private static DicomDirectory FinalizeDicomDirectoryLoad(
DicomDirectory df,
DicomFileReader reader,
DicomDirectoryReaderObserver dirObserver,
DicomReaderResult result)
{
if (result == DicomReaderResult.Processing)
{
throw new DicomFileException(df, "Invalid read return state: {state}", result);
}
if (result == DicomReaderResult.Error)
{
return(null);
}
df.IsPartial = result == DicomReaderResult.Stopped || result == DicomReaderResult.Suspended;
df.Format = reader.FileFormat;
df.Dataset.InternalTransferSyntax = reader.Syntax;
df._directoryRecordSequence = df.Dataset.Get <DicomSequence>(DicomTag.DirectoryRecordSequence);
df.RootDirectoryRecord = dirObserver.BuildDirectoryRecords();
return(df);
}
private async Task <bool> ParseItemSequenceValueAsync(IByteSource source)
{
if (this.parseStage == ParseStage.Value)
{
if (this.length != UndefinedLength)
{
if (!source.Require(this.length))
{
this.result = DicomReaderResult.Suspended;
return(false);
}
source.PushMilestone(this.length);
}
this.observer.OnBeginSequenceItem(source, this.length);
this.ResetState();
await this.ParseDatasetAsync(source).ConfigureAwait(false);
this.ResetState();
this.observer.OnEndSequenceItem();
}
return(true);
}
private bool ParseItemSequenceTag(IByteSource source)
{
if (this.parseStage == ParseStage.Tag)
{
source.Mark();
if (!source.Require(8))
{
this.result = DicomReaderResult.Suspended;
return(false);
}
var group = source.GetUInt16();
var element = source.GetUInt16();
this._tag = new DicomTag(@group, element);
if (this._tag != DicomTag.Item && this._tag != DicomTag.SequenceDelimitationItem)
{
// assume invalid sequence
source.Rewind();
if (!this._implicit)
{
source.PopMilestone();
}
this.observer.OnEndSequence();
if (this.badPrivateSequence)
{
this.isExplicitVR = !this.isExplicitVR;
this.badPrivateSequence = false;
}
return(false);
}
this.length = source.GetUInt32();
if (this._tag == DicomTag.SequenceDelimitationItem)
{
// #64, in case explicit length has been specified despite occurrence of Sequence Delimitation Item
if (source.HasReachedMilestone() && source.MilestonesCount > this.sequenceDepth)
{
this.ResetState();
return(true);
}
// end of sequence
this.observer.OnEndSequence();
if (this.badPrivateSequence)
{
this.isExplicitVR = !this.isExplicitVR;
this.badPrivateSequence = false;
}
this.ResetState();
return(false);
}
this.parseStage = ParseStage.Value;
}
return(true);
}
private bool ParseItemSequenceValue(IByteSource source)
{
if (this.parseStage == ParseStage.Value)
{
if (this.length != UndefinedLength)
{
if (!source.Require(this.length))
{
this.result = DicomReaderResult.Suspended;
return(false);
}
source.PushMilestone(this.length);
}
this.observer.OnBeginSequenceItem(source, this.length);
this.ResetState();
++this.sequenceDepth;
this.ParseDataset(source);
--this.sequenceDepth;
this.ResetState();
this.observer.OnEndSequenceItem();
}
return(true);
}
private void OnFileMetaInfoParseComplete(IAsyncResult result)
{
try {
if (_reader.EndRead(result) != DicomReaderResult.Stopped)
{
throw new DicomReaderException("DICOM File Meta Info ended prematurely");
}
// rewind to last marker (start of previous tag)... ugly because
// it requires knowledge of how the parser is implemented
_source.Rewind();
_source.Endian = _syntax.Endian;
_reader.IsExplicitVR = _syntax.IsExplicitVR;
_reader.BeginRead(_source, _dataObserver, null, OnDatasetParseComplete, null);
} catch (Exception e) {
if (_exception == null)
{
_exception = e;
}
_result = DicomReaderResult.Error;
} finally {
if (_result == DicomReaderResult.Error)
{
_async.Set();
}
}
}
public IAsyncResult BeginRead(IByteSource source, IDicomReaderObserver observer, DicomTag stop, AsyncCallback callback, object state) {
_stop = stop;
_observer = observer;
_result = DicomReaderResult.Processing;
_exception = null;
_async = new EventAsyncResult(callback, state);
ThreadPool.QueueUserWorkItem(ParseProc, source);
return _async;
}
public IAsyncResult BeginRead(IByteSource source, IDicomReaderObserver fileMetaInfo, IDicomReaderObserver dataset, AsyncCallback callback, object state) {
_result = DicomReaderResult.Processing;
_source = source;
_fmiObserver = fileMetaInfo;
_dataObserver = dataset;
_async = new EventAsyncResult(callback, state);
ParsePreamble(source, null); // ThreadPool?
return _async;
}
public IAsyncResult BeginRead(IByteSource source, IDicomReaderObserver fileMetaInfo, IDicomReaderObserver dataset, AsyncCallback callback, object state)
{
_result = DicomReaderResult.Processing;
_source = source;
_fmiObserver = fileMetaInfo;
_dataObserver = dataset;
_async = new EventAsyncResult(callback, state);
ParsePreamble(source, null); // ThreadPool?
return(_async);
}
public IAsyncResult BeginRead(IByteSource source, IDicomReaderObserver observer, DicomTag stop, AsyncCallback callback, object state)
{
_stop = stop;
_observer = observer;
_result = DicomReaderResult.Processing;
_exception = null;
_async = new EventAsyncResult(callback, state);
ThreadPool.QueueUserWorkItem(ParseProc, source);
return(_async);
}
private bool ParseTag(IByteSource source)
{
if (_parseStage == ParseStage.Tag)
{
source.Mark();
if (!source.Require(4))
{
_result = DicomReaderResult.Suspended;
return(false);
}
var group = source.GetUInt16();
var element = source.GetUInt16();
DicomPrivateCreator creator = null;
// according to
// http://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_7.8.html
// The requirements of this section do not allow any use of elements in the ranges
// (gggg,0001-000F) and (gggg,0100-0FFF) where gggg is odd.
// So element at [0x0100-0x0FFF] should not has a creator
if (@group.IsOdd() && element >= 0x1000)
{
var card = (uint)(@group << 16) + (uint)(element >> 8);
lock (_locker)
{
if (_private.TryGetValue(card, out string pvt))
{
creator = _dictionary.GetPrivateCreator(pvt);
}
}
}
_tag = new DicomTag(@group, element, creator);
_entry = _dictionary[_tag];
if (!_tag.IsPrivate && _entry != null && _entry.MaskTag == null)
{
_tag = _entry.Tag; // Use dictionary tag
}
if (_stop != null &&
_stop(new ParseState {
Tag = _tag, SequenceDepth = _sequenceDepth
}))
{
_result = DicomReaderResult.Stopped;
return(false);
}
_parseStage = ParseStage.VR;
}
return(true);
}
private void OnDatasetParseComplete(IAsyncResult result)
{
try {
_result = _reader.EndRead(result);
} catch (Exception e) {
if (_exception == null)
_exception = e;
_result = DicomReaderResult.Error;
} finally {
_async.Set();
}
}
/// <summary>
/// Throw if reading the file resulted in an error.
/// </summary>
/// <exception cref="DicomFileException">If the file could not be read properly.</exception>
protected static void HandleOpenError(DicomFile dicomFile, DicomReaderResult result)
{
switch (result)
{
case DicomReaderResult.Processing:
throw new DicomFileException(dicomFile,
$"Failed to parse {dicomFile} - probably not a valid DICOM file");
case DicomReaderResult.Error:
throw new DicomFileException(dicomFile, $"Not a valid DICOM file: {dicomFile}");
}
}
/// <summary>
/// Asynchronously read the byte source.
/// </summary>
/// <param name="source">Byte source to read.</param>
/// <returns>Awaitable read result.</returns>
internal async Task <DicomReaderResult> DoWorkAsync(IByteSource source)
{
ResetState();
source = ConvertSource(source);
await ParseDatasetAsync(source).ConfigureAwait(false);
if (_tag == DicomTag.SequenceDelimitationItem && _result == DicomReaderResult.Processing && source.IsEOF)
{
_result = DicomReaderResult.Success;
}
return(_result);
}
/// <summary>
/// Read the byte source.
/// </summary>
/// <param name="source">Byte source to read.</param>
/// <returns>Read result.</returns>
internal DicomReaderResult DoWork(IByteSource source)
{
ResetState();
source = ConvertSource(source);
ParseDataset(source);
if (_tag == DicomTag.SequenceDelimitationItem && _result == DicomReaderResult.Processing && source.IsEOF)
{
_result = DicomReaderResult.Success;
}
return(_result);
}
public void EndRead_ValidSource_ReturnsSuccess()
{
using (var stream = File.OpenRead(@".\Test Data\CT1_J2KI"))
{
var source = new StreamByteSource(stream);
var reader = new DicomFileReader();
const DicomReaderResult expected = DicomReaderResult.Success;
var actual = reader.EndRead(
reader.BeginRead(source, new MockObserver(), new MockObserver(), null, null));
Assert.Equal(expected, actual);
}
}
private bool ParseTag(IByteSource source)
{
if (this.parseStage == ParseStage.Tag)
{
source.Mark();
if (!source.Require(4))
{
this.result = DicomReaderResult.Suspended;
return(false);
}
var group = source.GetUInt16();
var element = source.GetUInt16();
DicomPrivateCreator creator = null;
if (@group.IsOdd() && element > 0x00ff)
{
var card = (uint)(@group << 16) + (uint)(element >> 8);
lock (this.locker)
{
string pvt;
if (this._private.TryGetValue(card, out pvt))
{
creator = this.dictionary.GetPrivateCreator(pvt);
}
}
}
this._tag = new DicomTag(@group, element, creator);
this._entry = this.dictionary[this._tag];
if (!this._tag.IsPrivate && this._entry != null && this._entry.MaskTag == null)
{
this._tag = this._entry.Tag; // Use dictionary tag
}
if (this.stop != null &&
this.stop(new ParseState {
Tag = this._tag, SequenceDepth = this.sequenceDepth
}))
{
this.result = DicomReaderResult.Stopped;
return(false);
}
this.parseStage = ParseStage.VR;
}
return(true);
}
private void OnDatasetParseComplete(IAsyncResult result)
{
try {
_result = _reader.EndRead(result);
} catch (Exception e) {
if (_exception == null)
{
_exception = e;
}
_result = DicomReaderResult.Error;
} finally {
_async.Set();
}
}
private void ParseDataset(IByteSource source)
{
if (this.isDeflated)
{
#if NET35
throw new NotSupportedException("Deflated datasets not supported in Unity.");
#else
source = this.Decompress(source);
#endif
}
this.result = DicomReaderResult.Processing;
while (!source.IsEOF && !source.HasReachedMilestone() && this.result == DicomReaderResult.Processing)
{
if (!this.ParseTag(source))
{
return;
}
if (!this.ParseVR(source))
{
return;
}
if (!this.ParseLength(source))
{
return;
}
if (!this.ParseValue(source))
{
return;
}
}
if (source.HasReachedMilestone())
{
// end of explicit length sequence item
source.PopMilestone();
return;
}
if (this.result != DicomReaderResult.Processing)
{
return;
}
// end of processing
this.result = DicomReaderResult.Success;
}
private async Task ParseFragmentSequenceAsync(IByteSource source)
{
_result = DicomReaderResult.Processing;
while (!source.IsEOF)
{
if (!ParseFragmentSequenceTag(source))
{
return;
}
if (!await ParseFragmentSequenceValueAsync(source).ConfigureAwait(false))
{
return;
}
}
}
private void ParseFragmentSequence(IByteSource source)
{
_result = DicomReaderResult.Processing;
while (!source.IsEOF)
{
if (!ParseFragmentSequenceTag(source))
{
return;
}
if (!ParseFragmentSequenceValue(source))
{
return;
}
}
}
private async Task <bool> ParseItemSequenceValueAsync(IByteSource source)
{
if (_parseStage == ParseStage.Value)
{
if (_length != _undefinedLength)
{
if (!source.Require(_length))
{
_result = DicomReaderResult.Suspended;
return(false);
}
source.PushMilestone(_length);
}
_observer.OnBeginSequenceItem(source, _length);
ResetState();
++_sequenceDepth;
await ParseDatasetAsync(source).ConfigureAwait(false);
--_sequenceDepth;
// bugfix k-pacs. there a sequence was not ended by ItemDelimitationItem>SequenceDelimitationItem, but directly with SequenceDelimitationItem
bool isEndSequence = (_tag == DicomTag.SequenceDelimitationItem);
ResetState();
_observer.OnEndSequenceItem();
if (isEndSequence)
{
// end of sequence
_observer.OnEndSequence();
// #565 Only reset the badPrivate sequence if we're in the correct depth
// This prevents prematurely resetting in case of sub-sequences contained in the bad private sequence
if (_badPrivateSequence && _sequenceDepth == _badPrivateSequenceDepth)
{
_isExplicitVR = !_isExplicitVR;
_badPrivateSequence = false;
}
ResetState();
return(false);
}
}
return(true);
}
private async Task ParseItemSequenceAsync(IByteSource source)
{
_result = DicomReaderResult.Processing;
while (!source.IsEOF && !source.HasReachedMilestone())
{
if (!ParseItemSequenceTag(source))
{
return;
}
if (!await ParseItemSequenceValueAsync(source).ConfigureAwait(false))
{
return;
}
}
ParseItemSequencePostProcess(source);
}
private void ParseItemSequence(IByteSource source)
{
_result = DicomReaderResult.Processing;
while (!source.IsEOF && !source.HasReachedMilestone())
{
if (!ParseItemSequenceTag(source))
{
return;
}
if (!ParseItemSequenceValue(source))
{
return;
}
}
ParseItemSequencePostProcess(source);
}
private bool ParseFragmentSequenceValue(IByteSource source)
{
if (_parseStage == ParseStage.Value)
{
if (!source.Require(_length))
{
_result = DicomReaderResult.Suspended;
return(false);
}
var buffer = source.GetBuffer(_length);
buffer = EndianByteBuffer.Create(buffer, source.Endian, _fragmentItem == 1 ? 4 : _vr.UnitSize);
_observer.OnFragmentSequenceItem(source, buffer);
_parseStage = ParseStage.Tag;
}
return(true);
}
private async Task ParseDatasetAsync(IByteSource source)
{
if (this.isDeflated)
{
source = this.Decompress(source);
}
this.result = DicomReaderResult.Processing;
while (!source.IsEOF && !source.HasReachedMilestone() && this.result == DicomReaderResult.Processing)
{
if (!this.ParseTag(source))
{
return;
}
if (!this.ParseVR(source))
{
return;
}
if (!this.ParseLength(source))
{
return;
}
if (!await this.ParseValueAsync(source).ConfigureAwait(false))
{
return;
}
}
if (source.HasReachedMilestone())
{
// end of explicit length sequence item
source.PopMilestone();
return;
}
if (this.result != DicomReaderResult.Processing)
{
return;
}
// end of processing
this.result = DicomReaderResult.Success;
}
private bool ParseItemSequenceValue(IByteSource source)
{
if (this.parseStage == ParseStage.Value)
{
if (this.length != UndefinedLength)
{
if (!source.Require(this.length))
{
this.result = DicomReaderResult.Suspended;
return(false);
}
source.PushMilestone(this.length);
}
this.observer.OnBeginSequenceItem(source, this.length);
this.ResetState();
++this.sequenceDepth;
this.ParseDataset(source);
--this.sequenceDepth;
// bugfix k-pacs. there a sequence was not ended by ItemDelimitationItem>SequenceDelimitationItem, but directly with SequenceDelimitationItem
bool isEndSequence = (this._tag == DicomTag.SequenceDelimitationItem);
this.ResetState();
this.observer.OnEndSequenceItem();
if (isEndSequence)
{
// end of sequence
this.observer.OnEndSequence();
// #565 Only reset the badPrivate sequence if we're in the correct depth
// This prevents prematurely resetting in case of sub-sequences contained in the bad private sequence
if (this.badPrivateSequence && this.sequenceDepth == this.badPrivateSequenceDepth)
{
this.isExplicitVR = !this.isExplicitVR;
this.badPrivateSequence = false;
}
this.ResetState();
return(false);
}
}
return(true);
}
private void ParseDataset(IByteSource source)
{
if (_isDeflated)
{
source = Decompress(source);
}
_result = DicomReaderResult.Processing;
while (!source.IsEOF && !source.HasReachedMilestone() && _result == DicomReaderResult.Processing)
{
if (!ParseTag(source))
{
return;
}
if (!ParseVR(source))
{
return;
}
if (!ParseLength(source))
{
return;
}
if (!ParseValue(source))
{
return;
}
}
if (source.HasReachedMilestone())
{
// end of explicit length sequence item
source.PopMilestone();
return;
}
if (_result != DicomReaderResult.Processing)
{
return;
}
// end of processing
_result = DicomReaderResult.Success;
}
private async Task <bool> ParseFragmentSequenceValueAsync(IByteSource source)
{
if (this.parseStage == ParseStage.Value)
{
if (!source.Require(this.length))
{
this.result = DicomReaderResult.Suspended;
return(false);
}
var buffer = await source.GetBufferAsync(this.length).ConfigureAwait(false);
buffer = EndianByteBuffer.Create(buffer, source.Endian, this.fragmentItem == 1 ? 4 : this._vr.UnitSize);
this.observer.OnFragmentSequenceItem(source, buffer);
this.parseStage = ParseStage.Tag;
}
return(true);
}
private async Task <bool> ParseItemSequenceValueAsync(IByteSource source)
{
if (this.parseStage == ParseStage.Value)
{
if (this.length != UndefinedLength)
{
if (!source.Require(this.length))
{
this.result = DicomReaderResult.Suspended;
return(false);
}
source.PushMilestone(this.length);
}
this.observer.OnBeginSequenceItem(source, this.length);
this.ResetState();
++this.sequenceDepth;
await this.ParseDatasetAsync(source).ConfigureAwait(false);
--this.sequenceDepth;
// bugfix k-pacs. there a sequence was not ended by ItemDelimitationItem>SequenceDelimitationItem, but directly with SequenceDelimitationItem
bool isEndSequence = (this._tag == DicomTag.SequenceDelimitationItem);
this.ResetState();
this.observer.OnEndSequenceItem();
if (isEndSequence)
{
// end of sequence
this.observer.OnEndSequence();
if (this.badPrivateSequence)
{
this.isExplicitVR = !this.isExplicitVR;
this.badPrivateSequence = false;
}
this.ResetState();
return(false);
}
}
return(true);
}
private void ParsePreamble(IByteSource source, object state)
{
try {
if (!source.Require(132, ParsePreamble, state))
{
return;
}
_source.Skip(128);
if (_source.GetUInt8() != 'D' ||
_source.GetUInt8() != 'I' ||
_source.GetUInt8() != 'C' ||
_source.GetUInt8() != 'M')
{
throw new DicomReaderException("Invalid preamble found in DICOM file parser");
}
DicomReaderCallbackObserver obs = new DicomReaderCallbackObserver();
obs.Add(DicomTag.TransferSyntaxUID, delegate(object sender, DicomReaderEventArgs ea) {
try {
string uid = Encoding.ASCII.GetString(ea.Data.Data);
_syntax = DicomTransferSyntax.Parse(uid);
} catch {
}
});
_source.Endian = _syntax.Endian;
_reader.IsExplicitVR = _syntax.IsExplicitVR;
_reader.BeginRead(_source, new DicomReaderMultiObserver(obs, _fmiObserver), FileMetaInfoStopTag, OnFileMetaInfoParseComplete, null);
} catch (Exception e) {
if (_exception == null)
{
_exception = e;
}
_result = DicomReaderResult.Error;
} finally {
if (_result != DicomReaderResult.Processing && _result != DicomReaderResult.Suspended)
{
_async.Set();
}
}
}
public void Read_ValidSource_ReturnsSuccess()
{
using var stream = File.OpenRead(TestData.Resolve("CT1_J2KI"));
var source = new StreamByteSource(stream);
var reader = new DicomFileReader();
var fileMetaInfo = new DicomFileMetaInformation();
var dataset = new DicomDataset();
const DicomReaderResult expected = DicomReaderResult.Success;
var actual = reader.Read(
source,
new DicomDatasetReaderObserver(fileMetaInfo),
new DicomDatasetReaderObserver(dataset));
Assert.Equal(expected, actual);
var modality = dataset.GetString(DicomTag.Modality);
Assert.Equal("CT", modality);
}
private bool ParseFragmentSequenceTag(IByteSource source)
{
if (_parseStage == ParseStage.Tag)
{
source.Mark();
if (!source.Require(8))
{
_result = DicomReaderResult.Suspended;
return(false);
}
var group = source.GetUInt16();
var element = source.GetUInt16();
var tag = new DicomTag(@group, element);
if (tag != DicomTag.Item && tag != DicomTag.SequenceDelimitationItem)
{
throw new DicomReaderException($"Unexpected tag in DICOM fragment sequence: {tag}");
}
_length = source.GetUInt32();
if (tag == DicomTag.SequenceDelimitationItem)
{
// end of fragment
_observer.OnEndFragmentSequence();
_fragmentItem = 0;
ResetState();
return(false);
}
_fragmentItem++;
_parseStage = ParseStage.Value;
}
return(true);
}
private void ParseDataset(IByteSource source)
{
if (this.isDeflated)
{
#if NET35
throw new NotSupportedException("Deflated datasets not supported in Unity.");
#else
source = this.Decompress(source);
#endif
}
this.result = DicomReaderResult.Processing;
while (!source.IsEOF && !source.HasReachedMilestone() && this.result == DicomReaderResult.Processing)
{
if (!this.ParseTag(source)) return;
if (!this.ParseVR(source)) return;
if (!this.ParseLength(source)) return;
if (!this.ParseValue(source)) return;
}
if (source.HasReachedMilestone())
{
// end of explicit length sequence item
source.PopMilestone();
return;
}
if (this.result != DicomReaderResult.Processing) return;
// end of processing
this.result = DicomReaderResult.Success;
}
private static DicomDirectory FinalizeDicomDirectoryLoad(
DicomDirectory df,
DicomFileReader reader,
DicomDirectoryReaderObserver dirObserver,
DicomReaderResult result)
{
if (result == DicomReaderResult.Processing)
{
throw new DicomFileException(df, "Invalid read return state: {state}", result);
}
if (result == DicomReaderResult.Error)
{
return null;
}
df.IsPartial = result == DicomReaderResult.Stopped || result == DicomReaderResult.Suspended;
df.Format = reader.FileFormat;
df.Dataset.InternalTransferSyntax = reader.Syntax;
df._directoryRecordSequence = df.Dataset.Get<DicomSequence>(DicomTag.DirectoryRecordSequence);
df.RootDirectoryRecord = dirObserver.BuildDirectoryRecords();
return df;
}
private void ParsePreamble(IByteSource source, object state)
{
try {
if (!source.Require(132, ParsePreamble, state))
return;
_source.Skip(128);
if (_source.GetUInt8() != 'D' ||
_source.GetUInt8() != 'I' ||
_source.GetUInt8() != 'C' ||
_source.GetUInt8() != 'M')
throw new DicomReaderException("Invalid preamble found in DICOM file parser");
DicomReaderCallbackObserver obs = new DicomReaderCallbackObserver();
obs.Add(DicomTag.TransferSyntaxUID, delegate(object sender, DicomReaderEventArgs ea) {
try {
string uid = Encoding.ASCII.GetString(ea.Data.Data);
_syntax = DicomTransferSyntax.Parse(uid);
} catch {
}
});
_source.Endian = _syntax.Endian;
_reader.IsExplicitVR = _syntax.IsExplicitVR;
_reader.BeginRead(_source, new DicomReaderMultiObserver(obs, _fmiObserver), FileMetaInfoStopTag, OnFileMetaInfoParseComplete, null);
} catch (Exception e) {
if (_exception == null)
_exception = e;
_result = DicomReaderResult.Error;
} finally {
if (_result != DicomReaderResult.Processing && _result != DicomReaderResult.Suspended) {
_async.Set();
}
}
}
private async Task<bool> ParseValueAsync(IByteSource source)
{
if (this.parseStage == ParseStage.Value)
{
// check dictionary for VR after reading length to handle 16-bit lengths
// check before reading value to handle SQ elements
var parsedVR = this._vr;
// check dictionary for VR after reading length to handle 16-bit lengths
// check before reading value to handle SQ elements
if (this._vr == DicomVR.Implicit || (this._vr == DicomVR.UN && this.isExplicitVR))
{
var entry = this.dictionary[this._tag];
if (entry != null)
{
this._vr = entry.ValueRepresentations.FirstOrDefault();
}
if (this._vr == null)
{
this._vr = DicomVR.UN;
}
}
if (this._tag == DicomTag.ItemDelimitationItem)
{
// end of sequence item
return false;
}
while (this._vr == DicomVR.SQ && this._tag.IsPrivate)
{
if (!IsPrivateSequence(source))
{
this._vr = DicomVR.UN;
break;
}
if (IsPrivateSequenceBad(source, this.isExplicitVR))
{
this.badPrivateSequence = true;
this.isExplicitVR = !this.isExplicitVR;
}
break;
}
if (this._vr == DicomVR.SQ)
{
// start of sequence
this.observer.OnBeginSequence(source, this._tag, this.length);
this.parseStage = ParseStage.Tag;
if (this.length != UndefinedLength)
{
this._implicit = false;
source.PushMilestone(this.length);
}
else
{
this._implicit = true;
}
var last = source.Position;
// Conformance with CP-246 (#177)
var needtoChangeEndian = false;
if (parsedVR == DicomVR.UN && !this._tag.IsPrivate)
{
this._implicit = true;
needtoChangeEndian = source.Endian == Endian.Big;
}
if (needtoChangeEndian)
{
source.Endian = Endian.Little;
}
await this.ParseItemSequenceAsync(source).ConfigureAwait(false);
if (needtoChangeEndian)
{
source.Endian = Endian.Big;
}
// Aeric Sylvan - https://github.com/rcd/fo-dicom/issues/62#issuecomment-46248073
// Fix reading of SQ with parsed VR of UN
if (source.Position > last || this.length == 0)
{
return true;
}
this.parseStage = ParseStage.Value;
this._vr = parsedVR;
}
if (this.length == UndefinedLength)
{
this.observer.OnBeginFragmentSequence(source, this._tag, this._vr);
this.parseStage = ParseStage.Tag;
await this.ParseFragmentSequenceAsync(source).ConfigureAwait(false);
return true;
}
if (!source.Require(this.length))
{
this.result = DicomReaderResult.Suspended;
return false;
}
var buffer = await source.GetBufferAsync(this.length).ConfigureAwait(false);
if (!this._vr.IsString)
{
buffer = EndianByteBuffer.Create(buffer, source.Endian, this._vr.UnitSize);
}
this.observer.OnElement(source, this._tag, this._vr, buffer);
// parse private creator value and add to lookup table
if (this._tag.IsPrivate && this._tag.Element != 0x0000 && this._tag.Element <= 0x00ff)
{
var creator =
DicomEncoding.Default.GetString(buffer.Data, 0, buffer.Data.Length)
.TrimEnd((char)DicomVR.LO.PaddingValue);
var card = (uint)(this._tag.Group << 16) + this._tag.Element;
lock (this.locker)
{
this._private[card] = creator;
}
}
this.ResetState();
}
return true;
}
private async Task<bool> ParseFragmentSequenceValueAsync(IByteSource source)
{
if (this.parseStage == ParseStage.Value)
{
if (!source.Require(this.length))
{
this.result = DicomReaderResult.Suspended;
return false;
}
var buffer = await source.GetBufferAsync(this.length).ConfigureAwait(false);
buffer = EndianByteBuffer.Create(buffer, source.Endian, this.fragmentItem == 1 ? 4 : this._vr.UnitSize);
this.observer.OnFragmentSequenceItem(source, buffer);
this.parseStage = ParseStage.Tag;
}
return true;
}
private void ParsePreamble(IByteSource source, object state) {
try {
if (!source.Require(132, ParsePreamble, state))
return;
// mark file origin
_source.Mark();
// test for DICM preamble
_source.Skip(128);
if (_source.GetUInt8() == 'D' &&
_source.GetUInt8() == 'I' &&
_source.GetUInt8() == 'C' &&
_source.GetUInt8() == 'M')
_fileFormat = DicomFileFormat.DICOM3;
// test for incorrect syntax in file meta info
do {
if (_fileFormat == DicomFileFormat.DICOM3) {
// move milestone to after preamble
_source.Mark();
} else {
// rewind to origin milestone
_source.Rewind();
}
// test for file meta info
var group = _source.GetUInt16();
if (group > 0x00ff) {
_source.Endian = Endian.Big;
_syntax = DicomTransferSyntax.ExplicitVRBigEndian;
group = Endian.Swap(group);
}
if (group > 0x00ff) {
// invalid starting tag
_fileFormat = DicomFileFormat.Unknown;
_source.Rewind();
break;
}
if (_fileFormat == DicomFileFormat.Unknown) {
if (group == 0x0002)
_fileFormat = DicomFileFormat.DICOM3NoPreamble;
else
_fileFormat = DicomFileFormat.DICOM3NoFileMetaInfo;
}
var element = _source.GetUInt16();
var tag = new DicomTag(group, element);
// test for explicit VR
var vrt = Encoding.UTF8.GetBytes(tag.DictionaryEntry.ValueRepresentations[0].Code);
var vrs = _source.GetBytes(2);
if (vrt[0] != vrs[0] || vrt[1] != vrs[1]) {
// implicit VR
if (_syntax.Endian == Endian.Little)
_syntax = DicomTransferSyntax.ImplicitVRLittleEndian;
else
_syntax = DicomTransferSyntax.ImplicitVRBigEndian;
}
_source.Rewind();
} while (_fileFormat == DicomFileFormat.Unknown);
if (_fileFormat == DicomFileFormat.Unknown)
throw new DicomReaderException("Attempted to read invalid DICOM file");
var obs = new DicomReaderCallbackObserver();
if (_fileFormat != DicomFileFormat.DICOM3) {
obs.Add(DicomTag.RecognitionCodeRETIRED, (object sender, DicomReaderEventArgs ea) => {
try {
string code = Encoding.UTF8.GetString(ea.Data.Data, 0, ea.Data.Data.Length);
if (code == "ACR-NEMA 1.0")
_fileFormat = DicomFileFormat.ACRNEMA1;
else if (code == "ACR-NEMA 2.0")
_fileFormat = DicomFileFormat.ACRNEMA2;
} catch {
}
});
}
obs.Add(DicomTag.TransferSyntaxUID, (object sender, DicomReaderEventArgs ea) => {
try {
string uid = Encoding.UTF8.GetString(ea.Data.Data, 0, ea.Data.Data.Length);
_syntax = DicomTransferSyntax.Parse(uid);
} catch {
}
});
_source.Endian = _syntax.Endian;
_reader.IsExplicitVR = _syntax.IsExplicitVR;
if (_fileFormat == DicomFileFormat.DICOM3NoFileMetaInfo)
_reader.BeginRead(_source, new DicomReaderMultiObserver(obs, _dataObserver), null, OnDatasetParseComplete, null);
else
_reader.BeginRead(_source, new DicomReaderMultiObserver(obs, _fmiObserver), FileMetaInfoStopTag, OnFileMetaInfoParseComplete, null);
} catch (Exception e) {
if (_exception == null)
_exception = e;
_result = DicomReaderResult.Error;
} finally {
if (_result != DicomReaderResult.Processing && _result != DicomReaderResult.Suspended) {
_async.Set();
}
}
}
private async Task ParseFragmentSequenceAsync(IByteSource source)
{
this.result = DicomReaderResult.Processing;
while (!source.IsEOF)
{
if (!this.ParseFragmentSequenceTag(source)) return;
if (!await this.ParseFragmentSequenceValueAsync(source).ConfigureAwait(false)) return;
}
}
private void autoCheckTransferSyntax(IByteSource source, ushort group, ushort element, object state)
{
//start checking Transfer Syntax after reading premable bytes
if (group > 0x0002 && !bAutoDetectVRType)
{
bAutoDetectVRType = true;//just check once
source.Mark();//mark the original position of pointer
//try to parse VR
uint tmpLength = 0;
source.Skip(2);
if (!source.Require(2, ParseDataset, state))
{
_result = DicomReaderResult.Suspended;
source.Rewind();
return;
}
tmpLength = source.GetUInt16();
try
{
if (!source.Require(tmpLength, ParseDataset, state))
{
_result = DicomReaderResult.Suspended;
source.Rewind();
return;
}
source.Skip((int)tmpLength);
if (!source.Require(4, ParseDataset, state))
{
_result = DicomReaderResult.Suspended;
source.Rewind();
return;
}
ushort group2 = source.GetUInt16();
ushort element2 = source.GetUInt16();
DicomPrivateCreator creator2 = null;
if (group2.IsOdd() && element2 > 0x00ff)
{
string pvt2 = null;
uint card2 = (uint)(group2 << 16) + (uint)(element2 >> 8);
if (_private.TryGetValue(card2, out pvt2))
creator2 = Dictionary.GetPrivateCreator(pvt2);
}
var tmpTag = new DicomTag(group2, element2, creator2);
var tmpEntry = Dictionary[tmpTag];
if (!tmpTag.IsPrivate && tmpEntry != null && tmpEntry.MaskTag == null)
{
tmpTag = tmpEntry.Tag; // Use dictionary tag
IsExplicitVR = true;
}
else
{
IsExplicitVR = false;
}
source.Rewind();
}
catch (Exception exin)
{
source.Rewind();
//说明有错误，直接抛出异常
throw new DicomIoException("Auto Check Transfer Syntax Exception by zssure,Details:{0}", exin.StackTrace);
}
}
}
private void ParseItemSequence(IByteSource source, object state) {
try {
_result = DicomReaderResult.Processing;
while (!source.IsEOF && !source.HasReachedMilestone()) {
if (_state == ParseState.Tag) {
source.Mark();
if (!source.Require(8, ParseItemSequence, state)) {
_result = DicomReaderResult.Suspended;
return;
}
ushort group = source.GetUInt16();
ushort element = source.GetUInt16();
_tag = new DicomTag(group, element);
if (_tag != DicomTag.Item && _tag != DicomTag.SequenceDelimitationItem) {
// assume invalid sequence
source.Rewind();
if (!_implicit)
source.PopMilestone();
_observer.OnEndSequence();
if (_badPrivateSequence) {
_explicit = !_explicit;
_badPrivateSequence = false;
}
return;
}
_length = source.GetUInt32();
if (_tag == DicomTag.SequenceDelimitationItem) {
// end of sequence
_observer.OnEndSequence();
if (_badPrivateSequence) {
_explicit = !_explicit;
_badPrivateSequence = false;
}
ResetState();
return;
}
_state = ParseState.Value;
}
if (_state == ParseState.Value) {
if (_length != UndefinedLength) {
if (!source.Require(_length, ParseItemSequence, state)) {
_result = DicomReaderResult.Suspended;
return;
}
source.PushMilestone(_length);
}
_observer.OnBeginSequenceItem(source, _length);
ResetState();
ParseDataset(source, state);
ResetState();
_observer.OnEndSequenceItem();
continue;
}
}
// end of explicit length sequence
if (source.HasReachedMilestone())
source.PopMilestone();
_observer.OnEndSequence();
if (_badPrivateSequence) {
_explicit = !_explicit;
_badPrivateSequence = false;
}
} catch (Exception e) {
_exception = e;
_result = DicomReaderResult.Error;
} finally {
if (_result != DicomReaderResult.Processing && _result != DicomReaderResult.Suspended) {
_async.Set();
}
}
}
private bool ParseItemSequenceTag(IByteSource source)
{
if (this.parseStage == ParseStage.Tag)
{
source.Mark();
if (!source.Require(8))
{
this.result = DicomReaderResult.Suspended;
return false;
}
var group = source.GetUInt16();
var element = source.GetUInt16();
this._tag = new DicomTag(@group, element);
if (this._tag != DicomTag.Item && this._tag != DicomTag.SequenceDelimitationItem)
{
// assume invalid sequence
source.Rewind();
if (!this._implicit)
{
source.PopMilestone();
}
this.observer.OnEndSequence();
if (this.badPrivateSequence)
{
this.isExplicitVR = !this.isExplicitVR;
this.badPrivateSequence = false;
}
return false;
}
this.length = source.GetUInt32();
if (this._tag == DicomTag.SequenceDelimitationItem)
{
// #64, in case explicit length has been specified despite occurrence of Sequence Delimitation Item
if (source.HasReachedMilestone() && source.MilestonesCount > this.sequenceDepth)
{
this.ResetState();
return true;
}
// end of sequence
this.observer.OnEndSequence();
if (this.badPrivateSequence)
{
this.isExplicitVR = !this.isExplicitVR;
this.badPrivateSequence = false;
}
this.ResetState();
return false;
}
this.parseStage = ParseStage.Value;
}
return true;
}
private async Task ParseItemSequenceAsync(IByteSource source)
{
this.result = DicomReaderResult.Processing;
while (!source.IsEOF && !source.HasReachedMilestone())
{
if (!this.ParseItemSequenceTag(source)) return;
if (!await this.ParseItemSequenceValueAsync(source).ConfigureAwait(false)) return;
}
this.ParseItemSequencePostProcess(source);
}
private void ParseItemSequence(IByteSource source)
{
this.result = DicomReaderResult.Processing;
while (!source.IsEOF && !source.HasReachedMilestone())
{
if (!this.ParseItemSequenceTag(source)) return;
if (!this.ParseItemSequenceValue(source)) return;
}
this.ParseItemSequencePostProcess(source);
}
public ParseResult(DicomReaderResult result, DicomFileFormat format, DicomTransferSyntax syntax)
{
this.Result = result;
this.Format = format;
this.Syntax = syntax;
}
private bool ParseFragmentSequenceTag(IByteSource source)
{
if (this.parseStage == ParseStage.Tag)
{
source.Mark();
if (!source.Require(8))
{
this.result = DicomReaderResult.Suspended;
return false;
}
var group = source.GetUInt16();
var element = source.GetUInt16();
DicomTag tag = new DicomTag(@group, element);
if (tag != DicomTag.Item && tag != DicomTag.SequenceDelimitationItem)
{
throw new DicomReaderException("Unexpected tag in DICOM fragment sequence: {0}", tag);
}
this.length = source.GetUInt32();
if (tag == DicomTag.SequenceDelimitationItem)
{
// end of fragment
this.observer.OnEndFragmentSequence();
this.fragmentItem = 0;
this.ResetState();
return false;
}
this.fragmentItem++;
this.parseStage = ParseStage.Value;
}
return true;
}
private bool ParseItemSequenceValue(IByteSource source)
{
if (this.parseStage == ParseStage.Value)
{
if (this.length != UndefinedLength)
{
if (!source.Require(this.length))
{
this.result = DicomReaderResult.Suspended;
return false;
}
source.PushMilestone(this.length);
}
this.observer.OnBeginSequenceItem(source, this.length);
this.ResetState();
++this.sequenceDepth;
this.ParseDataset(source);
--this.sequenceDepth;
this.ResetState();
this.observer.OnEndSequenceItem();
}
return true;
}
private bool ParseLength(IByteSource source)
{
while (this.parseStage == ParseStage.Length)
{
if (this._tag == DicomTag.Item || this._tag == DicomTag.ItemDelimitationItem
|| this._tag == DicomTag.SequenceDelimitationItem)
{
if (!source.Require(4))
{
this.result = DicomReaderResult.Suspended;
return false;
}
this.length = source.GetUInt32();
this.parseStage = ParseStage.Value;
break;
}
if (this.isExplicitVR)
{
if (this._vr == DicomVR.Implicit)
{
if (!source.Require(4))
{
this.result = DicomReaderResult.Suspended;
return false;
}
this.length = source.GetUInt32();
// assume that undefined length in implicit VR element is SQ
if (this.length == UndefinedLength)
{
this._vr = DicomVR.SQ;
}
}
else if (this._vr.Is16bitLength)
{
if (!source.Require(2))
{
this.result = DicomReaderResult.Suspended;
return false;
}
this.length = source.GetUInt16();
}
else
{
if (!source.Require(6))
{
this.result = DicomReaderResult.Suspended;
return false;
}
source.Skip(2);
this.length = source.GetUInt32();
// CP-246 (#177) handling
// assume that Undefined Length in explicit datasets with VR UN are sequences
// According to CP-246 the sequence shall be handled as ILE, but this will be handled later...
// in the current code this needs to be restricted to privates
if (this.length == UndefinedLength && this._vr == DicomVR.UN && this._tag.IsPrivate)
{
this._vr = DicomVR.SQ;
}
}
}
else
{
if (!source.Require(4))
{
this.result = DicomReaderResult.Suspended;
return false;
}
this.length = source.GetUInt32();
// assume that undefined length in implicit dataset is SQ
if (this.length == UndefinedLength && this._vr == DicomVR.UN)
{
this._vr = DicomVR.SQ;
}
}
this.parseStage = ParseStage.Value;
}
return true;
}
private async Task<bool> ParseItemSequenceValueAsync(IByteSource source)
{
if (this.parseStage == ParseStage.Value)
{
if (this.length != UndefinedLength)
{
if (!source.Require(this.length))
{
this.result = DicomReaderResult.Suspended;
return false;
}
source.PushMilestone(this.length);
}
this.observer.OnBeginSequenceItem(source, this.length);
this.ResetState();
await this.ParseDatasetAsync(source).ConfigureAwait(false);
this.ResetState();
this.observer.OnEndSequenceItem();
}
return true;
}
private void ParseFragmentSequence(IByteSource source)
{
this.result = DicomReaderResult.Processing;
while (!source.IsEOF)
{
if (!this.ParseFragmentSequenceTag(source)) return;
if (!this.ParseFragmentSequenceValue(source)) return;
}
}
private void ParseDataset(IByteSource source)
{
this.result = DicomReaderResult.Processing;
while (!source.IsEOF && !source.HasReachedMilestone() && this.result == DicomReaderResult.Processing)
{
if (!this.ParseTag(source)) return;
if (!this.ParseVR(source)) return;
if (!this.ParseLength(source)) return;
if (!this.ParseValue(source)) return;
}
if (source.HasReachedMilestone())
{
// end of explicit length sequence item
source.PopMilestone();
return;
}
if (this.result != DicomReaderResult.Processing) return;
// end of processing
this.result = DicomReaderResult.Success;
}
private void OnFileMetaInfoParseComplete(IAsyncResult result) {
try {
if (_reader.EndRead(result) != DicomReaderResult.Stopped)
throw new DicomReaderException("DICOM File Meta Info ended prematurely");
// rewind to last marker (start of previous tag)... ugly because
// it requires knowledge of how the parser is implemented
_source.Rewind();
_source.Endian = _syntax.Endian;
_reader.IsExplicitVR = _syntax.IsExplicitVR;
_reader.BeginRead(_source, _dataObserver, null, OnDatasetParseComplete, null);
} catch (Exception e) {
if (_exception == null)
_exception = e;
_result = DicomReaderResult.Error;
} finally {
if (_result == DicomReaderResult.Error) {
_async.Set();
}
}
}
private void ParseFragmentSequence(IByteSource source, object state) {
try {
_result = DicomReaderResult.Processing;
while (!source.IsEOF) {
if (_state == ParseState.Tag) {
source.Mark();
if (!source.Require(8, ParseFragmentSequence, state)) {
_result = DicomReaderResult.Suspended;
return;
}
ushort group = source.GetUInt16();
ushort element = source.GetUInt16();
DicomTag tag = new DicomTag(group, element);
if (tag != DicomTag.Item && tag != DicomTag.SequenceDelimitationItem)
throw new DicomReaderException("Unexpected tag in DICOM fragment sequence: {0}", tag);
_length = source.GetUInt32();
if (tag == DicomTag.SequenceDelimitationItem) {
// end of fragment
_observer.OnEndFragmentSequence();
_fragmentItem = 0;
ResetState();
ParseDataset(source, PopState());
return;
}
_fragmentItem++;
_state = ParseState.Value;
}
if (_state == ParseState.Value) {
if (!source.Require(_length, ParseFragmentSequence, state)) {
_result = DicomReaderResult.Suspended;
return;
}
IByteBuffer buffer = source.GetBuffer(_length);
if (_fragmentItem == 1)
buffer = EndianByteBuffer.Create(buffer, source.Endian, 4);
else
buffer = EndianByteBuffer.Create(buffer, source.Endian, _vr.UnitSize);
_observer.OnFragmentSequenceItem(source, buffer);
_state = ParseState.Tag;
}
}
} catch (Exception e) {
_exception = e;
_result = DicomReaderResult.Error;
} finally {
if (_result != DicomReaderResult.Processing && _result != DicomReaderResult.Suspended) {
_async.Set();
}
}
}
private async Task ParseDatasetAsync(IByteSource source)
{
this.result = DicomReaderResult.Processing;
while (!source.IsEOF && !source.HasReachedMilestone() && this.result == DicomReaderResult.Processing)
{
if (!this.ParseTag(source)) return;
if (!this.ParseVR(source)) return;
if (!this.ParseLength(source)) return;
if (!await this.ParseValueAsync(source).ConfigureAwait(false)) return;
}
if (source.HasReachedMilestone())
{
// end of explicit length sequence item
source.PopMilestone();
return;
}
if (this.result != DicomReaderResult.Processing) return;
// end of processing
this.result = DicomReaderResult.Success;
}
private void ParseDataset(IByteSource source, object state) {
try {
_result = DicomReaderResult.Processing;
while (!source.IsEOF && !source.HasReachedMilestone() && _result == DicomReaderResult.Processing) {
if (_state == ParseState.Tag) {
source.Mark();
if (!source.Require(4, ParseDataset, state)) {
_result = DicomReaderResult.Suspended;
return;
}
ushort group = source.GetUInt16();
ushort element = source.GetUInt16();
DicomPrivateCreator creator = null;
if (group.IsOdd() && element > 0x00ff) {
string pvt = null;
uint card = (uint)(group << 16) + (uint)(element >> 8);
if (_private.TryGetValue(card, out pvt))
creator = Dictionary.GetPrivateCreator(pvt);
}
_tag = new DicomTag(group, element, creator);
if (_stop != null && _tag.CompareTo(_stop) >= 0) {
_result = DicomReaderResult.Stopped;
return;
}
_state = ParseState.VR;
}
while (_state == ParseState.VR) {
if (_tag == DicomTag.Item || _tag == DicomTag.ItemDelimitationItem || _tag == DicomTag.SequenceDelimitationItem) {
_vr = DicomVR.NONE;
_state = ParseState.Length;
break;
}
if (IsExplicitVR) {
if (!source.Require(2, ParseDataset, state)) {
_result = DicomReaderResult.Suspended;
return;
}
byte[] bytes = source.GetBytes(2);
string vr = Encoding.UTF8.GetString(bytes, 0, bytes.Length);
try {
_vr = DicomVR.Parse(vr);
} catch {
// unable to parse VR
_vr = DicomVR.UN;
}
} else {
DicomDictionaryEntry entry = Dictionary[_tag];
if (entry != null) {
if (entry == DicomDictionary.UnknownTag)
_vr = DicomVR.UN;
else if (entry.ValueRepresentations.Contains(DicomVR.OB) && entry.ValueRepresentations.Contains(DicomVR.OW))
_vr = DicomVR.OW; // ???
else
_vr = entry.ValueRepresentations.FirstOrDefault();
}
}
if (_vr == null)
_vr = DicomVR.UN;
_state = ParseState.Length;
if (_vr == DicomVR.UN) {
if (_tag.Element == 0x0000) {
// Group Length to UL
_vr = DicomVR.UL;
break;
} else if (IsExplicitVR) {
break;
}
}
if (_tag.IsPrivate) {
if (_tag.Element != 0x0000 && _tag.Element <= 0x00ff && _vr == DicomVR.UN)
_vr = DicomVR.LO; // force private creator to LO
}
}
while (_state == ParseState.Length) {
if (_tag == DicomTag.Item || _tag == DicomTag.ItemDelimitationItem || _tag == DicomTag.SequenceDelimitationItem) {
if (!source.Require(4, ParseDataset, state)) {
_result = DicomReaderResult.Suspended;
return;
}
_length = source.GetUInt32();
_state = ParseState.Value;
break;
}
if (IsExplicitVR) {
if (_vr.Is16bitLength) {
if (!source.Require(2, ParseDataset, state)) {
_result = DicomReaderResult.Suspended;
return;
}
_length = source.GetUInt16();
} else {
if (!source.Require(6, ParseDataset, state)) {
_result = DicomReaderResult.Suspended;
return;
}
source.Skip(2);
_length = source.GetUInt32();
}
} else {
if (!source.Require(4, ParseDataset, state)) {
_result = DicomReaderResult.Suspended;
return;
}
_length = source.GetUInt32();
// assume that undefined length in implicit dataset is SQ
if (_length == UndefinedLength && _vr == DicomVR.UN)
_vr = DicomVR.SQ;
}
_state = ParseState.Value;
}
if (_state == ParseState.Value) {
// check dictionary for VR after reading length to handle 16-bit lengths
// check before reading value to handle SQ elements
if (_vr == DicomVR.UN && IsExplicitVR) {
var entry = Dictionary[_tag];
if (entry != null)
_vr = entry.ValueRepresentations.FirstOrDefault();
if (_vr == null)
_vr = DicomVR.UN;
}
if (_tag == DicomTag.ItemDelimitationItem) {
// end of sequence item
return;
}
while (_vr == DicomVR.SQ && _tag.IsPrivate) {
if (!IsPrivateSequence(source)) {
_vr = DicomVR.UN;
break;
}
if (IsPrivateSequenceBad(source)) {
_badPrivateSequence = true;
_explicit = !_explicit;
}
break;
}
if (_vr == DicomVR.SQ) {
// start of sequence
_observer.OnBeginSequence(source, _tag, _length);
_state = ParseState.Tag;
if (_length != UndefinedLength) {
_implicit = false;
source.PushMilestone(_length);
} else
_implicit = true;
PushState(state);
ParseItemSequence(source, null);
continue;
}
if (_length == UndefinedLength) {
_observer.OnBeginFragmentSequence(source, _tag, _vr);
_state = ParseState.Tag;
PushState(state);
ParseFragmentSequence(source, null);
continue;
}
if (!source.Require(_length, ParseDataset, state)) {
_result = DicomReaderResult.Suspended;
return;
}
IByteBuffer buffer = source.GetBuffer(_length);
if (!_vr.IsString)
buffer = EndianByteBuffer.Create(buffer, source.Endian, _vr.UnitSize);
_observer.OnElement(source, _tag, _vr, buffer);
// parse private creator value and add to lookup table
if (_tag.IsPrivate && _tag.Element != 0x0000 && _tag.Element <= 0x00ff) {
var creator = DicomEncoding.Default.GetString(buffer.Data, 0, buffer.Data.Length).TrimEnd((char)DicomVR.LO.PaddingValue);
var card = (uint)(_tag.Group << 16) + (uint)(_tag.Element);
_private[card] = creator;
}
ResetState();
}
}
if (source.HasReachedMilestone()) {
// end of explicit length sequence item
source.PopMilestone();
return;
}
if (_result != DicomReaderResult.Processing)
return;
// end of processing
_result = DicomReaderResult.Success;
} catch (Exception e) {
_exception = e;
_result = DicomReaderResult.Error;
} finally {
if (_result != DicomReaderResult.Processing && _result != DicomReaderResult.Suspended) {
_async.Set();
}
}
}
private bool ParseTag(IByteSource source)
{
if (this.parseStage == ParseStage.Tag)
{
source.Mark();
if (!source.Require(4))
{
this.result = DicomReaderResult.Suspended;
return false;
}
var group = source.GetUInt16();
var element = source.GetUInt16();
DicomPrivateCreator creator = null;
if (@group.IsOdd() && element > 0x00ff)
{
var card = (uint)(@group << 16) + (uint)(element >> 8);
lock (this.locker)
{
string pvt;
if (this._private.TryGetValue(card, out pvt))
{
creator = this.dictionary.GetPrivateCreator(pvt);
}
}
}
this._tag = new DicomTag(@group, element, creator);
this._entry = this.dictionary[this._tag];
if (!this._tag.IsPrivate && this._entry != null && this._entry.MaskTag == null)
{
this._tag = this._entry.Tag; // Use dictionary tag
}
if (this.stop != null
&& this.stop(new ParseState { Tag = this._tag, SequenceDepth = this.sequenceDepth }))
{
this.result = DicomReaderResult.Stopped;
return false;
}
this.parseStage = ParseStage.VR;
}
return true;
}
private void ParseDataset(IByteSource source, object state)
{
try {
_result = DicomReaderResult.Processing;
while (!source.IsEOF && !source.HasReachedMilestone() && _result == DicomReaderResult.Processing)
{
if (_state == ParseState.Tag)
{
source.Mark();
if (!source.Require(4, ParseDataset, state))
{
_result = DicomReaderResult.Suspended;
return;
}
ushort group = source.GetUInt16();
ushort element = source.GetUInt16();
DicomPrivateCreator creator = null;
if (group.IsOdd() && element > 0x00ff)
{
string pvt = null;
uint card = (uint)(group << 16) + (uint)(element >> 8);
if (_private.TryGetValue(card, out pvt))
{
creator = Dictionary.GetPrivateCreator(pvt);
}
}
_tag = new DicomTag(group, element, creator);
_entry = Dictionary[_tag];
if (!_tag.IsPrivate && _entry != null && _entry.MaskTag == null)
{
_tag = _entry.Tag; // Use dictionary tag
}
if (_stop != null && _tag.CompareTo(_stop) >= 0)
{
_result = DicomReaderResult.Stopped;
return;
}
_state = ParseState.VR;
}
while (_state == ParseState.VR)
{
if (_tag == DicomTag.Item || _tag == DicomTag.ItemDelimitationItem || _tag == DicomTag.SequenceDelimitationItem)
{
_vr = DicomVR.NONE;
_state = ParseState.Length;
break;
}
if (IsExplicitVR)
{
if (!source.Require(2, ParseDataset, state))
{
_result = DicomReaderResult.Suspended;
return;
}
byte[] bytes = source.GetBytes(2);
string vr = Encoding.UTF8.GetString(bytes, 0, bytes.Length);
if (!DicomVR.TryParse(vr, out _vr))
{
// unable to parse VR
_vr = DicomVR.UN;
}
}
else
{
if (_entry != null)
{
if (_entry == DicomDictionary.UnknownTag)
{
_vr = DicomVR.UN;
}
else if (_entry.ValueRepresentations.Contains(DicomVR.OB) && _entry.ValueRepresentations.Contains(DicomVR.OW))
{
_vr = DicomVR.OW; // ???
}
else
{
_vr = _entry.ValueRepresentations.FirstOrDefault();
}
}
}
if (_vr == null)
{
_vr = DicomVR.UN;
}
_state = ParseState.Length;
if (_vr == DicomVR.UN)
{
if (_tag.Element == 0x0000)
{
// Group Length to UL
_vr = DicomVR.UL;
break;
}
else if (IsExplicitVR)
{
break;
}
}
if (_tag.IsPrivate)
{
if (_tag.Element != 0x0000 && _tag.Element <= 0x00ff && _vr == DicomVR.UN)
{
_vr = DicomVR.LO; // force private creator to LO
}
}
}
while (_state == ParseState.Length)
{
if (_tag == DicomTag.Item || _tag == DicomTag.ItemDelimitationItem || _tag == DicomTag.SequenceDelimitationItem)
{
if (!source.Require(4, ParseDataset, state))
{
_result = DicomReaderResult.Suspended;
return;
}
_length = source.GetUInt32();
_state = ParseState.Value;
break;
}
if (IsExplicitVR)
{
if (_vr.Is16bitLength)
{
if (!source.Require(2, ParseDataset, state))
{
_result = DicomReaderResult.Suspended;
return;
}
_length = source.GetUInt16();
}
else
{
if (!source.Require(6, ParseDataset, state))
{
_result = DicomReaderResult.Suspended;
return;
}
source.Skip(2);
_length = source.GetUInt32();
}
}
else
{
if (!source.Require(4, ParseDataset, state))
{
_result = DicomReaderResult.Suspended;
return;
}
_length = source.GetUInt32();
// assume that undefined length in implicit dataset is SQ
if (_length == UndefinedLength && _vr == DicomVR.UN)
{
_vr = DicomVR.SQ;
}
}
_state = ParseState.Value;
}
if (_state == ParseState.Value)
{
// check dictionary for VR after reading length to handle 16-bit lengths
// check before reading value to handle SQ elements
var parsedVR = _vr;
// check dictionary for VR after reading length to handle 16-bit lengths
// check before reading value to handle SQ elements
if (_vr == DicomVR.UN && IsExplicitVR)
{
var entry = Dictionary[_tag];
if (entry != null)
{
_vr = entry.ValueRepresentations.FirstOrDefault();
}
if (_vr == null)
{
_vr = DicomVR.UN;
}
}
if (_tag == DicomTag.ItemDelimitationItem)
{
// end of sequence item
return;
}
while (_vr == DicomVR.SQ && _tag.IsPrivate)
{
if (!IsPrivateSequence(source))
{
_vr = DicomVR.UN;
break;
}
if (IsPrivateSequenceBad(source))
{
_badPrivateSequence = true;
_explicit = !_explicit;
}
break;
}
if (_vr == DicomVR.SQ)
{
// start of sequence
_observer.OnBeginSequence(source, _tag, _length);
_state = ParseState.Tag;
if (_length != UndefinedLength)
{
_implicit = false;
source.PushMilestone(_length);
}
else
{
_implicit = true;
}
PushState(state);
var last = source.Position;
ParseItemSequence(source, null);
// Aeric Sylvan - https://github.com/rcd/fo-dicom/issues/62#issuecomment-46248073
// Fix reading of SQ with parsed VR of UN
if (source.Position > last || _length == 0)
{
continue;
}
else
{
_state = ParseState.Value;
_vr = parsedVR;
}
}
if (_length == UndefinedLength)
{
_observer.OnBeginFragmentSequence(source, _tag, _vr);
_state = ParseState.Tag;
PushState(state);
ParseFragmentSequence(source, null);
continue;
}
if (!source.Require(_length, ParseDataset, state))
{
_result = DicomReaderResult.Suspended;
return;
}
IByteBuffer buffer = source.GetBuffer(_length);
if (!_vr.IsString)
{
buffer = EndianByteBuffer.Create(buffer, source.Endian, _vr.UnitSize);
}
_observer.OnElement(source, _tag, _vr, buffer);
// parse private creator value and add to lookup table
if (_tag.IsPrivate && _tag.Element != 0x0000 && _tag.Element <= 0x00ff)
{
var creator = DicomEncoding.Default.GetString(buffer.Data, 0, buffer.Data.Length).TrimEnd((char)DicomVR.LO.PaddingValue);
var card = (uint)(_tag.Group << 16) + (uint)(_tag.Element);
_private[card] = creator;
}
ResetState();
}
}
if (source.HasReachedMilestone())
{
// end of explicit length sequence item
source.PopMilestone();
return;
}
if (_result != DicomReaderResult.Processing)
{
return;
}
// end of processing
_result = DicomReaderResult.Success;
} catch (Exception e) {
_exception = e;
_result = DicomReaderResult.Error;
} finally {
if (_result != DicomReaderResult.Processing && _result != DicomReaderResult.Suspended)
{
_async.Set();
}
}
}
private bool ParseVR(IByteSource source)
{
while (this.parseStage == ParseStage.VR)
{
if (this._tag == DicomTag.Item || this._tag == DicomTag.ItemDelimitationItem
|| this._tag == DicomTag.SequenceDelimitationItem)
{
this._vr = DicomVR.NONE;
this.parseStage = ParseStage.Length;
break;
}
if (this.isExplicitVR)
{
if (!source.Require(2))
{
this.result = DicomReaderResult.Suspended;
return false;
}
source.Mark();
var bytes = source.GetBytes(2);
var vr = Encoding.UTF8.GetString(bytes, 0, bytes.Length);
if (string.IsNullOrWhiteSpace(vr))
{
if (this._entry != null)
{
this._vr = this._entry.ValueRepresentations.FirstOrDefault();
}
}
else if (!DicomVR.TryParse(vr, out this._vr))
{
// unable to parse VR; rewind VR bytes for continued attempt to interpret the data.
this._vr = DicomVR.Implicit;
source.Rewind();
}
}
else
{
if (this._entry != null)
{
if (this._entry == DicomDictionary.UnknownTag)
{
this._vr = DicomVR.UN;
}
else if (this._entry.ValueRepresentations.Contains(DicomVR.OB)
&& this._entry.ValueRepresentations.Contains(DicomVR.OW))
{
this._vr = DicomVR.OW; // ???
}
else
{
this._vr = this._entry.ValueRepresentations.FirstOrDefault();
}
}
}
if (this._vr == null)
{
this._vr = DicomVR.UN;
}
this.parseStage = ParseStage.Length;
if (this._vr == DicomVR.UN)
{
if (this._tag.Element == 0x0000)
{
// Group Length to UL
this._vr = DicomVR.UL;
break;
}
if (this.isExplicitVR)
{
break;
}
}
if (this._tag.IsPrivate)
{
if (this._tag.Element != 0x0000 && this._tag.Element <= 0x00ff && this._vr == DicomVR.UN)
{
this._vr = DicomVR.LO; // force private creator to LO
}
}
}
return true;
}
