450 lines
20 KiB
C#
450 lines
20 KiB
C#
using Dicom;
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using Dicom.Imaging.Codec;
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using EasyCaching.Core;
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using IRaCIS.Core.Application.Contracts.Dicom;
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using IRaCIS.Core.Infra.EFCore;
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using IRaCIS.Core.Domain.Share;
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using Microsoft.Extensions.Hosting;
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using System.Text;
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using IRaCIS.Core.Application.Contracts;
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namespace IRaCIS.Core.Application.Services
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{
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public class DicomArchiveService : IDicomArchiveService
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{
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private readonly IRepository<DicomStudy> _studyRepository;
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private readonly IRepository<DicomSeries> _seriesRepository;
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private readonly IRepository<DicomInstance> _instanceRepository;
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private readonly IEasyCachingProvider _provider;
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private readonly DicomFileStoreHelper _dicomFileStoreHelper;
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private static object lockCodeGenerate = new object();
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public DicomArchiveService(IRepository<DicomStudy> studyRepository,
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IRepository<DicomSeries> seriesRepository,
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IRepository<DicomInstance> instanceRepository,
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IHostEnvironment hostEnvironment,
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DicomFileStoreHelper dicomFileStoreHelper,
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IEasyCachingProvider provider)
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{
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_dicomFileStoreHelper = dicomFileStoreHelper;
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_studyRepository = studyRepository;
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_seriesRepository = seriesRepository;
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_instanceRepository = instanceRepository;
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_provider = provider;
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}
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public async Task<bool> DicomDBDataSaveChange()
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{
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var success = await _studyRepository.SaveChangesAsync();
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return success;
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}
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public async Task<Guid> ArchiveDicomStreamAsync(Stream dicomStream,
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DicomTrialSiteSubjectInfo addtionalInfo, List<string> seriesInstanceUidList, List<string> instanceUidList)
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{
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DicomFile dicomFile = await DicomFile.OpenAsync(dicomStream, Encoding.Default);
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DicomDataset dataset = dicomFile.Dataset;
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//如果数据库存在该instance 记录 那么就不处理
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string sopInstanceUid = dataset.GetString(DicomTag.SOPInstanceUID);
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string studyInstanceUid = dataset.GetString(DicomTag.StudyInstanceUID);
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if (instanceUidList.Any(t => t == sopInstanceUid))
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{
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return IdentifierHelper.CreateGuid(studyInstanceUid, addtionalInfo.TrialId.ToString());
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}
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var anonymize_AddFixedFiledList = _provider.Get<List<SystemAnonymization>>(StaticData.Anonymize_AddFixedFiled).Value;
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var anonymize_AddIRCInfoFiled = _provider.Get<List<SystemAnonymization>>(StaticData.Anonymize_AddIRCInfoFiled).Value;
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var anonymize_FixedField = _provider.Get<List<SystemAnonymization>>(StaticData.Anonymize_FixedField).Value;
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var anonymize_IRCInfoField = _provider.Get<List<SystemAnonymization>>(StaticData.Anonymize_IRCInfoField).Value;
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foreach (var item in anonymize_AddFixedFiledList.Union(anonymize_FixedField))
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{
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var dicomTag = new DicomTag(Convert.ToUInt16(item.Group, 16), Convert.ToUInt16(item.Element, 16));
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dataset.AddOrUpdate(dicomTag, item.ReplaceValue);
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}
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foreach (var item in anonymize_AddIRCInfoFiled.Union(anonymize_IRCInfoField))
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{
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var dicomTag = new DicomTag(Convert.ToUInt16(item.Group, 16), Convert.ToUInt16(item.Element, 16));
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if (dicomTag == DicomTag.ClinicalTrialProtocolID)
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{
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dataset.AddOrUpdate(dicomTag, addtionalInfo.TrialCode);
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}
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if (dicomTag == DicomTag.ClinicalTrialSiteID)
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{
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dataset.AddOrUpdate(dicomTag, addtionalInfo.TrialSiteCode);
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}
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if (dicomTag == DicomTag.ClinicalTrialSubjectID)
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{
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dataset.AddOrUpdate(dicomTag, addtionalInfo.SubjectCode);
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}
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if (dicomTag == DicomTag.ClinicalTrialTimePointID)
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{
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dataset.AddOrUpdate(dicomTag, addtionalInfo.VisitNum.ToString());
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}
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if (dicomTag == DicomTag.PatientID)
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{
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dataset.AddOrUpdate(dicomTag, addtionalInfo.TrialCode+"_"+ addtionalInfo.SubjectCode);
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}
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}
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#region 调整废弃
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////按照配置文件 匿名化
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//foreach (var anonymizeItem in SystemConfig.AnonymizeTagList)
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//{
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// if (anonymizeItem.Enable)
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// {
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// ushort group = Convert.ToUInt16(anonymizeItem.Group, 16);
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// ushort element = Convert.ToUInt16(anonymizeItem.Element, 16);
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// dataset.AddOrUpdate(new DicomTag(group, element), anonymizeItem.ReplaceValue);
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// }
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//}
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//if (AppSettings.AddClinicalInfo) //是否需要写入临床信息
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//{
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// //Dicom 文件中写入临床信息
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// dataset.AddOrUpdate(DicomTag.ClinicalTrialProtocolID, addtionalInfo.TrialCode); //Trial
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// dataset.AddOrUpdate(DicomTag.ClinicalTrialProtocolName, addtionalInfo.TrialIndication); //indication
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// dataset.AddOrUpdate(DicomTag.ClinicalTrialSponsorName, addtionalInfo.Sponsor);//sponsor
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// dataset.AddOrUpdate(DicomTag.ClinicalTrialSiteID, addtionalInfo.SiteCode); //SiteId
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// dataset.AddOrUpdate(DicomTag.ClinicalTrialSiteName, addtionalInfo.SiteName);//SiteName
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// dataset.AddOrUpdate(DicomTag.ClinicalTrialSubjectID, addtionalInfo.SubjectCode + " " + addtionalInfo.SubjectSex);//SubjectId
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// dataset.AddOrUpdate(DicomTag.ClinicalTrialTimePointID, addtionalInfo.VisitNum.ToString()); // TimePoint
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// dataset.AddOrUpdate(DicomTag.ClinicalTrialTimePointDescription, addtionalInfo.VisitName + " " + addtionalInfo.SVUPDES);
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//}
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//DicomStudy dicomStudy = null;
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//DicomSeries dicomSeries = null;
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//DicomInstance dicomInstance = null;
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//lock (lockTest)
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//{
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// dicomStudy = CreateDicomStudy(dataset, addtionalInfo, out bool isStudyNeedAdd);
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// dicomSeries = CreateDicomSeries(dataset, dicomStudy, out bool isSeriesNeedAdd);
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// dicomInstance = CreateDicomInstance(dataset, dicomStudy, dicomSeries);
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// if (isStudyNeedAdd) _studyRepository.Add(dicomStudy);
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// if (isSeriesNeedAdd) _seriesRepository.Add(dicomSeries);
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// _instanceRepository.Add(dicomInstance);
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//}
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#endregion
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DicomStudy dicomStudy = CreateDicomStudy(dataset, addtionalInfo, out bool isStudyNeedAdd);
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DicomSeries dicomSeries = CreateDicomSeries(dataset, dicomStudy, out bool isSeriesNeedAdd);
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DicomInstance dicomInstance = CreateDicomInstance(dataset, dicomStudy, dicomSeries);
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if (isStudyNeedAdd) await _studyRepository.AddAsync(dicomStudy);
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if (isSeriesNeedAdd) await _seriesRepository.AddAsync(dicomSeries);
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await _instanceRepository.AddAsync(dicomInstance);
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string filePath = _dicomFileStoreHelper.CreateInstanceFilePath(dicomStudy, dicomSeries.Id, dicomInstance.Id);
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var samplesPerPixel = dataset.GetSingleValueOrDefault(DicomTag.SamplesPerPixel, string.Empty);
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var photometricInterpretation = dataset.GetSingleValueOrDefault(DicomTag.PhotometricInterpretation, string.Empty);
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if (samplesPerPixel == "1" && (photometricInterpretation.ToUpper() == "MONOCHROME2" || photometricInterpretation.ToUpper() == "MONOCHROME1"))//MONOCHROME2
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{
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if (dataset.InternalTransferSyntax.IsEncapsulated)
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{
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await dicomFile.SaveAsync(filePath);
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}
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else
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{
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await dicomFile.Clone(DicomTransferSyntax.JPEGLSLossless).SaveAsync(filePath);
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}
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}
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else
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{
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if (dataset.InternalTransferSyntax.IsEncapsulated) await dicomFile.SaveAsync(filePath);
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else await dicomFile.Clone(DicomTransferSyntax.RLELossless).SaveAsync(filePath); //RLELossless
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}
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return dicomInstance.StudyId;
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}
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private DicomStudy CreateDicomStudy(DicomDataset dataset, DicomTrialSiteSubjectInfo addtionalInfo, out bool isStudyNeedAdd)
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{
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string studyInstanceUid = dataset.GetString(DicomTag.StudyInstanceUID);
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Guid studyId = IdentifierHelper.CreateGuid(studyInstanceUid, addtionalInfo.TrialId.ToString());
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// 每个线程都查询数据库最大的，和缓存中最大的，取最大值为基数生成Code
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//var id = Thread.CurrentThread.ManagedThreadId.ToString("00");
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//虽然每个文件都会进来，但是只要查询过，就会跟踪，不会再次查询数据库 这里线程并发会有问题，得加锁，不然生成Code 出错
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DicomStudy dicomStudy = _studyRepository.ImageFind(studyId, typeof(DicomStudy));
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if (dicomStudy != null)
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{
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isStudyNeedAdd = false;
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return dicomStudy;
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}
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//_logger.LogWarning($"Thread {id} ,studyUid{studyInstanceUid}， 生成StudyId：{studyId}");
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isStudyNeedAdd = true;
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dicomStudy = new DicomStudy
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{
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Id = studyId,
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StudyInstanceUid = studyInstanceUid,
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/* StudyTime = dataset.GetSingleValueOrDefault(DicomTag.StudyDate, DateTime.Now).Add(dataset.GetSingleValueOrDefault(DicomTag.StudyTime, DateTime.Now).TimeOfDay),*///dataset.GetDateTime(DicomTag.StudyDate, DicomTag.StudyTime),
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StudyTime = dataset.GetSingleValue<DateTime?>(DicomTag.StudyDate)?.Add(dataset.GetSingleValueOrDefault(DicomTag.StudyTime, TimeSpan.Zero)),
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Modalities = dataset.GetSingleValueOrDefault(DicomTag.Modality, string.Empty),
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Description = dataset.GetSingleValueOrDefault(DicomTag.StudyDescription, string.Empty),
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InstitutionName = dataset.GetSingleValueOrDefault(DicomTag.InstitutionName, string.Empty),
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PatientId = dataset.GetSingleValueOrDefault(DicomTag.PatientID, string.Empty),
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PatientName = dataset.GetSingleValueOrDefault(DicomTag.PatientName, string.Empty),
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PatientAge = dataset.GetSingleValueOrDefault(DicomTag.PatientAge, string.Empty),
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PatientSex = dataset.GetSingleValueOrDefault(DicomTag.PatientSex, string.Empty),
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BodyPartExamined = dataset.GetSingleValueOrDefault(DicomTag.BodyPartExamined, string.Empty),
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StudyId = dataset.GetSingleValueOrDefault(DicomTag.StudyID, string.Empty),
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AccessionNumber = dataset.GetSingleValueOrDefault(DicomTag.AccessionNumber, string.Empty),
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//需要特殊处理
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PatientBirthDate = dataset.GetSingleValueOrDefault(DicomTag.PatientBirthDate, string.Empty),
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AcquisitionTime = dataset.GetSingleValueOrDefault(DicomTag.AcquisitionTime, string.Empty),
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AcquisitionNumber = dataset.GetSingleValueOrDefault(DicomTag.AcquisitionNumber, string.Empty),
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TriggerTime = dataset.GetSingleValueOrDefault(DicomTag.TriggerTime, string.Empty),
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SiteId = addtionalInfo.SiteId,
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TrialId = addtionalInfo.TrialId,
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SubjectId = addtionalInfo.SubjectId,
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SubjectVisitId = addtionalInfo.SubjectVisitId,
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//IsDoubleReview = addtionalInfo.IsDoubleReview,
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SeriesCount = 0,
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InstanceCount = 0
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};
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if (dicomStudy.PatientBirthDate.Length == 8)
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{
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dicomStudy.PatientBirthDate = $"{dicomStudy.PatientBirthDate[0]}{dicomStudy.PatientBirthDate[1]}{dicomStudy.PatientBirthDate[2]}{dicomStudy.PatientBirthDate[3]}-{dicomStudy.PatientBirthDate[4]}{dicomStudy.PatientBirthDate[5]}-{dicomStudy.PatientBirthDate[6]}{dicomStudy.PatientBirthDate[7]}";
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}
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lock (lockCodeGenerate)
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{
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//查询数据库获取最大的Code 没有记录则为0
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var dbStudyCodeIntMax = _studyRepository.Where(s => s.TrialId == addtionalInfo.TrialId).Select(t => t.Code).DefaultIfEmpty().Max();
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//获取缓存中的值 并发的时候，需要记录，已被占用的值 这样其他线程在此占用的最大的值上递增
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var cacheMaxCodeInt = _provider.Get<int>($"{addtionalInfo.TrialId }_{ StaticData.StudyMaxCode}").Value;
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int currentNextCodeInt = cacheMaxCodeInt > dbStudyCodeIntMax ? cacheMaxCodeInt + 1 : dbStudyCodeIntMax + 1;
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dicomStudy.Code = currentNextCodeInt;
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dicomStudy.StudyCode = "ST" + currentNextCodeInt.ToString("D5");
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_provider.Set<int>($"{addtionalInfo.TrialId }_{ StaticData.StudyMaxCode}", dicomStudy.Code, TimeSpan.FromMinutes(30));
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}
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#region Setting Code old
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//var studyCode = _studyRepository.Where(s => s.TrialId == addtionalInfo.TrialId).Select(t => t.StudyCode).OrderByDescending(c => c).FirstOrDefault();
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//var cacheMaxCode = _provider.Get<string>($"{addtionalInfo.TrialId }_{ StaticData.StudyMaxCode}").Value;
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//if (studyCode == null && string.IsNullOrEmpty(cacheMaxCode))
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//{
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// dicomStudy.StudyCode = "ST" + 1.ToString().PadLeft(5, '0');
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// _logger.LogWarning($"Thread {id} DB：{studyCode} 生成{ dicomStudy.StudyCode}");
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//}
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//else
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//{
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// int dbNum = 0;
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// int cacheNum = 0;
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// if (studyCode != null)
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// {
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// int.TryParse(studyCode.Substring(studyCode.Length - 5, 5), out dbNum);
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// }
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// if (!string.IsNullOrEmpty(cacheMaxCode))
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// {
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// int.TryParse(cacheMaxCode.Substring(cacheMaxCode.Length - 5, 5), out cacheNum);
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// }
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// dbNum = cacheNum > dbNum ? cacheNum : dbNum;
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// dicomStudy.StudyCode = "ST" + (++dbNum).ToString().PadLeft(5, '0');
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// _logger.LogWarning($" Thread {id} DB：{studyCode} cache:{cacheNum} 生成{ dicomStudy.StudyCode}");
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//}
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//_provider.Set<string>($"{addtionalInfo.TrialId }_{ StaticData.StudyMaxCode}", dicomStudy.StudyCode, TimeSpan.FromMinutes(30));
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#endregion
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return dicomStudy;
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}
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private DicomSeries CreateDicomSeries(DicomDataset dataset, DicomStudy dicomStudy, out bool isSeriesNeedAdd)
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{
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string seriesInstanceUid = dataset.GetString(DicomTag.SeriesInstanceUID);
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Guid seriesId = IdentifierHelper.CreateGuid(dicomStudy.StudyInstanceUid, seriesInstanceUid, dicomStudy.TrialId.ToString());
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//有几个序列会查询几次
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DicomSeries dicomSeries = _seriesRepository.ImageFind(seriesId, typeof(DicomSeries));
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if (dicomSeries != null)
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{
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isSeriesNeedAdd = false;
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return dicomSeries;
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}
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else
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{
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//var id = Thread.CurrentThread.ManagedThreadId.ToString("00");
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isSeriesNeedAdd = true;
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dicomSeries = new DicomSeries
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{
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Id = seriesId,
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StudyId = dicomStudy.Id,
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StudyInstanceUid = dicomStudy.StudyInstanceUid,
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SeriesInstanceUid = seriesInstanceUid,
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SeriesNumber = dataset.GetSingleValueOrDefault(DicomTag.SeriesNumber, 1),
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//SeriesTime = dataset.GetSingleValueOrDefault(DicomTag.SeriesDate, DateTime.Now).Add(dataset.GetSingleValueOrDefault(DicomTag.SeriesTime, DateTime.Now).TimeOfDay),
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SeriesTime = dataset.GetSingleValue<DateTime?>(DicomTag.SeriesDate)?.Add(dataset.GetSingleValueOrDefault(DicomTag.SeriesTime, TimeSpan.Zero)),// dataset.GetDateTime(DicomTag.SeriesDate, DicomTag.SeriesTime),
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Modality = dataset.GetSingleValueOrDefault(DicomTag.Modality, string.Empty),
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Description = dataset.GetSingleValueOrDefault(DicomTag.SeriesDescription, string.Empty),
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SliceThickness = dataset.GetSingleValueOrDefault(DicomTag.SliceThickness, string.Empty),
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ImagePositionPatient = dataset.GetSingleValueOrDefault(DicomTag.ImagePositionPatient, string.Empty),
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ImageOrientationPatient = dataset.GetSingleValueOrDefault(DicomTag.ImageOrientationPatient, string.Empty),
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BodyPartExamined = dataset.GetSingleValueOrDefault(DicomTag.BodyPartExamined, string.Empty),
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SequenceName = dataset.GetSingleValueOrDefault(DicomTag.SequenceName, string.Empty),
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ProtocolName = dataset.GetSingleValueOrDefault(DicomTag.ProtocolName, string.Empty),
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ImagerPixelSpacing = dataset.GetSingleValueOrDefault(DicomTag.ImagerPixelSpacing, string.Empty),
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AcquisitionTime = dataset.GetSingleValueOrDefault(DicomTag.ImagerPixelSpacing, string.Empty),
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AcquisitionNumber = dataset.GetSingleValueOrDefault(DicomTag.ImagerPixelSpacing, string.Empty),
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TriggerTime = dataset.GetSingleValueOrDefault(DicomTag.ImagerPixelSpacing, string.Empty),
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SiteId = dicomStudy.SiteId,
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TrialId = dicomStudy.TrialId,
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SubjectId = dicomStudy.SubjectId,
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SubjectVisitId = dicomStudy.SubjectVisitId,
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InstanceCount = 0
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};
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++dicomStudy.SeriesCount;
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//_logger.LogWarning($"线程：{id},sericeId:{seriesId},count:{SeriesDic.Keys.Count}");
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return dicomSeries;
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}
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}
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private DicomInstance CreateDicomInstance(DicomDataset dataset, DicomStudy dicomStudy, DicomSeries dicomSeries)
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{
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string sopInstanceUid = dataset.GetString(DicomTag.SOPInstanceUID);
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Guid instanceId = IdentifierHelper.CreateGuid(dicomStudy.StudyInstanceUid, dicomSeries.SeriesInstanceUid, sopInstanceUid, dicomStudy.TrialId.ToString());
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DicomInstance dicomInstance = new DicomInstance
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{
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Id = instanceId,
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StudyId = dicomStudy.Id,
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SeriesId = dicomSeries.Id,
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SiteId = dicomStudy.SiteId,
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TrialId = dicomStudy.TrialId,
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SubjectId = dicomStudy.SubjectId,
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SubjectVisitId = dicomStudy.SubjectVisitId,
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StudyInstanceUid = dicomStudy.StudyInstanceUid,
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SeriesInstanceUid = dicomSeries.SeriesInstanceUid,
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SopInstanceUid = sopInstanceUid,
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InstanceNumber = dataset.GetSingleValueOrDefault(DicomTag.InstanceNumber, 1),
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InstanceTime = dataset.GetSingleValue<DateTime?>(DicomTag.ContentDate)?.Add(dataset.GetSingleValueOrDefault(DicomTag.ContentTime, TimeSpan.Zero)),
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//dataset.GetSingleValueOrDefault(DicomTag.ContentDate,DateTime.Now);//, DicomTag.ContentTime)
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CPIStatus = false,
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ImageRows = dataset.GetSingleValueOrDefault(DicomTag.Rows, 0),
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ImageColumns = dataset.GetSingleValueOrDefault(DicomTag.Columns, 0),
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SliceLocation = dataset.GetSingleValueOrDefault(DicomTag.SliceLocation, 0),
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SliceThickness = dataset.GetSingleValueOrDefault(DicomTag.SliceThickness, string.Empty),
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NumberOfFrames = dataset.GetSingleValueOrDefault(DicomTag.NumberOfFrames, 0),
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PixelSpacing = dataset.GetSingleValueOrDefault(DicomTag.PixelSpacing, string.Empty),
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ImagerPixelSpacing = dataset.GetSingleValueOrDefault(DicomTag.ImagerPixelSpacing, string.Empty),
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FrameOfReferenceUID = dataset.GetSingleValueOrDefault(DicomTag.FrameOfReferenceUID, string.Empty),
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WindowCenter = dataset.GetSingleValueOrDefault(DicomTag.WindowCenter, string.Empty),
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WindowWidth = dataset.GetSingleValueOrDefault(DicomTag.WindowWidth, string.Empty),
|
||
};
|
||
|
||
++dicomStudy.InstanceCount;
|
||
++dicomSeries.InstanceCount;
|
||
|
||
return dicomInstance;
|
||
|
||
|
||
|
||
}
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
}
|
||
}
|