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 void OnCompleteFileMetaInfo(IAsyncResult result)
{
try {
DicomDatasetWalker walker;
if (result != null)
{
walker = result.AsyncState as DicomDatasetWalker;
walker.EndWalk(result);
}
DicomTransferSyntax syntax = _fileMetaInfo.TransferSyntax;
DicomWriter writer = new DicomWriter(syntax, _options, _target);
walker = new DicomDatasetWalker(_dataset);
walker.BeginWalk(writer, OnCompleteDataset, walker);
} catch (Exception e) {
_exception = e;
_async.Set();
}
}
private void OnCompleteFileMetaInfo(IAsyncResult result)
{
try {
DicomDatasetWalker walker;
if (result != null)
{
walker = result.AsyncState as DicomDatasetWalker;
walker.EndWalk(result);
}
//DicomTransferSyntax syntax = _fileMetaInfo.TransferSyntax;
DicomTransferSyntax syntax = _fileMetaInfo.InternalTransferSyntax;
if (_options.KeepGroupLengths)
{
// update transfer syntax and recalculate existing group lengths
_dataset.InternalTransferSyntax = syntax;
_dataset.RecalculateGroupLengths(false);
}
else
{
// remove group lengths as suggested in PS 3.5 7.2
//
// 2. It is recommended that Group Length elements be removed during storage or transfer
// in order to avoid the risk of inconsistencies arising during coercion of data
// element values and changes in transfer syntax.
_dataset.RemoveGroupLengths();
}
DicomWriter writer = new DicomWriter(syntax, _options, _target);
walker = new DicomDatasetWalker(_dataset);
walker.BeginWalk(writer, OnCompleteDataset, walker);
} catch (Exception e) {
_exception = e;
_async.Set();
}
}
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 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.ASCII.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.ASCII.GetString(ea.Data.Data);
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.ASCII.GetString(ea.Data.Data);
_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 void ParseDataset(IByteSource source, object state)
{
try {
_result = DicomReaderResult.Processing;
while (!source.IsEOF && !source.HasReachedMilestone())
{
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.ASCII.GetString(bytes);
_vr = DicomVR.Parse(vr);
}
else
{
DicomDictionaryEntry entry = Dictionary[_tag];
if (entry != null)
{
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;
}
if (_tag.Group.IsOdd())
{
if (_tag.Element <= 0x00ff)
{
// Private Creator to LO
_vr = DicomVR.LO;
break;
}
else if (IsExplicitVR)
{
DicomDictionaryEntry entry = Dictionary[_tag];
if (entry != null)
{
_vr = entry.ValueRepresentations.FirstOrDefault();
}
if (_vr == null)
{
_vr = DicomVR.UN;
}
break;
}
}
}
}
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();
}
_state = ParseState.Value;
}
if (_state == ParseState.Value)
{
if (_tag == DicomTag.ItemDelimitationItem)
{
// end of sequence item
ParseItemSequence(source, state);
return;
}
if (_vr == DicomVR.SQ)
{
// start of sequence
_observer.OnBeginSequence(source, _tag, _length);
_state = ParseState.Tag;
if (_length != UndefinedLength)
{
source.PushMilestone(_length);
}
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);
ResetState();
}
}
if (source.HasReachedMilestone())
{
// end of explicit length sequence item
_observer.OnEndSequenceItem();
source.PopMilestone();
ParseItemSequence(source, state);
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();
}
}
}