X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkWriteDicomSeriesGenericFilter.txx;h=a2bccc4aa0daa52fbef3b8a34cb115b3eb9cc20c;hb=f48c960aef6e0a5a4edea516b062197db009e25f;hp=21612e4eaba3b927a5bc84ba3bc781c5f1b4727f;hpb=0b7c9b1e1215634b02cbd38d4e4ba101d6111ba8;p=clitk.git diff --git a/tools/clitkWriteDicomSeriesGenericFilter.txx b/tools/clitkWriteDicomSeriesGenericFilter.txx index 21612e4..a2bccc4 100644 --- a/tools/clitkWriteDicomSeriesGenericFilter.txx +++ b/tools/clitkWriteDicomSeriesGenericFilter.txx @@ -1,9 +1,9 @@ /*========================================================================= Program: vv http://www.creatis.insa-lyon.fr/rio/vv - Authors belong to: + Authors belong to: - University of LYON http://www.universite-lyon.fr/ - - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr + - Léon Bérard cancer center http://www.centreleonberard.fr - CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr This software is distributed WITHOUT ANY WARRANTY; without even @@ -14,197 +14,531 @@ - BSD See included LICENSE.txt file - CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html -======================================================================-====*/ +===========================================================================**/ #ifndef clitkWriteDicomSeriesGenericFilter_txx #define clitkWriteDicomSeriesGenericFilter_txx /* ================================================= * @file clitkWriteDicomSeriesGenericFilter.txx - * @author - * @date - * - * @brief - * + * @author + * @date + * + * @brief + * ===================================================*/ +// clitk +#include "clitkResampleImageWithOptionsFilter.h" +#if GDCM_MAJOR_VERSION >= 2 +#include "gdcmUIDGenerator.h" +#else +#include "gdcmFile.h" +#include "gdcmUtil.h" +#endif + namespace clitk { - //----------------------------------------------------------- - // Constructor - //----------------------------------------------------------- - template - WriteDicomSeriesGenericFilter::WriteDicomSeriesGenericFilter() - { - m_Verbose=false; - m_InputFileName=""; +//----------------------------------------------------------- +// Constructor +//----------------------------------------------------------- +template +WriteDicomSeriesGenericFilter::WriteDicomSeriesGenericFilter() +{ + m_Verbose=false; + m_InputFileName=""; +} + + +//----------------------------------------------------------- +// Update +//----------------------------------------------------------- +template +void WriteDicomSeriesGenericFilter::Update() +{ + // Read the Dimension and PixelType + int Dimension; + std::string PixelType; + ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType); + + + // Call UpdateWithDim + if(Dimension==2) UpdateWithDim<2>(PixelType); + else if(Dimension==3) UpdateWithDim<3>(PixelType); + // else if (Dimension==4)UpdateWithDim<4>(PixelType); + else { + std::cout<<"Error, Only for 2 or 3 Dimensions!!!"< +template +void +WriteDicomSeriesGenericFilter::UpdateWithDim(std::string PixelType) +{ + if (m_Verbose) std::cout << "Image was detected to be "< - void WriteDicomSeriesGenericFilter::Update() - { - // Read the Dimension and PixelType - int Dimension; - std::string PixelType; - ReadImageDimensionAndPixelType(m_InputFileName, Dimension, PixelType); + if(PixelType == "short") { + if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl; + UpdateWithDimAndPixelType(); + } + else if(PixelType == "unsigned_short"){ + if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_short..." << std::endl; + UpdateWithDimAndPixelType(); + } - - // Call UpdateWithDim - if(Dimension==2) UpdateWithDim<2>(PixelType); - else if(Dimension==3) UpdateWithDim<3>(PixelType); - // else if (Dimension==4)UpdateWithDim<4>(PixelType); - else - { - std::cout<<"Error, Only for 2 or 3 Dimensions!!!"<(); } - //------------------------------------------------------------------- - // Update with the number of dimensions - //------------------------------------------------------------------- - template - template - void - WriteDicomSeriesGenericFilter::UpdateWithDim(std::string PixelType) - { - if (m_Verbose) std::cout << "Image was detected to be "<(); + // } + else if (PixelType == "double") { + if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and double..." << std::endl; + UpdateWithDimAndPixelType(); + } + else { + if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl; + UpdateWithDimAndPixelType(); + } +} - if(PixelType == "short"){ - if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed short..." << std::endl; - UpdateWithDimAndPixelType(); +//------------------------------------------------------------------- +// Update with the number of dimensions and the pixeltype read from +// the dicom files. The MHD files may be resampled to match the +// dicom spacing (and number of slices). Rounding errors in resampling +// are handled by removing files when generating the output dicom +// series. +//------------------------------------------------------------------- +template +template +void +WriteDicomSeriesGenericFilter::UpdateWithDimAndPixelType() +{ + + // ImageTypes + typedef itk::Image InputImageType; + typedef itk::Image OutputImageType; + + // Read the dicom directory + typedef itk::ImageSeriesReader< InputImageType > ReaderType; + typedef itk::GDCMImageIO ImageIOType; + typedef itk::GDCMSeriesFileNames NamesGeneratorType; + + ImageIOType::Pointer gdcmIO = ImageIOType::New(); + NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New(); + namesGenerator->SetInputDirectory( m_ArgsInfo.inputDir_arg ); + namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg ); + typename ReaderType::FileNamesContainer filenames_in = namesGenerator->GetInputFileNames(); + typename ReaderType::FileNamesContainer filenames_out = namesGenerator->GetOutputFileNames(); + + // Output the dicom files + unsigned int numberOfFilenames = filenames_in.size(); + if (m_Verbose) { + std::cout << numberOfFilenames <<" were read in the directory "<(); - // } + } + + // Read the series + typename ReaderType::Pointer reader = ReaderType::New(); + if (m_ArgsInfo.preserve_flag) { +#if GDCM_MAJOR_VERSION >= 2 + gdcmIO->LoadPrivateTagsOn(); + gdcmIO->KeepOriginalUIDOn(); +#endif + } + reader->SetImageIO( gdcmIO ); + reader->SetFileNames( filenames_in ); + try { + reader->Update(); + } catch (itk::ExceptionObject &excp) { + std::cerr << "Error: Exception thrown while reading the DICOM series!!" << std::endl; + std::cerr << excp << std::endl; + } + + // Read the input (MHD file) + typedef typename InputImageType::RegionType RegionType; + typedef typename RegionType::SizeType SizeType; + typedef itk::ImageFileReader InputReaderType; + typename InputReaderType::Pointer volumeReader = InputReaderType::New(); + volumeReader->SetFileName( m_InputFileName); + volumeReader->Update(); + + typename InputImageType::Pointer input = volumeReader->GetOutput(); + if ((!m_ArgsInfo.useSizeAsReference_flag && (input->GetSpacing() != reader->GetOutput()->GetSpacing())) || + (m_ArgsInfo.useSizeAsReference_flag && (input->GetLargestPossibleRegion().GetSize() != reader->GetOutput()->GetLargestPossibleRegion().GetSize()))) { + + // resampling is carried out on the fly if resolution or size between + // the input mhd and input dicom series is different - else if (PixelType == "unsigned_char"){ - if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and unsigned_char..." << std::endl; - UpdateWithDimAndPixelType(); - } + // Filter + typedef clitk::ResampleImageWithOptionsFilter ResampleImageFilterType; + typename ResampleImageFilterType::Pointer filter = ResampleImageFilterType::New(); + filter->SetInput(input); + filter->SetVerboseOptions(m_Verbose); + filter->SetGaussianFilteringEnabled(false); + filter->SetDefaultPixelValue(0); - // else if (PixelType == "char"){ - // if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and signed_char..." << std::endl; - // UpdateWithDimAndPixelType(); - // } + if (!m_ArgsInfo.useSizeAsReference_flag) { + filter->SetOutputSpacing(reader->GetOutput()->GetSpacing()); + if (m_Verbose) { + std::cout << "Warning: The image spacing differs between the MHD file and the input dicom series. Performing resampling with default options using spacing as reference (for advanced options, use clitkResampleImage)." << std::endl; + std::cout << "MHD -> " << input->GetSpacing() << std::endl; + std::cout << "dicom -> " << reader->GetOutput()->GetSpacing() << std::endl; + } + } else { - if (m_Verbose) std::cout << "Launching filter in "<< Dimension <<"D and float..." << std::endl; - UpdateWithDimAndPixelType(); + const SizeType& dicom_size = reader->GetOutput()->GetLargestPossibleRegion().GetSize(); + SizeType output_size; + for (unsigned int i = 0; i < Dimension; i++) + output_size[i] = dicom_size[i]; + filter->SetOutputSize(output_size); + if (m_Verbose) { + std::cout << "Warning: The image size differs between the MHD file and the input dicom series. Performing resampling with default options using size as reference (for advanced options, use clitkResampleImage)." << std::endl; + std::cout << "MHD -> " << input->GetLargestPossibleRegion().GetSize() << std::endl; + std::cout << "dicom -> " << reader->GetOutput()->GetLargestPossibleRegion().GetSize() << std::endl; + } + } + + try { + filter->Update(); + input = filter->GetOutput(); + } catch( itk::ExceptionObject & excp ) { + std::cerr << "Error: Exception thrown while resampling!!" << std::endl; + std::cerr << excp << std::endl; } } + + // In some cases, due to resampling approximation issues, + // the number of slices in the MHD file may be different (smaller) + // from the number of files in the template dicom directory. + // To avoid ITK generating an exception, we reduce the number + // of DCM files to be considered, and a warning is printed + // in verbose mode + const RegionType volumeRegion = input->GetLargestPossibleRegion(); + const SizeType& volumeSize = volumeRegion.GetSize(); + if (m_Verbose) { + std::cout << volumeRegion << volumeSize << std::endl; + } + if (Dimension == 3 && volumeSize[2] < numberOfFilenames) { + if (m_Verbose) + std::cout << "Warning: The number of files in " << m_ArgsInfo.inputDir_arg << " (" << filenames_in.size() << " files) is greater than the number of slices in MHD (" << volumeSize[2] << " slices). Using only " << volumeSize[2] << " files." << std::endl; + + filenames_in.resize(volumeSize[2]); + filenames_out.resize(filenames_in.size()); + numberOfFilenames = filenames_in.size(); + } + // Modify the meta dictionary + typedef itk::MetaDataDictionary DictionaryType; + const std::vector* dictionary = reader->GetMetaDataDictionaryArray(); - //------------------------------------------------------------------- - // Update with the number of dimensions and the pixeltype - //------------------------------------------------------------------- - template - template - void - WriteDicomSeriesGenericFilter::UpdateWithDimAndPixelType() - { + // Get keys + unsigned int numberOfKeysGiven=m_ArgsInfo.key_given; + if (m_ArgsInfo.verbose_flag) + DD(numberOfKeysGiven); - // ImageTypes - typedef itk::Image InputImageType; - typedef itk::Image OutputImageType; - - // Read the input (volumetric) - typedef itk::ImageFileReader InputReaderType; - typename InputReaderType::Pointer volumeReader = InputReaderType::New(); - volumeReader->SetFileName( m_InputFileName); - volumeReader->Update(); - typename InputImageType::Pointer input= volumeReader->GetOutput(); - - // Read the dicom directory - typedef itk::ImageSeriesReader< InputImageType > ReaderType; - typedef itk::GDCMImageIO ImageIOType; - typedef itk::GDCMSeriesFileNames NamesGeneratorType; + std::string seriesUID; + std::string frameOfReferenceUID; + std::string studyUID; + + // one pass through the keys given on the cmd-line, to check what will be recreated + std::string seriesUIDkey = "0020|000e"; + std::string seriesNumberKey = "0020|0011"; + std::string seriesDescriptionKey = "0008|103e"; + std::string frameOfReferenceUIDKey = "0020|0052"; + std::string studyUIDKey = "0020|000d"; + std::string studyIDKey = "0020|0010"; + std::string studyDescriptionKey = "0008|1030"; + bool seriesUIDGiven = false; + bool seriesNumberGiven = false; + bool seriesDescriptionGiven = false; + bool studyUIDGiven = false; + bool studyIDGiven = false; + bool studyDescriptionGiven = false; + for (unsigned int i = 0; i < numberOfKeysGiven; i++) { + std::string entryId( m_ArgsInfo.key_arg[i] ); + if (m_ArgsInfo.verbose_flag) + DD(entryId); - ImageIOType::Pointer gdcmIO = ImageIOType::New(); - NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New(); - namesGenerator->SetInputDirectory( m_ArgsInfo.inputDir_arg ); - typename ReaderType::FileNamesContainer filenames = namesGenerator->GetInputFileNames(); - - // Output the dicom files - unsigned int numberOfFilenames = filenames.size(); - if (m_Verbose) - { - std::cout << numberOfFilenames <<" were read in the directory "<= 2 + gdcm::UIDGenerator suid; + seriesUID = suid.Generate(); + gdcm::UIDGenerator fuid; + frameOfReferenceUID = fuid.Generate(); +#else + seriesUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix()); + frameOfReferenceUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix()); +#endif + } + if (m_ArgsInfo.verbose_flag) { + DD(seriesUID); + DD(frameOfReferenceUID); + DD(studyUID); + } - // Modify the meta dictionary - typedef itk::MetaDataDictionary DictionaryType; - const std::vector* dictionary = reader->GetMetaDataDictionaryArray(); + // check if file UIDs will be be preserved + bool useInputFileUID = true; + if (m_ArgsInfo.newSeriesUID_flag || m_ArgsInfo.newStudyUID_flag || seriesUIDGiven || studyUIDGiven) { + useInputFileUID = false; + } + else { +#if GDCM_MAJOR_VERSION < 2 + gdcmIO->SetKeepOriginalUID(true); +#endif + namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg ); + } + + filenames_out.resize(numberOfFilenames); + + time_t t; + t = time(&t); + struct tm* instanceDateTimeTm = localtime(&t); + char datetime[16]; + strftime(datetime, 16, "%Y%m%d", instanceDateTimeTm); + std::ostringstream instanceDate; + instanceDate << datetime; + std::ostringstream instanceTime; + strftime(datetime, 16, "%H%M%S", instanceDateTimeTm); + instanceTime << datetime; + + // update output dicom keys/tags + for(unsigned int fni = 0; fni( *((*dictionary)[fni]), entryId, value ); + } + + // series UID + if (!seriesUIDGiven) { + if (m_ArgsInfo.newSeriesUID_flag) { + itk::EncapsulateMetaData( *((*dictionary)[fni]), seriesUIDkey, seriesUID ); + itk::EncapsulateMetaData( *((*dictionary)[fni]), frameOfReferenceUIDKey, frameOfReferenceUID ); + } + } + + // study UID + if (!studyUIDGiven) { + if (m_ArgsInfo.newStudyUID_flag) + itk::EncapsulateMetaData( *((*dictionary)[fni]), studyUIDKey, studyUID ); + } - // Get keys - unsigned int numberOfKeysGiven=0; - if(m_ArgsInfo.midP_flag && m_ArgsInfo.key_given) - std::cerr<<"Error: both keys and midP option are given"<( *((*dictionary)[fni]), studyIDKey,itksys::SystemTools::GetFilenameName( m_ArgsInfo.outputDir_arg )); + if (!studyDescriptionGiven) + itk::EncapsulateMetaData( *((*dictionary)[fni]), studyDescriptionKey,itksys::SystemTools::GetFilenameName( m_ArgsInfo.outputDir_arg )); + + itk::EncapsulateMetaData( *((*dictionary)[fni]), "0008|0020", instanceDate.str() ); + itk::EncapsulateMetaData( *((*dictionary)[fni]), "0008|0030", instanceTime.str() ); + } - for (unsigned int i = 0; i < numberOfKeysGiven; i++) - { - std::string entryId(m_ArgsInfo.key_arg[i] ); - std::string value( m_ArgsInfo.tag_arg[i] ); - for(unsigned int fni = 0; fni( *((*dictionary)[fni]), entryId, value ); - } + // series description/number + if (seriesUIDGiven || m_ArgsInfo.newSeriesUID_flag) { + if (!seriesDescriptionGiven) + itk::EncapsulateMetaData( *((*dictionary)[fni]), seriesDescriptionKey, itksys::SystemTools::GetFilenameName(m_ArgsInfo.outputDir_arg) ); + if (!seriesNumberGiven) + itk::EncapsulateMetaData( *((*dictionary)[fni]), seriesNumberKey, itksys::SystemTools::GetFilenameName(m_ArgsInfo.outputDir_arg) ); - // Output directory and filenames - itksys::SystemTools::MakeDirectory( m_ArgsInfo.outputDir_arg ); // create if it doesn't exist - typedef itk::ImageSeriesWriter SeriesWriterType; - typename SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New(); + itk::EncapsulateMetaData( *((*dictionary)[fni]), "0008|0012", instanceDate.str() ); + itk::EncapsulateMetaData( *((*dictionary)[fni]), "0008|0013", instanceTime.str() ); + } - seriesWriter->SetInput( volumeReader->GetOutput() ); - seriesWriter->SetImageIO( gdcmIO ); - namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg ); - seriesWriter->SetFileNames( namesGenerator->GetOutputFileNames() ); - //seriesWriter->SetMetaDataDictionaryArray( dictionary ); - seriesWriter->SetMetaDataDictionaryArray( dictionary ); - - // Write - try - { - seriesWriter->Update(); - } - catch( itk::ExceptionObject & excp ) - { - std::cerr << "Error: Exception thrown while writing the series!!" << std::endl; - std::cerr << excp << std::endl; - } + // file UIDs are recreated for new studies or series + if (!useInputFileUID) + { + if (m_ArgsInfo.verbose_flag) + std::cout << "Recreating file UIDs" << std::endl; + std::string fileUID; +#if GDCM_MAJOR_VERSION >= 2 + gdcm::UIDGenerator fid; + fileUID = fid.Generate(); +#else + fileUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix()); +#endif + itk::EncapsulateMetaData( *((*dictionary)[fni]), "0008|0018", fileUID ); + itk::EncapsulateMetaData( *((*dictionary)[fni]), "0002|0003", fileUID ); + + filenames_out[fni] = itksys::SystemTools::CollapseFullPath(fileUID.c_str(), m_ArgsInfo.outputDir_arg) + std::string(".dcm"); + } } + + // Output directory and filenames + itksys::SystemTools::MakeDirectory( m_ArgsInfo.outputDir_arg ); // create if it doesn't exist + typedef itk::ImageSeriesWriter SeriesWriterType; + typename SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New(); + seriesWriter->SetInput( input ); + seriesWriter->SetImageIO( gdcmIO ); + + seriesWriter->SetFileNames( filenames_out ); + seriesWriter->SetMetaDataDictionaryArray( dictionary ); + + // Write + try { + if (m_ArgsInfo.verbose_flag) + std::cout << seriesWriter << std::endl; + seriesWriter->Update(); + } catch( itk::ExceptionObject & excp ) { + std::cerr << "Error: Exception thrown while writing the series!!" << std::endl; + std::cerr << excp << std::endl; + } + +} + +/* +//------------------------------------------------------------------- +// Update with the number of dimensions and the pixeltype +//------------------------------------------------------------------- +template +template +void +WriteDicomSeriesGenericFilter::UpdateWithDimAndPixelType() +{ + + // ImageTypes + typedef itk::Image InputImageType; + typedef itk::Image OutputImageType; + + // Read the input (volumetric) + typedef itk::ImageFileReader InputReaderType; + typename InputReaderType::Pointer volumeReader = InputReaderType::New(); + volumeReader->SetFileName( m_InputFileName); + volumeReader->Update(); + typename InputImageType::Pointer input= volumeReader->GetOutput(); + + // Read the dicom directory + typedef itk::ImageSeriesReader< InputImageType > ReaderType; + typedef itk::GDCMImageIO ImageIOType; + typedef itk::GDCMSeriesFileNames NamesGeneratorType; + + ImageIOType::Pointer gdcmIO = ImageIOType::New(); + NamesGeneratorType::Pointer namesGenerator = NamesGeneratorType::New(); + namesGenerator->SetInputDirectory( m_ArgsInfo.inputDir_arg ); + namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg ); + typename ReaderType::FileNamesContainer filenames_in = namesGenerator->GetInputFileNames(); + typename ReaderType::FileNamesContainer filenames_out = namesGenerator->GetOutputFileNames(); + + // Output the dicom files + unsigned int numberOfFilenames = filenames_in.size(); + if (m_Verbose) { + std::cout << numberOfFilenames <<" were read in the directory "<SetImageIO( gdcmIO ); + reader->SetFileNames( filenames_in ); + try { + reader->Update(); + } catch (itk::ExceptionObject &excp) { + std::cerr << "Error: Exception thrown while reading the DICOM series!!" << std::endl; + std::cerr << excp << std::endl; + } + + + // Modify the meta dictionary + typedef itk::MetaDataDictionary DictionaryType; + const std::vector* dictionary = reader->GetMetaDataDictionaryArray(); + + // Get keys + unsigned int numberOfKeysGiven=0; + if(m_ArgsInfo.midP_flag && m_ArgsInfo.key_given) + std::cerr<<"Error: both keys and midP option are given"<( *((*dictionary)[fni]), entryId, value ); + } + + // Output directory and filenames + itksys::SystemTools::MakeDirectory( m_ArgsInfo.outputDir_arg ); // create if it doesn't exist + typedef itk::ImageSeriesWriter SeriesWriterType; + typename SeriesWriterType::Pointer seriesWriter = SeriesWriterType::New(); + + seriesWriter->SetInput( volumeReader->GetOutput() ); + seriesWriter->SetImageIO( gdcmIO ); + + seriesWriter->SetFileNames( filenames_out ); + seriesWriter->SetMetaDataDictionaryArray( dictionary ); + + // Write + try { + seriesWriter->Update(); + } catch( itk::ExceptionObject & excp ) { + std::cerr << "Error: Exception thrown while writing the series!!" << std::endl; + std::cerr << excp << std::endl; + } + +} +*/ }//end clitk - + #endif //#define clitkWriteDicomSeriesGenericFilter_txx