private void ProcessZipArchive(DataTable dt, IDataLoadEventListener listener, string zipFileName)
{
var skippedEntries = 0;
var corruptedEntries = 0;
try
{
using (var archive = ZipFile.Open(zipFileName, ZipArchiveMode.Read))
foreach (var f in archive.Entries)
{
//it's not a dicom file!
if (!AmbiguousFilePath.IsDicomReference(f.FullName))
{
skippedEntries++;
continue;
}
try
{
var buffer = ByteStreamHelper.ReadFully(f.Open());
using (var memoryStream = new MemoryStream(buffer))
ProcessFile(memoryStream, dt, zipFileName + "!" + f.FullName, listener);
}
catch (Exception e)
{
corruptedEntries++;
RecordError("Zip entry '" + f.FullName + "'", e);
if (corruptedEntries <= 3)
{
continue;
}
listener.OnNotify(this, new NotifyEventArgs(ProgressEventType.Warning, "Skipping the rest of '" + f.FullName + "'", e));
break;
}
}
}
catch (InvalidDataException e)
{
listener.OnNotify(this, new NotifyEventArgs(ProgressEventType.Warning, "Error processing zip file '" + zipFileName + "'", e));
}
if (skippedEntries > 0)
{
listener.OnNotify(this, new NotifyEventArgs(ProgressEventType.Warning, "Skipped '" + skippedEntries + "' in zip archive '" + zipFileName + "' because they did not have .dcm extensions"));
}
UpdateProgressListeners();
}
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));
}