Example #1
0
            private static bool IsPrivateSequenceBad(IByteSource source, bool isExplicitVR)
            {
                source.Mark();

                try
                {
                    source.GetUInt16(); // group
                    source.GetUInt16(); // element
                    source.GetUInt32(); // length

                    source.GetUInt16(); // group
                    source.GetUInt16(); // element

                    var     bytes = source.GetBytes(2);
                    var     vr    = Encoding.UTF8.GetString(bytes, 0, bytes.Length);
                    DicomVR dummy;
                    if (DicomVR.TryParse(vr, out dummy))
                    {
                        return(!isExplicitVR);
                    }
                    // unable to parse VR
                    if (isExplicitVR)
                    {
                        return(true);
                    }
                }
                finally
                {
                    source.Rewind();
                }

                return(false);
            }
Example #2
0
            private bool ParseItemSequenceTag(IByteSource source)
            {
                if (this.parseStage == ParseStage.Tag)
                {
                    source.Mark();

                    if (!source.Require(8))
                    {
                        this.result = DicomReaderResult.Suspended;
                        return(false);
                    }

                    var group   = source.GetUInt16();
                    var element = source.GetUInt16();

                    this._tag = new DicomTag(@group, element);

                    if (this._tag != DicomTag.Item && this._tag != DicomTag.SequenceDelimitationItem)
                    {
                        // assume invalid sequence
                        source.Rewind();
                        if (!this._implicit)
                        {
                            source.PopMilestone();
                        }
                        this.observer.OnEndSequence();
                        if (this.badPrivateSequence)
                        {
                            this.isExplicitVR       = !this.isExplicitVR;
                            this.badPrivateSequence = false;
                        }
                        return(false);
                    }

                    this.length = source.GetUInt32();

                    if (this._tag == DicomTag.SequenceDelimitationItem)
                    {
                        // #64, in case explicit length has been specified despite occurrence of Sequence Delimitation Item
                        if (source.HasReachedMilestone() && source.MilestonesCount > this.sequenceDepth)
                        {
                            this.ResetState();
                            return(true);
                        }

                        // end of sequence
                        this.observer.OnEndSequence();
                        if (this.badPrivateSequence)
                        {
                            this.isExplicitVR       = !this.isExplicitVR;
                            this.badPrivateSequence = false;
                        }
                        this.ResetState();
                        return(false);
                    }

                    this.parseStage = ParseStage.Value;
                }
                return(true);
            }
        private bool IsPrivateSequenceBad(IByteSource source)
        {
            source.Mark();

            try {
                var group   = source.GetUInt16();
                var element = source.GetUInt16();
                var tag     = new DicomTag(group, element);
                var length  = source.GetUInt32();

                group   = source.GetUInt16();
                element = source.GetUInt16();
                tag     = new DicomTag(group, element);

                byte[]  bytes = source.GetBytes(2);
                string  vr    = Encoding.UTF8.GetString(bytes, 0, bytes.Length);
                DicomVR dummy;
                if (DicomVR.TryParse(vr, out dummy))
                {
                    return(!_explicit);
                }
                // unable to parse VR
                if (_explicit)
                {
                    return(true);
                }
            } finally {
                source.Rewind();
            }

            return(false);
        }
Example #4
0
            private static bool IsPrivateSequenceBad(IByteSource source, bool isExplicitVR)
            {
                source.Mark();

                try
                {
                    // Skip "item" tags; continue skipping until length is non-zero (#223)
                    while (new DicomTag(source.GetUInt16(), source.GetUInt16()) == DicomTag.Item // group, element
                           & source.GetUInt32() == 0)                                            // length (using & instead of && enforces RHS to be evaluated regardless of LHS)
                    {
                    }

                    source.GetUInt16(); // group
                    source.GetUInt16(); // element

                    var     bytes = source.GetBytes(2);
                    var     vr    = Encoding.UTF8.GetString(bytes, 0, bytes.Length);
                    DicomVR dummy;
                    if (DicomVR.TryParse(vr, out dummy))
                    {
                        return(!isExplicitVR);
                    }
                    // unable to parse VR
                    if (isExplicitVR)
                    {
                        return(true);
                    }
                }
                finally
                {
                    source.Rewind();
                }

                return(false);
            }
Example #5
0
            private static bool IsPrivateSequenceBad(IByteSource source, uint count, bool isExplicitVR)
            {
                source.Mark();

                try
                {
                    // Skip "item" tags; continue skipping until length is non-zero (#223)
                    // Using & instead of && enforces RHS to be evaluated regardless of LHS
                    uint length;
                    while (source.GetUInt16() == DicomTag.Item.Group &
                           source.GetUInt16() == DicomTag.Item.Element &
                           (length = source.GetUInt32()) < uint.MaxValue)   // Dummy condition to ensure that length is included in parsing
                    {
                        // Length non-zero, end skipping (#223)
                        if (length > 0)
                        {
                            break;
                        }

                        // Handle scenario where last tag is private sequence with empty items (#487)
                        count -= 8;
                        if (count <= 0)
                        {
                            return(false);
                        }
                    }

                    source.GetUInt16(); // group
                    source.GetUInt16(); // element

                    var     bytes = source.GetBytes(2);
                    var     vr    = Encoding.UTF8.GetString(bytes, 0, bytes.Length);
                    DicomVR dummy;
                    if (DicomVR.TryParse(vr, out dummy))
                    {
                        return(!isExplicitVR);
                    }
                    // unable to parse VR
                    if (isExplicitVR)
                    {
                        return(true);
                    }
                }
                finally
                {
                    source.Rewind();
                }

                return(false);
            }
Example #6
0
            private bool ParseFragmentSequenceTag(IByteSource source)
            {
                if (_parseStage == ParseStage.Tag)
                {
                    source.Mark();

                    if (!source.Require(8))
                    {
                        _result = DicomReaderResult.Suspended;
                        return(false);
                    }

                    var group   = source.GetUInt16();
                    var element = source.GetUInt16();

                    var tag = new DicomTag(@group, element);

                    if (tag != DicomTag.Item && tag != DicomTag.SequenceDelimitationItem)
                    {
                        throw new DicomReaderException($"Unexpected tag in DICOM fragment sequence: {tag}");
                    }

                    _length = source.GetUInt32();

                    if (tag == DicomTag.SequenceDelimitationItem)
                    {
                        // end of fragment
                        _observer.OnEndFragmentSequence();
                        _fragmentItem = 0;
                        ResetState();
                        return(false);
                    }

                    _fragmentItem++;
                    _parseStage = ParseStage.Value;
                }
                return(true);
            }
        private void ParseFragmentSequence(IByteSource source, object state)
        {
            try {
                _result = DicomReaderResult.Processing;

                while (!source.IsEOF)
                {
                    if (_state == ParseState.Tag)
                    {
                        source.Mark();

                        if (!source.Require(8, ParseFragmentSequence, state))
                        {
                            _result = DicomReaderResult.Suspended;
                            return;
                        }

                        ushort group   = source.GetUInt16();
                        ushort element = source.GetUInt16();

                        DicomTag tag = new DicomTag(group, element);

                        if (tag != DicomTag.Item && tag != DicomTag.SequenceDelimitationItem)
                        {
                            throw new DicomReaderException("Unexpected tag in DICOM fragment sequence: {0}", tag);
                        }

                        _length = source.GetUInt32();

                        if (tag == DicomTag.SequenceDelimitationItem)
                        {
                            // end of fragment
                            _observer.OnEndFragmentSequence();
                            _fragmentItem = 0;
                            ResetState();
                            ParseDataset(source, PopState());
                            return;
                        }

                        _fragmentItem++;
                        _state = ParseState.Value;
                    }

                    if (_state == ParseState.Value)
                    {
                        if (!source.Require(_length, ParseFragmentSequence, state))
                        {
                            _result = DicomReaderResult.Suspended;
                            return;
                        }

                        IByteBuffer buffer = source.GetBuffer(_length);
                        if (_fragmentItem == 1)
                        {
                            buffer = EndianByteBuffer.Create(buffer, source.Endian, 4);
                        }
                        else
                        {
                            buffer = EndianByteBuffer.Create(buffer, source.Endian, _vr.UnitSize);
                        }
                        _observer.OnFragmentSequenceItem(source, buffer);

                        _state = ParseState.Tag;
                    }
                }
            } catch (Exception e) {
                _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() && _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 ParseItemSequence(IByteSource source, object state)
        {
            try {
                _result = DicomReaderResult.Processing;

                while (!source.IsEOF && !source.HasReachedMilestone())
                {
                    if (_state == ParseState.Tag)
                    {
                        source.Mark();

                        if (!source.Require(8, ParseItemSequence, state))
                        {
                            _result = DicomReaderResult.Suspended;
                            return;
                        }

                        ushort group   = source.GetUInt16();
                        ushort element = source.GetUInt16();

                        _tag = new DicomTag(group, element);

                        if (_tag != DicomTag.Item && _tag != DicomTag.SequenceDelimitationItem)
                        {
                            // assume invalid sequence
                            source.Rewind();
                            if (!_implicit)
                            {
                                source.PopMilestone();
                            }
                            _observer.OnEndSequence();
                            if (_badPrivateSequence)
                            {
                                _explicit           = !_explicit;
                                _badPrivateSequence = false;
                            }
                            return;
                        }

                        _length = source.GetUInt32();

                        if (_tag == DicomTag.SequenceDelimitationItem)
                        {
                            // end of sequence
                            _observer.OnEndSequence();
                            if (_badPrivateSequence)
                            {
                                _explicit           = !_explicit;
                                _badPrivateSequence = false;
                            }
                            ResetState();
                            return;
                        }

                        _state = ParseState.Value;
                    }

                    if (_state == ParseState.Value)
                    {
                        if (_length != UndefinedLength)
                        {
                            if (!source.Require(_length, ParseItemSequence, state))
                            {
                                _result = DicomReaderResult.Suspended;
                                return;
                            }

                            source.PushMilestone(_length);
                        }

                        _observer.OnBeginSequenceItem(source, _length);

                        ResetState();
                        ParseDataset(source, state);
                        ResetState();

                        _observer.OnEndSequenceItem();
                        continue;
                    }
                }

                // end of explicit length sequence
                if (source.HasReachedMilestone())
                {
                    source.PopMilestone();
                }

                _observer.OnEndSequence();
                if (_badPrivateSequence)
                {
                    _explicit           = !_explicit;
                    _badPrivateSequence = false;
                }
            } catch (Exception e) {
                _exception = e;
                _result    = DicomReaderResult.Error;
            } finally {
                if (_result != DicomReaderResult.Processing && _result != DicomReaderResult.Suspended)
                {
                    _async.Set();
                }
            }
        }
Example #10
0
            private static bool IsPrivateSequenceBad(IByteSource source, bool isExplicitVR)
            {
                source.Mark();

                try
                {
                    // Skip "item" tags; continue skipping until length is non-zero (#223)
                    while (new DicomTag(source.GetUInt16(), source.GetUInt16()) == DicomTag.Item    // group, element
                           & source.GetUInt32() == 0)   // length (using & instead of && enforces RHS to be evaluated regardless of LHS)
                    {
                    }

                    source.GetUInt16(); // group
                    source.GetUInt16(); // element

                    var bytes = source.GetBytes(2);
                    var vr = Encoding.UTF8.GetString(bytes, 0, bytes.Length);
                    DicomVR dummy;
                    if (DicomVR.TryParse(vr, out dummy)) return !isExplicitVR;
                    // unable to parse VR
                    if (isExplicitVR) return true;
                }
                finally
                {
                    source.Rewind();
                }

                return false;
            }
Example #11
0
		private void ParseFragmentSequence(IByteSource source, object state) {
			try {
				_result = DicomReaderResult.Processing;

				while (!source.IsEOF) {
					if (_state == ParseState.Tag) {
						source.Mark();

						if (!source.Require(8, ParseFragmentSequence, state)) {
							_result = DicomReaderResult.Suspended;
							return;
						}

						ushort group = source.GetUInt16();
						ushort element = source.GetUInt16();

						DicomTag tag = new DicomTag(group, element);

						if (tag != DicomTag.Item && tag != DicomTag.SequenceDelimitationItem)
							throw new DicomReaderException("Unexpected tag in DICOM fragment sequence: {0}", tag);

						_length = source.GetUInt32();

						if (tag == DicomTag.SequenceDelimitationItem) {
							// end of fragment
							_observer.OnEndFragmentSequence();
							_fragmentItem = 0;
							ResetState();
							ParseDataset(source, PopState());
							return;
						}

						_fragmentItem++;
						_state = ParseState.Value;
					}

					if (_state == ParseState.Value) {
						if (!source.Require(_length, ParseFragmentSequence, state)) {
							_result = DicomReaderResult.Suspended;
							return;
						}

						IByteBuffer buffer = source.GetBuffer(_length);
						if (_fragmentItem == 1)
							buffer = EndianByteBuffer.Create(buffer, source.Endian, 4);
						else
							buffer = EndianByteBuffer.Create(buffer, source.Endian, _vr.UnitSize);
						_observer.OnFragmentSequenceItem(source, buffer);

						_state = ParseState.Tag;
					}
				}
			} catch (Exception e) {
				_exception = e;
				_result = DicomReaderResult.Error;
			} finally {
				if (_result != DicomReaderResult.Processing && _result != DicomReaderResult.Suspended) {
					_async.Set();
				}
			}
		}
Example #12
0
		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);

						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);
							try {
								_vr = DicomVR.Parse(vr);
							} catch {
								// unable to parse VR
								_vr = DicomVR.UN;
							}
						} else {
							DicomDictionaryEntry entry = Dictionary[_tag];
							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
						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);
							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);

						// 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();
				}
			}
		}
Example #13
0
		private void ParseItemSequence(IByteSource source, object state) {
			try {
				_result = DicomReaderResult.Processing;

				while (!source.IsEOF && !source.HasReachedMilestone()) {
					if (_state == ParseState.Tag) {
						source.Mark();

						if (!source.Require(8, ParseItemSequence, state)) {
							_result = DicomReaderResult.Suspended;
							return;
						}

						ushort group = source.GetUInt16();
						ushort element = source.GetUInt16();

						_tag = new DicomTag(group, element);

						if (_tag != DicomTag.Item && _tag != DicomTag.SequenceDelimitationItem) {
							// assume invalid sequence
							source.Rewind();
							if (!_implicit)
								source.PopMilestone();
							_observer.OnEndSequence();
							if (_badPrivateSequence) {
								_explicit = !_explicit;
								_badPrivateSequence = false;
							}
							return;
						}

						_length = source.GetUInt32();

						if (_tag == DicomTag.SequenceDelimitationItem) {
							// end of sequence
							_observer.OnEndSequence();
							if (_badPrivateSequence) {
								_explicit = !_explicit;
								_badPrivateSequence = false;
							}
							ResetState();
							return;
						}

						_state = ParseState.Value;
					}

					if (_state == ParseState.Value) {
						if (_length != UndefinedLength) {
							if (!source.Require(_length, ParseItemSequence, state)) {
								_result = DicomReaderResult.Suspended;
								return;
							}

							source.PushMilestone(_length);
						}

						_observer.OnBeginSequenceItem(source, _length);

						ResetState();
						ParseDataset(source, state);
						ResetState();

						_observer.OnEndSequenceItem();
						continue;
					}
				}

				// end of explicit length sequence
				if (source.HasReachedMilestone())
					source.PopMilestone();

				_observer.OnEndSequence();
				if (_badPrivateSequence) {
					_explicit = !_explicit;
					_badPrivateSequence = false;
				}
			} catch (Exception e) {
				_exception = e;
				_result = DicomReaderResult.Error;
			} finally {
				if (_result != DicomReaderResult.Processing && _result != DicomReaderResult.Suspended) {
					_async.Set();
				}
			}
		}
Example #14
0
		private bool IsPrivateSequenceBad(IByteSource source) {
			source.Mark();

			try {
				var group = source.GetUInt16();
				var element = source.GetUInt16();
				var tag = new DicomTag(group, element);
				var length = source.GetUInt32();

				group = source.GetUInt16();
				element = source.GetUInt16();
				tag = new DicomTag(group, element);

				byte[] bytes = source.GetBytes(2);
				string vr = Encoding.UTF8.GetString(bytes, 0, bytes.Length);
				try {
					DicomVR.Parse(vr);
					return !_explicit;
				} catch {
					// unable to parse VR
					if (_explicit)
						return true;
				}
			} finally {
				source.Rewind();
			}

			return false;
		}
Example #15
0
            private bool ParseLength(IByteSource source)
            {
                while (_parseStage == ParseStage.Length)
                {
                    if (_tag == DicomTag.Item || _tag == DicomTag.ItemDelimitationItem ||
                        _tag == DicomTag.SequenceDelimitationItem)
                    {
                        if (!source.Require(4))
                        {
                            _result = DicomReaderResult.Suspended;
                            return(false);
                        }

                        _length = source.GetUInt32();

                        _parseStage = ParseStage.Value;
                        break;
                    }

                    if (_isExplicitVR || _badPrivateSequence)
                    {
                        if (_vr == DicomVR.Implicit)
                        {
                            if (!source.Require(4))
                            {
                                _result = DicomReaderResult.Suspended;
                                return(false);
                            }

                            _length = source.GetUInt32();

                            // assume that undefined length in implicit VR element is SQ
                            if (_length == _undefinedLength)
                            {
                                _vr = DicomVR.SQ;
                            }
                        }
                        else if (_vr.Is16bitLength)
                        {
                            if (!source.Require(2))
                            {
                                _result = DicomReaderResult.Suspended;
                                return(false);
                            }

                            _length = source.GetUInt16();
                        }
                        else
                        {
                            if (!source.Require(6))
                            {
                                _result = DicomReaderResult.Suspended;
                                return(false);
                            }

                            source.Skip(2);
                            _length = source.GetUInt32();

                            // CP-246 (#177) handling
                            // assume that Undefined Length in explicit datasets with VR UN are sequences
                            // According to CP-246 the sequence shall be handled as ILE, but this will be handled later...
                            // in the current code this needs to be restricted to privates
                            if (_length == _undefinedLength && _vr == DicomVR.UN && _tag.IsPrivate)
                            {
                                _vr = DicomVR.SQ;
                            }
                        }
                    }
                    else
                    {
                        if (!source.Require(4))
                        {
                            _result = DicomReaderResult.Suspended;
                            return(false);
                        }

                        _length = source.GetUInt32();

                        // assume that undefined length in implicit dataset is SQ
                        if (_length == _undefinedLength && _vr == DicomVR.UN)
                        {
                            _vr = DicomVR.SQ;
                        }
                    }

                    _parseStage = ParseStage.Value;
                }
                return(true);
            }
Example #16
0
            private bool ParseItemSequenceTag(IByteSource source)
            {
                if (_parseStage == ParseStage.Tag)
                {
                    source.Mark();

                    if (!source.Require(8))
                    {
                        _result = DicomReaderResult.Suspended;
                        return(false);
                    }

                    var group   = source.GetUInt16();
                    var element = source.GetUInt16();

                    _tag = new DicomTag(@group, element);

                    if (_tag != DicomTag.Item && _tag != DicomTag.SequenceDelimitationItem)
                    {
                        // assume invalid sequence
                        source.Rewind();
                        if (!_implicit)
                        {
                            source.PopMilestone();
                        }
                        _observer.OnEndSequence();
                        // #565 Only reset the badPrivate sequence if we're in the correct depth
                        // This prevents prematurely resetting in case of sub-sequences contained in the bad private sequence
                        if (_badPrivateSequence && _sequenceDepth == _badPrivateSequenceDepth)
                        {
                            _isExplicitVR       = !_isExplicitVR;
                            _badPrivateSequence = false;
                        }
                        return(false);
                    }

                    _length = source.GetUInt32();

                    if (_tag == DicomTag.SequenceDelimitationItem)
                    {
                        // #64, in case explicit length has been specified despite occurrence of Sequence Delimitation Item
                        if (source.HasReachedMilestone() && source.MilestonesCount > _sequenceDepth)
                        {
                            ResetState();
                            return(true);
                        }

                        // end of sequence
                        _observer.OnEndSequence();
                        // #565 Only reset the badPrivate sequence if we're in the correct depth
                        // This prevents prematurely resetting in case of sub-sequences contained in the bad private sequence
                        if (_badPrivateSequence && _sequenceDepth == _badPrivateSequenceDepth)
                        {
                            _isExplicitVR       = !_isExplicitVR;
                            _badPrivateSequence = false;
                        }
                        ResetState();
                        return(false);
                    }

                    _parseStage = ParseStage.Value;
                }
                return(true);
            }
Example #17
0
        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();
                }
            }
        }
Example #18
0
            private bool ParseFragmentSequenceTag(IByteSource source)
            {
                if (this.parseStage == ParseStage.Tag)
                {
                    source.Mark();

                    if (!source.Require(8))
                    {
                        this.result = DicomReaderResult.Suspended;
                        return false;
                    }

                    var group = source.GetUInt16();
                    var element = source.GetUInt16();

                    DicomTag tag = new DicomTag(@group, element);

                    if (tag != DicomTag.Item && tag != DicomTag.SequenceDelimitationItem)
                    {
                        throw new DicomReaderException("Unexpected tag in DICOM fragment sequence: {0}", tag);
                    }

                    this.length = source.GetUInt32();

                    if (tag == DicomTag.SequenceDelimitationItem)
                    {
                        // end of fragment
                        this.observer.OnEndFragmentSequence();
                        this.fragmentItem = 0;
                        this.ResetState();
                        return false;
                    }

                    this.fragmentItem++;
                    this.parseStage = ParseStage.Value;
                }
                return true;
            }
Example #19
0
            private bool ParseItemSequenceTag(IByteSource source)
            {
                if (this.parseStage == ParseStage.Tag)
                {
                    source.Mark();

                    if (!source.Require(8))
                    {
                        this.result = DicomReaderResult.Suspended;
                        return false;
                    }

                    var group = source.GetUInt16();
                    var element = source.GetUInt16();

                    this._tag = new DicomTag(@group, element);

                    if (this._tag != DicomTag.Item && this._tag != DicomTag.SequenceDelimitationItem)
                    {
                        // assume invalid sequence
                        source.Rewind();
                        if (!this._implicit)
                        {
                            source.PopMilestone();
                        }
                        this.observer.OnEndSequence();
                        if (this.badPrivateSequence)
                        {
                            this.isExplicitVR = !this.isExplicitVR;
                            this.badPrivateSequence = false;
                        }
                        return false;
                    }

                    this.length = source.GetUInt32();

                    if (this._tag == DicomTag.SequenceDelimitationItem)
                    {
                        // #64, in case explicit length has been specified despite occurrence of Sequence Delimitation Item
                        if (source.HasReachedMilestone() && source.MilestonesCount > this.sequenceDepth)
                        {
                            this.ResetState();
                            return true;
                        }

                        // end of sequence
                        this.observer.OnEndSequence();
                        if (this.badPrivateSequence)
                        {
                            this.isExplicitVR = !this.isExplicitVR;
                            this.badPrivateSequence = false;
                        }
                        this.ResetState();
                        return false;
                    }

                    this.parseStage = ParseStage.Value;
                }
                return true;
            }
Example #20
0
            private bool ParseLength(IByteSource source)
            {
                while (this.parseStage == ParseStage.Length)
                {
                    if (this._tag == DicomTag.Item || this._tag == DicomTag.ItemDelimitationItem
                        || this._tag == DicomTag.SequenceDelimitationItem)
                    {
                        if (!source.Require(4))
                        {
                            this.result = DicomReaderResult.Suspended;
                            return false;
                        }

                        this.length = source.GetUInt32();

                        this.parseStage = ParseStage.Value;
                        break;
                    }

                    if (this.isExplicitVR)
                    {
                        if (this._vr == DicomVR.Implicit)
                        {
                            if (!source.Require(4))
                            {
                                this.result = DicomReaderResult.Suspended;
                                return false;
                            }

                            this.length = source.GetUInt32();

                            // assume that undefined length in implicit VR element is SQ
                            if (this.length == UndefinedLength)
                            {
                                this._vr = DicomVR.SQ;
                            }
                        }
                        else if (this._vr.Is16bitLength)
                        {
                            if (!source.Require(2))
                            {
                                this.result = DicomReaderResult.Suspended;
                                return false;
                            }

                            this.length = source.GetUInt16();
                        }
                        else
                        {
                            if (!source.Require(6))
                            {
                                this.result = DicomReaderResult.Suspended;
                                return false;
                            }

                            source.Skip(2);
                            this.length = source.GetUInt32();

                            // CP-246 (#177) handling
                            // assume that Undefined Length in explicit datasets with VR UN are sequences 
                            // According to CP-246 the sequence shall be handled as ILE, but this will be handled later...
                            // in the current code this needs to be restricted to privates 
                            if (this.length == UndefinedLength && this._vr == DicomVR.UN && this._tag.IsPrivate)
                            {
                                this._vr = DicomVR.SQ;
                            }
                        }
                    }
                    else
                    {
                        if (!source.Require(4))
                        {
                            this.result = DicomReaderResult.Suspended;
                            return false;
                        }

                        this.length = source.GetUInt32();

                        // assume that undefined length in implicit dataset is SQ
                        if (this.length == UndefinedLength && this._vr == DicomVR.UN)
                        {
                            this._vr = DicomVR.SQ;
                        }
                    }

                    this.parseStage = ParseStage.Value;
                }
                return true;
            }
Example #21
0
            private static bool IsPrivateSequenceBad(IByteSource source, bool isExplicitVR)
            {
                source.Mark();

                try
                {
                    source.GetUInt16(); // group
                    source.GetUInt16(); // element
                    source.GetUInt32(); // length

                    source.GetUInt16(); // group
                    source.GetUInt16(); // element

                    var bytes = source.GetBytes(2);
                    var vr = Encoding.UTF8.GetString(bytes, 0, bytes.Length);
                    DicomVR dummy;
                    if (DicomVR.TryParse(vr, out dummy)) return !isExplicitVR;
                    // unable to parse VR
                    if (isExplicitVR) return true;
                }
                finally
                {
                    source.Rewind();
                }

                return false;
            }