public override DcmItem Clone()
{
DcmFragmentSequence sq = new DcmFragmentSequence(Tag, VR, StreamPosition, Endian);
sq.SetOffsetTable(OffsetTable);
foreach (ByteBuffer fragment in Fragments)
{
sq.AddFragment(fragment.Clone());
}
return(sq);
}
private static void SaveFragmentOffsetTable(XElement item, DcmFragmentSequence seq)
{
if (item.Value == String.Empty)
{
return;
}
string[] strs = item.FirstText().Split('\\');
foreach (string s in strs)
{
seq.OffsetTable.Add(uint.Parse(s, NumberStyles.HexNumber, CultureInfo.InvariantCulture));
}
}
private static void LoadSequence(XElement parent, IList <DcmItem> items, XDicomOptions options)
{
foreach (DcmItem item in items)
{
if (!Flags.IsSet(options, XDicomOptions.IncludePixelData) && item.Tag == DicomTags.PixelData)
{
continue;
}
XElement attr = new XElement("attr");
attr.SetAttributeValue("tag", item.Tag.Card.ToString("x8"));
attr.SetAttributeValue("vr", item.VR.VR);
if (item is DcmItemSequence)
{
DcmItemSequence seq = (DcmItemSequence)item;
attr.SetAttributeValue("len", -1);
foreach (DcmItemSequenceItem si in seq.SequenceItems)
{
XElement itm = new XElement("item");
LoadSequence(itm, si.Dataset.Elements, options);
attr.Add(itm);
}
}
else if (item is DcmFragmentSequence)
{
DcmFragmentSequence seq = (DcmFragmentSequence)item;
attr.SetAttributeValue("len", -1);
LoadFragmentOffsetTable(attr, seq);
foreach (ByteBuffer fi in seq.Fragments)
{
LoadFragmentItem(attr, seq.VR, fi);
}
}
else
{
DcmElement element = (DcmElement)item;
attr.SetAttributeValue("len", element.Length);
attr.Add(element.GetValueString());
}
if (Flags.IsSet(options, XDicomOptions.Comments))
{
parent.Add(new XComment(item.Tag.Entry.Name));
}
parent.Add(attr);
}
}
public void AddFrame(byte[] data)
{
_frames++;
if (IsFragmented)
{
DcmFragmentSequence sequence = PixelDataSequence;
uint offset = 0;
foreach (ByteBuffer fragment in sequence.Fragments)
{
offset += (uint)(8 + fragment.Length);
}
sequence.OffsetTable.Add(offset);
int pos = 0;
while (pos < data.Length)
{
int count = (int)Math.Min(FragmentSize, (uint)(data.Length - pos));
ByteBuffer buffer = new ByteBuffer();
buffer.Append(data, pos, count);
if ((buffer.Length % 2) != 0)
{
buffer.Append(new byte[1], 0, 1);
}
sequence.Fragments.Add(buffer);
pos += count;
}
}
else
{
if (BytesAllocated > 1 && TransferSyntax.Endian != Endian.LocalMachine)
{
Endian.SwapBytes(BytesAllocated, data);
}
else if (BytesAllocated == 1 && PixelDataItem.VR == DicomVR.OW && TransferSyntax.Endian == Endian.Big)
{
Endian.SwapBytes(2, data);
}
long pos = UncompressedFrameSize * (NumberOfFrames - 1);
PixelDataElement.ByteBuffer.Stream.Seek(pos, System.IO.SeekOrigin.Begin);
PixelDataElement.ByteBuffer.Stream.Write(data, 0, data.Length);
if ((PixelDataElement.ByteBuffer.Length % 2) != 0)
{
PixelDataElement.ByteBuffer.Stream.Write(new byte[1], 0, 1);
}
}
}
private static void LoadFragmentOffsetTable(XElement parent, DcmFragmentSequence seq) {
if (seq.HasOffsetTable) {
XElement item = new XElement("item");
item.SetAttributeValue("len", seq.OffsetTable.Count * 4);
StringBuilder sb = new StringBuilder();
foreach (uint offset in seq.OffsetTable) {
sb.AppendFormat("{0:X8}\\", offset);
}
item.Add(sb.ToString().TrimEnd('\\'));
parent.Add(item);
}
else {
XElement item = new XElement("item");
item.SetAttributeValue("len", 0);
parent.Add(item);
}
}
private static void Save(XElement parent, DcmDataset dataset)
{
foreach (XElement attr in parent.Elements("attr"))
{
DicomTag tag = DicomTag.Parse(attr.Attribute("tag").Value);
DicomVR vr = DicomVR.Lookup(attr.Attribute("vr").Value);
int len = int.Parse(attr.Attribute("len").Value, CultureInfo.InvariantCulture);
if (vr == DicomVR.SQ)
{
DcmItemSequence seq = new DcmItemSequence(tag);
foreach (XElement itm in attr.Elements("item"))
{
DcmItemSequenceItem item = new DcmItemSequenceItem();
Save(itm, item.Dataset);
seq.AddSequenceItem(item);
}
dataset.AddItem(seq);
}
else if (len == -1)
{
DcmFragmentSequence seq = new DcmFragmentSequence(tag, vr);
bool first = true;
foreach (XElement itm in attr.Elements("item"))
{
if (first)
{
SaveFragmentOffsetTable(itm, seq);
first = false;
}
else
{
SaveFragmentItem(itm, seq);
}
}
dataset.AddItem(seq);
}
else
{
DcmElement element = DcmElement.Create(tag, vr);
element.SetValueString(attr.FirstText());
dataset.AddItem(element);
}
}
}
private static void LoadFragmentOffsetTable(XElement parent, DcmFragmentSequence seq)
{
if (seq.HasOffsetTable)
{
XElement item = new XElement("item");
item.SetAttributeValue("len", seq.OffsetTable.Count * 4);
StringBuilder sb = new StringBuilder();
foreach (uint offset in seq.OffsetTable)
{
sb.AppendFormat("{0:X8}\\", offset);
}
item.Add(sb.ToString().TrimEnd('\\'));
parent.Add(item);
}
else
{
XElement item = new XElement("item");
item.SetAttributeValue("len", 0);
parent.Add(item);
}
}
private static void SaveFragmentItem(XElement item, DcmFragmentSequence seq)
{
ByteBuffer bb = new ByteBuffer();
string[] strs = item.FirstText().Split('\\');
if (seq.VR == DicomVR.OW)
{
foreach (string s in strs)
{
bb.Writer.Write(ushort.Parse(s, NumberStyles.HexNumber, CultureInfo.InvariantCulture));
}
}
else
{
foreach (string s in strs)
{
bb.Writer.Write(byte.Parse(s, NumberStyles.HexNumber, CultureInfo.InvariantCulture));
}
}
seq.AddFragment(bb);
}
public List <ByteBuffer> GetFrameFragments(int frame)
{
if (frame < 0 || frame >= NumberOfFrames)
{
throw new IndexOutOfRangeException("Requested frame out of range!");
}
if (!IsFragmented)
{
throw new InvalidOperationException("No fragmented pixel data!");
}
List <ByteBuffer> fragments = new List <ByteBuffer>();
DcmFragmentSequence sequence = PixelDataSequence;
int fragmentCount = sequence.Fragments.Count;
if (NumberOfFrames == 1)
{
fragments.AddRange(sequence.Fragments);
return(fragments);
}
if (fragmentCount == NumberOfFrames)
{
fragments.Add(sequence.Fragments[frame]);
return(fragments);
}
if (sequence.HasOffsetTable && sequence.OffsetTable.Count == NumberOfFrames)
{
uint offset = sequence.OffsetTable[frame];
uint stop = 0xffffffff;
uint pos = 0;
if ((frame + 1) < NumberOfFrames)
{
stop = sequence.OffsetTable[frame + 1];
}
int i = 0;
while (pos < offset && i < fragmentCount)
{
pos += (uint)(8 + sequence.Fragments[i].Length);
i++;
}
// check for invalid offset table
if (pos != offset)
{
goto GUESS_FRAME_OFFSET;
}
while (offset < stop && i < fragmentCount)
{
fragments.Add(sequence.Fragments[i]);
offset += (uint)(8 + sequence.Fragments[i].Length);
i++;
}
return(fragments);
}
GUESS_FRAME_OFFSET:
if (sequence.Fragments.Count > 0)
{
int fragmentSize = sequence.Fragments[0].Length;
bool allSameLength = true;
for (int i = 0; i < fragmentCount; i++)
{
if (sequence.Fragments[i].Length != fragmentSize)
{
allSameLength = false;
break;
}
}
if (allSameLength)
{
if ((fragmentCount % NumberOfFrames) != 0)
{
throw new DicomDataException("Unable to determine frame length from pixel data sequence!");
}
int count = fragmentCount / NumberOfFrames;
int start = frame * count;
for (int i = 0; i < fragmentCount; i++)
{
fragments.Add(sequence.Fragments[i]);
}
return(fragments);
}
else
{
// what if a single frame ends on a fragment boundary?
int count = 0;
int start = 0;
for (int i = 0; i < fragmentCount && count < frame; i++, start++)
{
if (sequence.Fragments[i].Length != fragmentSize)
{
count++;
}
}
for (int i = start; i < fragmentCount; i++)
{
fragments.Add(sequence.Fragments[i]);
if (sequence.Fragments[i].Length != fragmentSize)
{
break;
}
}
return(fragments);
}
}
return(fragments);
}
private DicomReadStatus InsertFragmentItem(DicomReadOptions options)
{
if (_tag == DicomTags.Item) {
if (_len > _remain)
return NeedMoreData(_len);
ByteBuffer data = CurrentBuffer(options);
_remain -= _len;
_read += _len;
if (!_fragment.HasOffsetTable)
_fragment.SetOffsetTable(data);
else
_fragment.AddFragment(data);
}
else if (_tag == DicomTags.SequenceDelimitationItem) {
_fragment = null;
}
else {
// unexpected tag
return DicomReadStatus.UnknownError;
}
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 override DcmItem Clone()
{
DcmFragmentSequence sq = new DcmFragmentSequence(Tag, VR, StreamPosition, Endian);
sq.SetOffsetTable(OffsetTable);
foreach (ByteBuffer fragment in Fragments)
{
sq.AddFragment(fragment.Clone());
}
return sq;
}
private static void SaveFragmentOffsetTable(XElement item, DcmFragmentSequence seq)
{
if (item.Value == String.Empty)
return;
string[] strs = item.FirstText().Split('\\');
foreach (string s in strs)
{
seq.OffsetTable.Add(uint.Parse(s, NumberStyles.HexNumber, CultureInfo.InvariantCulture));
}
}
private static void SaveFragmentItem(XElement item, DcmFragmentSequence seq)
{
ByteBuffer bb = new ByteBuffer();
string[] strs = item.FirstText().Split('\\');
if (seq.VR == DicomVR.OW)
{
foreach (string s in strs)
{
bb.Writer.Write(ushort.Parse(s, NumberStyles.HexNumber, CultureInfo.InvariantCulture));
}
}
else
{
foreach (string s in strs)
{
bb.Writer.Write(byte.Parse(s, NumberStyles.HexNumber, CultureInfo.InvariantCulture));
}
}
seq.AddFragment(bb);
}
private static void Save(XElement parent, DcmDataset dataset)
{
foreach (XElement attr in parent.Elements("attr"))
{
DicomTag tag = DicomTag.Parse(attr.Attribute("tag").Value);
DicomVR vr = DicomVR.Lookup(attr.Attribute("vr").Value);
int len = int.Parse(attr.Attribute("len").Value, CultureInfo.InvariantCulture);
if (vr == DicomVR.SQ)
{
DcmItemSequence seq = new DcmItemSequence(tag);
foreach (XElement itm in attr.Elements("item"))
{
DcmItemSequenceItem item = new DcmItemSequenceItem();
Save(itm, item.Dataset);
seq.AddSequenceItem(item);
}
dataset.AddItem(seq);
}
else if (len == -1)
{
DcmFragmentSequence seq = new DcmFragmentSequence(tag, vr);
bool first = true;
foreach (XElement itm in attr.Elements("item"))
{
if (first)
{
SaveFragmentOffsetTable(itm, seq);
first = false;
}
else
{
SaveFragmentItem(itm, seq);
}
}
dataset.AddItem(seq);
}
else
{
DcmElement element = DcmElement.Create(tag, vr);
element.SetValueString(attr.FirstText());
dataset.AddItem(element);
}
}
}