public DicomAttribute this[DicomTag tag]
{
get
{
if (_attributes.ContainsKey(tag))
{
return(_attributes[tag]);
}
if (!_fieldMap.ContainsKey(tag))
{
return(null);
}
DicomAttribute attr = tag.CreateDicomAttribute();
object value = _fieldMap[tag].GetValue(_entity, null);
if (value != null)
{
attr.SetStringValue(value.ToString());
}
_attributes.Add(tag, attr);
return(attr);
}
set
{
if (_fieldMap[tag] != null)
{
_fieldMap[tag].SetValue(_entity, value.ToString(), null);
}
}
}
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
{
_need = 0;
_remain = _stream.Length - _stream.Position;
while (_remain > 0)
{
if (_inGroup2 && _read >= _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 (_tag == 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)
{
_tag = DicomTagDictionary.GetDicomTag(g, e);
if (_tag == null)
{
_tag =
new DicomTag((uint)g << 16 | e, "Private Tag", "PrivateTag", DicomVr.UNvr, false, 1, uint.MaxValue, false);
}
}
else
{
if (e == 0x0000)
{
_tag = new DicomTag((uint)g << 16 | e, "Group Length", "GroupLength", DicomVr.ULvr, false, 1, 1, false);
}
else
{
_tag = DicomTagDictionary.GetDicomTag(g, e);
if (_tag == null)
{
_tag =
new DicomTag((uint)g << 16 | e, "Private Tag", "PrivateTag", DicomVr.UNvr, false, 1, uint.MaxValue, false);
}
}
}
_remain -= 4;
_bytes += 4;
_read += 4;
}
else
{
tagValue = _tag.TagValue;
}
if ((tagValue >= stopAtTag.TagValue) &&
(_sqrs.Count == 0)) // only exit in root message when after stop tag
{
return(DicomReadStatus.Success);
}
if (_vr == null)
{
if (_syntax.ExplicitVr)
{
if (_tag == DicomTag.Item ||
_tag == DicomTag.ItemDelimitationItem ||
_tag == DicomTag.SequenceDelimitationItem)
{
_vr = DicomVr.NONE;
}
else
{
if (_remain < 2)
{
return(NeedMoreData(2));
}
string vr = new string(_reader.ReadChars(2));
_vr = DicomVr.GetVR(vr);
_remain -= 2;
_bytes += 2;
_read += 2;
if (_tag.VR.Equals(DicomVr.UNvr))
{
_tag = new DicomTag(_tag.TagValue, "Private Tag", "PrivateTag", _vr, false, 1, uint.MaxValue, false);
}
else if (!_tag.VR.Equals(_vr))
{
if (!vr.Equals(" "))
{
DicomTag tag =
new DicomTag(_tag.TagValue, _tag.Name, _tag.VariableName, _vr, _tag.MultiVR,
_tag.VMLow, _tag.VMHigh,
_tag.Retired);
_tag = tag;
; // TODO, log something
}
}
}
}
else
{
_vr = _tag.VR;
}
if (_vr == DicomVr.UNvr)
{
if (_tag.IsPrivate)
{
if (_tag.Element <= 0x00ff && _tag.Element >= 0x0010)
{
// Reset the tag with the right VR and a more descriptive name.
_tag = new DicomTag(_tag.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;
l = _reader.ReadUInt32();
if (l == UndefinedLength)
{
_vr = DicomVr.SQvr;
}
}
_stream.Position = pos;
}
}
else if (!_syntax.ExplicitVr || Flags.IsSet(options, DicomReadOptions.UseDictionaryForExplicitUN))
{
_vr = _tag.VR;
}
}
}
// Read the value length
if (_len == UndefinedLength)
{
if (_syntax.ExplicitVr)
{
if (_tag == DicomTag.Item ||
_tag == DicomTag.ItemDelimitationItem ||
_tag == DicomTag.SequenceDelimitationItem)
{
if (_remain < 4)
{
return(NeedMoreData(4));
}
_len = _reader.ReadUInt32();
_remain -= 4;
_bytes += 4;
_read += 4;
}
else
{
if (_vr.Is16BitLengthField)
{
if (_remain < 2)
{
return(NeedMoreData(2));
}
_len = _reader.ReadUInt16();
_remain -= 2;
_bytes += 2;
_read += 2;
}
else
{
if (_remain < 6)
{
return(NeedMoreData(6));
}
_reader.ReadByte();
_reader.ReadByte();
_len = _reader.ReadUInt32();
_remain -= 6;
_bytes += 6;
_read += 6;
}
}
}
else
{
if (_remain < 4)
{
return(NeedMoreData(4));
}
_len = _reader.ReadUInt32();
_remain -= 4;
_bytes += 4;
_read += 4;
}
if ((_len != UndefinedLength) &&
!_vr.Equals(DicomVr.SQvr) &&
!(_tag.Equals(DicomTag.Item) &&
_fragment == null))
{
_bytes += _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 ((_tag.IsPrivate) &&
(_vr.Equals(DicomVr.UNvr)) &&
(_tag.Element <= 0x00ff))
{
_vr = DicomVr.LOvr;
}
if (_fragment != null)
{
// In the middle of parsing pixels
if (_tag == DicomTag.Item)
{
if (_remain < _len)
{
return(NeedMoreData(_remain - _len));
}
if (Flags.IsSet(options, DicomReadOptions.StorePixelDataReferences) &&
_fragment.HasOffsetTable)
{
FileReference reference = new FileReference(Filename, _stream.Position, _len, _endian, DicomVr.OBvr);
DicomFragment fragment =
new DicomFragment(reference);
_fragment.AddFragment(fragment);
_stream.Seek(_len, SeekOrigin.Current);
}
else
{
ByteBuffer data = new ByteBuffer(_endian);
data.CopyFrom(_stream, (int)_len);
if (!_fragment.HasOffsetTable)
{
_fragment.SetOffsetTable(data);
}
else
{
DicomFragment fragment = new DicomFragment(data);
_fragment.AddFragment(fragment);
}
}
_remain -= _len;
_read += _len;
}
else if (_tag == DicomTag.SequenceDelimitationItem)
{
_dataset[_fragment.Tag] = _fragment;
_fragment = null;
}
else
{
Platform.Log(LogLevel.Error, "Encountered unexpected tag in stream: {0}", _tag.ToString());
// unexpected tag
return(DicomReadStatus.UnknownError);
}
}
else if (_sqrs.Count > 0 &&
(_tag == DicomTag.Item ||
_tag == DicomTag.ItemDelimitationItem ||
_tag == DicomTag.SequenceDelimitationItem))
{
SequenceRecord rec = _sqrs.Peek();
if (_tag.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();
dr.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);
data.CopyFrom(_stream, (int)_len);
_remain -= _len;
_read += _len;
DicomStreamReader idsr = new DicomStreamReader(data.Stream);
idsr.Dataset = ds;
if (rec._tag.VR.Equals(DicomVr.UNvr))
{
idsr.TransferSyntax = TransferSyntax.ImplicitVrLittleEndian;
}
else
{
idsr.TransferSyntax = _syntax;
}
idsr.Filename = Filename;
DicomReadStatus stat = idsr.Read(null, options);
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 (_tag == DicomTag.ItemDelimitationItem)
{
}
else if (_tag == 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;
if (_tag.IsPrivate)
{
_tag = new DicomTag(_tag.TagValue, "Private Tag", "PrivateTag", DicomVr.SQvr, false, 1, uint.MaxValue, false);
}
else
{
_tag = new DicomTag(_tag.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.",
_tag, _stream.Position);
return(DicomReadStatus.UnknownError);
}
}
if (_vr.Equals(DicomVr.SQvr))
{
SequenceRecord rec = new SequenceRecord();
if (_sqrs.Count > 0)
{
rec._parent = _sqrs.Peek()._current;
}
else
{
rec._parent = _dataset;
}
rec._current = null;
rec._tag = _tag;
rec._len = UndefinedLength;
_sqrs.Push(rec);
}
else
{
_fragment = new DicomFragmentSequence(_tag);
_dataset.LoadDicomFields(_fragment);
}
}
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[_tag].SetNullValue();
}
else
{
SequenceRecord rec = new SequenceRecord();
rec._len = _len;
rec._pos = _pos;
rec._tag = _tag;
if (_sqrs.Count > 0)
{
rec._parent = _sqrs.Peek()._current;
}
else
{
rec._parent = _dataset;
}
_sqrs.Push(rec);
}
}
else
{
if (_remain < _len)
{
return(NeedMoreData(_len - _remain));
}
if ((_tag.TagValue == DicomTags.PixelData) &&
Flags.IsSet(options, DicomReadOptions.DoNotStorePixelDataInDataSet))
{
// Skip PixelData !!
_stream.Seek((int)_len, SeekOrigin.Current);
_remain -= _len;
_read += _len;
}
else if ((_tag.TagValue == DicomTags.PixelData) &&
Flags.IsSet(options, DicomReadOptions.StorePixelDataReferences))
{
FileReference reference =
new FileReference(Filename, _stream.Position, _len, _endian,
_tag.VR);
_stream.Seek((int)_len, SeekOrigin.Current);
if (_tag.VR.Equals(DicomVr.OWvr))
{
DicomAttributeOW elem = new DicomAttributeOW(_tag, reference);
_dataset[_tag] = elem;
}
else if (_tag.VR.Equals(DicomVr.OBvr))
{
DicomAttributeOB elem = new DicomAttributeOB(_tag, reference);
_dataset[_tag] = elem;
}
else
{
DicomAttributeOF elem = new DicomAttributeOF(_tag, reference);
_dataset[_tag] = elem;
}
_remain -= _len;
_read += _len;
}
else
{
ByteBuffer bb = new ByteBuffer();
// If the tag is impacted by specific character set,
// set the encoding properly.
if (_tag.VR.SpecificCharacterSet)
{
if (_sqrs.Count > 0)
{
SequenceRecord rec = _sqrs.Peek();
bb.SpecificCharacterSet = rec._current.SpecificCharacterSet;
}
else
{
bb.SpecificCharacterSet = _dataset.SpecificCharacterSet;
}
}
bb.Endian = _endian;
bb.CopyFrom(_stream, (int)_len);
DicomAttribute elem = _tag.CreateDicomAttribute(bb);
_remain -= _len;
_read += _len;
if (_sqrs.Count > 0)
{
SequenceRecord rec = _sqrs.Peek();
DicomAttributeCollection ds = rec._current;
if (elem.Tag.TagValue == DicomTags.SpecificCharacterSet)
{
ds.SpecificCharacterSet = elem.ToString();
}
if (_tag.Element == 0x0000)
{
if (Flags.IsSet(options, DicomReadOptions.KeepGroupLengths))
{
ds[_tag] = elem;
}
}
else
{
ds[_tag] = elem;
}
if (rec._curlen != UndefinedLength)
{
long end = rec._curpos + rec._curlen;
if (_stream.Position >= end)
{
rec._current = null;
}
}
}
else
{
if (_tag.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 = _read + group2len;
}
else if (_tag.TagValue == DicomTags.SpecificCharacterSet)
{
_dataset.SpecificCharacterSet = elem.ToString();
}
if (_tag.Element == 0x0000)
{
if (Flags.IsSet(options, DicomReadOptions.KeepGroupLengths))
{
_dataset[_tag] = elem;
}
}
else
{
_dataset[_tag] = elem;
}
}
}
}
}
}
_tag = 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);
}
}