/// <summary>
/// Anonymises every DICOM file in the specified folder path and saves locally to the
/// correct dry run folder.
/// </summary>
/// <param name="anonymisationProtocolId">The anonymisation protocol unique identifier.</param>
/// <param name="anonymisationProtocol">The anonymisation protocol.</param>
/// <param name="uploadQueueItem">The upload queue item.</param>
/// <param name="aETConfigType">Type of application entity title configuration.</param>
/// <returns>The async task.</returns>
private async Task AnonymiseAndSaveDicomFilesAsync(
Guid anonymisationProtocolId,
IEnumerable <DicomTagAnonymisation> anonymisationProtocol,
UploadQueueItem uploadQueueItem,
AETConfigType aETConfigType)
{
var dryRunFolder = DryRunFolders.GetFolder(aETConfigType);
var resultFolderPath = Path.Combine(uploadQueueItem.RootDicomFolderPath, dryRunFolder, uploadQueueItem.AssociationGuid.ToString());
foreach (var filePath in EnumerateFiles(uploadQueueItem.AssociationFolderPath, uploadQueueItem))
{
var dicomFile = TryOpenDicomFile(filePath, uploadQueueItem);
// Not a DICOM file or is not a structure set file.
if (dicomFile == null)
{
EnqueueMessage(new DeleteQueueItem(uploadQueueItem, filePath), _deleteQueuePath);
continue;
}
var anonymizedDicomFile = _innerEyeSegmentationClient.AnonymizeDicomFile(
dicomFile: dicomFile,
anonymisationProtocolId: anonymisationProtocolId,
anonymisationProtocol: anonymisationProtocol);
await SaveDicomFilesAsync(resultFolderPath, anonymizedDicomFile).ConfigureAwait(false);
// This item has been saved, we can now delete this file
EnqueueMessage(new DeleteQueueItem(uploadQueueItem, filePath), _deleteQueuePath);
}
}
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 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;
}
}
}
}
}
