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);
}
}
