private void Anonymize(IBackgroundTaskContext context)
{
//TODO (Marmot) This probably should be its own WorkItem type and have it done in the background there.
var study = (StudyTableItem) context.UserState;
var anonymizedInstances = new AuditedInstances();
try
{
context.ReportProgress(new BackgroundTaskProgress(0, SR.MessageAnonymizingStudy));
var loader = study.Server.GetService<IStudyLoader>();
int numberOfSops = loader.Start(new StudyLoaderArgs(study.StudyInstanceUid, null));
if (numberOfSops <= 0)
return;
var anonymizer = new DicomAnonymizer {StudyDataPrototype = _component.AnonymizedData};
if (_component.PreserveSeriesData)
{
//The default anonymizer removes the series data, so we just clone the original.
anonymizer.AnonymizeSeriesDataDelegate = original => original.Clone();
}
// Setup the ImportFilesUtility to perform the import
var configuration = DicomServer.GetConfiguration();
// setup auditing information
var result = EventResult.Success;
string patientsSex = null;
for (int i = 0; i < numberOfSops; ++i)
{
using (var sop = loader.LoadNextSop())
{
if (sop != null &&
(_component.KeepReportsAndAttachments || !IsReportOrAttachmentSopClass(sop.SopClassUid)))
{
//preserve the patient sex.
if (patientsSex == null)
anonymizer.StudyDataPrototype.PatientsSex = patientsSex = sop.PatientsSex ?? "";
var localSopDataSource = sop.DataSource as ILocalSopDataSource;
if (localSopDataSource != null)
{
string filename = string.Format("{0}.dcm", i);
DicomFile file = (localSopDataSource).File;
// make sure we anonymize a new instance, not the same instance that the Sop cache holds!!
file = new DicomFile(filename, file.MetaInfo.Copy(), file.DataSet.Copy());
anonymizer.Anonymize(file);
// TODO (CR Jun 2012): Importing each file separately?
Platform.GetService((IPublishFiles w) => w.PublishLocal(new List<DicomFile> {file}));
string studyInstanceUid = file.DataSet[DicomTags.StudyInstanceUid].ToString();
string patientId = file.DataSet[DicomTags.PatientId].ToString();
string patientsName = file.DataSet[DicomTags.PatientsName].ToString();
anonymizedInstances.AddInstance(patientId, patientsName, studyInstanceUid);
var progressPercent = (int)Math.Floor((i + 1) / (float)numberOfSops * 100);
var progressMessage = String.Format(SR.MessageAnonymizingStudy, file.MediaStorageSopInstanceUid);
context.ReportProgress(new BackgroundTaskProgress(progressPercent, progressMessage));
}
}
}
}
AuditHelper.LogCreateInstances(new[]{configuration.AETitle}, anonymizedInstances, EventSource.CurrentUser, result);
context.Complete();
}
catch (Exception e)
{
AuditHelper.LogCreateInstances(new[] { string.Empty }, anonymizedInstances, EventSource.CurrentUser, EventResult.MajorFailure);
context.Error(e);
}
}
public AnonymizeStudyOutput AnonymizeStudy(AnonymizeStudyInput input)
{
// load study to anonymize
IDataStoreReader reader = DataAccessLayer.GetIDataStoreReader();
IStudy study = reader.GetStudy(input.StudyInstanceUID);
List<ISopInstance> sops = new List<ISopInstance>(study.GetSopInstances());
// ensure there is a valid output location
if(string.IsNullOrEmpty(input.OutputDirectory))
{
// create temp dir
}
string fullPath = Path.GetFullPath(input.OutputDirectory);
if (!Directory.Exists(fullPath))
{
Directory.CreateDirectory(fullPath);
}
// set up anonymization data
StudyData studyData = new StudyData();
studyData.PatientId = input.PatientId;
studyData.PatientsNameRaw = input.PatientsName;
studyData.PatientsBirthDate = input.PatientsBirthDate;
studyData.PatientsSex = input.PatientsSex;
studyData.AccessionNumber = input.AccessionNumber;
studyData.StudyDescription = input.StudyDescription;
studyData.StudyDate = input.StudyDate;
DicomAnonymizer anonymizer = new DicomAnonymizer();
anonymizer.StudyDataPrototype = studyData;
//The default anonymizer removes the series data, so we just clone the original.
anonymizer.AnonymizeSeriesDataDelegate =
delegate(SeriesData original) { return original.Clone(); };
// anonymize each image in the study
for (int i = 0; i < sops.Count; ++i)
{
ISopInstance sop = sops[i];
DicomFile file = new DicomFile(sop.GetLocationUri().LocalDiskPath);
anonymizer.Anonymize(file);
file.Save(string.Format("{0}\\{1}.dcm", fullPath, i));
}
return new AnonymizeStudyOutput(sops.Count);
}
private bool Initialize()
{
_synchronizationContext = SynchronizationContext.Current;
_exportedInstances = new AuditedInstances();
_canceled = false;
_overwrite = false;
if (Anonymize)
{
ExportComponent component = new ExportComponent();
component.OutputPath = OutputPath;
if (DialogBoxAction.Ok != DesktopWindow.ShowDialogBox(component, SR.Export))
return false;
OutputPath = component.OutputPath;
StudyData studyData = new StudyData
{
PatientId = component.PatientId,
PatientsNameRaw = component.PatientsName,
PatientsBirthDate = component.PatientsDateOfBirth,
StudyId = component.StudyId,
StudyDescription = component.StudyDescription,
AccessionNumber = component.AccessionNumber,
StudyDate = component.StudyDate
};
_anonymizer = new DicomAnonymizer();
_anonymizer.ValidationOptions = ValidationOptions.RelaxAllChecks;
_anonymizer.StudyDataPrototype = studyData;
}
else
{
SelectFolderDialogCreationArgs args = new SelectFolderDialogCreationArgs();
args.Prompt = SR.MessageSelectOutputLocation;
args.Path = OutputPath;
FileDialogResult result = DesktopWindow.ShowSelectFolderDialogBox(args);
if (result.Action != DialogBoxAction.Ok)
return false;
OutputPath = result.FileName;
}
return true;
}
private List<SopInstanceNode> DoBuildTree()
{
bool doAnonymize = _anonymize;
Dictionary<string, string> uidMap = new Dictionary<string, string>();
List<SopInstanceNode> sops = new List<SopInstanceNode>();
// TODO: perform some performance tests to adjust these weights
float aweight = doAnonymize ? 0.45f : 0; // portion of the work to anonymize the instances
float pweight = (1 - aweight)*0.75f; // portion of the work to reassign uids
float mweight = 1 - pweight - aweight; // portion of the work to remap related uids
int count = _patients.Count;
int now = 0;
this.Progress = 0;
// traverse the tree assign new instance uids
foreach (PatientNode patient in _patients)
{
if (patient.Parent != _rootNode)
throw new NullReferenceException("Unsynchronized parent-child relationship");
now++;
foreach (StudyNode study in patient.Studies)
{
if (study.Parent != patient)
throw new NullReferenceException("Unsynchronized parent-child relationship");
string studyUid = NewUid();
uidMap.Add(study.InstanceUid, studyUid);
study.InstanceUid = studyUid;
foreach (SeriesNode series in study.Series)
{
if (series.Parent != study)
throw new NullReferenceException("Unsynchronized parent-child relationship");
string seriesUid = NewUid();
uidMap.Add(series.InstanceUid, seriesUid);
series.InstanceUid = seriesUid;
foreach (SopInstanceNode sop in series.Images)
{
if (sop.Parent != series)
throw new NullReferenceException("Unsynchronized parent-child relationship");
string sopUid = NewUid();
uidMap.Add(sop.InstanceUid, sopUid);
sop.InstanceUid = sopUid;
patient.Update(sop.DicomData);
study.Update(sop.DicomData, true);
series.Update(sop.DicomData, true);
sop.Update(sop.DicomData, true);
sops.Add(sop);
}
}
}
this.Progress = mweight*now/count;
}
// map any uids that point to an instance that was just reassigned
count = sops.Count;
now = 0;
foreach (SopInstanceNode sop in sops)
{
MapKnownUids(sop.DicomData, uidMap);
now++;
this.Progress = mweight*now/count;
}
// run the anonymizer if required
if (doAnonymize)
{
DicomAnonymizer anonymizer = new DicomAnonymizer();
anonymizer.ValidationOptions = ValidationOptions.RelaxAllChecks;
count = sops.Count;
now = 0;
foreach (SopInstanceNode sop in sops)
{
anonymizer.Anonymize(sop.DicomFile);
SeriesNode series = sop.Parent;
StudyNode study = series.Parent;
PatientNode patient = study.Parent;
// overwrite the anonymized data with any edited properties
// anonymizer writes in new anonymized uids based on the new structure, so don't overwrite them!
// instead, get the new uids and put them back into the node
patient.Update(sop.DicomData);
study.Update(sop.DicomData, false);
study.InstanceUid = sop.DicomData[DicomTags.StudyInstanceUid].GetString(0, "");
series.Update(sop.DicomData, false);
series.InstanceUid = sop.DicomData[DicomTags.SeriesInstanceUid].GetString(0, "");
sop.Update(sop.DicomData, false);
sop.InstanceUid = sop.DicomData[DicomTags.SopInstanceUid].GetString(0, "");
now++;
this.Progress = mweight*now/count;
}
}
return sops;
}
