private void DoExport(IBackgroundTaskContext context)
{
try
{
int i = 0;
int fileCount = _files.Count;
foreach (string filename in _files)
{
string message = String.Format(SR.MessageFormatExportingFiles, i + 1, fileCount);
BackgroundTaskProgress progress = new BackgroundTaskProgress(i, fileCount, message);
context.ReportProgress(progress);
SaveFile(filename);
if (_canceled || context.CancelRequested)
{
_canceled = true;
context.Cancel();
return;
}
i++;
}
context.Complete();
}
catch (Exception e)
{
context.Error(e);
}
}
private void DoImport(IBackgroundTaskContext context)
{
int lineCount = 0;
int batch = 0;
try
{
lineCount = PrescanFile();
using (StreamReader reader = File.OpenText(_filename))
{
// treat as csv
List <string> lines = null;
while ((lines = ReadLines(reader, _batchSize)).Count > 0)
{
if (context.CancelRequested)
{
break;
}
try
{
Platform.GetService <IImportService>(
delegate(IImportService service)
{
service.ImportCsv(new ImportCsvRequest(_importType, lines));
});
}
catch (FaultException <ImportException> e)
{
// unwrap the fault exception
throw e.Detail;
}
UpdateProgress(context, "Importing", batch++, lineCount);
}
}
if (context.CancelRequested)
{
UpdateProgress(context, "Cancelled", batch, lineCount);
context.Cancel();
}
else
{
UpdateProgress(context, "Completed", batch, lineCount);
context.Complete(null);
}
}
catch (Exception e)
{
UpdateProgress(context, "Error", batch, lineCount);
context.Error(e);
}
}
private void Go(IBackgroundTaskContext context)
{
string studyUid = DicomUid.GenerateUid().UID;
string seriesUid = DicomUid.GenerateUid().UID;
PixelAspectRatioChanger changer =
new PixelAspectRatioChanger
{
IncreasePixelDimensions = _component.IncreasePixelDimensions,
NewAspectRatio = new PixelAspectRatio(_component.AspectRatioRow, _component.AspectRatioColumn),
RemoveCalibration = _component.RemoveCalibration
};
int i = 0;
context.ReportProgress(new BackgroundTaskProgress(i, _dicomFileNames.Count, "Exporting ..."));
try
{
foreach (string originalFile in _dicomFileNames)
{
var file = new DicomFile(originalFile);
file.Load(DicomReadOptions.None);
string sopInstanceUid = DicomUid.GenerateUid().UID;
file.DataSet[DicomTags.StudyInstanceUid].SetStringValue(studyUid);
file.DataSet[DicomTags.SeriesInstanceUid].SetStringValue(seriesUid);
file.DataSet[DicomTags.SopInstanceUid].SetStringValue(sopInstanceUid);
changer.ChangeAspectRatio(file);
string outputFileName = Path.Combine(_outputDirectory, String.Format("{0}.dcm", sopInstanceUid));
file.Save(outputFileName);
if (context.CancelRequested)
{
context.Cancel();
return;
}
context.ReportProgress(new BackgroundTaskProgress(++i, _dicomFileNames.Count + 1, "Exporting ..."));
}
}
catch (Exception e)
{
context.Error(e);
return;
}
context.Complete();
}
private void LoadVolume(IBackgroundTaskContext context)
{
try
{
ProgressTask mainTask = new ProgressTask();
mainTask.AddSubTask("BUILD", 90);
mainTask.AddSubTask("LAYOUT", 10);
context.ReportProgress(new BackgroundTaskProgress(mainTask.IntPercent, string.Format(SR.MessageInitializingMpr, mainTask.Progress)));
BackgroundTaskParams @params = (BackgroundTaskParams)context.UserState;
Volume volume = Volume.Create(@params.Frames,
delegate(int i, int count)
{
if (context.CancelRequested)
{
throw new BackgroundTaskCancelledException();
}
if (i == 0)
{
mainTask["BUILD"].AddSubTask("", count);
}
mainTask["BUILD"][""].Increment();
string message = string.Format(SR.MessageBuildingMprVolumeProgress, mainTask.Progress, i + 1, count, mainTask["BUILD"].Progress);
context.ReportProgress(new BackgroundTaskProgress(mainTask.IntPercent, message));
});
mainTask["BUILD"].MarkComplete();
context.ReportProgress(new BackgroundTaskProgress(mainTask.IntPercent, string.Format(SR.MessagePerformingMprWorkspaceLayout, mainTask.Progress)));
//call layout here b/c it could take a while
@params.SynchronizationContext.Send(delegate
{
_viewer = new MprViewerComponent(volume);
_viewer.Layout();
}, null);
mainTask["LAYOUT"].MarkComplete();
context.ReportProgress(new BackgroundTaskProgress(mainTask.IntPercent, string.Format(SR.MessageDone, mainTask.Progress)));
context.Complete();
}
catch (BackgroundTaskCancelledException)
{
context.Cancel();
}
catch (Exception ex)
{
context.Error(ex);
}
}
private static void LoadWorker(IBackgroundTaskContext context)
{
State state = context.UserState as State;
if (state == null)
{
context.Cancel();
return;
}
context.ReportProgress(new BackgroundTaskProgress(0, 1000, SR.MessageLoading));
if (context.CancelRequested)
{
context.Cancel();
return;
}
List <string> fileList = new List <string>();
try
{
foreach (string path in state.Paths)
{
fileList.AddRange(EnumerateFiles(path, state.Recursive));
}
}
catch (Exception ex)
{
context.Error(ex);
return;
}
for (int n = 0; n < fileList.Count; n++)
{
context.ReportProgress(new BackgroundTaskProgress(n, fileList.Count, SR.MessageLoading));
if (context.CancelRequested)
{
context.Cancel();
return;
}
state.SynchronizationContext.Send(i => state.Component.Load(fileList[(int)i]), n);
}
if (context.CancelRequested)
{
context.Cancel();
return;
}
context.Complete();
}
private void ChangeToSyntax(IBackgroundTaskContext context)
{
var study = (StudyTableItem)context.UserState;
try
{
_tempPath = System.IO.Path.Combine(System.IO.Path.GetTempPath(), "ClearCanvas");
_tempPath = System.IO.Path.Combine(_tempPath, "Compression");
_tempPath = System.IO.Path.Combine(_tempPath, Path.GetRandomFileName());
string message = String.Format("Changing transfer syntax to: {0}", _syntax);
context.ReportProgress(new BackgroundTaskProgress(0, message));
var loader = study.Server.GetService <IStudyLoader>();
int numberOfSops = loader.Start(new StudyLoaderArgs(study.StudyInstanceUid, null));
if (numberOfSops <= 0)
{
return;
}
for (int i = 0; i < numberOfSops; ++i)
{
Sop sop = loader.LoadNextSop();
if (sop != null)
{
if (sop.DataSource is ILocalSopDataSource)
{
string filename = Path.Combine(_tempPath, string.Format("{0}.dcm", i));
DicomFile file = ((ILocalSopDataSource)sop.DataSource).File;
file.ChangeTransferSyntax(_syntax);
file.Save(filename);
}
}
int progressPercent = (int)Math.Floor((i + 1) / (float)numberOfSops * 100);
context.ReportProgress(new BackgroundTaskProgress(progressPercent, message));
}
//trigger an import of the anonymized files.
var client = new DicomFileImportBridge();
client.ImportFileList(new List <string> {
_tempPath
}, BadFileBehaviourEnum.Move, FileImportBehaviourEnum.Move);
context.Complete();
}
catch (Exception e)
{
context.Error(e);
}
}
private void BackgroundSendAnnotationsToAimService(IBackgroundTaskContext context)
{
var xmlAnnotations = context.UserState as Dictionary <string, string>;
try
{
if (xmlAnnotations != null && xmlAnnotations.Count > 0)
{
var progress = new BackgroundTaskProgress(20, string.Format("Sending {0} annotation(s) to AIM data service.", xmlAnnotations.Count));
context.ReportProgress(progress);
AIMTCGAService.AIMTCGASubmit.sendAIMTCGAAnnotation(new List <string>(xmlAnnotations.Values).ToArray());
}
context.Complete();
}
catch (Exception ex)
{
SaveAnnotationsToQueue(xmlAnnotations, AIMTCGAService.AIMTCGASubmit.ServiceUrl);
context.Error(ex);
}
}
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);
}
}
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);
}
}
private void DoExport(IBackgroundTaskContext context)
{
try
{
int i = 0;
int fileCount = _files.Count;
foreach (string filename in _files)
{
string message = String.Format(SR.MessageFormatExportingFiles, i + 1, fileCount);
BackgroundTaskProgress progress = new BackgroundTaskProgress(i, fileCount, message);
context.ReportProgress(progress);
SaveFile(filename);
if (_canceled || context.CancelRequested)
{
_canceled = true;
context.Cancel();
return;
}
i++;
}
context.Complete();
}
catch (Exception e)
{
context.Error(e);
}
}
private void LoadVolume(IBackgroundTaskContext context)
{
try
{
ProgressTask mainTask = new ProgressTask();
mainTask.AddSubTask("BUILD", 90);
mainTask.AddSubTask("LAYOUT", 10);
context.ReportProgress(new BackgroundTaskProgress(mainTask.IntPercent, string.Format(SR.MessageInitializingMpr, mainTask.Progress)));
BackgroundTaskParams @params = (BackgroundTaskParams) context.UserState;
Volume volume = Volume.Create(@params.Frames,
delegate(int i, int count)
{
if (context.CancelRequested)
throw new BackgroundTaskCancelledException();
if (i == 0)
mainTask["BUILD"].AddSubTask("", count);
mainTask["BUILD"][""].Increment();
string message = string.Format(SR.MessageBuildingMprVolumeProgress, mainTask.Progress, i + 1, count, mainTask["BUILD"].Progress);
context.ReportProgress(new BackgroundTaskProgress(mainTask.IntPercent, message));
});
mainTask["BUILD"].MarkComplete();
context.ReportProgress(new BackgroundTaskProgress(mainTask.IntPercent, string.Format(SR.MessagePerformingMprWorkspaceLayout, mainTask.Progress)));
//call layout here b/c it could take a while
@params.SynchronizationContext.Send(delegate
{
_viewer = new MprViewerComponent(volume);
_viewer.Layout();
}, null);
mainTask["LAYOUT"].MarkComplete();
context.ReportProgress(new BackgroundTaskProgress(mainTask.IntPercent, string.Format(SR.MessageDone, mainTask.Progress)));
context.Complete();
}
catch (BackgroundTaskCancelledException)
{
context.Cancel();
}
catch (Exception ex)
{
context.Error(ex);
}
}
private void ChangeToSyntax(IBackgroundTaskContext context)
{
var study = (StudyTableItem)context.UserState;
try
{
_tempPath = System.IO.Path.Combine(System.IO.Path.GetTempPath(), "ClearCanvas");
_tempPath = System.IO.Path.Combine(_tempPath, "Compression");
_tempPath = System.IO.Path.Combine(_tempPath, Path.GetRandomFileName());
string message = String.Format("Changing transfer syntax to: {0}", _syntax);
context.ReportProgress(new BackgroundTaskProgress(0, message));
var loader = study.Server.GetService<IStudyLoader>();
int numberOfSops = loader.Start(new StudyLoaderArgs(study.StudyInstanceUid, null, StudyLoaderOptions.Default));
if (numberOfSops <= 0)
return;
for (int i = 0; i < numberOfSops; ++i)
{
Sop sop = loader.LoadNextSop();
if (sop != null)
{
if (sop.DataSource is ILocalSopDataSource)
{
string filename = Path.Combine(_tempPath, string.Format("{0}.dcm", i));
DicomFile file = ((ILocalSopDataSource)sop.DataSource).File;
file.ChangeTransferSyntax(_syntax);
file.Save(filename);
}
}
int progressPercent = (int)Math.Floor((i + 1) / (float)numberOfSops * 100);
context.ReportProgress(new BackgroundTaskProgress(progressPercent, message));
}
//trigger an import of the anonymized files.
var client = new DicomFileImportBridge();
client.ImportFileList(new List<string> {_tempPath}, BadFileBehaviourEnum.Move, FileImportBehaviourEnum.Move);
context.Complete();
}
catch(Exception e)
{
context.Error(e);
}
}
private void Rename(IBackgroundTaskContext context)
{
try
{
_tempPath = String.Format(".\\temp\\{0}", Path.GetRandomFileName());
Directory.CreateDirectory(_tempPath);
_tempPath = Path.GetFullPath(_tempPath);
context.ReportProgress(new BackgroundTaskProgress(0, "Renaming Study"));
int numberOfSops = LocalStudyLoader.Start(new StudyLoaderArgs(this.Context.SelectedStudy.StudyInstanceUid, null));
if (numberOfSops <= 0)
{
return;
}
for (int i = 0; i < numberOfSops; ++i)
{
string message = String.Format("{0} of {1}", i.ToString(), numberOfSops.ToString());
Platform.Log(LogLevel.Info, message);
Sop sop = LocalStudyLoader.LoadNextSop();
ILocalSopDataSource localsource = (ILocalSopDataSource)sop.DataSource;
string progressMessage = localsource.Filename.ToString();
DicomFile file = ((ILocalSopDataSource)sop.DataSource).File;
//renamer.Anonymize(file);
StudyData originalData = new StudyData();
file.DataSet.LoadDicomFields(originalData);
originalData.PatientId = _component.PatientId;
originalData.PatientsBirthDate = _component.PatientsBirthDate;
originalData.PatientsNameRaw = _component.PatientsName;
originalData.AccessionNumber = _component.AccessionNumber;
originalData.StudyDate = _component.StudyDate;
originalData.StudyDescription = _component.StudyDescription;
file.DataSet.SaveDicomFields(originalData);
file.Save(String.Format("{0}\\{1}.dcm", _tempPath, i));
int progressPercent = (int)Math.Floor((i + 1) / (float)numberOfSops * 100);
//string progressMessage = String.Format(SR.MessageAnonymizingStudy, _tempPath);
context.ReportProgress(new BackgroundTaskProgress(progressPercent, progressMessage));
// This code deletes the study from the database, so that when it is re-imported the changed fields
// will appear
}
using (IDataStoreStudyRemover studyRemover = DataAccessLayer.GetIDataStoreStudyRemover())
{
studyRemover.RemoveStudy(this.Context.SelectedStudy.StudyInstanceUid);
}
//trigger an import of the Renamed files.
LocalDataStoreServiceClient client = new LocalDataStoreServiceClient();
client.Open();
try
{
FileImportRequest request = new FileImportRequest();
request.BadFileBehaviour = BadFileBehaviour.Move;
request.FileImportBehaviour = FileImportBehaviour.Move;
List <string> filePaths = new List <string>();
filePaths.Add(_tempPath);
request.FilePaths = filePaths;
request.Recursive = true;
client.Import(request);
client.Close();
// Need to refresh study list in order for changed values to appear
// This method doesn't work. Need to manually click 'Search' again
//this.Context.RefreshStudyList();
}
catch
{
client.Abort();
throw;
}
//this.Context.RefreshStudyList();
context.Complete();
}
catch (Exception e)
{
context.Error(e);
}
}
private void Go(IBackgroundTaskContext context)
{
string studyUid = DicomUid.GenerateUid().UID;
string seriesUid = DicomUid.GenerateUid().UID;
PixelAspectRatioChanger changer =
new PixelAspectRatioChanger
{
IncreasePixelDimensions = _component.IncreasePixelDimensions,
NewAspectRatio = new PixelAspectRatio(_component.AspectRatioRow, _component.AspectRatioColumn),
RemoveCalibration = _component.RemoveCalibration
};
int i = 0;
context.ReportProgress(new BackgroundTaskProgress(i, _dicomFileNames.Count, "Exporting ..."));
try
{
foreach (string originalFile in _dicomFileNames)
{
var file = new DicomFile(originalFile);
file.Load(DicomReadOptions.None);
string sopInstanceUid = DicomUid.GenerateUid().UID;
file.DataSet[DicomTags.StudyInstanceUid].SetStringValue(studyUid);
file.DataSet[DicomTags.SeriesInstanceUid].SetStringValue(seriesUid);
file.DataSet[DicomTags.SopInstanceUid].SetStringValue(sopInstanceUid);
changer.ChangeAspectRatio(file);
string outputFileName = Path.Combine(_outputDirectory, String.Format("{0}.dcm", sopInstanceUid));
file.Save(outputFileName);
if (context.CancelRequested)
{
context.Cancel();
return;
}
context.ReportProgress(new BackgroundTaskProgress(++i, _dicomFileNames.Count + 1, "Exporting ..."));
}
}
catch (Exception e)
{
context.Error(e);
return;
}
context.Complete();
}
private static void LoadWorker(IBackgroundTaskContext context)
{
State state = context.UserState as State;
if (state == null)
{
context.Cancel();
return;
}
context.ReportProgress(new BackgroundTaskProgress(0, 1000, SR.MessageLoading));
if (context.CancelRequested)
{
context.Cancel();
return;
}
List<string> fileList = new List<string>();
try
{
foreach (string path in state.Paths)
fileList.AddRange(EnumerateFiles(path, state.Recursive));
}
catch (Exception ex)
{
context.Error(ex);
return;
}
for (int n = 0; n < fileList.Count; n++)
{
context.ReportProgress(new BackgroundTaskProgress(n, fileList.Count, SR.MessageLoading));
if (context.CancelRequested)
{
context.Cancel();
return;
}
state.SynchronizationContext.Send(i => state.Component.Load(fileList[(int) i]), n);
}
if (context.CancelRequested)
{
context.Cancel();
return;
}
context.Complete();
}