public async Task GenerateAndTestDeAnonymisedStructureSetFile() { var image = @"Images\LargeSeriesWithContour"; var tempFolder = CreateTemporaryDirectory(); var segmentationClient = GetMockInnerEyeSegmentationClient(); var configType = AETConfigType.ModelWithResultDryRun; var dryRunFolder = DryRunFolders.GetFolder(configType); var testAETConfigModel = GetTestAETConfigModel(); var newTestAETConfigModel = testAETConfigModel.With( aetConfig: new ClientAETConfig( new AETConfig( configType, testAETConfigModel.AETConfig.Config.ModelsConfig), testAETConfigModel.AETConfig.Destination, false)); var aetConfigProvider = new MockAETConfigProvider(newTestAETConfigModel); var receivePort = 160; using (var deleteService = CreateDeleteService()) using (var pushService = CreatePushService(aetConfigProvider.AETConfigModels)) using (var downloadService = CreateDownloadService(segmentationClient)) using (var uploadService = CreateUploadService(segmentationClient, aetConfigProvider.AETConfigModels)) using (var receiveService = CreateReceiveService(receivePort, tempFolder)) { deleteService.Start(); pushService.Start(); downloadService.Start(); uploadService.Start(); receiveService.Start(); DcmtkHelpers.SendFolderUsingDCMTK( image, receivePort, ScuProfile.LEExplicitCT, TestContext, applicationEntityTitle: newTestAETConfigModel.CallingAET, calledAETitle: newTestAETConfigModel.CalledAET); SpinWait.SpinUntil(() => tempFolder.GetDirectories().FirstOrDefault(x => x.FullName.Contains(dryRunFolder)) != null); var dryRunFolderDirectory = tempFolder.GetDirectories().First(x => x.FullName.Contains(dryRunFolder)).GetDirectories().First(); // Wait until we have all image files. SpinWait.SpinUntil(() => dryRunFolderDirectory.GetFiles().Length == 1); // Wait for all files to save. await Task.Delay(1000); var originalSlice = DicomFile.Open(new DirectoryInfo(image).GetFiles().First().FullName); Assert.IsNotNull(originalSlice); foreach (var file in dryRunFolderDirectory.GetFiles()) { var dicomFile = DicomFile.Open(file.FullName, FileReadOption.ReadAll); Assert.AreEqual(originalSlice.Dataset.GetSingleValue <string>(DicomTag.StudyDate), dicomFile.Dataset.GetSingleValue <string>(DicomTag.StudyDate)); Assert.AreEqual(originalSlice.Dataset.GetSingleValue <string>(DicomTag.AccessionNumber), dicomFile.Dataset.GetSingleValue <string>(DicomTag.AccessionNumber)); Assert.AreEqual("RTSTRUCT", dicomFile.Dataset.GetSingleValue <string>(DicomTag.Modality)); Assert.AreEqual("Microsoft Corporation", dicomFile.Dataset.GetSingleValue <string>(DicomTag.Manufacturer)); Assert.AreEqual(originalSlice.Dataset.GetSingleValue <string>(DicomTag.ReferringPhysicianName), dicomFile.Dataset.GetSingleValue <string>(DicomTag.ReferringPhysicianName)); Assert.AreEqual(originalSlice.Dataset.GetSingleValueOrDefault(DicomTag.StudyDescription, string.Empty), dicomFile.Dataset.GetSingleValueOrDefault(DicomTag.StudyDescription, string.Empty)); Assert.AreEqual(originalSlice.Dataset.GetSingleValue <string>(DicomTag.PatientName), dicomFile.Dataset.GetSingleValue <string>(DicomTag.PatientName)); Assert.AreEqual(originalSlice.Dataset.GetSingleValue <string>(DicomTag.PatientID), dicomFile.Dataset.GetSingleValue <string>(DicomTag.PatientID)); Assert.AreEqual(originalSlice.Dataset.GetSingleValue <string>(DicomTag.PatientBirthDate), dicomFile.Dataset.GetSingleValue <string>(DicomTag.PatientBirthDate)); Assert.AreEqual(originalSlice.Dataset.GetSingleValue <string>(DicomTag.StudyInstanceUID), dicomFile.Dataset.GetSingleValue <string>(DicomTag.StudyInstanceUID)); Assert.AreEqual(originalSlice.Dataset.GetSingleValue <string>(DicomTag.StudyID), dicomFile.Dataset.GetSingleValue <string>(DicomTag.StudyID)); Assert.IsTrue(dicomFile.Dataset.GetString(DicomTag.SoftwareVersions).StartsWith("Microsoft InnerEye Gateway:")); Assert.IsTrue(dicomFile.Dataset.GetValue <string>(DicomTag.SoftwareVersions, 1).StartsWith("InnerEye AI Model:")); Assert.IsTrue(dicomFile.Dataset.GetValue <string>(DicomTag.SoftwareVersions, 2).StartsWith("InnerEye AI Model ID:")); Assert.IsTrue(dicomFile.Dataset.GetValue <string>(DicomTag.SoftwareVersions, 3).StartsWith("InnerEye Model Created:")); Assert.IsTrue(dicomFile.Dataset.GetValue <string>(DicomTag.SoftwareVersions, 4).StartsWith("InnerEye Version:")); Assert.AreEqual("1.2.840.10008.5.1.4.1.1.481.3", dicomFile.Dataset.GetSingleValue <string>(DicomTag.SOPClassUID)); Assert.AreEqual($"{DateTime.UtcNow.Year}{DateTime.UtcNow.Month.ToString("D2")}{DateTime.UtcNow.Day.ToString("D2")}", dicomFile.Dataset.GetSingleValue <string>(DicomTag.SeriesDate)); Assert.IsTrue(dicomFile.Dataset.GetSingleValueOrDefault(DicomTag.SeriesInstanceUID, string.Empty).StartsWith("1.2.826.0.1.3680043.2")); Assert.AreEqual("511091532", dicomFile.Dataset.GetSingleValueOrDefault(DicomTag.SeriesNumber, string.Empty)); Assert.AreEqual("NOT FOR CLINICAL USE", dicomFile.Dataset.GetSingleValueOrDefault(DicomTag.SeriesDescription, string.Empty)); Assert.IsTrue(dicomFile.Dataset.GetSingleValueOrDefault(DicomTag.SOPInstanceUID, string.Empty).StartsWith("1.2.826.0.1.3680043.2")); Assert.AreEqual("ANONYM", dicomFile.Dataset.GetSingleValueOrDefault(DicomTag.OperatorsName, string.Empty)); VerifyDicomFile(file.FullName); } } }
public async Task GatewayLiveEndToEndTest() { var testAETConfigModel = GetTestAETConfigModel(); var resultDirectory = CreateTemporaryDirectory(); using (var dicomDataReceiver = new ListenerDataReceiver(new ListenerDicomSaver(resultDirectory.FullName))) { var eventCount = 0; var folderPath = string.Empty; dicomDataReceiver.DataReceived += (sender, e) => { folderPath = e.FolderPath; Interlocked.Increment(ref eventCount); }; StartDicomDataReceiver(dicomDataReceiver, testAETConfigModel.AETConfig.Destination.Port); var receivePort = 141; using (var segmentationClient = GetMockInnerEyeSegmentationClient()) using (var deleteService = CreateDeleteService()) using (var pushService = CreatePushService()) using (var downloadService = CreateDownloadService(segmentationClient)) using (var uploadService = CreateUploadService(segmentationClient)) using (var receiveService = CreateReceiveService(receivePort)) { deleteService.Start(); pushService.Start(); downloadService.Start(); uploadService.Start(); receiveService.Start(); var dicomDataSender = new DicomDataSender(); var echoResult = await dicomDataSender.DicomEchoAsync( testAETConfigModel.CallingAET, testAETConfigModel.CalledAET, receivePort, "127.0.0.1").ConfigureAwait(false); Assert.IsTrue(echoResult == DicomOperationResult.Success); DcmtkHelpers.SendFolderUsingDCMTK( @"Images\1ValidSmall", receivePort, ScuProfile.LEExplicitCT, TestContext, applicationEntityTitle: testAETConfigModel.CallingAET, calledAETitle: testAETConfigModel.CalledAET); // Wait for all events to finish on the data received SpinWait.SpinUntil(() => eventCount >= 3, TimeSpan.FromMinutes(3)); #pragma warning disable CA1508 // Avoid dead conditional code Assert.IsFalse(string.IsNullOrWhiteSpace(folderPath)); #pragma warning restore CA1508 // Avoid dead conditional code var dicomFile = await DicomFile.OpenAsync(new DirectoryInfo(folderPath).GetFiles()[0].FullName).ConfigureAwait(false); Assert.IsNotNull(dicomFile); } } }
public async Task GenerateAndTestAnonymisedRTFile() { var tempFolder = CreateTemporaryDirectory(); { var configType = AETConfigType.ModelDryRun; var dryRunFolder = DryRunFolders.GetFolder(configType); var segmentationClient = GetMockInnerEyeSegmentationClient(); var testAETConfigModel = GetTestAETConfigModel(); var newTestAETConfigModel = testAETConfigModel.With( aetConfig: new ClientAETConfig( new AETConfig( configType, null), testAETConfigModel.AETConfig.Destination, false)); var aetConfigProvider = new MockAETConfigProvider(newTestAETConfigModel); var receivePort = 162; using (var deleteService = CreateDeleteService()) using (var pushService = CreatePushService(aetConfigProvider.AETConfigModels)) using (var downloadService = CreateDownloadService(segmentationClient)) using (var uploadService = CreateUploadService(segmentationClient, aetConfigProvider.AETConfigModels)) using (var receiveService = CreateReceiveService(receivePort, tempFolder)) { deleteService.Start(); pushService.Start(); downloadService.Start(); uploadService.Start(); receiveService.Start(); DcmtkHelpers.SendFolderUsingDCMTK( @"Images\1ValidSmall", receivePort, ScuProfile.LEExplicitRTCT, TestContext, applicationEntityTitle: newTestAETConfigModel.CallingAET, calledAETitle: newTestAETConfigModel.CalledAET); SpinWait.SpinUntil(() => tempFolder.GetDirectories().FirstOrDefault(x => x.FullName.Contains(dryRunFolder)) != null); var dryRunFolderDirectory = tempFolder.GetDirectories().First(x => x.FullName.Contains(dryRunFolder)).GetDirectories().First(); // Wait until we have all image files. SpinWait.SpinUntil(() => dryRunFolderDirectory.GetFiles().Length == 1); // Wait for all files to save. await Task.Delay(1000); var savedSampleFile = false; foreach (var file in dryRunFolderDirectory.GetFiles()) { var dicomFile = DicomFile.Open(file.FullName); AssertDicomFileIsAnonymised(dicomFile); if (!savedSampleFile) { WriteDicomFileForBuildPackage("AnonymisedRT.dcm", dicomFile); savedSampleFile = true; } } } } }
public async Task IntegrationTestEndToEnd() { var sourceDirectory = CreateTemporaryDirectory(); var resultDirectory = CreateTemporaryDirectory(); var random = new Random(); // Get file names for all in directory var sourceDicomFileNames = new DirectoryInfo(@"Images\HN").GetFiles().ToArray(); // Load all DICOM files var sourceDicomFiles = sourceDicomFileNames.Select(f => DicomFile.Open(f.FullName, FileReadOption.ReadAll)).ToArray(); // Add/Update random tags for the source DICOM files. DicomAnonymisationTests.AddRandomTags(random, sourceDicomFiles); // Save them all to the sourceDirectory. var sourcePairs = sourceDicomFileNames.Zip(sourceDicomFiles, (f, d) => Tuple.Create(f, d)).ToArray(); foreach (var sourcePair in sourcePairs) { var sourceImageFilePath = Path.Combine(sourceDirectory.FullName, sourcePair.Item1.Name); sourcePair.Item2.Save(sourceImageFilePath); } // Keep the first as a reference for deanonymization later. var originalSlice = sourceDicomFiles.First(); var testAETConfigModel = GetTestAETConfigModel(); var receivePort = 160; using (var dicomDataReceiver = new ListenerDataReceiver(new ListenerDicomSaver(resultDirectory.FullName))) using (var deleteService = CreateDeleteService()) using (var pushService = CreatePushService()) using (var downloadService = CreateDownloadService()) using (var uploadService = CreateUploadService()) using (var receiveService = CreateReceiveService(receivePort)) { // Start a DICOM receiver for the final DICOM-RT file var eventCount = new ConcurrentDictionary <DicomReceiveProgressCode, int>(); var folderPath = string.Empty; dicomDataReceiver.DataReceived += (sender, e) => { folderPath = e.FolderPath; eventCount.AddOrUpdate(e.ProgressCode, 1, (k, v) => v + 1); }; StartDicomDataReceiver(dicomDataReceiver, testAETConfigModel.AETConfig.Destination.Port); // Start the services. deleteService.Start(); pushService.Start(); downloadService.Start(); uploadService.Start(); receiveService.Start(); // Try a DICOM C-ECHO var dicomDataSender = new DicomDataSender(); var echoResult = await dicomDataSender.DicomEchoAsync( testAETConfigModel.CallingAET, testAETConfigModel.CalledAET, receivePort, "127.0.0.1").ConfigureAwait(false); Assert.IsTrue(echoResult == DicomOperationResult.Success); // Send the image stack DcmtkHelpers.SendFolderUsingDCMTK( sourceDirectory.FullName, receivePort, ScuProfile.LEExplicitCT, TestContext, applicationEntityTitle: testAETConfigModel.CallingAET, calledAETitle: testAETConfigModel.CalledAET); // Wait for DICOM-RT file to be received. Func <DicomReceiveProgressCode, int, bool> TestEventCount = (progressCode, count) => eventCount.ContainsKey(progressCode) && eventCount[progressCode] == count; SpinWait.SpinUntil(() => TestEventCount(DicomReceiveProgressCode.AssociationEstablished, 1)); SpinWait.SpinUntil(() => TestEventCount(DicomReceiveProgressCode.FileReceived, 1)); SpinWait.SpinUntil(() => TestEventCount(DicomReceiveProgressCode.AssociationReleased, 1)); SpinWait.SpinUntil(() => TestEventCount(DicomReceiveProgressCode.ConnectionClosed, 1)); Assert.IsTrue(eventCount[DicomReceiveProgressCode.AssociationEstablished] == 1); Assert.IsTrue(eventCount[DicomReceiveProgressCode.FileReceived] == 1); Assert.IsTrue(eventCount[DicomReceiveProgressCode.AssociationReleased] == 1); Assert.IsTrue(eventCount[DicomReceiveProgressCode.ConnectionClosed] == 1); var receivedFiles = new DirectoryInfo(folderPath).GetFiles(); Assert.AreEqual(1, receivedFiles.Length); var receivedFilePath = receivedFiles.First().FullName; var dicomFile = await DicomFile.OpenAsync(receivedFilePath, FileReadOption.ReadAll).ConfigureAwait(false); Assert.IsNotNull(dicomFile); var matchedModel = ApplyAETModelConfigProvider.ApplyAETModelConfig(testAETConfigModel.AETConfig.Config.ModelsConfig, sourceDicomFiles); var segmentationClient = TestGatewayProcessorConfigProvider.CreateInnerEyeSegmentationClient().Invoke(); DicomAnonymisationTests.AssertDeanonymizedFile( originalSlice, dicomFile, segmentationClient.TopLevelReplacements, matchedModel.Result.TagReplacements, false); AssertIsDicomRtFile(DateTime.UtcNow, dicomFile, matchedModel.Result.ModelId); } }