/// <summary>
/// Method for adding a <see cref="DicomSequenceItem"/> to an attributes value.
/// </summary>
/// <param name="item">The <see cref="DicomSequenceItem"/> to add to the attribute.</param>
/// <remarks>
/// This method is value for <see cref="DicomAttributeSQ"/> attributes only.
/// </remarks>
public override void AddSequenceItem(DicomSequenceItem item)
{
if (_values == null)
{
_values = new DicomSequenceItem[1];
_values[0] = item;
}
else
{
DicomSequenceItem[] oldValues = _values;
_values = new DicomSequenceItem[oldValues.Length + 1];
oldValues.CopyTo(_values, 0);
_values[oldValues.Length] = item;
}
if (item.SpecificCharacterSet == null)
item.SpecificCharacterSet = ParentCollection.SpecificCharacterSet;
base.Count = _values.Length;
base.StreamLength = (uint)base.Count;
}
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
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(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, _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)
{
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,
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 (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);
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[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 !!
_stream.Seek((int) _len, SeekOrigin.Current);
_remain -= _len;
BytesRead += _len;
}
else if ((LastTagRead.TagValue == DicomTags.PixelData) &&
Flags.IsSet(options, DicomReadOptions.StorePixelDataReferences))
{
FileReference reference =
new FileReference(Filename, _stream.Position, _len, _endian,
LastTagRead.VR);
_stream.Seek((int) _len, SeekOrigin.Current);
if (LastTagRead.VR.Equals(DicomVr.OWvr))
{
DicomAttributeOW elem = new DicomAttributeOW(LastTagRead, reference);
Dataset[LastTagRead] = elem;
}
else if (LastTagRead.VR.Equals(DicomVr.OBvr))
{
DicomAttributeOB elem = new DicomAttributeOB(LastTagRead, reference);
Dataset[LastTagRead] = elem;
}
else
{
DicomAttributeOF elem = new DicomAttributeOF(LastTagRead, reference);
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;
}
}
/// <summary>
/// Initializes a new instance of the <see cref="VoiLutMacro"/> class.
/// </summary>
/// <param name="dicomSequenceItem">The dicom sequence item.</param>
public VoiLutMacro(DicomSequenceItem dicomSequenceItem) : base(dicomSequenceItem) {}
/// <summary>
/// Initializes a new instance of the <see cref="VoiLutSequenceItem"/> class.
/// </summary>
/// <param name="dicomSequenceItem">The dicom sequence item.</param>
public VoiLutSequenceItem(DicomSequenceItem dicomSequenceItem) : base(dicomSequenceItem) {}
/// <summary>
/// Method for adding a <see cref="DicomSequenceItem"/> to an attributes value.
/// </summary>
/// <remarks>
/// This method is value for <see cref="DicomAttributeSQ"/> attributes only.
/// </remarks>
/// <param name="item">The <see cref="DicomSequenceItem"/> to add to the attribute.</param>
public virtual void AddSequenceItem(DicomSequenceItem item)
{
throw new DicomException(SR.InvalidType);
}
/// <summary>
/// Update an <see cref="DicomAttributeCollection"/> with pixel data related tags.
/// </summary>
/// <param name="dataset">The collection to update.</param>
public override void UpdateAttributeCollection(DicomAttributeCollection dataset)
{
if (dataset.Contains(DicomTags.NumberOfFrames) || NumberOfFrames > 1)
dataset[DicomTags.NumberOfFrames].SetInt32(0, NumberOfFrames);
if (dataset.Contains(DicomTags.PlanarConfiguration))
dataset[DicomTags.PlanarConfiguration].SetInt32(0, PlanarConfiguration);
if (dataset.Contains(DicomTags.LossyImageCompression) || LossyImageCompression.Length > 0)
dataset[DicomTags.LossyImageCompression].SetString(0, LossyImageCompression);
if (dataset.Contains(DicomTags.LossyImageCompressionRatio) || (LossyImageCompressionRatio != 1.0f && LossyImageCompressionRatio != 0.0f))
dataset[DicomTags.LossyImageCompressionRatio].SetFloat32(0, LossyImageCompressionRatio);
if (dataset.Contains(DicomTags.LossyImageCompressionMethod) || LossyImageCompressionMethod.Length > 0)
dataset[DicomTags.LossyImageCompressionMethod].SetString(0, LossyImageCompressionMethod);
if (dataset.Contains(DicomTags.DerivationDescription) || DerivationDescription.Length > 0)
{
string currentValue = dataset[DicomTags.DerivationDescription].ToString();
dataset[DicomTags.DerivationDescription].SetStringValue(DerivationDescription);
if (!currentValue.Equals(DerivationDescription))
{
DicomSequenceItem item = new DicomSequenceItem();
CodeSequenceMacro macro = new CodeSequenceMacro(item);
macro.CodeMeaning = "Lossy Compression";
macro.CodeValue = "113040";
macro.CodingSchemeDesignator = "DCM";
macro.ContextGroupVersion = new DateTime(2005, 8, 22);
macro.ContextIdentifier = "7203";
macro.MappingResource = "DCMR";
dataset[DicomTags.DerivationCodeSequence].AddSequenceItem(item);
}
}
if (dataset.Contains(DicomTags.RescaleSlope) || DecimalRescaleSlope != 1.0M || DecimalRescaleIntercept != 0.0M)
dataset[DicomTags.RescaleSlope].SetString(0, RescaleSlope);
if (dataset.Contains(DicomTags.RescaleIntercept) || DecimalRescaleSlope != 1.0M || DecimalRescaleIntercept != 0.0M)
dataset[DicomTags.RescaleIntercept].SetString(0, RescaleIntercept);
if (dataset.Contains(DicomTags.WindowCenter) || LinearVoiLuts.Count > 0)
Window.SetWindowCenterAndWidth(dataset, LinearVoiLuts);
//Remove the palette color lut, if the pixels were translated to RGB
if (dataset.Contains(DicomTags.RedPaletteColorLookupTableData)
&& dataset.Contains(DicomTags.BluePaletteColorLookupTableData)
&& dataset.Contains(DicomTags.GreenPaletteColorLookupTableData)
&& !HasPaletteColorLut)
{
dataset.RemoveAttribute(DicomTags.BluePaletteColorLookupTableDescriptor);
dataset.RemoveAttribute(DicomTags.BluePaletteColorLookupTableData);
dataset.RemoveAttribute(DicomTags.RedPaletteColorLookupTableDescriptor);
dataset.RemoveAttribute(DicomTags.RedPaletteColorLookupTableData);
dataset.RemoveAttribute(DicomTags.GreenPaletteColorLookupTableDescriptor);
dataset.RemoveAttribute(DicomTags.GreenPaletteColorLookupTableData);
}
dataset.SaveDicomFields(this);
dataset[DicomTags.PixelData] = _sq;
}