484 lines
22 KiB
C#
484 lines
22 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.Domain.Share;
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using System.Text;
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using IRaCIS.Core.Application.Contracts;
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using IRaCIS.Core.Application.Helper;
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using Microsoft.AspNetCore.Hosting;
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using IRaCIS.Core.Infrastructure;
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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 IRepository<Dictionary> _dictionaryRepository;
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private readonly IEasyCachingProvider _provider;
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private readonly IWebHostEnvironment _hostEnvironment;
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private static object lockCodeGenerate = new object();
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private List<Guid> _instanceIdList = new List<Guid>();
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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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IWebHostEnvironment hostEnvironment,
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IRepository<Dictionary> dictionaryRepository,
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IEasyCachingProvider provider)
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{
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_hostEnvironment = hostEnvironment;
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_studyRepository = studyRepository;
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_seriesRepository = seriesRepository;
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_instanceRepository = instanceRepository;
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_dictionaryRepository = dictionaryRepository;
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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 StudyId, string StudyCode)> 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()), string.Empty);
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}
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var anonymize_AddFixedFiledList = _provider.Get<List<SystemAnonymization>>(StaticData.Anonymize.Anonymize_AddFixedFiled).Value ?? new List<SystemAnonymization>();
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var anonymize_AddIRCInfoFiledList = _provider.Get<List<SystemAnonymization>>(StaticData.Anonymize.Anonymize_AddIRCInfoFiled).Value ?? new List<SystemAnonymization>();
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var anonymize_FixedFieldList = _provider.Get<List<SystemAnonymization>>(StaticData.Anonymize.Anonymize_FixedField).Value ?? new List<SystemAnonymization>();
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var anonymize_IRCInfoFieldList = _provider.Get<List<SystemAnonymization>>(StaticData.Anonymize.Anonymize_IRCInfoField).Value ?? new List<SystemAnonymization>();
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if (anonymize_AddFixedFiledList.Union(anonymize_AddIRCInfoFiledList).Union(anonymize_FixedFieldList).Union(anonymize_IRCInfoFieldList).Count() == 0)
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{
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throw new BusinessValidationFailedException("未取到缓存匿名化配置数据，上传停止,请联系开发人员核实");
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}
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foreach (var item in anonymize_AddFixedFiledList.Union(anonymize_FixedFieldList))
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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_AddIRCInfoFiledList.Union(anonymize_IRCInfoFieldList))
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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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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,out bool isInstanceNeedAdd);
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dicomSeries.DicomStudy = dicomStudy;
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var createtime = DateTime.Now;
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if (isStudyNeedAdd)
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{
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// 添加检查
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await _studyRepository.AddAsync(dicomStudy);
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}
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if (isSeriesNeedAdd)
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{
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dicomSeries.DicomStudy = dicomStudy;
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// 添加序列
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await _seriesRepository.AddAsync(dicomSeries);
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}
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var (physicalPath, relativePath) = FileStoreHelper.GetDicomInstanceFilePath(_hostEnvironment, dicomStudy.TrialId, dicomStudy.SiteId, dicomStudy.SubjectId, dicomStudy.SubjectVisitId, dicomStudy.Id, dicomInstance.Id);
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dicomInstance.Path = relativePath;
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if (isInstanceNeedAdd)
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{
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await _instanceRepository.AddAsync(dicomInstance);
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}
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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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//正常保存 不做处理
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await dicomFile.SaveAsync(physicalPath);
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}
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else
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{ //JPEGLSLossless 保存
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await dicomFile.Clone(DicomTransferSyntax.JPEGLSLossless).SaveAsync(physicalPath);
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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)
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{
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//正常保存 不做处理
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await dicomFile.SaveAsync(physicalPath);
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}
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else
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{
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//RLELossless 保存
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await dicomFile.Clone(DicomTransferSyntax.RLELossless).SaveAsync(physicalPath); //RLELossless
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}
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}
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return (dicomInstance.StudyId, dicomStudy.StudyCode);
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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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//dataset.GetSingleValue<string>(DicomTag.StudyDate) + dataset.GetSingleValue<string>(DicomTag.StudyTime)
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var modality = dataset.GetSingleValueOrDefault(DicomTag.Modality, string.Empty);
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var dicModalityList = _dictionaryRepository.Where(t => t.Code == "Modality").SelectMany(t => t.ChildList.Select(c => c.Value)).ToList();
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var modalityForEdit = dicModalityList.Contains(modality) ? modality : String.Empty;
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if (modality == "MR")
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{
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modalityForEdit = "MRI";
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}
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if (modality == "PT")
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{
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modalityForEdit = "PET";
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}
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if(modality== "PT、CT")
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{
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modalityForEdit = "PET-CT";
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}
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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.GetSingleValueOrDefault(DicomTag.StudyDate, string.Empty) == string.Empty ? null : dataset.GetSingleValue<DateTime>(DicomTag.StudyDate).Add(dataset.GetSingleValueOrDefault(DicomTag.StudyTime, string.Empty) == string.Empty ? TimeSpan.Zero : dataset.GetSingleValue<DateTime>(DicomTag.StudyTime).TimeOfDay),
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Modalities = modality,
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ModalityForEdit = modalityForEdit,
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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.CacheKey.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 = AppSettings.GetCodeStr(currentNextCodeInt, nameof(DicomStudy));
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_provider.Set<int>($"{addtionalInfo.TrialId}_{StaticData.CacheKey.StudyMaxCode}", dicomStudy.Code, TimeSpan.FromMinutes(30));
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}
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#region Setting Code old
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//var studyCode = _studyRepository.Where(s => s.TrialId == addtionalInfo.TrialId).Select(t => t.StudyCode).OrderByDescending(c => c).FirstOrDefault();
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//var cacheMaxCode = _provider.Get<string>($"{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 = DateTime.TryParse(dataset.GetSingleValue<string>(DicomTag.SeriesDate) + dataset.GetSingleValue<string>(DicomTag.SeriesTime), out DateTime dt) ? dt : null,
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SeriesTime = dataset.GetSingleValueOrDefault(DicomTag.SeriesDate, string.Empty) == string.Empty ? null : dataset.GetSingleValue<DateTime>(DicomTag.SeriesDate).Add(dataset.GetSingleValueOrDefault(DicomTag.SeriesTime, string.Empty) == string.Empty ? TimeSpan.Zero : dataset.GetSingleValue<DateTime>(DicomTag.SeriesTime).TimeOfDay),
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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.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 = 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, out bool isInstanceNeedAdd)
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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.GetSingleValueOrDefault(DicomTag.ContentDate, string.Empty) == string.Empty ? null : dataset.GetSingleValue<DateTime>(DicomTag.ContentDate).Add(dataset.GetSingleValueOrDefault(DicomTag.ContentTime, string.Empty) == string.Empty ? TimeSpan.Zero : dataset.GetSingleValue<DateTime>(DicomTag.ContentTime).TimeOfDay),
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//InstanceTime = DateTime.TryParse(dataset.GetSingleValue<string>(DicomTag.ContentDate) + dataset.GetSingleValue<string>(DicomTag.ContentTime), out DateTime dt) ? dt : null,
|
||
//InstanceTime = dataset.GetSingleValueOrDefault(DicomTag.ContentDate,(DateTime?)null)?.Add(dataset.GetSingleValueOrDefault(DicomTag.ContentTime, TimeSpan.Zero)),
|
||
//dataset.GetSingleValueOrDefault(DicomTag.ContentDate,DateTime.Now);//, DicomTag.ContentTime)
|
||
CPIStatus = false,
|
||
ImageRows = dataset.GetSingleValueOrDefault(DicomTag.Rows, 0),
|
||
ImageColumns = dataset.GetSingleValueOrDefault(DicomTag.Columns, 0),
|
||
SliceLocation = dataset.GetSingleValueOrDefault(DicomTag.SliceLocation, 0),
|
||
|
||
SliceThickness = dataset.GetSingleValueOrDefault(DicomTag.SliceThickness, string.Empty),
|
||
NumberOfFrames = dataset.GetSingleValueOrDefault(DicomTag.NumberOfFrames, 0),
|
||
PixelSpacing = dataset.GetSingleValueOrDefault(DicomTag.PixelSpacing, string.Empty),
|
||
ImagerPixelSpacing = dataset.GetSingleValueOrDefault(DicomTag.ImagerPixelSpacing, string.Empty),
|
||
FrameOfReferenceUID = dataset.GetSingleValueOrDefault(DicomTag.FrameOfReferenceUID, string.Empty),
|
||
WindowCenter = dataset.GetSingleValueOrDefault(DicomTag.WindowCenter, string.Empty),
|
||
WindowWidth = dataset.GetSingleValueOrDefault(DicomTag.WindowWidth, string.Empty),
|
||
};
|
||
|
||
isInstanceNeedAdd = false;
|
||
|
||
if (!_instanceIdList.Contains(instanceId))
|
||
{
|
||
++dicomStudy.InstanceCount;
|
||
++dicomSeries.InstanceCount;
|
||
|
||
isInstanceNeedAdd = true;
|
||
|
||
_instanceIdList.Add(instanceId);
|
||
}
|
||
|
||
return dicomInstance;
|
||
|
||
}
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
|
||
}
|
||
}
|