Improved the dicom plugins handling of different slice positions
This commit is contained in:
Robert Osfield
parent
723ebd3334
commit
c03b64731b
@ -236,7 +236,7 @@ class ReaderWriterDICOM : public osgDB::ReaderWriter
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++itr)
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++itr)
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{
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{
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std::string localFile = path + "/" + *itr;
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std::string localFile = path + "/" + *itr;
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std::cout<<"contents = "<<localFile<<std::endl;
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osg::notify(osg::INFO)<<"contents = "<<localFile<<std::endl;
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if (osgDB::getLowerCaseFileExtension(localFile)=="dcm" &&
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if (osgDB::getLowerCaseFileExtension(localFile)=="dcm" &&
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osgDB::fileType(localFile) == osgDB::REGULAR_FILE)
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osgDB::fileType(localFile) == osgDB::REGULAR_FILE)
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{
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{
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@ -296,13 +296,155 @@ class ReaderWriterDICOM : public osgDB::ReaderWriter
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GLenum pixelFormat = 0;
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GLenum pixelFormat = 0;
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GLenum dataType = 0;
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GLenum dataType = 0;
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unsigned int pixelSize = 0;
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unsigned int pixelSize = 0;
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bool invertOrigiantion = true;
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bool invertOrigiantion = false;
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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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for(Files::iterator itr = files.begin();
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for(Files::iterator itr = files.begin();
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itr != files.end();
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itr != files.end();
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++itr)
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++itr)
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{
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{
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std::auto_ptr<DicomImage> dcmImage(new DicomImage((*itr).c_str()));
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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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if (fileformat.getDataset()->findAndGetFloat64(DCM_PixelSpacing, pixelSize_y,0).good())
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{
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fileInfo.matrix(1,1) = pixelSize_y;
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}
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double pixelSize_x = 1.0;
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if (fileformat.getDataset()->findAndGetFloat64(DCM_PixelSpacing, pixelSize_x,1).good())
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{
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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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double sliceThickness = 1.0;
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if (fileformat.getDataset()->findAndGetFloat64(DCM_SliceThickness, sliceThickness).good())
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{
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fileInfo.matrix(2,2) = sliceThickness;
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}
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double imagePositionPatient[3] = {0, 0, 0};
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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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osg::notify(osg::INFO)<<"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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osg::notify(osg::INFO)<<"Have not read DCM_ImagePositionPatient["<<i<<"]"<<std::endl;
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}
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}
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fileInfo.matrix.setTrans(imagePositionPatient[0],imagePositionPatient[1],imagePositionPatient[2]);
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double imageOrientationPatient[6] = { 1.0, 0.0, 0.0,
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0.0, -1.0, 0.0 };
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for(int i=0; i<6; ++i)
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{
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if (fileformat.getDataset()->findAndGetFloat64(DCM_ImageOrientationPatient, imageOrientationPatient[i],i).good())
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{
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osg::notify(osg::INFO)<<"Read imageOrientationPatient["<<i<<"], "<<imageOrientationPatient[i]<<std::endl;
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}
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else
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{
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osg::notify(osg::INFO)<<"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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osg::notify(osg::INFO)<<"dirX = "<<dirX<<std::endl;
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osg::notify(osg::INFO)<<"dirY = "<<dirY<<std::endl;
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osg::notify(osg::INFO)<<"dirZ = "<<dirZ<<std::endl;
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osg::notify(osg::INFO)<<"matrix = "<<fileInfo.matrix<<std::endl;
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osg::notify(osg::INFO)<<"pos = "<<osg::Vec3d(0.0,0.0,0.0)*fileInfo.matrix<<std::endl;
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osg::notify(osg::INFO)<<"dist = "<<fileInfo.distance<<std::endl;
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osg::notify(osg::INFO)<<std::endl;
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(orientationFileInfoMap[dirZ])[fileInfo.distance] = fileInfo;
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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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osg::notify(osg::INFO)<<"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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osg::notify(osg::INFO)<<" d = "<<fileInfo.distance<<" "<<fileInfo.filename<<std::endl;
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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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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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fileInfoList.push_back(fileInfo);
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osg::notify(osg::INFO)<<" d = "<<fileInfo.distance<<" "<<fileInfo.filename<<std::endl;
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}
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double totalDistance = dfim.rbegin()->first - dfim.begin()->first;
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double averageThickness = dfim.size()<=1 ? 1.0 : totalDistance / double(dfim.size()-1);
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osg::notify(osg::INFO)<<"Average thickness "<<averageThickness<<std::endl;
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for(FileInfoList::iterator itr = fileInfoList.begin();
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itr != fileInfoList.end();
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++itr)
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{
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FileInfo& fileInfo = *itr;
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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.get())
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{
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{
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if (dcmImage->getStatus()==EIS_Normal)
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if (dcmImage->getStatus()==EIS_Normal)
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@ -313,60 +455,6 @@ class ReaderWriterDICOM : public osgDB::ReaderWriter
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if (!image)
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if (!image)
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{
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{
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// read dicom file format to extra spacing info
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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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double pixelSize_y = 1.0;
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if (fileformat.getDataset()->findAndGetFloat64(DCM_PixelSpacing, pixelSize_y,0).good())
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{
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(*matrix)(1,1) = pixelSize_y;
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}
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double pixelSize_x = 1.0;
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if (fileformat.getDataset()->findAndGetFloat64(DCM_PixelSpacing, pixelSize_x,1).good())
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{
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(*matrix)(0,0) = pixelSize_x;
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}
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// Get slice thickness
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double sliceThickness = 1.0;
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if (fileformat.getDataset()->findAndGetFloat64(DCM_SliceThickness, sliceThickness).good())
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{
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(*matrix)(2,2) = sliceThickness;
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}
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double imagePositionPatient[3] = {0};
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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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osg::notify(osg::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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osg::notify(osg::NOTICE)<<"Have not read DCM_ImagePositionPatient["<<i<<"]"<<std::endl;
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}
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}
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double imageOrientationPatient[6] = { 1.0, 0.0, 0.0,
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0.0, -1.0, 0.0 };
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for(int i=0; i<6; ++i)
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{
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if (fileformat.getDataset()->findAndGetFloat64(DCM_ImageOrientationPatient, imageOrientationPatient[i],i).good())
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{
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osg::notify(osg::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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osg::notify(osg::NOTICE)<<"Have not read imageOrientationPatient["<<i<<"]"<<std::endl;
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}
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}
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osg::notify(osg::NOTICE)<<"dcmImage->getWidth() = "<<dcmImage->getWidth()<<std::endl;
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osg::notify(osg::NOTICE)<<"dcmImage->getWidth() = "<<dcmImage->getWidth()<<std::endl;
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osg::notify(osg::NOTICE)<<"dcmImage->getHeight() = "<<dcmImage->getHeight()<<std::endl;
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osg::notify(osg::NOTICE)<<"dcmImage->getHeight() = "<<dcmImage->getHeight()<<std::endl;
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osg::notify(osg::NOTICE)<<"dcmImage->getFrameCount() = "<<dcmImage->getFrameCount()<<std::endl;
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osg::notify(osg::NOTICE)<<"dcmImage->getFrameCount() = "<<dcmImage->getFrameCount()<<std::endl;
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@ -434,11 +522,24 @@ class ReaderWriterDICOM : public osgDB::ReaderWriter
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break;
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break;
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}
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}
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(*matrix)(0,0) = fileInfo.matrix(0,0);
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(*matrix)(1,0) = fileInfo.matrix(1,0);
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(*matrix)(2,0) = fileInfo.matrix(2,0);
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(*matrix)(0,1) = fileInfo.matrix(0,1);
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(*matrix)(1,1) = fileInfo.matrix(1,1);
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(*matrix)(2,1) = fileInfo.matrix(2,1);
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(*matrix)(0,2) = fileInfo.matrix(0,2) * averageThickness;
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(*matrix)(1,2) = fileInfo.matrix(1,2) * averageThickness;
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(*matrix)(2,2) = fileInfo.matrix(2,2) * averageThickness;
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image = new osg::Image;
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image = new osg::Image;
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image->setUserData(matrix.get());
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image->setUserData(matrix.get());
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image->setFileName(fileName.c_str());
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image->setFileName(fileName.c_str());
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image->allocateImage(dcmImage->getWidth(), dcmImage->getHeight(), files.size() * dcmImage->getFrameCount(),
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image->allocateImage(dcmImage->getWidth(), dcmImage->getHeight(), files.size() * dcmImage->getFrameCount(),
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pixelFormat, dataType);
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pixelFormat, dataType);
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osg::notify(osg::NOTICE)<<"Image dimensions = "<<image->s()<<", "<<image->t()<<", "<<image->r()<<std::endl;
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}
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}
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if (pixelData->getPlanes()==numPlanes &&
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if (pixelData->getPlanes()==numPlanes &&
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@ -481,6 +582,42 @@ class ReaderWriterDICOM : public osgDB::ReaderWriter
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}
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}
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#endif
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#endif
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struct FileInfo
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{
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FileInfo():
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numX(0),
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numY(0),
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numSlices(0),
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distance(0.0) {}
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FileInfo(const FileInfo& rhs):
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filename(rhs.filename),
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matrix(rhs.matrix),
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numX(rhs.numX),
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numY(rhs.numY),
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numSlices(rhs.numSlices),
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distance(distance) {}
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FileInfo& operator = (const FileInfo& rhs)
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{
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if (&rhs == this) return *this;
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filename = rhs.filename;
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matrix = rhs.matrix;
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numX = rhs.numX;
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numY = rhs.numY;
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numSlices = rhs.numSlices;
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distance = rhs.distance;
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}
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std::string filename;
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osg::Matrixd matrix;
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unsigned int numX;
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unsigned int numY;
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unsigned int numSlices;
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double distance;
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};
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};
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};
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// now register with Registry to instantiate the above
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// now register with Registry to instantiate the above
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