr << e.GetDescription() << std::endl;
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std::cerr << e.GetLocation() << std::endl;
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return ReadResult::ERROR_IN_READING_FILE;
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}
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ImageType::Pointer inputImage = reader->GetOutput();
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ImageType::RegionType region = inputImage->GetBufferedRegion();
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ImageType::SizeType size = region.GetSize();
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ImageType::IndexType start = region.GetIndex();
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//inputImage->GetSpacing();
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//inputImage->GetOrigin();
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unsigned int width = size[0];
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unsigned int height = size[1];
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unsigned int depth = size[2];
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osg::RefMatrix* matrix = new osg::RefMatrix;
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notice()<<"width = "<<width<<" height = "<<height<<" depth = "<<depth<<std::endl;
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for(unsigned int i=0; i<Dimension; ++i)
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{
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(*matrix)(i,i) = inputImage->GetSpacing()[i];
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(*matrix)(3,i) = inputImage->GetOrigin()[i];
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}
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osg::Image* image = new osg::Image;
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image->allocateImage(width, height, depth, GL_LUMINANCE, GL_UNSIGNED_BYTE, 1);
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unsigned char* data = image->data();
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typedef itk::ImageRegionConstIterator< ImageType > IteratorType;
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IteratorType it(inputImage, region);
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it.GoToBegin();
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while (!it.IsAtEnd())
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{
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*data = it.Get();
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++data;
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++it;
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}
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image->setUserData(matrix);
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return image;
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}
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#endif
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#ifdef USE_DCMTK
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void convertPixelTypes(const DiPixel* pixelData,
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EP_Representation& pixelRep, int& numPlanes,
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GLenum& dataType, GLenum& pixelFormat, unsigned int& pixelSize) const
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{
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dataType = GL_UNSIGNED_BYTE;
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pixelRep = pixelData->getRepresentation();
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switch(pixelRep)
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{
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case(EPR_Uint8):
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dataType = GL_UNSIGNED_BYTE;
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pixelSize = 1;
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break;
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case(EPR_Sint8):
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dataType = GL_BYTE;
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pixelSize = 1;
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break;
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case(EPR_Uint16):
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dataType = GL_UNSIGNED_SHORT;
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pixelSize = 2;
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break;
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case(EPR_Sint16):
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dataType = GL_SHORT;
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pixelSize = 2;
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break;
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case(EPR_Uint32):
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dataType = GL_UNSIGNED_INT;
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pixelSize = 4;
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break;
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case(EPR_Sint32):
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dataType = GL_INT;
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pixelSize = 4;
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break;
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default:
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dataType = 0;
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break;
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}
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pixelFormat = GL_INTENSITY;
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numPlanes = pixelData->getPlanes();
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switch(numPlanes)
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{
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case(1):
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pixelFormat = GL_LUMINANCE;
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break;
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case(2):
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pixelFormat = GL_LUMINANCE_ALPHA;
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pixelSize *= 2;
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break;
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case(3):
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pixelFormat = GL_RGB;
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pixelSize *= 3;
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break;
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case(4):
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pixelFormat = GL_RGBA;
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pixelSize *= 4;
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break;
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}
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}
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typedef std::vector<std::string> Files;
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bool getDicomFilesInDirectory(const std::string& path, Files& files) const
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{
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osgDB::DirectoryContents contents = osgDB::getDirectoryContents(path);
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std::sort(contents.begin(), contents.end());
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for(osgDB::DirectoryContents::iterator itr = contents.begin();
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itr != contents.end();
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++itr)
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{
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std::string localFile = path + "/" + *itr;
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info()<<"contents = "<<localFile<<std::endl;
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if (acceptsExtension(osgDB::getLowerCaseFileExtension(localFile)) &&
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osgDB::fileType(localFile) == osgDB::REGULAR_FILE)
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{
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files.push_back(localFile);
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}
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}
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return !files.empty();
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}
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virtual ReadResult readImage(const std::string& file, const osgDB::ReaderWriter::Options* options) const
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{
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notice()<<"Reading DICOM file "<<file<<" using DCMTK"<<std::endl;
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std::string ext = osgDB::getLowerCaseFileExtension(file);
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if (!acceptsExtension(ext)) return ReadResult::FILE_NOT_HANDLED;
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std::string fileName = file;
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if (ext=="dicom")
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{
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fileName = osgDB::getNameLessExtension(file);
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}
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fileName = osgDB::findDataFile( fileName, options );
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if (fileName.empty()) return ReadResult::FILE_NOT_FOUND;
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Files files;
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osgDB::FileType fileType = osgDB::fileType(fileName);
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if (fileType==osgDB::DIRECTORY)
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{
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getDicomFilesInDirectory(fileName, files);
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}
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else
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{
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#if 1
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files.push_back(fileName);
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#else
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if (!getDicomFilesInDirectory(osgDB::getFilePath(fileName), files))
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{
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files.push_back(fileName);
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}
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#endif
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}
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if (files.empty())
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{
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return ReadResult::FILE_NOT_FOUND;
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}
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osg::ref_ptr<osg::RefMatrix> matrix = new osg::RefMatrix;
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osg::ref_ptr<osg::Image> image;
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unsigned int imageNum = 0;
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EP_Representation pixelRep;
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int numPlanes = 0;
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GLenum pixelFormat = 0;
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GLenum dataType = 0;
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unsigned int pixelSize = 0;
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typedef std::list<FileInfo> FileInfoList;
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FileInfoList fileInfoList;
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typedef std::map<double, FileInfo> DistanceFileInfoMap;
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typedef std::map<osg::Vec3d, DistanceFileInfoMap> OrientationFileInfoMap;
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OrientationFileInfoMap orientationFileInfoMap;
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unsigned int totalNumSlices = 0;
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for(Files::iterator itr = files.begin();
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itr != files.end();
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++itr)
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{
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DcmFileFormat fileformat;
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OFCondition status = fileformat.loadFile((*itr).c_str());
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if(!status.good()) return ReadResult::ERROR_IN_READING_FILE;
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FileInfo fileInfo;
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fileInfo.filename = *itr;
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double pixelSize_y = 1.0;
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double pixelSize_x = 1.0;
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double sliceThickness = 1.0;
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double imagePositionPatient[3] = {0, 0, 0};
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double imageOrientationPatient[6] = {1.0, 0.0, 0.0, 0.0, 1.0, 0.0 };
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Uint16 numOfSlices = 1;
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double value = 0.0;
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if (fileformat.getDataset()->findAndGetFloat64(DCM_PixelSpacing, value,0).good())
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{
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pixelSize_y = value;
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fileInfo.matrix(1,1) = pixelSize_y;
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}
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if (fileformat.getDataset()->findAndGetFloat64(DCM_PixelSpacing, value,1).good())
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{
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pixelSize_x = value;
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fileInfo.matrix(0,0) = pixelSize_x;
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}
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// Get slice thickness
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if (fileformat.getDataset()->findAndGetFloat64(DCM_SliceThickness, value).good())
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{
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sliceThickness = value;
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notice()<<"sliceThickness = "<<sliceThickness<<std::endl;
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fileInfo.sliceThickness = sliceThickness;
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}
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notice()<<"tagExistsWithValue(DCM_NumberOfFrames)="<<fileformat.getDataset()->tagExistsWithValue(DCM_NumberOfFrames)<<std::endl;
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notice()<<"tagExistsWithValue(DCM_NumberOfSlices)="<<fileformat.getDataset()->tagExistsWithValue(DCM_NumberOfSlices)<<std::endl;
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Uint32 numFrames;
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if (fileformat.getDataset()->findAndGetUint32(DCM_NumberOfFrames, numFrames).good())
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{
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fileInfo.numSlices = numFrames;
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notice()<<"Read number of frames = "<<numFrames<<std::endl;
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}
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OFString numFramesStr;
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if (fileformat.getDataset()->findAndGetOFString(DCM_NumberOfFrames, numFramesStr).good())
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{
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fileInfo.numSlices = atoi(numFramesStr.c_str());
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notice()<<"Read number of frames = "<<numFramesStr<<std::endl;
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}
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if (fileformat.getDataset()->findAndGetUint16(DCM_NumberOfFrames, numOfSlices).good())
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{
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fileInfo.numSlices = numOfSlices;
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notice()<<"Read number of frames = "<<numOfSlices<<std::endl;
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}
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if (fileformat.getDataset()->findAndGetUint16(DCM_NumberOfSlices, numOfSlices).good())
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{
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fileInfo.numSlices = numOfSlices;
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notice()<<"Read number of slices = "<<numOfSlices<<std::endl;
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}
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// patient position
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for(int i=0; i<3; ++i)
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{
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if (fileformat.getDataset()->findAndGetFloat64(DCM_ImagePositionPatient, imagePositionPatient[i],i).good())
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{
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notice()<<"Read DCM_ImagePositionPatient["<<i<<"], "<<imagePositionPatient[i]<<std::endl;
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}
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else
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{
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notice()<<"Have not read DCM_ImagePositionPatient["<<i<<"]"<<std::endl;
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}
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}
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//notice()<<"imagePositionPatient[2]="<<imagePositionPatient[2]<<std::endl;
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fileInfo.matrix.setTrans(imagePositionPatient[0],imagePositionPatient[1],imagePositionPatient[2]);
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for(int i=0; i<6; ++i)
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{
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double value = 0.0;
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if (fileformat.getDataset()->findAndGetFloat64(DCM_ImageOrientationPatient, value,i).good())
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{
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imageOrientationPatient[i] = value;
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notice()<<"Read imageOrientationPatient["<<i<<"], "<<imageOrientationPatient[i]<<std::endl;
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}
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else
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{
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notice()<<"Have not read imageOrientationPatient["<<i<<"]"<<std::endl;
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}
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}
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osg::Vec3d dirX(imageOrientationPatient[0],imageOrientationPatient[1],imageOrientationPatient[2]);
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osg::Vec3d dirY(imageOrientationPatient[3],imageOrientationPatient[4],imageOrientationPatient[5]);
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osg::Vec3d dirZ = dirX ^ dirY;
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dirZ.normalize();
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dirX *= pixelSize_x;
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dirY *= pixelSize_y;
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fileInfo.matrix(0,0) = dirX[0];
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fileInfo.matrix(1,0) = dirX[1];
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fileInfo.matrix(2,0) = dirX[2];
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fileInfo.matrix(0,1) = dirY[0];
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fileInfo.matrix(1,1) = dirY[1];
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fileInfo.matrix(2,1) = dirY[2];
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fileInfo.matrix(0,2) = dirZ[0];
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fileInfo.matrix(1,2) = dirZ[1];
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fileInfo.matrix(2,2) = dirZ[2];
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fileInfo.distance = dirZ * (osg::Vec3d(0.0,0.0,0.0)*fileInfo.matrix);
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notice()<<"dirX = "<<dirX<<std::endl;
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notice()<<"dirY = "<<dirY<<std::endl;
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notice()<<"dirZ = "<<dirZ<<std::endl;
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notice()<<"matrix = "<<fileInfo.matrix<<std::endl;
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notice()<<"pos = "<<osg::Vec3d(0.0,0.0,0.0)*fileInfo.matrix<<std::endl;
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notice()<<"dist = "<<fileInfo.distance<<std::endl;
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notice()<<std::endl;
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(orientationFileInfoMap[dirZ])[fileInfo.distance] = fileInfo;
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totalNumSlices += fileInfo.numSlices;
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}
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if (orientationFileInfoMap.empty()) return 0;
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typedef std::map<double, FileInfo> DistanceFileInfoMap;
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typedef std::map<osg::Vec3d, DistanceFileInfoMap> OrientationFileInfoMap;
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for(OrientationFileInfoMap::iterator itr = orientationFileInfoMap.begin();
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itr != orientationFileInfoMap.end();
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++itr)
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{
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notice()<<"Orientation = "<<itr->first<<std::endl;
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DistanceFileInfoMap& dfim = itr->second;
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for(DistanceFileInfoMap::iterator ditr = dfim.begin();
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ditr != dfim.end();
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++ditr)
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{
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FileInfo& fileInfo = ditr->second;
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notice()<<" d = "<<fileInfo.distance<<" "<<fileInfo.filename<<std::endl;
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}
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}
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|
|
|
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DistanceFileInfoMap& dfim = orientationFileInfoMap.begin()->second;
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if (dfim.empty()) return 0;
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|
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double totalDistance = 0.0;
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if (dfim.size()>1)
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{
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totalDistance = fabs(dfim.rbegin()->first - dfim.begin()->first);
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}
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else
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{
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totalDistance = dfim.begin()->second.sliceThickness * double(dfim.begin()->second.numSlices);
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}
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|
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notice()<<"Total Distance including ends "<<totalDistance<<std::endl;
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|
|
|
double averageThickness = totalNumSlices<=1 ? 1.0 : totalDistance / double(totalNumSlices-1);
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|
|
|
notice()<<"Average thickness "<<averageThickness<<std::endl;
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|
|
|
for(DistanceFileInfoMap::iterator ditr = dfim.begin();
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|
ditr != dfim.end();
|
|
++ditr)
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|
{
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|
FileInfo& fileInfo = ditr->second;
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|
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|
std::auto_ptr<DicomImage> dcmImage(new DicomImage(fileInfo.filename.c_str()));
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|
if (dcmImage.get())
|
|
{
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|
if (dcmImage->getStatus()==EIS_Normal)
|
|
{
|
|
|
|
// get the pixel data
|
|
const DiPixel* pixelData = dcmImage->getInterData();
|
|
if(!pixelData)
|
|
{
|
|
warning()<<"Error: no data in DicomImage object."<<std::endl;
|
|
return ReadResult::ERROR_IN_READING_FILE;
|
|
}
|
|
|
|
osg::ref_ptr<osg::Image> imageAdapter = new osg::Image;
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|
|
|
EP_Representation curr_pixelRep;
|
|
int curr_numPlanes;
|
|
GLenum curr_pixelFormat;
|
|
GLenum curr_dataType;
|
|
unsigned int curr_pixelSize;
|
|
|
|
// create the new image
|
|
convertPixelTypes(pixelData,
|
|
curr_pixelRep, curr_numPlanes,
|
|
curr_dataType, curr_pixelFormat, curr_pixelSize);
|
|
|
|
imageAdapter->setImage(dcmImage->getWidth(), dcmImage->getHeight(), dcmImage->getFrameCount(),
|
|
curr_pixelFormat,
|
|
curr_pixelFormat,
|
|
curr_dataType,
|
|
(unsigned char*)(pixelData->getData()),
|
|
osg::Image::NO_DELETE);
|
|
if (!image)
|
|
{
|
|
pixelRep = curr_pixelRep;
|
|
numPlanes = curr_numPlanes;
|
|
dataType = curr_dataType;
|
|
pixelFormat = curr_pixelFormat;
|
|
pixelSize = curr_pixelSize;
|
|
|
|
(*matrix)(0,0) = fileInfo.matrix(0,0);
|
|
(*matrix)(1,0) = fileInfo.matrix(1,0);
|
|
(*matrix)(2,0) = fileInfo.matrix(2,0);
|
|
(*matrix)(0,1) = fileInfo.matrix(0,1);
|
|
(*matrix)(1,1) = fileInfo.matrix(1,1);
|
|
(*matrix)(2,1) = fileInfo.matrix(2,1);
|
|
(*matrix)(0,2) = fileInfo.matrix(0,2) * averageThickness;
|
|
(*matrix)(1,2) = fileInfo.matrix(1,2) * averageThickness;
|
|
(*matrix)(2,2) = fileInfo.matrix(2,2) * averageThickness;
|
|
|
|
image = new osg::Image;
|
|
image->setUserData(matrix.get());
|
|
image->setFileName(fileName.c_str());
|
|
image->allocateImage(dcmImage->getWidth(), dcmImage->getHeight(), totalNumSlices,
|
|
pixelFormat, dataType);
|
|
|
|
|
|
notice()<<"Image dimensions = "<<image->s()<<", "<<image->t()<<", "<<image->r()<<" pixelFormat=0x"<<std::hex<<pixelFormat<<" dataType=0x"<<std::hex<<dataType<<std::endl;
|
|
}
|
|
else if (pixelData->getPlanes()>numPlanes ||
|
|
pixelData->getRepresentation()>pixelRep)
|
|
{
|
|
notice()<<"Need to reallocated "<<image->s()<<", "<<image->t()<<", "<<image->r()<<std::endl;
|
|
|
|
// record the previous image settings to use when we copy back the content.
|
|
osg::ref_ptr<osg::Image> previous_image = image;
|
|
|
|
// create the new image
|
|
convertPixelTypes(pixelData,
|
|
pixelRep, numPlanes,
|
|
dataType, pixelFormat, pixelSize);
|
|
|
|
image = new osg::Image;
|
|
image->setUserData(previous_image->getUserData());
|
|
image->setFileName(fileName.c_str());
|
|
image->allocateImage(dcmImage->getWidth(), dcmImage->getHeight(), totalNumSlices,
|
|
pixelFormat, dataType);
|
|
|
|
osg::copyImage(previous_image.get(), 0,0,0, previous_image->s(), previous_image->t(), imageNum,
|
|
image.get(), 0, 0, 0,
|
|
false);
|
|
|
|
}
|
|
|
|
osg::copyImage(imageAdapter.get(), 0,0,0, imageAdapter->s(), imageAdapter->t(), imageAdapter->r(),
|
|
image.get(), 0, 0, imageNum,
|
|
false);
|
|
|
|
imageNum += dcmImage->getFrameCount();
|
|
}
|
|
else
|
|
{
|
|
warning()<<"Error in reading dicom file "<<fileName.c_str()<<", error = "<<DicomImage::getString(dcmImage->getStatus())<<std::endl;
|
|
}
|
|
}
|
|
}
|
|
|
|
if (!image)
|
|
{
|
|
return ReadResult::ERROR_IN_READING_FILE;
|
|
}
|
|
|
|
notice()<<"Spacing = "<<*matrix<<std::endl;
|
|
|
|
return image.get();
|
|
}
|
|
#endif
|
|
|
|
struct FileInfo
|
|
{
|
|
FileInfo():
|
|
numX(0),
|
|
numY(0),
|
|
numSlices(1),
|
|
sliceThickness(0.0),
|
|
distance(0.0) {}
|
|
|
|
FileInfo(const FileInfo& rhs):
|
|
filename(rhs.filename),
|
|
matrix(rhs.matrix),
|
|
numX(rhs.numX),
|
|
numY(rhs.numY),
|
|
numSlices(rhs.numSlices),
|
|
sliceThickness(rhs.sliceThickness),
|
|
distance(distance) {}
|
|
|
|
FileInfo& operator = (const FileInfo& rhs)
|
|
{
|
|
if (&rhs == this) return *this;
|
|
|
|
filename = rhs.filename;
|
|
matrix = rhs.matrix;
|
|
numX = rhs.numX;
|
|
numY = rhs.numY;
|
|
sliceThickness = rhs.sliceThickness;
|
|
numSlices = rhs.numSlices;
|
|
distance = rhs.distance;
|
|
|
|
return *this;
|
|
}
|
|
|
|
std::string filename;
|
|
osg::Matrixd matrix;
|
|
unsigned int numX;
|
|
unsigned int numY;
|
|
unsigned int numSlices;
|
|
double sliceThickness;
|
|
double distance;
|
|
};
|
|
|
|
};
|
|
|
|
// now register with Registry to instantiate the above
|
|
// reader/writer.
|
|
REGISTER_OSGPLUGIN(dicom, ReaderWriterDICOM)
|