/// <summary>
/// Loads a dicom file, stopping at a certain tag
/// </summary>
/// <param name="file">Filename</param>
/// <param name="stopTag">Tag to stop parsing at</param>
/// <param name="options">DICOM read options</param>
public DicomReadStatus Load(String file, DicomTag stopTag, DicomReadOptions options)
{
using (FileStream fs = File.OpenRead(file)) {
fs.Seek(128, SeekOrigin.Begin);
CheckFileHeader(fs);
DicomStreamReader dsr = new DicomStreamReader(fs);
_metainfo = new DcmFileMetaInfo();
dsr.Dataset = _metainfo;
dsr.Read(DcmFileMetaInfo.StopTag, options | DicomReadOptions.FileMetaInfoOnly);
if (_metainfo.TransferSyntax.IsDeflate)
{
MemoryStream ms = StreamUtility.Deflate(fs, false);
dsr = new DicomStreamReader(ms);
}
_dataset = new DcmDataset(_metainfo.TransferSyntax);
dsr.Dataset = _dataset;
DicomReadStatus status = dsr.Read(stopTag, options);
fs.Close();
return(status);
}
}
private DicomReadStatus ParseSequenceItemDataset(DicomTransferSyntax syntax, long len, out DcmDataset dataset, DicomReadOptions options)
{
long pos = _stream.Position;
dataset = new DcmDataset(pos, (uint)len, syntax);
Stream stream = (len != UndefinedLength) ? new SegmentStream(_stream, _stream.Position, _len) : _stream;
DicomStreamReader idsr = new DicomStreamReader(stream);
idsr.Dataset = dataset;
idsr.Encoding = _encoding;
if (len != UndefinedLength)
{
idsr.PositionOffset = dataset.StreamPosition;
}
DicomReadStatus status = idsr.Read(null, options);
if (status != DicomReadStatus.Success)
{
_stream.Seek(pos, SeekOrigin.Begin);
dataset = null;
}
else
{
if (len == UndefinedLength)
{
// rewind delimitation item tag
_stream.Seek(-4, SeekOrigin.Current);
len = _stream.Position - pos;
}
_remain -= len;
_bytes += len;
_read += len;
}
return(status);
}
public DicomReadStatus Read(DicomTag stopAtTag, DicomReadOptions options)
{
if (stopAtTag == null)
{
stopAtTag = new DicomTag(0xFFFFFFFF, "Bogus Tag", "BogusTag", DicomVr.UNvr, false, 1, 1, false);
}
// Counters:
// _remain - bytes remaining in stream
// _bytes - estimates bytes to end of dataset
// _read - number of bytes read from stream
try
{
BytesNeeded = 0;
_remain = _stream.Length - _stream.Position;
while (_remain > 0)
{
if (_inGroup2 && BytesRead >= _endGroup2)
{
_inGroup2 = false;
// Only change if we're still reading the meta info
if (Dataset.StartTagValue < DicomTags.TransferSyntaxUid)
{
TransferSyntax group2Syntax =
TransferSyntax.GetTransferSyntax(
Dataset[DicomTags.TransferSyntaxUid].GetString(0, String.Empty));
if (group2Syntax == null)
{
throw new DicomException("Unsupported transfer syntax in group 2 elements");
}
TransferSyntax = group2Syntax;
}
}
uint tagValue;
if (LastTagRead == null)
{
if (_remain < 4)
{
return(NeedMoreData(4));
}
_pos = _stream.Position;
ushort g = _reader.ReadUInt16();
ushort e = _reader.ReadUInt16();
tagValue = DicomTag.GetTagValue(g, e);
if (DicomTag.IsPrivateGroup(g) && e > 0x00ff)
{
SaveTagRead = LastTagRead = DicomTagDictionary.GetDicomTag(g, e) ??
new DicomTag((uint)g << 16 | e, "Private Tag", "PrivateTag", DicomVr.UNvr, false, 1, uint.MaxValue, false);
}
else
{
if (e == 0x0000)
{
SaveTagRead = LastTagRead = new DicomTag((uint)g << 16 | e, "Group Length", "GroupLength", DicomVr.ULvr, false, 1, 1, false);
}
else
{
SaveTagRead = LastTagRead = DicomTagDictionary.GetDicomTag(g, e) ??
new DicomTag((uint)g << 16 | e, "Private Tag", "PrivateTag", DicomVr.UNvr, false, 1, uint.MaxValue, false);
}
}
_remain -= 4;
BytesEstimated += 4;
BytesRead += 4;
}
else
{
tagValue = LastTagRead.TagValue;
}
if ((tagValue >= stopAtTag.TagValue) &&
(_sqrs.Count == 0)) // only exit in root message when after stop tag
{
if (_inGroup2 && tagValue > 0x0002FFFF)
{
if (_endGroup2 != BytesRead - 4)
{
Platform.Log(LogLevel.Debug, "File Meta Info Length, {0}, not equal to actual bytes read in file, {1}, overwriting length.",
EndGroupTwo, BytesRead - 4);
_endGroup2 = BytesRead - 4;
}
_inGroup2 = false;
}
EncounteredStopTag = true;
return(DicomReadStatus.Success);
}
bool twoByteLength;
if (_vr == null)
{
if (_syntax.ExplicitVr)
{
if (LastTagRead == DicomTag.Item ||
LastTagRead == DicomTag.ItemDelimitationItem ||
LastTagRead == DicomTag.SequenceDelimitationItem)
{
_vr = DicomVr.NONE;
twoByteLength = _vr.Is16BitLengthField;
}
else
{
if (_remain < 2)
{
return(NeedMoreData(2));
}
string vr = new string(_reader.ReadChars(2));
_vr = DicomVr.GetVR(vr);
twoByteLength = _vr.Is16BitLengthField;
_remain -= 2;
BytesEstimated += 2;
BytesRead += 2;
if (LastTagRead.VR.Equals(DicomVr.UNvr))
{
LastTagRead = new DicomTag(LastTagRead.TagValue, "Private Tag", "PrivateTag", _vr, false, 1, uint.MaxValue, false);
if (vr.Equals("??"))
{
twoByteLength = true;
}
}
else if (!LastTagRead.VR.Equals(_vr))
{
if (!vr.Equals(" "))
{
DicomTag tag =
new DicomTag(LastTagRead.TagValue, LastTagRead.Name, LastTagRead.VariableName, _vr, LastTagRead.MultiVR,
LastTagRead.VMLow, LastTagRead.VMHigh,
LastTagRead.Retired);
LastTagRead = tag;
; // TODO, log something
}
}
}
}
else
{
_vr = LastTagRead.VR;
twoByteLength = _vr.Is16BitLengthField;
}
if (_vr == DicomVr.UNvr)
{
if (LastTagRead.IsPrivate)
{
if (LastTagRead.Element <= 0x00ff && LastTagRead.Element >= 0x0010)
{
// Reset the tag with the right VR and a more descriptive name.
LastTagRead = new DicomTag(LastTagRead.TagValue, "Private Creator Code", "PrivateCreatorCode", DicomVr.LOvr, false, 1, uint.MaxValue, false);
// private creator id
// Only set the VR to LO for Implicit VR, if we do it for
// Explicit VR syntaxes, we would incorrectly read the tag
// length below.
if (!_syntax.ExplicitVr)
{
_vr = DicomVr.LOvr;
}
}
else if (_stream.CanSeek && Flags.IsSet(options, DicomReadOptions.AllowSeekingForContext))
{
// attempt to identify private sequence by checking if the tag has
// an undefined length
long pos = _stream.Position;
int bytesToCheck = _syntax.ExplicitVr ? 6 : 4;
if (_remain >= bytesToCheck)
{
if (_syntax.ExplicitVr)
{
_reader.ReadUInt16();
}
uint l = _reader.ReadUInt32();
if (l == _undefinedLength)
{
_vr = DicomVr.SQvr;
}
}
_stream.Position = pos;
}
}
}
}
else
{
twoByteLength = _vr.Is16BitLengthField;
}
// Read the value length
if (_len == _undefinedLength)
{
if (_syntax.ExplicitVr)
{
if (LastTagRead == DicomTag.Item ||
LastTagRead == DicomTag.ItemDelimitationItem ||
LastTagRead == DicomTag.SequenceDelimitationItem)
{
if (_remain < 4)
{
return(NeedMoreData(4));
}
_len = _reader.ReadUInt32();
_remain -= 4;
BytesEstimated += 4;
BytesRead += 4;
}
else
{
if (twoByteLength)
{
if (_remain < 2)
{
return(NeedMoreData(2));
}
_len = _reader.ReadUInt16();
_remain -= 2;
BytesEstimated += 2;
BytesRead += 2;
}
else
{
if (_remain < 6)
{
return(NeedMoreData(6));
}
_reader.ReadByte();
_reader.ReadByte();
_len = _reader.ReadUInt32();
_remain -= 6;
BytesEstimated += 6;
BytesRead += 6;
}
}
}
else
{
if (_remain < 4)
{
return(NeedMoreData(4));
}
_len = _reader.ReadUInt32();
_remain -= 4;
BytesEstimated += 4;
BytesRead += 4;
}
if ((_len != _undefinedLength) &&
!_vr.Equals(DicomVr.SQvr) &&
!(LastTagRead.Equals(DicomTag.Item) &&
_fragment == null))
{
BytesEstimated += _len;
}
}
// If we have a private creator code, set the VR to LO, because
// that is what it is. We must do this after we read the length
// so that the 32 bit length is read properly.
if ((LastTagRead.IsPrivate) &&
(_vr.Equals(DicomVr.UNvr)) &&
(LastTagRead.Element <= 0x00ff))
{
_vr = DicomVr.LOvr;
}
if (_fragment != null)
{
// In the middle of parsing pixels
if (LastTagRead == DicomTag.Item)
{
if (_remain < _len)
{
return(NeedMoreData(_remain - _len));
}
if (Flags.IsSet(options, DicomReadOptions.StorePixelDataReferences) &&
_fragment.HasOffsetTable)
{
FileReference reference = new FileReference(StreamOpener, _stream.Position, _len, _endian, DicomVr.OBvr);
DicomFragment fragment = new DicomFragment(reference);
_fragment.AddFragment(fragment);
if (_stream.CanSeek)
{
_stream.Seek(_len, SeekOrigin.Current);
}
else
{
ConsumeStreamBytes(_stream, _len);
}
}
else
{
ByteBuffer data = new ByteBuffer(_endian, _len);
data.CopyFrom(_stream, (int)_len);
if (!_fragment.HasOffsetTable)
{
_fragment.SetOffsetTable(data);
}
else
{
DicomFragment fragment = new DicomFragment(data);
_fragment.AddFragment(fragment);
}
}
_remain -= _len;
BytesRead += _len;
}
else if (LastTagRead == DicomTag.SequenceDelimitationItem)
{
if (_sqrs.Count > 0)
{
SequenceRecord rec = _sqrs.Peek();
DicomAttributeCollection ds = rec.Current;
ds[_fragment.Tag] = _fragment;
if (rec.Curlen != _undefinedLength)
{
long end = rec.Curpos + rec.Curlen;
if (_stream.Position >= end)
{
rec.Current = null;
}
}
}
else
{
Dataset[_fragment.Tag] = _fragment;
}
_fragment = null;
}
else
{
Platform.Log(LogLevel.Error, "Encountered unexpected tag in stream: {0}", LastTagRead.ToString());
// unexpected tag
return(DicomReadStatus.UnknownError);
}
}
else if (_sqrs.Count > 0 &&
(LastTagRead == DicomTag.Item ||
LastTagRead == DicomTag.ItemDelimitationItem ||
LastTagRead == DicomTag.SequenceDelimitationItem))
{
SequenceRecord rec = _sqrs.Peek();
if (LastTagRead.Equals(DicomTag.Item))
{
if (_len != _undefinedLength)
{
if (_len > _remain)
{
return(NeedMoreData(_remain - _len));
}
}
DicomSequenceItem ds;
if (rec.Tag.TagValue.Equals(DicomTags.DirectoryRecordSequence))
{
DirectoryRecordSequenceItem dr = new DirectoryRecordSequenceItem
{
Offset = (uint)_pos
};
ds = dr;
}
else
{
ds = new DicomSequenceItem();
}
rec.Current = ds;
if (rec.Tag.VR.Equals(DicomVr.UNvr))
{
DicomTag tag = new DicomTag(rec.Tag.TagValue, rec.Tag.Name,
rec.Tag.VariableName, DicomVr.SQvr, rec.Tag.MultiVR, rec.Tag.VMLow,
rec.Tag.VMHigh, rec.Tag.Retired);
rec.Parent[tag].AddSequenceItem(ds);
}
else
{
rec.Parent[rec.Tag].AddSequenceItem(ds);
}
// Specific character set is inherited, save it. It will be overwritten
// if a new value of the tag is encountered in the sequence.
rec.Current.SpecificCharacterSet = rec.Parent.SpecificCharacterSet;
// save the sequence length
rec.Curpos = _pos + 8;
rec.Curlen = _len;
_sqrs.Pop();
_sqrs.Push(rec);
if (_len != _undefinedLength)
{
ByteBuffer data = new ByteBuffer(_endian, _len);
data.CopyFrom(_stream, (int)_len);
data.Stream.Position = 0;
_remain -= _len;
BytesRead += _len;
DicomStreamReader idsr = new DicomStreamReader(data.Stream)
{
Dataset = ds,
TransferSyntax = rec.Tag.VR.Equals(DicomVr.UNvr)
? TransferSyntax.ImplicitVrLittleEndian
: _syntax,
StreamOpener = StreamOpener
};
DicomReadStatus stat = idsr.Read(null, options & ~DicomReadOptions.StorePixelDataReferences);
if (stat != DicomReadStatus.Success)
{
Platform.Log(LogLevel.Error, "Unexpected parsing error ({0}) when reading sequence attribute: {1}.", stat, rec.Tag.ToString());
return(stat);
}
}
}
else if (LastTagRead == DicomTag.ItemDelimitationItem)
{
}
else if (LastTagRead == DicomTag.SequenceDelimitationItem)
{
SequenceRecord rec2 = _sqrs.Pop();
if (rec2.Current == null)
{
rec2.Parent[rec.Tag].SetNullValue();
}
}
if (rec.Len != _undefinedLength)
{
long end = rec.Pos + 8 + rec.Len;
if (_syntax.ExplicitVr)
{
end += 2 + 2;
}
if (_stream.Position >= end)
{
_sqrs.Pop();
}
}
}
else
{
if (_len == _undefinedLength)
{
if (_vr.Equals(DicomVr.UNvr))
{
if (!_syntax.ExplicitVr)
{
_vr = DicomVr.SQvr;
LastTagRead = LastTagRead.IsPrivate
? new DicomTag(LastTagRead.TagValue, "Private Tag", "PrivateTag", DicomVr.SQvr, false, 1, uint.MaxValue, false)
: new DicomTag(LastTagRead.TagValue, "Unknown Tag", "UnknownTag", DicomVr.SQvr, false, 1, uint.MaxValue, false);
}
else
{
// To handle this case, we'd have to add a new mechanism to transition the parser to implicit VR parsing,
// and then return back to implicit once the parsing of the SQ is complete.
Platform.Log(LogLevel.Error,
"Encountered unknown tag {0}, encoded as undefined length in an Explicit VR transfer syntax at offset {1}. Unable to parse.",
LastTagRead, _stream.Position);
return(DicomReadStatus.UnknownError);
}
}
if (_vr.Equals(DicomVr.SQvr))
{
SequenceRecord rec = new SequenceRecord
{
Parent = _sqrs.Count > 0
? _sqrs.Peek().Current
: Dataset,
Current = null,
Tag = LastTagRead,
Len = _undefinedLength
};
_sqrs.Push(rec);
}
else
{
_fragment = new DicomFragmentSequence(LastTagRead);
}
}
else
{
if (_vr.Equals(DicomVr.SQvr))
{
if (_len == 0)
{
DicomAttributeCollection ds;
if (_sqrs.Count > 0)
{
SequenceRecord rec = _sqrs.Peek();
ds = rec.Current;
}
else
{
ds = Dataset;
}
ds[LastTagRead].SetNullValue();
}
else
{
SequenceRecord rec = new SequenceRecord
{
Len = _len,
Pos = _pos,
Tag = LastTagRead,
Parent = _sqrs.Count > 0
? _sqrs.Peek().Current
: Dataset
};
_sqrs.Push(rec);
}
}
else
{
if (_remain < _len)
{
return(NeedMoreData(_len - _remain));
}
if ((LastTagRead.TagValue == DicomTags.PixelData) &&
Flags.IsSet(options, DicomReadOptions.DoNotStorePixelDataInDataSet))
{
// Skip PixelData !!
if (_stream.CanSeek)
{
_stream.Seek((int)_len, SeekOrigin.Current);
}
else
{
ConsumeStreamBytes(_stream, _len);
}
_remain -= _len;
BytesRead += _len;
}
else if ((LastTagRead.TagValue == DicomTags.PixelData) &&
Flags.IsSet(options, DicomReadOptions.StorePixelDataReferences))
{
var reference = new FileReference(StreamOpener, _stream.Position, _len, _endian, LastTagRead.VR);
if (_stream.CanSeek)
{
_stream.Seek((int)_len, SeekOrigin.Current);
}
else
{
ConsumeStreamBytes(_stream, _len);
}
DicomAttribute elem;
if (LastTagRead.VR.Equals(DicomVr.OWvr))
{
elem = new DicomAttributeOW(LastTagRead, reference);
}
else if (LastTagRead.VR.Equals(DicomVr.OBvr))
{
elem = new DicomAttributeOB(LastTagRead, reference);
}
else if (LastTagRead.VR.Equals(DicomVr.ODvr))
{
elem = new DicomAttributeOD(LastTagRead, reference);
}
else
{
elem = new DicomAttributeOF(LastTagRead, reference);
}
if (_sqrs.Count > 0)
{
SequenceRecord rec = _sqrs.Peek();
DicomAttributeCollection ds = rec.Current;
ds[LastTagRead] = elem;
if (rec.Curlen != _undefinedLength)
{
long end = rec.Curpos + rec.Curlen;
if (_stream.Position >= end)
{
rec.Current = null;
}
}
}
else
{
Dataset[LastTagRead] = elem;
}
_remain -= _len;
BytesRead += _len;
}
else
{
ByteBuffer bb = new ByteBuffer(_len);
// If the tag is impacted by specific character set,
// set the encoding properly.
if (LastTagRead.VR.SpecificCharacterSet)
{
if (_sqrs.Count > 0)
{
SequenceRecord rec = _sqrs.Peek();
bb.SpecificCharacterSet = rec.Current.SpecificCharacterSet;
}
else
{
bb.SpecificCharacterSet = Dataset.SpecificCharacterSet;
}
}
if (LastTagRead.VR.Equals(DicomVr.UNvr) &&
!SaveTagRead.VR.Equals(DicomVr.UNvr) &&
!SaveTagRead.VR.Equals(DicomVr.SQvr) &&
Flags.IsSet(options, DicomReadOptions.UseDictionaryForExplicitUN))
{
LastTagRead = SaveTagRead;
bb.Endian = Endian.Little;
}
else
{
bb.Endian = _endian;
}
bb.CopyFrom(_stream, (int)_len);
DicomAttribute elem = LastTagRead.CreateDicomAttribute(bb);
_remain -= _len;
BytesRead += _len;
if (_sqrs.Count > 0)
{
SequenceRecord rec = _sqrs.Peek();
DicomAttributeCollection ds = rec.Current;
if (elem.Tag.TagValue == DicomTags.SpecificCharacterSet)
{
ds.SpecificCharacterSet = elem.ToString();
}
if (LastTagRead.Element == 0x0000)
{
if (Flags.IsSet(options, DicomReadOptions.KeepGroupLengths))
{
ds[LastTagRead] = elem;
}
}
else
{
ds[LastTagRead] = elem;
}
if (rec.Curlen != _undefinedLength)
{
long end = rec.Curpos + rec.Curlen;
if (_stream.Position >= end)
{
rec.Current = null;
}
}
}
else
{
if (LastTagRead.TagValue == DicomTags.FileMetaInformationGroupLength)
{
// Save the end of the group 2 elements, so that we can automatically
// check and change our transfer syntax when needed.
_inGroup2 = true;
uint group2Len;
elem.TryGetUInt32(0, out group2Len);
_endGroup2 = BytesRead + group2Len;
}
else if (LastTagRead.TagValue == DicomTags.SpecificCharacterSet)
{
Dataset.SpecificCharacterSet = elem.ToString();
}
if (LastTagRead.Element == 0x0000)
{
if (Flags.IsSet(options, DicomReadOptions.KeepGroupLengths))
{
Dataset[LastTagRead] = elem;
}
}
else
{
Dataset[LastTagRead] = elem;
}
}
}
}
}
}
LastTagRead = null;
_vr = null;
_len = _undefinedLength;
}
return(DicomReadStatus.Success);
}
catch (EndOfStreamException e)
{
// should never happen
Platform.Log(LogLevel.Error, "Unexpected exception when reading file: {0}", e.ToString());
return(DicomReadStatus.UnknownError);
}
}
private DicomReadStatus InsertSequenceItem(DicomReadOptions options)
{
if (_tag.Equals(DicomTags.Item))
{
if (_len != UndefinedLength && _len > _remain)
{
return(NeedMoreData(_len));
}
if (_sds.Count > _sqs.Count)
{
_sds.Pop();
}
DcmItemSequenceItem si = new DcmItemSequenceItem(_pos, _len);
if (_len != UndefinedLength || (_stream.CanSeek && Flags.IsSet(options, DicomReadOptions.AllowSeekingForContext)))
{
if (_len == UndefinedLength)
{
options |= DicomReadOptions.SequenceItemOnly;
}
DcmDataset ds = null;
DicomReadStatus status = ParseSequenceItemDataset(TransferSyntax, _len, out ds, options);
if (status != DicomReadStatus.Success)
{
Dicom.Debug.Log.Warn("Unknown error while attempting to read sequence item. Trying again with alternate encodings.");
DicomTransferSyntax[] syntaxes = null;
if (TransferSyntax == DicomTransferSyntax.ExplicitVRBigEndian)
{
syntaxes = new DicomTransferSyntax[] { DicomTransferSyntax.ImplicitVRLittleEndian, DicomTransferSyntax.ExplicitVRLittleEndian }
}
;
else if (TransferSyntax.IsExplicitVR)
{
syntaxes = new DicomTransferSyntax[] { DicomTransferSyntax.ImplicitVRLittleEndian, DicomTransferSyntax.ExplicitVRBigEndian }
}
;
else
{
syntaxes = new DicomTransferSyntax[] { DicomTransferSyntax.ExplicitVRLittleEndian, DicomTransferSyntax.ExplicitVRBigEndian }
};
foreach (DicomTransferSyntax tx in syntaxes)
{
status = ParseSequenceItemDataset(tx, _len, out ds, options);
if (status == DicomReadStatus.Success)
{
break;
}
}
}
if (status != DicomReadStatus.Success)
{
return(DicomReadStatus.UnknownError);
}
si.Dataset = ds;
if (_len == UndefinedLength)
{
if (8 > _remain)
{
// need more data?
_sds.Push(ds);
}
else
{
// skip delimitation item
_stream.Seek(8, SeekOrigin.Current);
_remain -= 8;
_bytes += 8;
_read += 8;
}
}
}
else
{
DcmDataset ds = new DcmDataset(_pos + 8, _len, TransferSyntax);
_sds.Push(ds);
}
_sqs.Peek().AddSequenceItem(si);
}
else if (_tag == DicomTags.ItemDelimitationItem)
{
if (_sds.Count == _sqs.Count)
{
_sds.Pop();
}
}
else if (_tag == DicomTags.SequenceDelimitationItem)
{
if (_sds.Count == _sqs.Count)
{
_sds.Pop();
}
_sqs.Pop();
}
return(DicomReadStatus.Success);
}
/// <summary>
/// Read dataset from stream
/// </summary>
/// <param name="stopAtTag">End parsing at this tag</param>
/// <param name="options">DICOM read options</param>
/// <returns>Status code</returns>
public DicomReadStatus Read(DicomTag stopAtTag, DicomReadOptions options)
{
// Counters:
// _remain - bytes remaining in stream
// _bytes - estimates bytes to end of dataset
// _read - number of bytes read from stream
try {
_need = 0;
_remain = _stream.Length - _stream.Position;
while (_remain > 0)
{
DicomReadStatus status = ParseTag(stopAtTag, options);
if (status == DicomReadStatus.SuccessEndRead)
{
return(DicomReadStatus.Success);
}
if (status != DicomReadStatus.Success)
{
return(status);
}
status = ParseVR(options);
if (status != DicomReadStatus.Success)
{
return(status);
}
status = ParseLength(options);
if (status != DicomReadStatus.Success)
{
return(status);
}
if (_tag.IsPrivate)
{
if (_tag.Element != 0x0000 && _tag.Element <= 0x00ff)
{
// handle UN private creator id
if (_vr != DicomVR.LO && Flags.IsSet(options, DicomReadOptions.ForcePrivateCreatorToLO))
{
Dicom.Debug.Log.Warn("Converting Private Creator VR from '{0}' to 'LO'", _vr.VR);
_vr = DicomVR.LO;
}
}
}
if (_vr == DicomVR.UN && _syntax.IsExplicitVR && Flags.IsSet(options, DicomReadOptions.UseDictionaryForExplicitUN))
{
_vr = _tag.Entry.DefaultVR;
}
if (_fragment != null)
{
status = InsertFragmentItem(options);
if (status != DicomReadStatus.Success)
{
return(status);
}
}
else if (_sqs.Count > 0 &&
(_tag == DicomTags.Item ||
_tag == DicomTags.ItemDelimitationItem ||
_tag == DicomTags.SequenceDelimitationItem))
{
status = InsertSequenceItem(options);
if (status != DicomReadStatus.Success)
{
return(status);
}
}
else
{
if (_sqs.Count > 0)
{
DcmItemSequence sq = _sqs.Peek();
if (sq.StreamLength != UndefinedLength)
{
long end = sq.StreamPosition + 8 + sq.StreamLength;
if (_syntax.IsExplicitVR)
{
end += 2 + 2;
}
if ((_stream.Position - _offset) >= end)
{
if (_sds.Count == _sqs.Count)
{
_sds.Pop();
}
_sqs.Pop();
}
}
}
if (_len == UndefinedLength)
{
if (_vr == DicomVR.SQ)
{
DcmItemSequence sq = new DcmItemSequence(_tag, _pos, _len, _endian);
InsertDatasetItem(sq, options);
_sqs.Push(sq);
}
else
{
_fragment = new DcmFragmentSequence(_tag, _vr, _pos, _endian);
InsertDatasetItem(_fragment, options);
}
}
else
{
if (_vr == DicomVR.SQ)
{
DcmItemSequence sq = new DcmItemSequence(_tag, _pos, _len, _endian);
InsertDatasetItem(sq, options);
_sqs.Push(sq);
}
else
{
if (_len > _remain)
{
return(NeedMoreData(_len));
}
DcmElement elem = DcmElement.Create(_tag, _vr, _pos, _endian, CurrentBuffer(options));
_remain -= _len;
_read += _len;
InsertDatasetItem(elem, options);
}
}
}
_tag = null;
_vr = null;
_len = UndefinedLength;
}
return(DicomReadStatus.Success);
}
catch (EndOfStreamException) {
// should never happen
return(DicomReadStatus.UnknownError);
}
}
public DcmDimseInfo()
{
IsNewDimse = true;
ParseDatasetStatus = DicomReadStatus.NeedMoreData;
DatasetStopTag = null;
StreamMessage = false;
}
private void LoadCore(Stream stream, DicomStreamOpener streamOpener, DicomTag stopTag, DicomReadOptions options)
{
// TODO CR (24 Jan 2014): DICOM stream read only uses tag value, so the real implementation should be the uint overload!
if (stopTag == null)
{
stopTag = new DicomTag(0xFFFFFFFF, "Bogus Tag", "BogusTag", DicomVr.NONE, false, 1, 1, false);
}
DicomStreamReader dsr;
var iStream = stream ?? streamOpener.Open();
if (iStream.CanSeek)
{
iStream.Seek(128, SeekOrigin.Begin);
if (!FileHasPart10Header(iStream))
{
if (!Flags.IsSet(options, DicomReadOptions.ReadNonPart10Files))
{
throw new DicomException(String.Format("File is not part 10 format file: {0}", Filename));
}
iStream.Seek(0, SeekOrigin.Begin);
dsr = new DicomStreamReader(iStream)
{
StreamOpener = streamOpener,
TransferSyntax = TransferSyntax.ImplicitVrLittleEndian,
Dataset = DataSet
};
DicomReadStatus stat = dsr.Read(stopTag, options);
if (stat != DicomReadStatus.Success)
{
Platform.Log(LogLevel.Error, "Unexpected error when reading file: {0}", Filename);
throw new DicomException("Unexpected read error with file: " + Filename);
}
TransferSyntax = TransferSyntax.ImplicitVrLittleEndian;
if (DataSet.Contains(DicomTags.SopClassUid))
{
MediaStorageSopClassUid = DataSet[DicomTags.SopClassUid].ToString();
}
if (DataSet.Contains(DicomTags.SopInstanceUid))
{
MediaStorageSopInstanceUid = DataSet[DicomTags.SopInstanceUid].ToString();
}
Loaded = true;
return;
}
}
else
{
// TODO CR (04 Apr 2014): this code here is almost identical to the seekable stream above, except that we use the 4CC wrapper
// we can combine these two when we trust that the wrapper works in all cases
iStream = FourCcReadStream.Create(iStream);
// Read the 128 byte header first, then check for DICM
iStream.SeekEx(128, SeekOrigin.Begin);
if (!FileHasPart10Header(iStream))
{
if (!Flags.IsSet(options, DicomReadOptions.ReadNonPart10Files))
{
throw new DicomException(String.Format("File is not part 10 format file: {0}", Filename));
}
iStream.Seek(0, SeekOrigin.Begin);
dsr = new DicomStreamReader(iStream)
{
StreamOpener = streamOpener,
TransferSyntax = TransferSyntax.ImplicitVrLittleEndian,
Dataset = DataSet
};
DicomReadStatus stat = dsr.Read(stopTag, options);
if (stat != DicomReadStatus.Success)
{
Platform.Log(LogLevel.Error, "Unexpected error when reading file: {0}", Filename);
throw new DicomException("Unexpected read error with file: " + Filename);
}
TransferSyntax = TransferSyntax.ImplicitVrLittleEndian;
if (DataSet.Contains(DicomTags.SopClassUid))
{
MediaStorageSopClassUid = DataSet[DicomTags.SopClassUid].ToString();
}
if (DataSet.Contains(DicomTags.SopInstanceUid))
{
MediaStorageSopInstanceUid = DataSet[DicomTags.SopInstanceUid].ToString();
}
Loaded = true;
return;
}
}
dsr = new DicomStreamReader(iStream)
{
TransferSyntax = TransferSyntax.ExplicitVrLittleEndian,
StreamOpener = streamOpener,
Dataset = MetaInfo
};
DicomReadStatus readStat =
dsr.Read(new DicomTag(0x0002FFFF, "Bogus Tag", "BogusTag", DicomVr.UNvr, false, 1, 1, false), options);
if (readStat != DicomReadStatus.Success)
{
Platform.Log(LogLevel.Error, "Unexpected error when reading file Meta info for file: {0}", Filename);
throw new DicomException("Unexpected failure reading file Meta info for file: " + Filename);
}
MetaInfoFileLength = dsr.EndGroupTwo + 128 + 4;
dsr.Dataset = DataSet;
dsr.TransferSyntax = TransferSyntax;
readStat = dsr.Read(stopTag, options);
if (readStat != DicomReadStatus.Success)
{
Platform.Log(LogLevel.Error, "Unexpected error ({0}) when reading file at offset {2}: {1}", readStat, Filename, dsr.BytesRead);
throw new DicomException("Unexpected failure (" + readStat + ") reading file at offset " + dsr.BytesRead + ": " + Filename);
}
Loaded = true;
}
/// <summary>
/// Load a DICOM file from an input stream.
/// </summary>
/// <remarks>
/// Note: If the file does not contain DICM encoded in it, and
/// <see cref="Stream.CanSeek"/> is true for <paramref name="iStream"/>,
/// the routine will assume the file is not a Part 10 format file, and is
/// instead encoded as just a DataSet with the transfer syntax set to
/// Implicit VR Little Endian.
/// </remarks>
/// <param name="iStream">The input stream to read from.</param>
/// <param name="stopTag">The dicom tag to stop the reading at.</param>
/// <param name="options">The dicom read options to consider.</param>
public void Load(Stream iStream, DicomTag stopTag, DicomReadOptions options)
{
if (iStream == null)
{
throw new ArgumentNullException("iStream");
}
if (stopTag == null)
{
stopTag = new DicomTag(0xFFFFFFFF, "Bogus Tag", "BogusTag", DicomVr.NONE, false, 1, 1, false);
}
DicomStreamReader dsr;
if (iStream.CanSeek)
{
iStream.Seek(128, SeekOrigin.Begin);
if (!FileHasPart10Header(iStream))
{
if (!Flags.IsSet(options, DicomReadOptions.ReadNonPart10Files))
{
throw new DicomException(String.Format("File is not part 10 format file: {0}", Filename));
}
iStream.Seek(0, SeekOrigin.Begin);
dsr = new DicomStreamReader(iStream)
{
Filename = Filename,
TransferSyntax = TransferSyntax.ImplicitVrLittleEndian,
Dataset = DataSet
};
DicomReadStatus stat = dsr.Read(stopTag, options);
if (stat != DicomReadStatus.Success)
{
Platform.Log(LogLevel.Error, "Unexpected error when reading file: {0}", Filename);
throw new DicomException("Unexpected read error with file: " + Filename);
}
TransferSyntax = TransferSyntax.ImplicitVrLittleEndian;
if (DataSet.Contains(DicomTags.SopClassUid))
{
MediaStorageSopClassUid = DataSet[DicomTags.SopClassUid].ToString();
}
if (DataSet.Contains(DicomTags.SopInstanceUid))
{
MediaStorageSopInstanceUid = DataSet[DicomTags.SopInstanceUid].ToString();
}
return;
}
}
else
{
// Read the 128 byte header first, then check for DICM
iStream.Read(new byte[128], 0, 128);
if (!FileHasPart10Header(iStream))
{
Platform.Log(LogLevel.Error, "Reading DICOM file from stream, file does not have part 10 format header.");
throw new DicomException("File being read from stream is not a part 10 format file");
}
}
dsr = new DicomStreamReader(iStream)
{
TransferSyntax = TransferSyntax.ExplicitVrLittleEndian,
Filename = Filename,
Dataset = MetaInfo
};
DicomReadStatus readStat =
dsr.Read(new DicomTag(0x0002FFFF, "Bogus Tag", "BogusTag", DicomVr.UNvr, false, 1, 1, false), options);
if (readStat != DicomReadStatus.Success)
{
Platform.Log(LogLevel.Error, "Unexpected error when reading file Meta info for file: {0}", Filename);
throw new DicomException("Unexpected failure reading file Meta info for file: " + Filename);
}
dsr.Dataset = DataSet;
dsr.TransferSyntax = TransferSyntax;
readStat = dsr.Read(stopTag, options);
if (readStat != DicomReadStatus.Success)
{
Platform.Log(LogLevel.Error, "Unexpected error ({0}) when reading file at offset {2}: {1}", readStat, Filename, dsr.BytesRead);
throw new DicomException("Unexpected failure (" + readStat + ") reading file at offset " + dsr.BytesRead + ": " + Filename);
}
}
