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(); } } }