X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=tools%2FclitkWriteDicomSeriesGenericFilter.txx;h=a2bccc4aa0daa52fbef3b8a34cb115b3eb9cc20c;hb=HEAD;hp=3a8446fadabb4c4f5f7ec775d9ca165cc156f28b;hpb=4454c06e212fb6af58d206f2d6f9b76778858967;p=clitk.git diff --git a/tools/clitkWriteDicomSeriesGenericFilter.txx b/tools/clitkWriteDicomSeriesGenericFilter.txx index 3a8446f..a2bccc4 100644 --- a/tools/clitkWriteDicomSeriesGenericFilter.txx +++ b/tools/clitkWriteDicomSeriesGenericFilter.txx @@ -153,6 +153,12 @@ WriteDicomSeriesGenericFilter::UpdateWithDimAndPixelType() // 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 { @@ -241,10 +247,52 @@ WriteDicomSeriesGenericFilter::UpdateWithDimAndPixelType() // Get keys unsigned int numberOfKeysGiven=m_ArgsInfo.key_given; + if (m_ArgsInfo.verbose_flag) + DD(numberOfKeysGiven); std::string seriesUID; std::string frameOfReferenceUID; - if (m_ArgsInfo.newSeriesUID_flag) { + 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); + + seriesUIDGiven |= (entryId == seriesUIDkey || entryId == frameOfReferenceUIDKey); + seriesNumberGiven |= (entryId == seriesNumberKey); + seriesDescriptionGiven |= (entryId == seriesDescriptionKey); + studyUIDGiven |= (entryId == studyUIDKey); + studyIDGiven |= (entryId == studyIDKey); + studyDescriptionGiven |= (entryId == studyDescriptionKey); + } + + // force the creation of a new series if a new study was specified + if (!studyUIDGiven && m_ArgsInfo.newStudyUID_flag) { + m_ArgsInfo.newSeriesUID_flag = true; +#if GDCM_MAJOR_VERSION >= 2 + gdcm::UIDGenerator suid; + studyUID = suid.Generate(); +#else + studyUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix()); +#endif + } + + if (!seriesUIDGiven && m_ArgsInfo.newSeriesUID_flag) { #if GDCM_MAJOR_VERSION >= 2 gdcm::UIDGenerator suid; seriesUID = suid.Generate(); @@ -254,60 +302,90 @@ WriteDicomSeriesGenericFilter::UpdateWithDimAndPixelType() seriesUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix()); frameOfReferenceUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix()); #endif - if (m_ArgsInfo.verbose_flag) - { - DD(seriesUID); - DD(frameOfReferenceUID); - } } - - std::string studyUID; - if (m_ArgsInfo.newStudyUID_flag) { -#if GDCM_MAJOR_VERSION >= 2 - gdcm::UIDGenerator suid; - studyUID = suid.Generate(); -#else - studyUID = gdcm::Util::CreateUniqueUID( gdcmIO->GetUIDPrefix()); -#endif - if (m_ArgsInfo.verbose_flag) - DD(studyUID); + if (m_ArgsInfo.verbose_flag) { + DD(seriesUID); + DD(frameOfReferenceUID); + DD(studyUID); } + + // 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 - else - gdcmIO->KeepOriginalUID(); + gdcmIO->SetKeepOriginalUID(true); #endif + namesGenerator->SetOutputDirectory( m_ArgsInfo.outputDir_arg ); + } - std::string seriesUIDkey = "0020|000e"; - std::string frameOfReferenceUIDKey = "0020|0052"; - std::string studyUIDKey = "0020|000d"; + 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 ); - if (entryId == seriesUIDkey || entryId == frameOfReferenceUIDKey) - series_id_given = true; - if (entryId == studyUIDKey) - study_id_given = true; } - - if (!series_id_given) { + + // series UID + if (!seriesUIDGiven) { if (m_ArgsInfo.newSeriesUID_flag) { itk::EncapsulateMetaData( *((*dictionary)[fni]), seriesUIDkey, seriesUID ); itk::EncapsulateMetaData( *((*dictionary)[fni]), frameOfReferenceUIDKey, frameOfReferenceUID ); } } - if (!study_id_given) { + // study UID + if (!studyUIDGiven) { if (m_ArgsInfo.newStudyUID_flag) itk::EncapsulateMetaData( *((*dictionary)[fni]), studyUIDKey, studyUID ); } + + // study description + if (studyUIDGiven || m_ArgsInfo.newStudyUID_flag) { + if (!studyIDGiven) + itk::EncapsulateMetaData( *((*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() ); + } + + // 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) ); + + itk::EncapsulateMetaData( *((*dictionary)[fni]), "0008|0012", instanceDate.str() ); + itk::EncapsulateMetaData( *((*dictionary)[fni]), "0008|0013", instanceTime.str() ); + } + + // file UIDs are recreated for new studies or series + if (!useInputFileUID) + { + if (m_ArgsInfo.verbose_flag) + std::cout << "Recreating file UIDs" << std::endl; - if (m_ArgsInfo.newSeriesUID_flag || m_ArgsInfo.newStudyUID_flag || series_id_given || study_id_given) { std::string fileUID; #if GDCM_MAJOR_VERSION >= 2 gdcm::UIDGenerator fid; @@ -317,10 +395,11 @@ WriteDicomSeriesGenericFilter::UpdateWithDimAndPixelType() #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; @@ -334,6 +413,8 @@ WriteDicomSeriesGenericFilter::UpdateWithDimAndPixelType() // 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;