diff --git a/Core/Code/IO/mitkDicomSeriesReader.txx b/Core/Code/IO/mitkDicomSeriesReader.txx index c7d55d2242..deadb68a27 100644 --- a/Core/Code/IO/mitkDicomSeriesReader.txx +++ b/Core/Code/IO/mitkDicomSeriesReader.txx @@ -1,270 +1,270 @@ /*========================================================================= Program: Medical Imaging & Interaction Toolkit Language: C++ Date: $Date$ Version: $Revision$ Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. See MITKCopyright.txt or http://www.mitk.org/copyright.html for details. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the above copyright notices for more information. =========================================================================*/ #ifndef MITKDICOMSERIESREADER_TXX_ #define MITKDICOMSERIESREADER_TXX_ #include #include namespace mitk { template void DicomSeriesReader::LoadDicom(const StringContainer &filenames, DataNode &node, bool sort, bool load4D, UpdateCallBackMethod callback) { const char* previousCLocale = setlocale(LC_NUMERIC, NULL); setlocale(LC_NUMERIC, "C"); std::locale previousCppLocale( std::cin.getloc() ); std::locale l( "C" ); std::cin.imbue(l); try { mitk::Image::Pointer image = mitk::Image::New(); CallbackCommand *command = callback ? new CallbackCommand(callback) : 0; /* special case for Philips 3D+t ultrasound images */ if ( DicomSeriesReader::IsPhilips3DDicom(filenames.front().c_str()) ) { ReadPhilips3DDicom(filenames.front().c_str(), image); } else { /* default case: assume "normal" image blocks, possibly 3D+t */ bool canLoadAs4D(true); std::list imageBlocks = SortIntoBlocksFor3DplusT( filenames, sort, canLoadAs4D ); unsigned int volume_count = imageBlocks.size(); - if (!canLoadAs4D || !load4D) + if (volume_count == 1 || !canLoadAs4D || !load4D) { image = LoadDICOMByITK( imageBlocks.front() , command ); // load first 3D block } else { // It is 3D+t! Read it and store into mitk image typedef itk::Image ImageType; typedef itk::ImageSeriesReader ReaderType; DcmIoType::Pointer io = DcmIoType::New(); typename ReaderType::Pointer reader = ReaderType::New(); reader->SetImageIO(io); reader->ReverseOrderOff(); if (command) { reader->AddObserver(itk::ProgressEvent(), command); } unsigned int act_volume = 1u; reader->SetFileNames(imageBlocks.front()); reader->Update(); image->InitializeByItk(reader->GetOutput(), 1, volume_count); image->SetImportVolume(reader->GetOutput()->GetBufferPointer(), 0u); DicomSeriesReader::CopyMetaDataToImageProperties( imageBlocks.front(), io, image ); MITK_DEBUG << "Volume dimension: [" << image->GetDimension(0) << ", " << image->GetDimension(1) << ", " << image->GetDimension(2) << ", " << image->GetDimension(3) << "]"; #if (GDCM_MAJOR_VERSION == 2) && (GDCM_MINOR_VERSION < 1) && (GDCM_BUILD_VERSION < 15) // workaround for a GDCM 2 bug until version 2.0.15: // GDCM read spacing vector wrongly. Instead of "row spacing, column spacing", it misinterprets the DICOM tag as "column spacing, row spacing". // this is undone here, until we use a GDCM that has this issue fixed. // From the commit comments, GDCM 2.0.15 fixed the spacing interpretation with bug 2901181 // http://sourceforge.net/tracker/index.php?func=detail&aid=2901181&group_id=137895&atid=739587 Vector3D correctedImageSpacing = image->GetGeometry()->GetSpacing(); std::swap( correctedImageSpacing[0], correctedImageSpacing[1] ); image->GetGeometry()->SetSpacing( correctedImageSpacing ); #endif MITK_DEBUG << "Volume spacing: [" << image->GetGeometry()->GetSpacing()[0] << ", " << image->GetGeometry()->GetSpacing()[1] << ", " << image->GetGeometry()->GetSpacing()[2] << "]"; for (std::list::iterator df_it = ++imageBlocks.begin(); df_it != imageBlocks.end(); ++df_it) { reader->SetFileNames(*df_it); reader->Update(); image->SetImportVolume(reader->GetOutput()->GetBufferPointer(), act_volume++); } } } node.SetData( image ); setlocale(LC_NUMERIC, previousCLocale); std::cin.imbue(previousCppLocale); } catch (std::exception& e) { // reset locale then throw up setlocale(LC_NUMERIC, previousCLocale); std::cin.imbue(previousCppLocale); throw e; } } template Image::Pointer DicomSeriesReader::LoadDICOMByITK( const StringContainer& filenames, CallbackCommand* command ) { /******** Normal Case, 3D (also for GDCM < 2 usable) ***************/ mitk::Image::Pointer image = mitk::Image::New(); typedef itk::Image ImageType; typedef itk::ImageSeriesReader ReaderType; DcmIoType::Pointer io = DcmIoType::New(); typename ReaderType::Pointer reader = ReaderType::New(); reader->SetImageIO(io); reader->ReverseOrderOff(); if (command) { reader->AddObserver(itk::ProgressEvent(), command); } reader->SetFileNames(filenames); reader->Update(); image->InitializeByItk(reader->GetOutput()); image->SetImportVolume(reader->GetOutput()->GetBufferPointer()); MITK_DEBUG << "Volume dimension: [" << image->GetDimension(0) << ", " << image->GetDimension(1) << ", " << image->GetDimension(2) << "]"; #if (GDCM_MAJOR_VERSION == 2) && (GDCM_MINOR_VERSION < 1) && (GDCM_BUILD_VERSION < 15) // workaround for a GDCM 2 bug until version 2.0.15: // GDCM read spacing vector wrongly. Instead of "row spacing, column spacing", it misinterprets the DICOM tag as "column spacing, row spacing". // this is undone here, until we use a GDCM that has this issue fixed. // From the commit comments, GDCM 2.0.15 fixed the spacing interpretation with bug 2901181 // http://sourceforge.net/tracker/index.php?func=detail&aid=2901181&group_id=137895&atid=739587 Vector3D correctedImageSpacing = image->GetGeometry()->GetSpacing(); std::swap( correctedImageSpacing[0], correctedImageSpacing[1] ); image->GetGeometry()->SetSpacing( correctedImageSpacing ); #endif MITK_DEBUG << "Volume spacing: [" << image->GetGeometry()->GetSpacing()[0] << ", " << image->GetGeometry()->GetSpacing()[1] << ", " << image->GetGeometry()->GetSpacing()[2] << "]"; return image; } std::list DicomSeriesReader::SortIntoBlocksFor3DplusT( const StringContainer& presortedFilenames, bool sort, bool& canLoadAs4D ) { std::list imageBlocks; // ignore sort request, because most likely re-sorting is now needed due to changes in GetSeries(bug #8022) StringContainer sorted_filenames = DicomSeriesReader::SortSeriesSlices(presortedFilenames); gdcm::Tag ippTag(0x0020,0x0032); //Image position (Patient) gdcm::Scanner scanner; scanner.AddTag(ippTag); scanner.Scan(sorted_filenames); // make available image position for each file std::string firstPosition; unsigned int numberOfBlocks(0); // number of 3D image blocks // loop files to determine number of image blocks for (StringContainer::const_iterator fileIter = sorted_filenames.begin(); fileIter != sorted_filenames.end(); ++fileIter) { std::string position = scanner.GetValue( fileIter->c_str(), ippTag); MITK_DEBUG << "File " << *fileIter << " at " << position; if (firstPosition.empty()) { firstPosition = position; } if ( position == firstPosition ) { ++numberOfBlocks; } else { break; // enough information to know the number of image blocks } } MITK_DEBUG << "Assuming " << numberOfBlocks << " image blocks"; if (numberOfBlocks == 0) return imageBlocks; // only possible if called with no files // loop files to sort them into image blocks unsigned int numberOfExpectedSlices(0); for (unsigned int block = 0; block < numberOfBlocks; ++block) { StringContainer filesOfCurrentBlock; for ( StringContainer::const_iterator fileIter = sorted_filenames.begin() + block; fileIter != sorted_filenames.end(); //fileIter += numberOfBlocks) // TODO shouldn't this work? give invalid iterators on first attempts ) { filesOfCurrentBlock.push_back( *fileIter ); for (unsigned int b = 0; b < numberOfBlocks; ++b) { if (fileIter != sorted_filenames.end()) ++fileIter; } } imageBlocks.push_back(filesOfCurrentBlock); if (block == 0) { numberOfExpectedSlices = filesOfCurrentBlock.size(); } else { if (filesOfCurrentBlock.size() != numberOfExpectedSlices) { MITK_WARN << "DicomSeriesReader expected " << numberOfBlocks << " image blocks of " << numberOfExpectedSlices << " images each. Block " << block << " got " << filesOfCurrentBlock.size() << " instead. Cannot load this as 3D+t"; // TODO implement recovery (load as many slices 3D+t as much as possible) canLoadAs4D = false; } } } return imageBlocks; } } #endif