public DicomFile GetDataset(ZipPool pool = null)
{
if (IsZipReference(FullPath))
{
var bits = FullPath.Split('!');
var zip = pool != null?pool.OpenRead(bits[0]) : ZipFile.Open(bits[0], ZipArchiveMode.Read);
try
{
var entry = zip.GetEntry(bits[1]);
if (!IsDicomReference(bits[1]))
{
throw new AmbiguousFilePathResolutionException("Path provided '" + FullPath + "' was to a zip file but not to a dicom file entry");
}
var buffer = ByteStreamHelper.ReadFully(entry.Open());
//todo: when GH-627 goes live we can use FileReadOption https://github.com/fo-dicom/fo-dicom/blob/GH-627/DICOM/DicomFile.cs
//using (var memoryStream = new MemoryStream(buffer))
var memoryStream = new MemoryStream(buffer);
return(DicomFile.Open(memoryStream));
}
finally
{
if (pool == null)
{
zip.Dispose();
}
}
}
if (!IsDicomReference(FullPath))
{
throw new AmbiguousFilePathResolutionException("Path provided '" + FullPath + "' was not to either an entry in a zip file or to a dicom file");
}
return(DicomFile.Open(FullPath));
}
public DicomFile GetDataset(ZipPool pool = null)
{
if (IsZipReference(FullPath))
{
var bits = FullPath.Split('!');
var zip = pool != null?pool.OpenRead(bits[0]) : ZipFile.Open(bits[0], ZipArchiveMode.Read);
try
{
var entry = zip.GetEntry(bits[1]);
if (entry == null)
{
//Maybe user has formatted it dodgy
//e.g. \2015\3\18\2.25.177481563701402448825228719253578992342.dcm
string adjusted = bits[1].TrimStart('\\', '/');
//if that doesn't work
if ((entry = zip.GetEntry(adjusted)) == null)
{
//try normalizing the slashes
adjusted = adjusted.Replace('\\', '/');
//nope we just cannot get a legit path in this zip
if ((entry = zip.GetEntry(adjusted)) == null)
{
throw new AmbiguousFilePathResolutionException($"Could not find path '{bits[1]}' within zip archive '{bits[0]}'");
}
}
//we fixed it to something that actually exists so update our state that we don't make the same mistake again
FullPath = bits[0] + '!' + adjusted;
}
if (!IsDicomReference(bits[1]))
{
throw new AmbiguousFilePathResolutionException("Path provided '" + FullPath + "' was to a zip file but not to a dicom file entry");
}
var buffer = ByteStreamHelper.ReadFully(entry.Open());
//todo: when GH-627 goes live we can use FileReadOption https://github.com/fo-dicom/fo-dicom/blob/GH-627/DICOM/DicomFile.cs
//using (var memoryStream = new MemoryStream(buffer))
var memoryStream = new MemoryStream(buffer);
return(DicomFile.Open(memoryStream));
}
finally
{
if (pool == null)
{
zip.Dispose();
}
}
}
if (!IsDicomReference(FullPath))
{
throw new AmbiguousFilePathResolutionException("Path provided '" + FullPath + "' was not to either an entry in a zip file or to a dicom file");
}
return(DicomFile.Open(FullPath));
}
public DataTable ProcessPipelineData(DataTable toProcess, IDataLoadEventListener listener, GracefulCancellationToken cancellationToken)
{
//Things we ignore, Lookups, SupportingSql etc
if (_extractCommand == null)
{
listener.OnNotify(this, new NotifyEventArgs(ProgressEventType.Information, "Ignoring non dataset command "));
return(toProcess);
}
//if it isn't a dicom dataset don't process it
if (!toProcess.Columns.Contains(RelativeArchiveColumnName))
{
listener.OnNotify(this, new NotifyEventArgs(ProgressEventType.Warning, "Dataset " + _extractCommand.DatasetBundle.DataSet + " did not contain field '" + RelativeArchiveColumnName + "' so we will not attempt to extract images"));
return(toProcess);
}
if (_putter == null)
{
_putter = (IPutDicomFilesInExtractionDirectories) new ObjectConstructor().Construct(PutterType);
}
var projectNumber = _extractCommand.Configuration.Project.ProjectNumber.Value;
var mappingServer = new MappingRepository(UIDMappingServer);
var destinationDirectory = new DirectoryInfo(Path.Combine(_extractCommand.GetExtractionDirectory().FullName, "Images"));
var releaseCol = _extractCommand.QueryBuilder.SelectColumns.Select(c => c.IColumn).Single(c => c.IsExtractionIdentifier);
// See: ftp://medical.nema.org/medical/dicom/2011/11_15pu.pdf
var flags = DicomAnonymizer.SecurityProfileOptions.BasicProfile |
DicomAnonymizer.SecurityProfileOptions.CleanStructdCont |
DicomAnonymizer.SecurityProfileOptions.CleanDesc |
DicomAnonymizer.SecurityProfileOptions.RetainUIDs;
if (RetainDates)
{
flags |= DicomAnonymizer.SecurityProfileOptions.RetainLongFullDates;
}
var profile = DicomAnonymizer.SecurityProfile.LoadProfile(null, flags);
var anonymiser = new DicomAnonymizer(profile);
using (var pool = new ZipPool())
{
_sw.Start();
foreach (DataRow row in toProcess.Rows)
{
if (_errors > 0 && _errors > ErrorThreshold)
{
throw new Exception($"Number of errors reported ({_errors}) reached the threshold ({ErrorThreshold})");
}
cancellationToken.ThrowIfAbortRequested();
var path = new AmbiguousFilePath(ArchiveRootIfAny, (string)row[RelativeArchiveColumnName]);
DicomFile dicomFile;
try
{
dicomFile = path.GetDataset(pool);
}
catch (Exception e)
{
listener.OnNotify(this, new NotifyEventArgs(ProgressEventType.Error, $"Failed to get image at path '{path.FullPath}'", e));
_errors++;
continue;
}
//get the new patient ID
var releaseId = row[releaseCol.GetRuntimeName()].ToString();
DicomDataset ds;
try
{
ds = anonymiser.Anonymize(dicomFile.Dataset);
}
catch (Exception e)
{
listener.OnNotify(this, new NotifyEventArgs(ProgressEventType.Error, $"Failed to anonymize image at path '{path.FullPath}'", e));
_errors++;
continue;
}
//now we want to explicitly use our own release Id regardless of what FoDicom said
ds.AddOrUpdate(DicomTag.PatientID, releaseId);
//rewrite the UIDs
foreach (var kvp in UIDMapping.SupportedTags)
{
if (!ds.Contains(kvp.Key))
{
continue;
}
var value = ds.GetValue <string>(kvp.Key, 0);
//if it has a value for this UID
if (value == null)
{
continue;
}
var releaseValue = mappingServer.GetOrAllocateMapping(value, projectNumber, kvp.Value);
//change value in dataset
ds.AddOrUpdate(kvp.Key, releaseValue);
//and change value in DataTable
if (toProcess.Columns.Contains(kvp.Key.DictionaryEntry.Keyword))
{
row[kvp.Key.DictionaryEntry.Keyword] = releaseValue;
}
}
var newPath = _putter.WriteOutDataset(destinationDirectory, releaseId, ds);
row[RelativeArchiveColumnName] = newPath;
_anonymisedImagesCount++;
listener.OnProgress(this, new ProgressEventArgs("Writing ANO images", new ProgressMeasurement(_anonymisedImagesCount, ProgressType.Records), _sw.Elapsed));
}
_sw.Stop();
}
return(toProcess);
}
