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);
}
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);
}
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);
}
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);
}
public void ExportBytes(IByteSource editvar)
{
var dlg = new SaveFileDialog();
var bytes = editvar.GetBytes();
dlg.Filter = string.Join("|", ImportExportUtility.GetPossibleExtensions(bytes, (CVariable)editvar));
dlg.InitialDirectory = MainController.Get().Configuration.InitialExportDirectory;
if (dlg.ShowDialog() == DialogResult.OK)
{
MainController.Get().Configuration.InitialExportDirectory = Path.GetDirectoryName(dlg.FileName);
using (var fs = new FileStream(dlg.FileName, FileMode.Create, FileAccess.Write))
using (var writer = new BinaryWriter(fs))
{
bytes = ImportExportUtility.GetExportBytes(bytes, Path.GetExtension(dlg.FileName), (CVariable)editvar);
writer.Write(bytes);
MainController.LogString(
$"{((CVariable) editvar).GetFullDependencyStringName()} succesfully exported to {dlg.FileName}",
Logtype.Success);
}
}
}
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 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();
}
}
}
public SimpleByteSource(IByteSource source)
{
_bytes = source.GetBytes();
}
private static void Preprocess(
IByteSource source,
ref DicomFileFormat fileFormat,
ref DicomTransferSyntax syntax)
{
// 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)
{
fileFormat = @group == 0x0002
? DicomFileFormat.DICOM3NoPreamble
: DicomFileFormat.DICOM3NoFileMetaInfo;
}
var element = source.GetUInt16();
var tag = new DicomTag(@group, element);
// test for explicit VR
var vrt = Encoding.UTF8.GetBytes(tag.DictionaryEntry.ValueRepresentations[0].Code);
var vrs = source.GetBytes(2);
if (vrt[0] != vrs[0] || vrt[1] != vrs[1])
{
// implicit VR
syntax = syntax.Endian == Endian.Little
? DicomTransferSyntax.ImplicitVRLittleEndian
: DicomTransferSyntax.ImplicitVRBigEndian;
}
source.Rewind();
}while (fileFormat == DicomFileFormat.Unknown);
if (fileFormat == DicomFileFormat.Unknown)
{
throw new DicomReaderException("Attempted to read invalid DICOM file");
}
// Adopt transfer syntax endianess to byte source.
source.Endian = syntax.Endian;
}
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;
}
private bool ParseVR(IByteSource source)
{
while (this.parseStage == ParseStage.VR)
{
if (this._tag == DicomTag.Item || this._tag == DicomTag.ItemDelimitationItem
|| this._tag == DicomTag.SequenceDelimitationItem)
{
this._vr = DicomVR.NONE;
this.parseStage = ParseStage.Length;
break;
}
if (this.isExplicitVR)
{
if (!source.Require(2))
{
this.result = DicomReaderResult.Suspended;
return false;
}
source.Mark();
var bytes = source.GetBytes(2);
var vr = Encoding.UTF8.GetString(bytes, 0, bytes.Length);
if (string.IsNullOrWhiteSpace(vr))
{
if (this._entry != null)
{
this._vr = this._entry.ValueRepresentations.FirstOrDefault();
}
}
else if (!DicomVR.TryParse(vr, out this._vr))
{
// unable to parse VR; rewind VR bytes for continued attempt to interpret the data.
this._vr = DicomVR.Implicit;
source.Rewind();
}
}
else
{
if (this._entry != null)
{
if (this._entry == DicomDictionary.UnknownTag)
{
this._vr = DicomVR.UN;
}
else if (this._entry.ValueRepresentations.Contains(DicomVR.OB)
&& this._entry.ValueRepresentations.Contains(DicomVR.OW))
{
this._vr = DicomVR.OW; // ???
}
else
{
this._vr = this._entry.ValueRepresentations.FirstOrDefault();
}
}
}
if (this._vr == null)
{
this._vr = DicomVR.UN;
}
this.parseStage = ParseStage.Length;
if (this._vr == DicomVR.UN)
{
if (this._tag.Element == 0x0000)
{
// Group Length to UL
this._vr = DicomVR.UL;
break;
}
if (this.isExplicitVR)
{
break;
}
}
if (this._tag.IsPrivate)
{
if (this._tag.Element != 0x0000 && this._tag.Element <= 0x00ff && this._vr == DicomVR.UN)
{
this._vr = DicomVR.LO; // force private creator to LO
}
}
}
return true;
}
private bool ParseVR(IByteSource source)
{
while (_parseStage == ParseStage.VR)
{
if (_tag == DicomTag.Item || _tag == DicomTag.ItemDelimitationItem ||
_tag == DicomTag.SequenceDelimitationItem)
{
_vr = DicomVR.NONE;
_parseStage = ParseStage.Length;
break;
}
if (_isExplicitVR || _badPrivateSequence)
{
if (!source.Require(2))
{
_result = DicomReaderResult.Suspended;
return(false);
}
source.Mark();
var bytes = source.GetBytes(2);
var vr = Encoding.UTF8.GetString(bytes, 0, bytes.Length);
if (string.IsNullOrEmpty(vr.Trim()))
{
if (_entry != null)
{
_vr = _entry.ValueRepresentations.FirstOrDefault();
}
}
else if (!DicomVR.TryParse(vr, out _vr))
{
// unable to parse VR; rewind VR bytes for continued attempt to interpret the data.
_vr = DicomVR.Implicit;
source.Rewind();
}
}
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;
}
_parseStage = ParseStage.Length;
if (_vr == DicomVR.UN)
{
if (_tag.Element == 0x0000)
{
// Group Length to UL
// change 20161216: if changing from UN to UL then ParseLength causes a error, since length in UL is 2 bytes while length in UN is 6 bytes.
// so the source hat UN and coded the length in 6 bytes. if here the VR was changed to UL then ParseLength would only read 2 bytes and the parser is then wrong.
// but no worry: in ParseValue in the first lines there is a lookup in the Dictionary of DicomTags and there the VR is changed to UL so that the value is finally interpreted correctly as UL.
// _vr = DicomVR.UL;
break;
}
if (_isExplicitVR)
{
break;
}
}
if (_tag.IsPrivate)
{
// according to
// http://dicom.nema.org/medical/dicom/current/output/chtml/part05/sect_7.8.html
// Private Creator Data Elements numbered (gggg,0010-00FF) (gggg is odd)
// The VR of the private identification code shall be LO (Long String) and the VM shall be equal to 1.
if (_tag.Element >= 0x0010 && _tag.Element <= 0x00ff && _vr == DicomVR.UN)
{
_vr = DicomVR.LO; // force private creator to LO
}
}
}
return(true);
}
private static void Preprocess(
IByteSource source,
ref DicomFileFormat fileFormat,
ref DicomTransferSyntax syntax)
{
// 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)
{
fileFormat = @group == 0x0002
? DicomFileFormat.DICOM3NoPreamble
: DicomFileFormat.DICOM3NoFileMetaInfo;
}
var element = source.GetUInt16();
var tag = new DicomTag(@group, element);
// test for explicit VR
var vrt = Encoding.UTF8.GetBytes(tag.DictionaryEntry.ValueRepresentations[0].Code);
var vrs = source.GetBytes(2);
if (vrt[0] != vrs[0] || vrt[1] != vrs[1])
{
// implicit VR
syntax = syntax.Endian == Endian.Little
? DicomTransferSyntax.ImplicitVRLittleEndian
: DicomTransferSyntax.ImplicitVRBigEndian;
}
source.Rewind();
}
while (fileFormat == DicomFileFormat.Unknown);
if (fileFormat == DicomFileFormat.Unknown)
{
throw new DicomReaderException("Attempted to read invalid DICOM file");
}
// Adopt transfer syntax endianess to byte source.
source.Endian = syntax.Endian;
}
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;
}
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();
}
}
}
private bool ParseVR(IByteSource source)
{
while (this.parseStage == ParseStage.VR)
{
if (this._tag == DicomTag.Item || this._tag == DicomTag.ItemDelimitationItem ||
this._tag == DicomTag.SequenceDelimitationItem)
{
this._vr = DicomVR.NONE;
this.parseStage = ParseStage.Length;
break;
}
if (this.isExplicitVR)
{
if (!source.Require(2))
{
this.result = DicomReaderResult.Suspended;
return(false);
}
source.Mark();
var bytes = source.GetBytes(2);
var vr = Encoding.UTF8.GetString(bytes, 0, bytes.Length);
if (string.IsNullOrWhiteSpace(vr))
{
if (this._entry != null)
{
this._vr = this._entry.ValueRepresentations.FirstOrDefault();
}
}
else if (!DicomVR.TryParse(vr, out this._vr))
{
// unable to parse VR; rewind VR bytes for continued attempt to interpret the data.
this._vr = DicomVR.Implicit;
source.Rewind();
}
}
else
{
if (this._entry != null)
{
if (this._entry == DicomDictionary.UnknownTag)
{
this._vr = DicomVR.UN;
}
else if (this._entry.ValueRepresentations.Contains(DicomVR.OB) &&
this._entry.ValueRepresentations.Contains(DicomVR.OW))
{
this._vr = DicomVR.OW; // ???
}
else
{
this._vr = this._entry.ValueRepresentations.FirstOrDefault();
}
}
}
if (this._vr == null)
{
this._vr = DicomVR.UN;
}
this.parseStage = ParseStage.Length;
if (this._vr == DicomVR.UN)
{
if (this._tag.Element == 0x0000)
{
// Group Length to UL
this._vr = DicomVR.UL;
break;
}
if (this.isExplicitVR)
{
break;
}
}
if (this._tag.IsPrivate)
{
if (this._tag.Element != 0x0000 && this._tag.Element <= 0x00ff && this._vr == DicomVR.UN)
{
this._vr = DicomVR.LO; // force private creator to LO
}
}
}
return(true);
}
private bool ParseVR(IByteSource source)
{
while (this.parseStage == ParseStage.VR)
{
if (this._tag == DicomTag.Item || this._tag == DicomTag.ItemDelimitationItem ||
this._tag == DicomTag.SequenceDelimitationItem)
{
this._vr = DicomVR.NONE;
this.parseStage = ParseStage.Length;
break;
}
if (this.isExplicitVR || this.badPrivateSequence)
{
if (!source.Require(2))
{
this.result = DicomReaderResult.Suspended;
return(false);
}
source.Mark();
var bytes = source.GetBytes(2);
var vr = Encoding.UTF8.GetString(bytes, 0, bytes.Length);
if (string.IsNullOrEmpty(vr.Trim()))
{
if (this._entry != null)
{
this._vr = this._entry.ValueRepresentations.FirstOrDefault();
}
}
else if (!DicomVR.TryParse(vr, out this._vr))
{
// unable to parse VR; rewind VR bytes for continued attempt to interpret the data.
this._vr = DicomVR.Implicit;
source.Rewind();
}
}
else
{
if (this._entry != null)
{
if (this._entry == DicomDictionary.UnknownTag)
{
this._vr = DicomVR.UN;
}
else if (this._entry.ValueRepresentations.Contains(DicomVR.OB) &&
this._entry.ValueRepresentations.Contains(DicomVR.OW))
{
this._vr = DicomVR.OW; // ???
}
else
{
this._vr = this._entry.ValueRepresentations.FirstOrDefault();
}
}
}
if (this._vr == null)
{
this._vr = DicomVR.UN;
}
this.parseStage = ParseStage.Length;
if (this._vr == DicomVR.UN)
{
if (this._tag.Element == 0x0000)
{
// Group Length to UL
// change 20161216: if changing from UN to UL then ParseLength causes a error, since length in UL is 2 bytes while length in UN is 6 bytes.
// so the source hat UN and coded the length in 6 bytes. if here the VR was changed to UL then ParseLength would only read 2 bytes and the parser is then wrong.
// but no worry: in ParseValue in the first lines there is a lookup in the Dictionary of DicomTags and there the VR is changed to UL so that the value is finally interpreted correctly as UL.
// this._vr = DicomVR.UL;
break;
}
if (this.isExplicitVR)
{
break;
}
}
if (this._tag.IsPrivate)
{
if (this._tag.Element != 0x0000 && this._tag.Element <= 0x00ff && this._vr == DicomVR.UN)
{
this._vr = DicomVR.LO; // force private creator to LO
}
}
}
return(true);
}
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;
}
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();
}
}
}