public void SetupRequiredMathMrtData(DicomTypes.RequiredMathMrtData data, uint rows, uint columns, uint frames, byte[] pixelArray)
{
dicomFile.DataSet[DicomTags.SliceThickness].SetStringValue(data.SliceThickness);
dicomFile.DataSet[DicomTags.SpacingBetweenSlices].SetStringValue(data.SpacingBetweenSlices);
dicomFile.DataSet[DicomTags.ImagePositionPatient].SetString(0, data.ImagePositionPatient0);
dicomFile.DataSet[DicomTags.ImagePositionPatient].SetString(1, data.ImagePositionPatient1);
dicomFile.DataSet[DicomTags.ImagePositionPatient].SetString(2, data.ImagePositionPatient2);
dicomFile.DataSet[DicomTags.ImageOrientationPatient].SetString(0, data.ImageOrientationPatient0);
dicomFile.DataSet[DicomTags.ImageOrientationPatient].SetString(1, data.ImageOrientationPatient1);
dicomFile.DataSet[DicomTags.ImageOrientationPatient].SetString(2, data.ImageOrientationPatient2);
dicomFile.DataSet[DicomTags.ImageOrientationPatient].SetString(3, data.ImageOrientationPatient3);
dicomFile.DataSet[DicomTags.ImageOrientationPatient].SetString(4, data.ImageOrientationPatient4);
dicomFile.DataSet[DicomTags.ImageOrientationPatient].SetString(5, data.ImageOrientationPatient5);
dicomFile.DataSet[DicomTags.SamplesPerPixel].SetStringValue(data.SamplesPerPixel);
dicomFile.DataSet[DicomTags.Rows].SetUInt32(0, rows);
dicomFile.DataSet[DicomTags.Columns].SetUInt32(0, columns);
dicomFile.DataSet[DicomTags.PixelSpacing].SetString(0, data.PixelSpacing0);
dicomFile.DataSet[DicomTags.PixelSpacing].SetString(1, data.PixelSpacing1);
dicomFile.DataSet[DicomTags.PixelRepresentation].SetStringValue(data.PixelRepresentation);
dicomFile.DataSet[DicomTags.BitsAllocated].SetStringValue(data.BitsAllocated);
dicomFile.DataSet[DicomTags.BitsStored].SetStringValue(data.BitsStored);
dicomFile.DataSet[DicomTags.HighBit].SetStringValue(data.HighBit);
uint length = rows * columns * frames;
if (length % 2 == 1)
{
length++;
}
DicomAttributeOW pixels = new DicomAttributeOW(DicomTags.PixelData);
pixelArray[length - 1] = 0x00;
pixels.Values = pixelArray;
dicomFile.DataSet[DicomTags.PixelData] = pixels;
}
public DicomReadStatus Read(DicomTag stopAtTag, DicomReadOptions options)
{
if (stopAtTag == null)
{
stopAtTag = new DicomTag(0xFFFFFFFF, "Bogus Tag", "BogusTag", DicomVr.UNvr, false, 1, 1, false);
}
// Counters:
// _remain - bytes remaining in stream
// _bytes - estimates bytes to end of dataset
// _read - number of bytes read from stream
try
{
BytesNeeded = 0;
_remain = _stream.Length - _stream.Position;
while (_remain > 0)
{
if (_inGroup2 && BytesRead >= _endGroup2)
{
_inGroup2 = false;
// Only change if we're still reading the meta info
if (Dataset.StartTagValue < DicomTags.TransferSyntaxUid)
{
TransferSyntax group2Syntax =
TransferSyntax.GetTransferSyntax(
Dataset[DicomTags.TransferSyntaxUid].GetString(0, String.Empty));
if (group2Syntax == null)
{
throw new DicomException("Unsupported transfer syntax in group 2 elements");
}
TransferSyntax = group2Syntax;
}
}
uint tagValue;
if (LastTagRead == null)
{
if (_remain < 4)
{
return(NeedMoreData(4));
}
_pos = _stream.Position;
ushort g = _reader.ReadUInt16();
ushort e = _reader.ReadUInt16();
tagValue = DicomTag.GetTagValue(g, e);
if (DicomTag.IsPrivateGroup(g) && e > 0x00ff)
{
SaveTagRead = LastTagRead = DicomTagDictionary.GetDicomTag(g, e) ??
new DicomTag((uint)g << 16 | e, "Private Tag", "PrivateTag", DicomVr.UNvr, false, 1, uint.MaxValue, false);
}
else
{
if (e == 0x0000)
{
SaveTagRead = LastTagRead = new DicomTag((uint)g << 16 | e, "Group Length", "GroupLength", DicomVr.ULvr, false, 1, 1, false);
}
else
{
SaveTagRead = LastTagRead = DicomTagDictionary.GetDicomTag(g, e) ??
new DicomTag((uint)g << 16 | e, "Private Tag", "PrivateTag", DicomVr.UNvr, false, 1, uint.MaxValue, false);
}
}
_remain -= 4;
BytesEstimated += 4;
BytesRead += 4;
}
else
{
tagValue = LastTagRead.TagValue;
}
if ((tagValue >= stopAtTag.TagValue) &&
(_sqrs.Count == 0)) // only exit in root message when after stop tag
{
if (_inGroup2 && tagValue > 0x0002FFFF)
{
if (_endGroup2 != BytesRead - 4)
{
Platform.Log(LogLevel.Debug, "File Meta Info Length, {0}, not equal to actual bytes read in file, {1}, overwriting length.",
EndGroupTwo, BytesRead - 4);
_endGroup2 = BytesRead - 4;
}
_inGroup2 = false;
}
EncounteredStopTag = true;
return(DicomReadStatus.Success);
}
bool twoByteLength;
if (_vr == null)
{
if (_syntax.ExplicitVr)
{
if (LastTagRead == DicomTag.Item ||
LastTagRead == DicomTag.ItemDelimitationItem ||
LastTagRead == DicomTag.SequenceDelimitationItem)
{
_vr = DicomVr.NONE;
twoByteLength = _vr.Is16BitLengthField;
}
else
{
if (_remain < 2)
{
return(NeedMoreData(2));
}
string vr = new string(_reader.ReadChars(2));
_vr = DicomVr.GetVR(vr);
twoByteLength = _vr.Is16BitLengthField;
_remain -= 2;
BytesEstimated += 2;
BytesRead += 2;
if (LastTagRead.VR.Equals(DicomVr.UNvr))
{
LastTagRead = new DicomTag(LastTagRead.TagValue, "Private Tag", "PrivateTag", _vr, false, 1, uint.MaxValue, false);
if (vr.Equals("??"))
{
twoByteLength = true;
}
}
else if (!LastTagRead.VR.Equals(_vr))
{
if (!vr.Equals(" "))
{
DicomTag tag =
new DicomTag(LastTagRead.TagValue, LastTagRead.Name, LastTagRead.VariableName, _vr, LastTagRead.MultiVR,
LastTagRead.VMLow, LastTagRead.VMHigh,
LastTagRead.Retired);
LastTagRead = tag;
; // TODO, log something
}
}
}
}
else
{
_vr = LastTagRead.VR;
twoByteLength = _vr.Is16BitLengthField;
}
if (_vr == DicomVr.UNvr)
{
if (LastTagRead.IsPrivate)
{
if (LastTagRead.Element <= 0x00ff && LastTagRead.Element >= 0x0010)
{
// Reset the tag with the right VR and a more descriptive name.
LastTagRead = new DicomTag(LastTagRead.TagValue, "Private Creator Code", "PrivateCreatorCode", DicomVr.LOvr, false, 1, uint.MaxValue, false);
// private creator id
// Only set the VR to LO for Implicit VR, if we do it for
// Explicit VR syntaxes, we would incorrectly read the tag
// length below.
if (!_syntax.ExplicitVr)
{
_vr = DicomVr.LOvr;
}
}
else if (_stream.CanSeek && Flags.IsSet(options, DicomReadOptions.AllowSeekingForContext))
{
// attempt to identify private sequence by checking if the tag has
// an undefined length
long pos = _stream.Position;
int bytesToCheck = _syntax.ExplicitVr ? 6 : 4;
if (_remain >= bytesToCheck)
{
if (_syntax.ExplicitVr)
{
_reader.ReadUInt16();
}
uint l = _reader.ReadUInt32();
if (l == _undefinedLength)
{
_vr = DicomVr.SQvr;
}
}
_stream.Position = pos;
}
}
}
}
else
{
twoByteLength = _vr.Is16BitLengthField;
}
// Read the value length
if (_len == _undefinedLength)
{
if (_syntax.ExplicitVr)
{
if (LastTagRead == DicomTag.Item ||
LastTagRead == DicomTag.ItemDelimitationItem ||
LastTagRead == DicomTag.SequenceDelimitationItem)
{
if (_remain < 4)
{
return(NeedMoreData(4));
}
_len = _reader.ReadUInt32();
_remain -= 4;
BytesEstimated += 4;
BytesRead += 4;
}
else
{
if (twoByteLength)
{
if (_remain < 2)
{
return(NeedMoreData(2));
}
_len = _reader.ReadUInt16();
_remain -= 2;
BytesEstimated += 2;
BytesRead += 2;
}
else
{
if (_remain < 6)
{
return(NeedMoreData(6));
}
_reader.ReadByte();
_reader.ReadByte();
_len = _reader.ReadUInt32();
_remain -= 6;
BytesEstimated += 6;
BytesRead += 6;
}
}
}
else
{
if (_remain < 4)
{
return(NeedMoreData(4));
}
_len = _reader.ReadUInt32();
_remain -= 4;
BytesEstimated += 4;
BytesRead += 4;
}
if ((_len != _undefinedLength) &&
!_vr.Equals(DicomVr.SQvr) &&
!(LastTagRead.Equals(DicomTag.Item) &&
_fragment == null))
{
BytesEstimated += _len;
}
}
// If we have a private creator code, set the VR to LO, because
// that is what it is. We must do this after we read the length
// so that the 32 bit length is read properly.
if ((LastTagRead.IsPrivate) &&
(_vr.Equals(DicomVr.UNvr)) &&
(LastTagRead.Element <= 0x00ff))
{
_vr = DicomVr.LOvr;
}
if (_fragment != null)
{
// In the middle of parsing pixels
if (LastTagRead == DicomTag.Item)
{
if (_remain < _len)
{
return(NeedMoreData(_remain - _len));
}
if (Flags.IsSet(options, DicomReadOptions.StorePixelDataReferences) &&
_fragment.HasOffsetTable)
{
FileReference reference = new FileReference(StreamOpener, _stream.Position, _len, _endian, DicomVr.OBvr);
DicomFragment fragment = new DicomFragment(reference);
_fragment.AddFragment(fragment);
if (_stream.CanSeek)
{
_stream.Seek(_len, SeekOrigin.Current);
}
else
{
ConsumeStreamBytes(_stream, _len);
}
}
else
{
ByteBuffer data = new ByteBuffer(_endian, _len);
data.CopyFrom(_stream, (int)_len);
if (!_fragment.HasOffsetTable)
{
_fragment.SetOffsetTable(data);
}
else
{
DicomFragment fragment = new DicomFragment(data);
_fragment.AddFragment(fragment);
}
}
_remain -= _len;
BytesRead += _len;
}
else if (LastTagRead == DicomTag.SequenceDelimitationItem)
{
if (_sqrs.Count > 0)
{
SequenceRecord rec = _sqrs.Peek();
DicomAttributeCollection ds = rec.Current;
ds[_fragment.Tag] = _fragment;
if (rec.Curlen != _undefinedLength)
{
long end = rec.Curpos + rec.Curlen;
if (_stream.Position >= end)
{
rec.Current = null;
}
}
}
else
{
Dataset[_fragment.Tag] = _fragment;
}
_fragment = null;
}
else
{
Platform.Log(LogLevel.Error, "Encountered unexpected tag in stream: {0}", LastTagRead.ToString());
// unexpected tag
return(DicomReadStatus.UnknownError);
}
}
else if (_sqrs.Count > 0 &&
(LastTagRead == DicomTag.Item ||
LastTagRead == DicomTag.ItemDelimitationItem ||
LastTagRead == DicomTag.SequenceDelimitationItem))
{
SequenceRecord rec = _sqrs.Peek();
if (LastTagRead.Equals(DicomTag.Item))
{
if (_len != _undefinedLength)
{
if (_len > _remain)
{
return(NeedMoreData(_remain - _len));
}
}
DicomSequenceItem ds;
if (rec.Tag.TagValue.Equals(DicomTags.DirectoryRecordSequence))
{
DirectoryRecordSequenceItem dr = new DirectoryRecordSequenceItem
{
Offset = (uint)_pos
};
ds = dr;
}
else
{
ds = new DicomSequenceItem();
}
rec.Current = ds;
if (rec.Tag.VR.Equals(DicomVr.UNvr))
{
DicomTag tag = new DicomTag(rec.Tag.TagValue, rec.Tag.Name,
rec.Tag.VariableName, DicomVr.SQvr, rec.Tag.MultiVR, rec.Tag.VMLow,
rec.Tag.VMHigh, rec.Tag.Retired);
rec.Parent[tag].AddSequenceItem(ds);
}
else
{
rec.Parent[rec.Tag].AddSequenceItem(ds);
}
// Specific character set is inherited, save it. It will be overwritten
// if a new value of the tag is encountered in the sequence.
rec.Current.SpecificCharacterSet = rec.Parent.SpecificCharacterSet;
// save the sequence length
rec.Curpos = _pos + 8;
rec.Curlen = _len;
_sqrs.Pop();
_sqrs.Push(rec);
if (_len != _undefinedLength)
{
ByteBuffer data = new ByteBuffer(_endian, _len);
data.CopyFrom(_stream, (int)_len);
data.Stream.Position = 0;
_remain -= _len;
BytesRead += _len;
DicomStreamReader idsr = new DicomStreamReader(data.Stream)
{
Dataset = ds,
TransferSyntax = rec.Tag.VR.Equals(DicomVr.UNvr)
? TransferSyntax.ImplicitVrLittleEndian
: _syntax,
StreamOpener = StreamOpener
};
DicomReadStatus stat = idsr.Read(null, options & ~DicomReadOptions.StorePixelDataReferences);
if (stat != DicomReadStatus.Success)
{
Platform.Log(LogLevel.Error, "Unexpected parsing error ({0}) when reading sequence attribute: {1}.", stat, rec.Tag.ToString());
return(stat);
}
}
}
else if (LastTagRead == DicomTag.ItemDelimitationItem)
{
}
else if (LastTagRead == DicomTag.SequenceDelimitationItem)
{
SequenceRecord rec2 = _sqrs.Pop();
if (rec2.Current == null)
{
rec2.Parent[rec.Tag].SetNullValue();
}
}
if (rec.Len != _undefinedLength)
{
long end = rec.Pos + 8 + rec.Len;
if (_syntax.ExplicitVr)
{
end += 2 + 2;
}
if (_stream.Position >= end)
{
_sqrs.Pop();
}
}
}
else
{
if (_len == _undefinedLength)
{
if (_vr.Equals(DicomVr.UNvr))
{
if (!_syntax.ExplicitVr)
{
_vr = DicomVr.SQvr;
LastTagRead = LastTagRead.IsPrivate
? new DicomTag(LastTagRead.TagValue, "Private Tag", "PrivateTag", DicomVr.SQvr, false, 1, uint.MaxValue, false)
: new DicomTag(LastTagRead.TagValue, "Unknown Tag", "UnknownTag", DicomVr.SQvr, false, 1, uint.MaxValue, false);
}
else
{
// To handle this case, we'd have to add a new mechanism to transition the parser to implicit VR parsing,
// and then return back to implicit once the parsing of the SQ is complete.
Platform.Log(LogLevel.Error,
"Encountered unknown tag {0}, encoded as undefined length in an Explicit VR transfer syntax at offset {1}. Unable to parse.",
LastTagRead, _stream.Position);
return(DicomReadStatus.UnknownError);
}
}
if (_vr.Equals(DicomVr.SQvr))
{
SequenceRecord rec = new SequenceRecord
{
Parent = _sqrs.Count > 0
? _sqrs.Peek().Current
: Dataset,
Current = null,
Tag = LastTagRead,
Len = _undefinedLength
};
_sqrs.Push(rec);
}
else
{
_fragment = new DicomFragmentSequence(LastTagRead);
}
}
else
{
if (_vr.Equals(DicomVr.SQvr))
{
if (_len == 0)
{
DicomAttributeCollection ds;
if (_sqrs.Count > 0)
{
SequenceRecord rec = _sqrs.Peek();
ds = rec.Current;
}
else
{
ds = Dataset;
}
ds[LastTagRead].SetNullValue();
}
else
{
SequenceRecord rec = new SequenceRecord
{
Len = _len,
Pos = _pos,
Tag = LastTagRead,
Parent = _sqrs.Count > 0
? _sqrs.Peek().Current
: Dataset
};
_sqrs.Push(rec);
}
}
else
{
if (_remain < _len)
{
return(NeedMoreData(_len - _remain));
}
if ((LastTagRead.TagValue == DicomTags.PixelData) &&
Flags.IsSet(options, DicomReadOptions.DoNotStorePixelDataInDataSet))
{
// Skip PixelData !!
if (_stream.CanSeek)
{
_stream.Seek((int)_len, SeekOrigin.Current);
}
else
{
ConsumeStreamBytes(_stream, _len);
}
_remain -= _len;
BytesRead += _len;
}
else if ((LastTagRead.TagValue == DicomTags.PixelData) &&
Flags.IsSet(options, DicomReadOptions.StorePixelDataReferences))
{
var reference = new FileReference(StreamOpener, _stream.Position, _len, _endian, LastTagRead.VR);
if (_stream.CanSeek)
{
_stream.Seek((int)_len, SeekOrigin.Current);
}
else
{
ConsumeStreamBytes(_stream, _len);
}
DicomAttribute elem;
if (LastTagRead.VR.Equals(DicomVr.OWvr))
{
elem = new DicomAttributeOW(LastTagRead, reference);
}
else if (LastTagRead.VR.Equals(DicomVr.OBvr))
{
elem = new DicomAttributeOB(LastTagRead, reference);
}
else if (LastTagRead.VR.Equals(DicomVr.ODvr))
{
elem = new DicomAttributeOD(LastTagRead, reference);
}
else
{
elem = new DicomAttributeOF(LastTagRead, reference);
}
if (_sqrs.Count > 0)
{
SequenceRecord rec = _sqrs.Peek();
DicomAttributeCollection ds = rec.Current;
ds[LastTagRead] = elem;
if (rec.Curlen != _undefinedLength)
{
long end = rec.Curpos + rec.Curlen;
if (_stream.Position >= end)
{
rec.Current = null;
}
}
}
else
{
Dataset[LastTagRead] = elem;
}
_remain -= _len;
BytesRead += _len;
}
else
{
ByteBuffer bb = new ByteBuffer(_len);
// If the tag is impacted by specific character set,
// set the encoding properly.
if (LastTagRead.VR.SpecificCharacterSet)
{
if (_sqrs.Count > 0)
{
SequenceRecord rec = _sqrs.Peek();
bb.SpecificCharacterSet = rec.Current.SpecificCharacterSet;
}
else
{
bb.SpecificCharacterSet = Dataset.SpecificCharacterSet;
}
}
if (LastTagRead.VR.Equals(DicomVr.UNvr) &&
!SaveTagRead.VR.Equals(DicomVr.UNvr) &&
!SaveTagRead.VR.Equals(DicomVr.SQvr) &&
Flags.IsSet(options, DicomReadOptions.UseDictionaryForExplicitUN))
{
LastTagRead = SaveTagRead;
bb.Endian = Endian.Little;
}
else
{
bb.Endian = _endian;
}
bb.CopyFrom(_stream, (int)_len);
DicomAttribute elem = LastTagRead.CreateDicomAttribute(bb);
_remain -= _len;
BytesRead += _len;
if (_sqrs.Count > 0)
{
SequenceRecord rec = _sqrs.Peek();
DicomAttributeCollection ds = rec.Current;
if (elem.Tag.TagValue == DicomTags.SpecificCharacterSet)
{
ds.SpecificCharacterSet = elem.ToString();
}
if (LastTagRead.Element == 0x0000)
{
if (Flags.IsSet(options, DicomReadOptions.KeepGroupLengths))
{
ds[LastTagRead] = elem;
}
}
else
{
ds[LastTagRead] = elem;
}
if (rec.Curlen != _undefinedLength)
{
long end = rec.Curpos + rec.Curlen;
if (_stream.Position >= end)
{
rec.Current = null;
}
}
}
else
{
if (LastTagRead.TagValue == DicomTags.FileMetaInformationGroupLength)
{
// Save the end of the group 2 elements, so that we can automatically
// check and change our transfer syntax when needed.
_inGroup2 = true;
uint group2Len;
elem.TryGetUInt32(0, out group2Len);
_endGroup2 = BytesRead + group2Len;
}
else if (LastTagRead.TagValue == DicomTags.SpecificCharacterSet)
{
Dataset.SpecificCharacterSet = elem.ToString();
}
if (LastTagRead.Element == 0x0000)
{
if (Flags.IsSet(options, DicomReadOptions.KeepGroupLengths))
{
Dataset[LastTagRead] = elem;
}
}
else
{
Dataset[LastTagRead] = elem;
}
}
}
}
}
}
LastTagRead = null;
_vr = null;
_len = _undefinedLength;
}
return(DicomReadStatus.Success);
}
catch (EndOfStreamException e)
{
// should never happen
Platform.Log(LogLevel.Error, "Unexpected exception when reading file: {0}", e.ToString());
return(DicomReadStatus.UnknownError);
}
}
public DicomFile Serialize(SegmentationSerializerCallback callback)
{
Platform.CheckForNullReference(callback, "callback");
Debug.Assert(!_segDocument.Saved, "Cannot serialize previously saved document");
// TODO: validate that all Segs are coming from the same study!
IPresentationImage firstIPresentationImage = null;
if (_segDocument.Segs != null)
{
var oneSeg = _segDocument.Segs.FirstOrDefault(item => item != null && item.SegGraphics != null && item.SegGraphics.OfType<PolygonalRoiSegGraphic>().Any());
if (oneSeg != null)
{
var polyGraphic = oneSeg.SegGraphics.OfType<PolygonalRoiSegGraphic>().First();
firstIPresentationImage = callback(polyGraphic.ImageSopInstanceUid, polyGraphic.ImageFrameNumber);
}
}
var firstImageSopProvider = firstIPresentationImage as IImageSopProvider;
if (firstImageSopProvider == null)
return null;
var sourceSop = firstImageSopProvider.ImageSop; // source of the common DICOM attributes
var dicomFile = _sopInstanceFactory.CreateFile(sourceSop);
// NOTE. These modules are initialized by the factory:
// patient IE
// - PatientModule
// - ClinicalTrialSubjectModule
// study IE
// - GeneralStudyModule
// - PatientStudyModule
// - ClinicalTrialStudyModule
// equipment IE
// - GeneralEquipmentModule
// Data values
const int instanceNumber = 1;
var contentDateTime = DateTime.Now;
var segDocumentIod = new SegmentationDocumentIod(dicomFile.DataSet);
// PatientModule
var patientModule = segDocumentIod.PatientModuleIod;
// patientModule.PatientBreedDescription = null; // bug in CC code
patientModule.DicomAttributeProvider[DicomTags.PatientBreedDescription].SetEmptyValue();
// GeneralEquipmentModule
var generalEquipmentModuleIod = segDocumentIod.GeneralEquipmentModuleIod;
generalEquipmentModuleIod.DeviceSerialNumber = EnvironmentUtilities.MachineIdentifier;
// GeneralSeriesModule
var srcGeneralSeriesModuleIod = new GeneralSeriesModuleIod(sourceSop.DataSource);
var generalSeriesModuleIod = segDocumentIod.GeneralSeriesModuleIod;
generalSeriesModuleIod.SeriesDescription = _segDocument.SeriesDescription;
generalSeriesModuleIod.SeriesNumber = _segDocument.SeriesNumber;
generalSeriesModuleIod.Modality = Modality.Seg;
generalSeriesModuleIod.SeriesInstanceUid = DicomUid.GenerateUid().UID;
generalSeriesModuleIod.Laterality = srcGeneralSeriesModuleIod.Laterality;
generalSeriesModuleIod.SeriesDateTime = _segDocument.CreationDateTime;
generalSeriesModuleIod.PerformingPhysiciansName = srcGeneralSeriesModuleIod.PerformingPhysiciansName;
generalSeriesModuleIod.PerformingPhysicianIdentificationSequence = srcGeneralSeriesModuleIod.PerformingPhysicianIdentificationSequence;
generalSeriesModuleIod.ProtocolName = srcGeneralSeriesModuleIod.ProtocolName;
{
// General Description Code Sequence is missing from the GeneralSeriesModuleIod implementation
var seriesDescriptionCodeSequence = new CodeSequenceMacro
{
CodeValue = "113076",
CodeMeaning = "Segmentation",
CodingSchemeDesignator = "DCM"
};
var result = new[] { seriesDescriptionCodeSequence.DicomSequenceItem };
generalSeriesModuleIod.DicomAttributeProvider[DicomTags.SeriesDescriptionCodeSequence].Values = result;
}
string userDicomName = null;
if (_segDocument.UserInfo != null && !string.IsNullOrEmpty(_segDocument.UserInfo.Name))
{
userDicomName = FormatDicomName(_segDocument.UserInfo.Name);
if (userDicomName != null)
generalSeriesModuleIod.OperatorsName = userDicomName;
// NOTE: Login name is being ignored for now
}
generalSeriesModuleIod.BodyPartExamined = srcGeneralSeriesModuleIod.BodyPartExamined;
generalSeriesModuleIod.PatientPosition = srcGeneralSeriesModuleIod.PatientPosition;
generalSeriesModuleIod.RequestAttributesSequence = srcGeneralSeriesModuleIod.RequestAttributesSequence;
//generalSeriesModuleIod.AnatomicalOrientationType = srcGeneralSeriesModuleIod.AnatomicalOrientationType; // Not needed
// FrameOfReferenceModule
var srcFrameOfReferenceModuleIod = new FrameOfReferenceModuleIod(sourceSop.DataSource);
segDocumentIod.FrameOfReferenceModuleIod.FrameOfReferenceUid = srcFrameOfReferenceModuleIod.FrameOfReferenceUid;
segDocumentIod.FrameOfReferenceModuleIod.PositionReferenceIndicator = srcFrameOfReferenceModuleIod.PositionReferenceIndicator;
// Initialize Segmentation Image Module first
var segmentationImageModuleIod = segDocumentIod.SegmentationImageModuleIod;
segmentationImageModuleIod.InitializeAttributes();
// General Image Module and Segmentation Image Module
var srcGeneralImageModuleIod = new GeneralImageModuleIod(sourceSop.DataSource);
var generalImageModuleIod = segDocumentIod.GeneralImageModuleIod;
generalImageModuleIod.InstanceNumber = instanceNumber;
generalImageModuleIod.PatientOrientation = srcGeneralImageModuleIod.PatientOrientation;
generalImageModuleIod.ContentDateTime = contentDateTime;
generalImageModuleIod.ImageType = "DERIVED\\PRIMARY";
generalImageModuleIod.AcquisitionNumber = srcGeneralImageModuleIod.AcquisitionNumber;
generalImageModuleIod.AcquisitionDateTime = srcGeneralImageModuleIod.AcquisitionDateTime;
generalImageModuleIod.QualityControlImage = srcGeneralImageModuleIod.QualityControlImage;
generalImageModuleIod.BurnedInAnnotation = srcGeneralImageModuleIod.BurnedInAnnotation;
generalImageModuleIod.RecognizableVisualFeatures = srcGeneralImageModuleIod.RecognizableVisualFeatures;
generalImageModuleIod.LossyImageCompression = srcGeneralImageModuleIod.LossyImageCompression.HasValue && srcGeneralImageModuleIod.LossyImageCompression.Value;
generalImageModuleIod.LossyImageCompressionMethod = srcGeneralImageModuleIod.LossyImageCompressionMethod;
generalImageModuleIod.LossyImageCompressionRatio = srcGeneralImageModuleIod.LossyImageCompressionRatio;
generalImageModuleIod.IrradiationEventUid = srcGeneralImageModuleIod.IrradiationEventUid;
// Image Pixel Module and Segmentation Image Module
var srcImagePixelModule = new ImagePixelMacroIod(sourceSop.DataSource);
var imagePixelModule = segDocumentIod.ImagePixelModuleIod;
imagePixelModule.Rows = srcImagePixelModule.Rows; // same height as the the image
imagePixelModule.Columns = srcImagePixelModule.Columns; // same width as the image
//imagePixelModule.PixelAspectRatio = srcImagePixelModule.PixelAspectRatio; // same as the image
// Continue initialization of non-default values for the Segmentation Image Module
segmentationImageModuleIod.ContentLabel = SanitizeDicomCsValue(_segDocument.ContentLabel);
if (!string.IsNullOrEmpty(userDicomName))
segmentationImageModuleIod.ContentCreatorsName = userDicomName;
segmentationImageModuleIod.SegmentationType = SegmentationType.BINARY;
// Per segmentation and per frame item initialization
var docHasOneFrame = _segDocument.Segs.Where(item => item != null && item.SegGraphics != null).Sum(seg => seg.SegGraphics.OfType<PolygonalRoiSegGraphic>().Count()) == 1;
var docHasOneSeg = _segDocument.Segs.Count(item => item != null && item.SegGraphics != null && item.SegGraphics.OfType<PolygonalRoiSegGraphic>().Any()) == 1;
var multiFrameDimensionsModuleIod = segDocumentIod.MultiFrameDimensionModuleIod;
multiFrameDimensionsModuleIod.InitializeAttributes();
var segmentSequenceItems = new List<SegmentSequence>();
var dimensionIndexSequenceItems = new List<DimensionIndexSequenceItem>();
var dimensionOrganizationSequenceItems = new List<DimensionOrganizationSequenceItem>();
var multiFrameFunctionalGroupsModuleIod = segDocumentIod.MultiFrameFunctionalGroupsModuleIod;
multiFrameFunctionalGroupsModuleIod.InitializeAttributes();
var perFrameFunctionalGroupSequenceItems = new List<FunctionalGroupsSequenceItem>();
var frameBytesList = new List<byte[]>(); // list of pixel data for each frame
var seriesUidToSopClassUidToSopInstanceUid = new Dictionary<string, Dictionary<string, HashSet<string>>>();
var segmentNumber = 0;
foreach (var seg in _segDocument.Segs)
{
segmentNumber++;
Debug.Assert(segmentNumber == 1, "We're only supposed to create one Segment per document for now");
// Segment Sequence initialization
var segmentSequenceItemIod = segmentationImageModuleIod.CreateSegmentSequence();
segmentSequenceItemIod.SegmentNumber = segmentNumber;
segmentSequenceItemIod.SegmentLabel = seg.Label;
segmentSequenceItemIod.SegmentDescription = seg.Description;
segmentSequenceItemIod.SegmentAlgorithmType = "MANUAL";
#region Category, Type, Anatomic Region, Anatomic Region Modifier
var selectedCategory = seg.SelectedCategory;
if (selectedCategory != null)
{
// Category
var segmentedPropertyCategoryCodeSequenceItem = segmentSequenceItemIod.CreateSegmentedPropertyCategoryCodeSequence();
segmentedPropertyCategoryCodeSequenceItem.CodeValue = selectedCategory.CodeValue;
segmentedPropertyCategoryCodeSequenceItem.CodeMeaning = selectedCategory.CodeMeaning;
segmentedPropertyCategoryCodeSequenceItem.CodingSchemeDesignator = selectedCategory.CodingSchemeDesignator;
//if (!string.IsNullOrEmpty(selectedCategory.CodingSchemeVersion))
// segmentedPropertyCategoryCodeSequenceItem.CodingSchemeVersion = selectedCategory.CodingSchemeVersion;
segmentSequenceItemIod.SegmentedPropertyCategoryCodeSequence = new[] { segmentedPropertyCategoryCodeSequenceItem };
// Type
if (selectedCategory.SelectedType != null)
{
var segmentedPropertyTypeCodeSequenceItem = segmentSequenceItemIod.CreateSegmentedPropertyTypeCodeSequence();
segmentedPropertyTypeCodeSequenceItem.CodeValue = selectedCategory.SelectedType.CodeValue;
segmentedPropertyTypeCodeSequenceItem.CodeMeaning = selectedCategory.SelectedType.CodeMeaning;
segmentedPropertyTypeCodeSequenceItem.CodingSchemeDesignator = selectedCategory.SelectedType.CodingSchemeDesignator;
//if (!string.IsNullOrEmpty(selectedCategory.SelectedType.CodingSchemeVersion))
// segmentedPropertyTypeCodeSequenceItem.CodingSchemeVersion = selectedCategory.SelectedType.CodingSchemeVersion;
// Type modifier
if (selectedCategory.SelectedType.SelectedTypeModifier != null)
{
var segmentedPropertyTypeModifierCodeSequenceItem = new CodeSequenceMacro();
segmentedPropertyTypeModifierCodeSequenceItem.CodeValue = selectedCategory.SelectedType.SelectedTypeModifier.CodeValue;
segmentedPropertyTypeModifierCodeSequenceItem.CodeMeaning = selectedCategory.SelectedType.SelectedTypeModifier.CodeMeaning;
segmentedPropertyTypeModifierCodeSequenceItem.CodingSchemeDesignator = selectedCategory.SelectedType.SelectedTypeModifier.CodingSchemeDesignator;
//if (!string.IsNullOrEmpty(selectedCategory.SelectedType.SelectedTypeModifier.CodingSchemeVersion))
// segmentedPropertyTypeModifierCodeSequenceItem.CodingSchemeVersion = selectedCategory.SelectedType.SelectedTypeModifier.CodingSchemeVersion;
segmentedPropertyTypeCodeSequenceItem.SegmentedPropertyTypeModifierCodeSequence = new[] {segmentedPropertyTypeModifierCodeSequenceItem};
}
segmentSequenceItemIod.SegmentedPropertyTypeCodeSequence = new[] { segmentedPropertyTypeCodeSequenceItem };
}
// Anatomic Region
var selectedAnatomicRegion = selectedCategory.SelectedAnatomicRegion;
if (selectedAnatomicRegion != null)
{
var anatomicRegionSequenceItem = segmentSequenceItemIod.CreateAnatomicRegionSequence();
anatomicRegionSequenceItem.CodeValue = selectedAnatomicRegion.CodeValue;
anatomicRegionSequenceItem.CodeMeaning = selectedAnatomicRegion.CodeMeaning;
anatomicRegionSequenceItem.CodingSchemeDesignator = selectedAnatomicRegion.CodingSchemeDesignator;
//if (!string.IsNullOrEmpty(selectedAnatomicRegion.CodingSchemeVersion))
// anatomicRegionSequenceItem.CodingSchemeVersion = selectedAnatomicRegion.CodingSchemeVersion;
// Anatomic region Modifier
if (selectedAnatomicRegion.SelectedAnatomicRegionModifier != null)
{
var anatomicRegionModifierSequenceItem = new CodeSequenceMacro();
anatomicRegionModifierSequenceItem.CodeValue = selectedAnatomicRegion.SelectedAnatomicRegionModifier.CodeValue;
anatomicRegionModifierSequenceItem.CodeMeaning = selectedAnatomicRegion.SelectedAnatomicRegionModifier.CodeMeaning;
anatomicRegionModifierSequenceItem.CodingSchemeDesignator = selectedAnatomicRegion.SelectedAnatomicRegionModifier.CodingSchemeDesignator;
//if (!string.IsNullOrEmpty(selectedAnatomicRegion.SelectedAnatomicRegionModifier.CodingSchemeVersion))
// anatomicRegionModifierSequenceItem.CodingSchemeVersion = selectedAnatomicRegion.SelectedAnatomicRegionModifier.CodingSchemeVersion;
anatomicRegionSequenceItem.AnatomicRegionModifierSequence = new[] { anatomicRegionModifierSequenceItem };
}
segmentSequenceItemIod.AnatomicRegionSequence = new[] { anatomicRegionSequenceItem };
}
}
#endregion
segmentSequenceItemIod.RecomendedDisplayCIELabValue = LabColorHelpers.RgbColorToCIELabColor(seg.Color);
segmentSequenceItems.Add(segmentSequenceItemIod);
// Dimension Organization Sequence item
var dimensionOrganizationUid = DicomUid.GenerateUid().UID;
var dimensionOrganizationSequenceItem = multiFrameDimensionsModuleIod.CreateDimensionOrganizationSequenceItem();
dimensionOrganizationSequenceItem.DimensionOrganizationUid = dimensionOrganizationUid;
dimensionOrganizationSequenceItems.Add(dimensionOrganizationSequenceItem);
// Dimension Index Sequence items
var dimensionIndexSequenceItem1 = multiFrameDimensionsModuleIod.CreateDimensionIndexSequenceItem();
dimensionIndexSequenceItem1.DimensionIndexPointer = DicomTags.StackId;
dimensionIndexSequenceItem1.FunctionalGroupPointer = DicomTags.FrameContentSequence;
dimensionIndexSequenceItem1.DimensionOrganizationUid = dimensionOrganizationUid;
dimensionIndexSequenceItem1.DimensionDescriptionLabel = "Stack ID";
dimensionIndexSequenceItems.Add(dimensionIndexSequenceItem1);
var dimensionIndexSequenceItem2 = multiFrameDimensionsModuleIod.CreateDimensionIndexSequenceItem();
dimensionIndexSequenceItem2.DimensionIndexPointer = DicomTags.InStackPositionNumber;
dimensionIndexSequenceItem2.FunctionalGroupPointer = DicomTags.FrameContentSequence;
dimensionIndexSequenceItem2.DimensionOrganizationUid = dimensionOrganizationUid;
dimensionIndexSequenceItem2.DimensionDescriptionLabel = "In Stack Position Number";
dimensionIndexSequenceItems.Add(dimensionIndexSequenceItem2);
var inStackPositionIndex = 0;
var presentationImagePolygons = new Dictionary<IPresentationImage, List<PolygonalRoiSegGraphic>>();
foreach (var polygonalSegGraphic in seg.SegGraphics.OfType<PolygonalRoiSegGraphic>())
{
var poly = polygonalSegGraphic.PolygonalRoiGraphic.Roi as PolygonalRoi;
if (poly != null)
{
var currentPresentationImage = callback(polygonalSegGraphic.ImageSopInstanceUid, polygonalSegGraphic.ImageFrameNumber);
if (presentationImagePolygons.ContainsKey(currentPresentationImage))
presentationImagePolygons[currentPresentationImage].Add(polygonalSegGraphic);
else
presentationImagePolygons.Add(poly.PresentationImage, new List<PolygonalRoiSegGraphic> { polygonalSegGraphic });
}
else
{
Debug.Assert(false, "Encountered non-polygonal graphic during segmentation serialization");
}
}
foreach (var presentationImage in presentationImagePolygons.Keys)
{
var currentImageSopProvider = presentationImage as IImageSopProvider;
if (presentationImage == null)
{
Debug.Assert(false, "Failed to get IImageSopProvider for the current Segmentation graphic");
continue;
}
Debug.Assert(presentationImagePolygons[presentationImage].FirstOrDefault().ImageFrameNumber ==
currentImageSopProvider.Frame.FrameNumber,
"Stored frame number must match with the current SOP Instance's value");
#region PerFrameFunctionalGroupSequenceItem
// Initialize Per Frame Functional Groups here and groups
var perFrameFunctionalGroupSequenceItem = multiFrameFunctionalGroupsModuleIod.CreatePerFrameFunctionalGroupsSequence();
if (!docHasOneSeg)
{
// Pixel Measures Functional Group (per frame)
InitializePixelMeasureFunctionalGroup(perFrameFunctionalGroupSequenceItem, currentImageSopProvider.Frame);
// Initialize Segmentation Functional Group (per frame)
InitializeSegmentationFunctionalGroup(perFrameFunctionalGroupSequenceItem, segmentNumber);
// Plane Orientation (Patient) Functional Group
InitializePlaneOrientationPatientFunctionalGroup(perFrameFunctionalGroupSequenceItem, currentImageSopProvider.Frame.ImageOrientationPatient);
}
if (!docHasOneFrame)
{
// Plain Position Patient Functional Group (per frame)
InitializePlanePositionPatientFunctionalGroup(perFrameFunctionalGroupSequenceItem, currentImageSopProvider.Frame.ImagePositionPatient);
// Derivation Image Functional Group (per frame)
InitializeDerivationImageFunctionalGroup(perFrameFunctionalGroupSequenceItem, currentImageSopProvider.ImageSop, currentImageSopProvider.Frame.FrameNumber);
}
else
{
Debug.Assert(firstImageSopProvider.ImageSop.SeriesInstanceUid == currentImageSopProvider.Frame.SeriesInstanceUid &&
firstImageSopProvider.ImageSop.SopInstanceUid == currentImageSopProvider.ImageSop.SopInstanceUid,
"initial image reference and the single image reference must be the same");
}
// Initialize Frame Content Functional Group
InitializeFrameContentFunctionalGroup(perFrameFunctionalGroupSequenceItem, segmentNumber, ++inStackPositionIndex);
perFrameFunctionalGroupSequenceItems.Add(perFrameFunctionalGroupSequenceItem);
#endregion PerFrameFunctionalGroupSequenceItem
// Store referenced image info in a dictionary for later use
{
var currentSeriesInstanceUid = currentImageSopProvider.ImageSop.SeriesInstanceUid;
var currentSopClassUid = currentImageSopProvider.ImageSop.SopClassUid;
var currentSopInstanceUid = currentImageSopProvider.ImageSop.SopInstanceUid;
if (!seriesUidToSopClassUidToSopInstanceUid.ContainsKey(currentSeriesInstanceUid))
seriesUidToSopClassUidToSopInstanceUid.Add(currentSeriesInstanceUid, new Dictionary<string, HashSet<string>>());
var sopClassToSopInstanceDic = seriesUidToSopClassUidToSopInstanceUid[currentSeriesInstanceUid];
if (!sopClassToSopInstanceDic.ContainsKey(currentSopClassUid))
sopClassToSopInstanceDic.Add(currentSopClassUid, new HashSet<string>());
sopClassToSopInstanceDic[currentSopClassUid].Add(currentSopInstanceUid);
}
var polygons = new List<IList<PointF>>();
// Get frame's pixel data here
foreach (var polygonalSegGraphic in presentationImagePolygons[presentationImage])
{
var poly = polygonalSegGraphic.PolygonalRoiGraphic.Roi as PolygonalRoi;
if (poly != null)
{
polygons.Add(poly.Polygon.Vertices);
}
else
{
Debug.Assert(false, "Encountered non-polygonal graphic during segmentation serialization");
}
}
var grayscalePixelData = CreateFramePixelData(presentationImage, polygons);
frameBytesList.Add(grayscalePixelData.Raw);
}
}
segmentationImageModuleIod.SegmentSequence = segmentSequenceItems.ToArray();
// Per Frame Functional Groups module
multiFrameFunctionalGroupsModuleIod.PerFrameFunctionalGroupsSequence = perFrameFunctionalGroupSequenceItems.ToArray();
#region SharedFunctionalGroupSequence
// Shared Functional Group Sequence Item
var sharedFunctionalGroupSequenceItem = multiFrameFunctionalGroupsModuleIod.CreateSharedFunctionalGroupsSequence();
if (docHasOneSeg)
{
Debug.Assert(segmentNumber == 1, "This is for a single segment only");
// Pixel Measures Functional Group (shared)
InitializePixelMeasureFunctionalGroup(sharedFunctionalGroupSequenceItem, firstImageSopProvider.Frame);
// Initialize Segmentation Functional Group (shared)
InitializeSegmentationFunctionalGroup(sharedFunctionalGroupSequenceItem, segmentNumber);
// Plane Orientation (Patient) Functional Group
InitializePlaneOrientationPatientFunctionalGroup(sharedFunctionalGroupSequenceItem, firstImageSopProvider.Frame.ImageOrientationPatient);
}
if (docHasOneFrame)
{
// Plain Position Patient Functional Group
InitializePlanePositionPatientFunctionalGroup(sharedFunctionalGroupSequenceItem, firstImageSopProvider.Frame.ImagePositionPatient);
// Derivation Image Functional Group
InitializeDerivationImageFunctionalGroup(sharedFunctionalGroupSequenceItem, firstImageSopProvider.ImageSop, firstImageSopProvider.Frame.FrameNumber);
}
multiFrameFunctionalGroupsModuleIod.SharedFunctionalGroupsSequence = sharedFunctionalGroupSequenceItem;
#endregion SharedFunctionalGroupSequence
// Multi-frame Dimensions module
multiFrameDimensionsModuleIod.DimensionIndexSequence = dimensionIndexSequenceItems.ToArray();
multiFrameDimensionsModuleIod.DimensionOrganizationSequence = dimensionOrganizationSequenceItems.ToArray();
multiFrameDimensionsModuleIod.DimensionOrganizationType = "3D";
// Multi-frame Functional Groups module
multiFrameFunctionalGroupsModuleIod.SharedFunctionalGroupsSequence = sharedFunctionalGroupSequenceItem;
multiFrameFunctionalGroupsModuleIod.PerFrameFunctionalGroupsSequence = perFrameFunctionalGroupSequenceItems.ToArray();
multiFrameFunctionalGroupsModuleIod.NumberOfFrames = perFrameFunctionalGroupSequenceItems.Count;
// Specimen Module
var srcSpecimenModuleIod = new SpecimenModuleIod(sourceSop.DataSource);
var specimenModuleIod = segDocumentIod.SpecimenModuleIod;
//specimenModuleIod.ContainerIdentifier = srcSpecimenModuleIod.ContainerIdentifier;
specimenModuleIod.IssuerOfTheContainterIdentifier = srcSpecimenModuleIod.IssuerOfTheContainterIdentifier;
specimenModuleIod.AlternateContainerIdentifierSequence = srcSpecimenModuleIod.AlternateContainerIdentifierSequence;
specimenModuleIod.ContainerTypeCodeSequence = srcSpecimenModuleIod.ContainerTypeCodeSequence;
//specimenModuleIod.ContainerDescription = srcSpecimenModuleIod.ContainerDescription;
specimenModuleIod.ContainerComponentSequence = srcSpecimenModuleIod.ContainerComponentSequence;
specimenModuleIod.SpecimenDescriptionSequence = srcSpecimenModuleIod.SpecimenDescriptionSequence;
// Common Instance Reference Module
var referencedSeriesSequenceItems = new List<ReferencedSeriesSequenceIod>();
foreach (
var seriesToSopClassToSopInstanceDic in
seriesUidToSopClassUidToSopInstanceUid.Where(seriesToSopClassToSopInstanceDic => seriesToSopClassToSopInstanceDic.Value != null))
{
var referencedSopInstances = new List<ReferencedInstanceSequenceIod>();
foreach (var sopClassToSopInstanceDic in seriesToSopClassToSopInstanceDic.Value.Where(sopClassToSopInstanceDic => sopClassToSopInstanceDic.Value != null))
{
referencedSopInstances.AddRange(sopClassToSopInstanceDic.Value.Select(sopInstanceUid => new ReferencedInstanceSequenceIod
{
ReferencedSopClassUid = sopClassToSopInstanceDic.Key,
ReferencedSopInstanceUid = sopInstanceUid
}));
}
if (referencedSopInstances.Count > 0)
{
referencedSeriesSequenceItems.Add(new ReferencedSeriesSequenceIod
{
SeriesInstanceUid = seriesToSopClassToSopInstanceDic.Key,
ReferencedInstanceSequence = referencedSopInstances.ToArray()
});
}
}
if (referencedSeriesSequenceItems.Count > 0)
{
var commonInstanceReferenceModuleIod = segDocumentIod.CommonInstanceReferenceModuleIod;
commonInstanceReferenceModuleIod.InitializeAttributes();
commonInstanceReferenceModuleIod.ReferencedSeriesSequence = referencedSeriesSequenceItems.ToArray();
}
// SOP Common Module
var srcSopCommonModuleIod = new SopCommonModuleIod(sourceSop.DataSource);
var sopCommonModuleIod = segDocumentIod.SopCommonModuleIod;
sopCommonModuleIod.SopClass = SopClass.SegmentationStorage;
sopCommonModuleIod.SopInstanceUid = DicomUid.GenerateUid().UID;
//sopCommonModuleIod.SpecificCharacterSet = "UTF-8"; // TBD -it's ISO_IR 192 by default
sopCommonModuleIod.InstanceCreationDateTime = contentDateTime;
sopCommonModuleIod.InstanceCreatorUid = InstanceCreatorUid;
sopCommonModuleIod.TimezoneOffsetFromUtc = contentDateTime.ToString("zzz", DateTimeFormatInfo.InvariantInfo);
//sopCommonModuleIod.LongitudinalTemporalInformationModified = srcSopCommonModuleIod.LongitudinalTemporalInformationModified; // has a bug in CC
// Pixel data
{
Debug.Assert(frameBytesList.TrueForAll(bytes => bytes.Length == frameBytesList[0].Length), "Allocated buffers for all frames must be of the same size");
var byteBuffer = new byte[frameBytesList[0].Length * frameBytesList.Count];
using (var stream = new MemoryStream(byteBuffer))
{
foreach (var frameBytes in frameBytesList)
stream.Write(frameBytes, 0, frameBytes.Length);
}
// Byte Packing
// TODO FIXME: we can do in-place byte packing without allocating the second array!
var packetBuffer = new byte[(int) Math.Ceiling(byteBuffer.Length/8.0)];
var numberOfFullBytes = byteBuffer.Length/8;
for (var i = 0; i < numberOfFullBytes; i++)
{
var newByte = packetBuffer[i];
for (var y = 0; y < 8; y++)
{
var bitMask = (byte) (1 << y);
newByte = (byte) ((byteBuffer[8*i + y] & 0xFF) > 0 ? newByte | bitMask : newByte & ~bitMask);
}
packetBuffer[i] = newByte;
}
// last byte(s) TODO VK: handle padding for non-even number of bytes. make sure padded bits are initialized to 0
if (numberOfFullBytes < packetBuffer.Length)
{
// Pack leftover bytes ( < 8)
Debug.Assert(packetBuffer.Length - numberOfFullBytes == 1, "Wrong destination bytes count during packing");
Debug.Assert(byteBuffer.Length - numberOfFullBytes*8 < 8, "Wrong leftover bytes count during packing");
var newByte = packetBuffer[packetBuffer.Length - 1];
for (var y = numberOfFullBytes * 8; y < byteBuffer.Length; y++)
{
var bitMask = (byte) (1 << (y%8));
newByte = (byte) ((byteBuffer[y] & 0xFF) > 0 ? newByte | bitMask : newByte & ~bitMask);
}
packetBuffer[packetBuffer.Length - 1] = newByte;
}
var pdAttribute = new DicomAttributeOW(DicomTags.PixelData);
using (var stream = pdAttribute.AsStream())
{
stream.Write(packetBuffer, 0, packetBuffer.Length);
}
multiFrameFunctionalGroupsModuleIod.DicomAttributeProvider[DicomTags.PixelData] = pdAttribute;
}
dicomFile.MediaStorageSopClassUid = SopClass.SegmentationStorageUid;
dicomFile.MediaStorageSopInstanceUid = segDocumentIod.SopInstanceUid;
// Update the original document with new values
_segDocument.SeriesInstanceUid = segDocumentIod.SeriesInstanceUid;
_segDocument.SopInstanceUid = segDocumentIod.SopInstanceUid;
return dicomFile;
}
/// <summary>
/// Initializes the frame data container from an OW Pixel Data attribute.
/// </summary>
public FrameDataOW(DicomUncompressedPixelData owner, DicomAttributeOW pixelDataAttribute, int frameIndex)
: base(owner)
{
_owAttrib = pixelDataAttribute;
_frameIndex = frameIndex;
}
public static bool Convert2Dicom(byte[] pixelData, string rawFileName, DataRow patientInfo, bool delbeforeSave, string AutoWLPath)
{
try
{
const string colPid = "PID";
const string colKVP = "KVP";
const string colMAS = "MAS";
const string colDepartmentName = "Department_Name";
const string colPatientName = "Patient_Name";
const string colPatientSex = "Patient_Sex";
const string colPatientAge = "Patient_Age";
const string colPatientBirthdate = "Patient_Birthdate";
const string colRegDate = "Reg_Date";
const string colRegNum = "Reg_Num";
const string colImgWidth = "IMGWidth";
const string colImgHeight = "IMGHeigh";
const string colModalityCode = "Modality_Code";
const string colAtonomyCode = "Atonomy_Code";
const string colProjectionCode = "Projection_Code";
const string colHostpitalName = "Hostpital_Name";
const string colMonoChrome = "MonoChrome";
const string _colStudyInstanceUID = "StudyInstanceUID";
const string colSeriesInstanceUID = "SeriesInstanceUID";
const string colSOPInstanceUID = "SOPInstanceUID";
const string colAcqDate = "AcqDate";
const string colAppName = "AppName";
const string colBitsStored = "BitsStored";
const string colHightBit = "HightBit";
const string colBitsAllocated = "BitsAllocated";
_bitsStored = TryGetBitsStored(patientInfo, colBitsStored);
var _HightBit = TryGetBitsStored(patientInfo, colHightBit);
var _BitsAllocated = TryGetBitsStored(patientInfo, colBitsAllocated);
var MonoChrome = TryGetString(patientInfo, colMonoChrome, "MONOCHROME2");
var pid = TryGetString(patientInfo, colPid);
var _KVP = TryGetString(patientInfo, colKVP);
var _MAS = TryGetString(patientInfo, colMAS);
var patientName = TryGetString(patientInfo, colPatientName);
var patientSex = TryGetString(patientInfo, colPatientSex);
var patientAge = TryGetString(patientInfo, colPatientAge);
var patientBirthdate = TryGetString(patientInfo, colPatientBirthdate);
var regDate = TryGetString(patientInfo, colRegDate);
var regNum = TryGetString(patientInfo, colRegNum);
var imgWidth = TryGetString(patientInfo, colImgWidth);
var imgHeigh = TryGetString(patientInfo, colImgHeight);
var modalityCode = TryGetString(patientInfo, colModalityCode);
var atonomyCode = TryGetString(patientInfo, colAtonomyCode);
var projectionCode = TryGetString(patientInfo, colProjectionCode);
var hostpitalName = TryGetString(patientInfo, colHostpitalName, "BACH MAI HOSTPITAL");
var departmentName = TryGetString(patientInfo, colDepartmentName, "Khoa chan doan hinh anh");
string defaultStudyInstanceUID = ClearCanvas.Dicom.DicomUid.GenerateUid().UID;
string defaultSeriesInstanceUID = defaultStudyInstanceUID + ".1";
string defaultSOPInstanceUID = defaultSeriesInstanceUID + ".1";
var StudyInstanceUID = TryGetString(patientInfo, _colStudyInstanceUID, defaultStudyInstanceUID);
var SeriesInstanceUID = TryGetString(patientInfo, colSeriesInstanceUID, defaultSeriesInstanceUID);
var SOPInstanceUID = TryGetString(patientInfo, colSOPInstanceUID, defaultSOPInstanceUID);
var AppName = TryGetString(patientInfo, colAppName, "VBIT");
string dicomPath = Path.GetDirectoryName(rawFileName);
// Lấy về tên file Dicom từ file raw
string dicomFileName = string.Format("{0}{1}{2}.DCM", dicomPath, Path.DirectorySeparatorChar,
Path.GetFileNameWithoutExtension(rawFileName));
if (delbeforeSave && File.Exists(dicomFileName)) Try2DelFile(dicomFileName);
else
try2RenameExistedFile(dicomFileName);
//FileStream fs = File.OpenRead(rawFileName);
//long length = fs.Length;
long dataLength = pixelData.Length;
string col = imgWidth.ToString();
string row = imgHeigh.ToString();
// GetSize(dataLength, out col, out row);
// Tạo File Dicom để lưu thông tin
var dcmFile = new DicomFile(dicomFileName);
DicomAttributeCollection dicomDataSet = dcmFile.DataSet;
//Set Tag For File
DateTime studyTime = DateTime.Now;
dicomDataSet[DicomTags.SpecificCharacterSet].SetStringValue("ISO_IR 100");
dicomDataSet[DicomTags.ImageType].SetStringValue("ORIGINAL\\PRIMARY\\OTHER\\M\\FFE");
dicomDataSet[DicomTags.InstanceCreationDate].SetStringValue(DateParser.ToDicomString(studyTime));
dicomDataSet[DicomTags.InstanceCreationTime].SetStringValue(TimeParser.ToDicomString(studyTime));
dicomDataSet[DicomTags.SopClassUid].SetStringValue(SopClass.MrImageStorageUid);
dicomDataSet[DicomTags.SopInstanceUid].SetStringValue(SOPInstanceUID);
dicomDataSet[DicomTags.StudyDate].SetStringValue(regDate);
dicomDataSet[DicomTags.ApplicationName].SetStringValue(AppName);
dicomDataSet[DicomTags.StudyTime].SetStringValue(TimeParser.ToDicomString(studyTime));
dicomDataSet[DicomTags.SeriesDate].SetStringValue(regDate);
dicomDataSet[DicomTags.SeriesTime].SetStringValue(TimeParser.ToDicomString(studyTime));
dicomDataSet[DicomTags.AccessionNumber].SetStringValue(regNum);
dicomDataSet[DicomTags.Modality].SetStringValue(modalityCode);
dicomDataSet[DicomTags.Manufacturer].SetStringValue("VBIT");
dicomDataSet[DicomTags.StationName].SetStringValue(AppName);
dicomDataSet[DicomTags.ExposureInMas].SetStringValue(_MAS);
dicomDataSet[DicomTags.Kvp].SetStringValue(_KVP);
dicomDataSet[DicomTags.ManufacturersModelName].SetNullValue();
dicomDataSet[DicomTags.InstitutionName].SetStringValue(hostpitalName);
dicomDataSet[DicomTags.InstitutionalDepartmentName].SetStringValue(departmentName);
//dicomDataSet[DicomTags.StudyDescription].SetStringValue("HEART");
//dicomDataSet[DicomTags.SeriesDescription].SetStringValue("Heart 2D EPI BH TRA");
//dicomDataSet[DicomTags.PatientsName].SetStringValue("Patient^Test");
dicomDataSet[DicomTags.PatientsName].SetStringValue(patientName);
dicomDataSet[DicomTags.PatientId].SetStringValue(pid);
dicomDataSet[DicomTags.PatientsBirthDate].SetStringValue(patientBirthdate);
dicomDataSet[DicomTags.PatientsSex].SetStringValue(patientSex);
dicomDataSet[DicomTags.PatientsAge].SetStringValue(patientAge);
dicomDataSet[DicomTags.PatientsWeight].SetStringValue("70");
dicomDataSet[DicomTags.SequenceVariant].SetStringValue("OTHER");
dicomDataSet[DicomTags.ScanOptions].SetStringValue("CG");
dicomDataSet[DicomTags.MrAcquisitionType].SetStringValue("2D");
dicomDataSet[DicomTags.SliceThickness].SetStringValue("2");
dicomDataSet[DicomTags.RepetitionTime].SetStringValue("857.142883");
dicomDataSet[DicomTags.EchoTime].SetStringValue("8.712100");
dicomDataSet[DicomTags.NumberOfAverages].SetStringValue("1");
dicomDataSet[DicomTags.ImagingFrequency].SetStringValue("63.901150");
dicomDataSet[DicomTags.ImagedNucleus].SetStringValue("1H");
dicomDataSet[DicomTags.EchoNumbers].SetStringValue("1");
dicomDataSet[DicomTags.MagneticFieldStrength].SetStringValue("1.500000");
dicomDataSet[DicomTags.SpacingBetweenSlices].SetStringValue("10.00000");
dicomDataSet[DicomTags.NumberOfPhaseEncodingSteps].SetStringValue("81");
dicomDataSet[DicomTags.EchoTrainLength].SetStringValue("0");
dicomDataSet[DicomTags.PercentSampling].SetStringValue("63.281250");
dicomDataSet[DicomTags.PercentPhaseFieldOfView].SetStringValue("68.75000");
dicomDataSet[DicomTags.DeviceSerialNumber].SetStringValue("1234");
dicomDataSet[DicomTags.SoftwareVersions].SetStringValue("V1.0");
dicomDataSet[DicomTags.ProtocolName].SetStringValue("2D EPI BH");
dicomDataSet[DicomTags.TriggerTime].SetStringValue("14.000000");
dicomDataSet[DicomTags.LowRRValue].SetStringValue("948");
dicomDataSet[DicomTags.HighRRValue].SetStringValue("1178");
dicomDataSet[DicomTags.IntervalsAcquired].SetStringValue("102");
dicomDataSet[DicomTags.IntervalsRejected].SetStringValue("0");
dicomDataSet[DicomTags.HeartRate].SetStringValue("56");
dicomDataSet[DicomTags.ReceiveCoilName].SetStringValue("B");
dicomDataSet[DicomTags.TransmitCoilName].SetStringValue("B");
dicomDataSet[DicomTags.InPlanePhaseEncodingDirection].SetStringValue("COL");
dicomDataSet[DicomTags.FlipAngle].SetStringValue("50.000000");
dicomDataSet[DicomTags.PatientPosition].SetStringValue("HFS");
dicomDataSet[DicomTags.StudyInstanceUid].SetStringValue(StudyInstanceUID);
dicomDataSet[DicomTags.SeriesInstanceUid].SetStringValue(SeriesInstanceUID);
//dicomDataSet[DicomTags.StudyId].SetStringValue(pid);
dicomDataSet[DicomTags.SeriesNumber].SetStringValue("1");
dicomDataSet[DicomTags.AcquisitionNumber].SetStringValue("7");
dicomDataSet[DicomTags.InstanceNumber].SetStringValue("1");
dicomDataSet[DicomTags.ImagePositionPatient].SetStringValue("-61.7564\\-212.04848\\-99.6208");
dicomDataSet[DicomTags.ImageOrientationPatient].SetStringValue("0.861\\0.492\\0.126\\-0.2965");
dicomDataSet[DicomTags.FrameOfReferenceUid].SetStringValue(DicomUid.GenerateUid().UID);
dicomDataSet[DicomTags.PositionReferenceIndicator].SetStringValue(null);
//dicomDataSet[DicomTags.ImageComments].SetStringValue("Test MR Image");
dicomDataSet[DicomTags.SamplesPerPixel].SetStringValue("1");
dicomDataSet[DicomTags.PhotometricInterpretation].SetStringValue(MonoChrome);
dicomDataSet[DicomTags.Rows].SetStringValue(row);
dicomDataSet[DicomTags.Columns].SetStringValue(col);
dicomDataSet[DicomTags.PixelSpacing].SetStringValue("0.168\\0.168");
dicomDataSet[DicomTags.BitsAllocated].SetStringValue(_BitsAllocated.ToString());
dicomDataSet[DicomTags.BitsStored].SetStringValue(_bitsStored.ToString());
dicomDataSet[DicomTags.HighBit].SetStringValue(_HightBit.ToString());
dicomDataSet[DicomTags.PixelRepresentation].SetStringValue("0");
if (File.Exists(AutoWLPath))
{
switch (_bitsStored)
{
case 12:
dicomDataSet[DicomTags.WindowCenter].SetStringValue("2048");
dicomDataSet[DicomTags.WindowWidth].SetStringValue("4095");
break;
case 14:
dicomDataSet[DicomTags.WindowCenter].SetStringValue("8192");
dicomDataSet[DicomTags.WindowWidth].SetStringValue("16383");
break;
case 16:
dicomDataSet[DicomTags.WindowCenter].SetStringValue("32767");
dicomDataSet[DicomTags.WindowWidth].SetStringValue("65535");
break;
default:
dicomDataSet[DicomTags.WindowCenter].SetStringValue("32767");
dicomDataSet[DicomTags.WindowWidth].SetStringValue("65535");
break;
}
}
//dicomDataSet[DicomTags.SmallestImagePixelValue].SetStringValue("32772");
//dicomDataSet[DicomTags.LargestImagePixelValue].SetStringValue("47745");
dicomDataSet[DicomTags.RescaleIntercept].SetStringValue("0.");
dicomDataSet[DicomTags.RescaleSlope].SetStringValue("1.");
dicomDataSet[DicomTags.ViewPosition].SetStringValue(projectionCode);
dicomDataSet[DicomTags.BodyPartExamined].SetStringValue(atonomyCode);
//Gán Dữ liệu ảnh
var pixels = new DicomAttributeOW(DicomTags.PixelData) { Values = pixelData };
dicomDataSet[DicomTags.PixelData] = pixels;
var item = new DicomSequenceItem();
dicomDataSet[DicomTags.RequestAttributesSequence].AddSequenceItem(item);
item[DicomTags.RequestedProcedureId].SetStringValue("MRR1234");
item[DicomTags.ScheduledProcedureStepId].SetStringValue("MRS1234");
item = new DicomSequenceItem();
dicomDataSet[DicomTags.RequestAttributesSequence].AddSequenceItem(item);
item[DicomTags.RequestedProcedureId].SetStringValue("MR2R1234");
item[DicomTags.ScheduledProcedureStepId].SetStringValue("MR2S1234");
var studyItem = new DicomSequenceItem();
item[DicomTags.ReferencedStudySequence].AddSequenceItem(studyItem);
studyItem[DicomTags.ReferencedSopClassUid].SetStringValue(SopClass.MrImageStorageUid);
studyItem[DicomTags.ReferencedSopInstanceUid].SetStringValue("1.2.3.4.5.6.7.8.9");
//Set Meta Info
dicomDataSet[DicomTags.MediaStorageSopClassUid].SetStringValue(
dcmFile.DataSet[DicomTags.SopClassUid].GetString(0, ""));
dicomDataSet[DicomTags.MediaStorageSopInstanceUid].SetStringValue(
dcmFile.DataSet[DicomTags.SopInstanceUid].GetString(0, ""));
dcmFile.TransferSyntax = TransferSyntax.ExplicitVrLittleEndian;
dicomDataSet[DicomTags.ImplementationClassUid].SetStringValue("1.1.1.1.1.11.1");
dicomDataSet[DicomTags.ImplementationVersionName].SetStringValue("droc 1.0");
// Lưu File
dcmFile.Save();
return true;
}
catch (Exception ex)
{
return false;
}
}
public void SetupMultiframeXA(DicomAttributeCollection theSet, uint rows, uint columns, uint frames)
{
DateTime studyTime = DateTime.Now;
theSet[DicomTags.SpecificCharacterSet].SetStringValue("ISO_IR 100");
theSet[DicomTags.ImageType].SetStringValue("DERIVED\\SECONDARY\\SINGLE PLANE\\SINGLE A");
theSet[DicomTags.InstanceCreationDate].SetStringValue(DateParser.ToDicomString(DateTime.Now));
theSet[DicomTags.InstanceCreationTime].SetStringValue(TimeParser.ToDicomString(DateTime.Now));
theSet[DicomTags.SopClassUid].SetStringValue(SopClass.XRayAngiographicImageStorageUid);
theSet[DicomTags.SopInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.StudyDate].SetStringValue(DateParser.ToDicomString(studyTime));
theSet[DicomTags.StudyTime].SetStringValue(TimeParser.ToDicomString(studyTime));
theSet[DicomTags.SeriesDate].SetStringValue(DateParser.ToDicomString(studyTime));
theSet[DicomTags.SeriesTime].SetStringValue(TimeParser.ToDicomString(studyTime));
theSet[DicomTags.AccessionNumber].SetStringValue("A4567");
theSet[DicomTags.Modality].SetStringValue("XA");
theSet[DicomTags.Manufacturer].SetStringValue("ClearCanvas");
theSet[DicomTags.InstitutionName].SetStringValue("KardiologieUniklinikHeidelberg");
theSet[DicomTags.ReferringPhysiciansName].SetStringValue("Last^First");
theSet[DicomTags.StudyDescription].SetStringValue("HEART");
theSet[DicomTags.SeriesDescription].SetStringValue("Heart 2D EPI BH TRA");
theSet[DicomTags.PatientsName].SetStringValue("Patient^Test");
theSet[DicomTags.PatientId].SetStringValue("ID123-45-9999");
theSet[DicomTags.PatientsBirthDate].SetStringValue("19600101");
theSet[DicomTags.PatientsSex].SetStringValue("M");
theSet[DicomTags.PatientsWeight].SetStringValue("80");
theSet[DicomTags.PatientsSize].SetStringValue("10.000244140625");
theSet[DicomTags.Kvp].SetStringValue("80");
theSet[DicomTags.ProtocolName].SetStringValue("25 FPS Koronarien");
theSet[DicomTags.FrameTime].SetStringValue("40");
theSet[DicomTags.FrameDelay].SetStringValue("0");
theSet[DicomTags.DistanceSourceToDetector].SetStringValue("1018");
theSet[DicomTags.ExposureTime].SetStringValue("7");
theSet[DicomTags.XRayTubeCurrent].SetStringValue("815");
theSet[DicomTags.RadiationSetting].SetStringValue("GR");
theSet[DicomTags.IntensifierSize].SetStringValue("169.99998");
theSet[DicomTags.PositionerMotion].SetStringValue("STATIC");
theSet[DicomTags.PositionerPrimaryAngle].SetStringValue("-40.2999999");
theSet[DicomTags.PositionerSecondaryAngle].SetStringValue("-15.5");
theSet[DicomTags.DeviceSerialNumber].SetStringValue("1234");
theSet[DicomTags.SoftwareVersions].SetStringValue("V1.0");
theSet[DicomTags.StudyInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.SeriesInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.StudyId].SetStringValue("20021208125233");
theSet[DicomTags.SeriesNumber].SetStringValue("1");
theSet[DicomTags.AcquisitionNumber].SetStringValue("3");
theSet[DicomTags.InstanceNumber].SetStringValue("13");
theSet[DicomTags.PatientOrientation].SetNullValue();
theSet[DicomTags.ImagesInAcquisition].SetStringValue("1");
theSet[DicomTags.SamplesPerPixel].SetStringValue("1");
theSet[DicomTags.PhotometricInterpretation].SetStringValue("MONOCHROME2");
theSet[DicomTags.NumberOfFrames].SetUInt32(0, frames);
theSet[DicomTags.Rows].SetUInt32(0,rows);
theSet[DicomTags.Columns].SetUInt32(0, columns);
theSet[DicomTags.FrameIncrementPointer].SetUInt32(0,DicomTags.FrameTime);
theSet[DicomTags.BitsAllocated].SetStringValue("8");
theSet[DicomTags.BitsStored].SetStringValue("8");
theSet[DicomTags.HighBit].SetStringValue("7");
theSet[DicomTags.PixelRepresentation].SetStringValue("0");
theSet[DicomTags.WindowCenter].SetStringValue("128");
theSet[DicomTags.WindowWidth].SetStringValue("204.8");
theSet[DicomTags.PerformedProcedureStepStartDate].SetStringValue("20080219");
theSet[DicomTags.PerformedProcedureStepStartTime].SetStringValue("143600");
theSet[DicomTags.PerformedProcedureStepId].SetStringValue("UNKNOWN");
// Null SQ Test
theSet[DicomTags.ReferencedStudySequence].SetNullValue();
// FL & FD tags for testing
theSet[DicomTags.SlabThickness].SetFloat64(0,0.1234567d);
theSet[DicomTags.CalciumScoringMassFactorPatient].SetFloat32(0, 0.7654321f);
uint length = rows * columns * frames;
if (length % 2 == 1)
length++;
DicomAttributeOW pixels = new DicomAttributeOW(DicomTags.PixelData);
byte[] pixelArray = new byte[length];
pixelArray[length - 1] = 0x00; // Padding char
for (uint frameCount = 0; frameCount < frames; frameCount++)
for (uint i = frameCount * rows * columns, val = frameCount + 1; i < (frameCount + 1) * rows * columns; i++, val++)
pixelArray[i] = (byte)(val % 255);
pixels.Values = pixelArray;
theSet[DicomTags.PixelData] = pixels;
DicomSequenceItem item = new DicomSequenceItem();
theSet[DicomTags.RequestAttributesSequence].AddSequenceItem(item);
item[DicomTags.RequestedProcedureId].SetStringValue("XA123");
item[DicomTags.ScheduledProcedureStepId].SetStringValue("XA1234");
item = new DicomSequenceItem();
theSet[DicomTags.RequestAttributesSequence].AddSequenceItem(item);
item[DicomTags.RequestedProcedureId].SetStringValue("XA123");
item[DicomTags.ScheduledProcedureStepId].SetStringValue("XA1234");
}
public void SetupSecondaryCapture(DicomAttributeCollection theSet)
{
DateTime studyTime = DateTime.Now;
theSet[DicomTags.SpecificCharacterSet].SetStringValue("ISO_IR 100");
theSet[DicomTags.ImageType].SetStringValue("ORIGINAL\\PRIMARY\\OTHER\\");
theSet[DicomTags.InstanceCreationDate].SetStringValue(DateParser.ToDicomString(DateTime.Now));
theSet[DicomTags.InstanceCreationTime].SetStringValue(TimeParser.ToDicomString(DateTime.Now));
theSet[DicomTags.SopClassUid].SetStringValue(SopClass.SecondaryCaptureImageStorageUid);
theSet[DicomTags.SopInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.StudyDate].SetStringValue(DateParser.ToDicomString(studyTime));
theSet[DicomTags.StudyTime].SetStringValue(TimeParser.ToDicomString(studyTime));
theSet[DicomTags.SeriesDate].SetStringValue(DateParser.ToDicomString(studyTime));
theSet[DicomTags.SeriesTime].SetStringValue(TimeParser.ToDicomString(studyTime));
theSet[DicomTags.AccessionNumber].SetStringValue("A1234");
theSet[DicomTags.Modality].SetStringValue("MR");
theSet[DicomTags.Manufacturer].SetStringValue("ClearCanvas");
theSet[DicomTags.ManufacturersModelName].SetNullValue();
theSet[DicomTags.InstitutionName].SetStringValue("Toronto General Hospital");
theSet[DicomTags.ReferringPhysiciansName].SetStringValue("Last^First");
theSet[DicomTags.StudyDescription].SetStringValue("TEST");
theSet[DicomTags.SeriesDescription].SetStringValue("TEST");
theSet[DicomTags.PatientsName].SetStringValue("Patient^Test");
theSet[DicomTags.PatientId].SetStringValue("ID123-45-9999");
theSet[DicomTags.PatientsBirthDate].SetStringValue("19600102");
theSet[DicomTags.PatientsSize].SetStringValue("10.000244140625");
theSet[DicomTags.SequenceVariant].SetStringValue("OTHER");
theSet[DicomTags.DeviceSerialNumber].SetStringValue("1234");
theSet[DicomTags.SoftwareVersions].SetStringValue("V1.0");
theSet[DicomTags.PatientPosition].SetStringValue("HFS");
theSet[DicomTags.StudyInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.SeriesInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.StudyId].SetStringValue("1933");
theSet[DicomTags.SeriesNumber].SetStringValue("1");
theSet[DicomTags.InstanceNumber].SetStringValue("1");
theSet[DicomTags.ImageComments].SetStringValue("Test SC Image");
theSet[DicomTags.SamplesPerPixel].SetStringValue("1");
theSet[DicomTags.PhotometricInterpretation].SetStringValue("MONOCHROME2");
theSet[DicomTags.Rows].SetStringValue("256");
theSet[DicomTags.Columns].SetStringValue("256");
theSet[DicomTags.BitsAllocated].SetStringValue("16");
theSet[DicomTags.BitsStored].SetStringValue("12");
theSet[DicomTags.HighBit].SetStringValue("11");
theSet[DicomTags.PixelRepresentation].SetStringValue("0");
uint length = 256 * 256 * 2;
DicomAttributeOW pixels = new DicomAttributeOW(DicomTags.PixelData);
byte[] pixelArray = new byte[length];
for (uint i = 0; i < length; i += 2)
pixelArray[i] = (byte)(i % 255);
pixels.Values = pixelArray;
theSet[DicomTags.PixelData] = pixels;
DicomSequenceItem item = new DicomSequenceItem();
theSet[DicomTags.RequestAttributesSequence].AddSequenceItem(item);
item[DicomTags.RequestedProcedureId].SetStringValue("MRR1234");
item[DicomTags.ScheduledProcedureStepId].SetStringValue("MRS1234");
item = new DicomSequenceItem();
theSet[DicomTags.RequestAttributesSequence].AddSequenceItem(item);
item[DicomTags.RequestedProcedureId].SetStringValue("MR2R1234");
item[DicomTags.ScheduledProcedureStepId].SetStringValue("MR2S1234");
DicomSequenceItem studyItem = new DicomSequenceItem();
item[DicomTags.ReferencedStudySequence].AddSequenceItem(studyItem);
studyItem[DicomTags.ReferencedSopClassUid].SetStringValue(SopClass.SecondaryCaptureImageStorageUid);
studyItem[DicomTags.ReferencedSopInstanceUid].SetStringValue("1.2.3.4.5.6.7.8.9");
}
public void SetupMR(DicomAttributeCollection theSet)
{
DateTime studyTime = DateTime.Now;
theSet[DicomTags.SpecificCharacterSet].SetStringValue("ISO_IR 100");
theSet[DicomTags.ImageType].SetStringValue("ORIGINAL\\PRIMARY\\OTHER\\M\\FFE");
theSet[DicomTags.InstanceCreationDate].SetStringValue(DateParser.ToDicomString(DateTime.Now));
theSet[DicomTags.InstanceCreationTime].SetStringValue(TimeParser.ToDicomString(DateTime.Now));
theSet[DicomTags.AcquisitionDatetime].SetDateTime(0, DateTime.Now);
theSet[DicomTags.SopClassUid].SetStringValue(SopClass.MrImageStorageUid);
theSet[DicomTags.SopInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.StudyDate].SetStringValue(DateParser.ToDicomString(studyTime));
theSet[DicomTags.StudyTime].SetStringValue(TimeParser.ToDicomString(studyTime));
theSet[DicomTags.SeriesDate].SetStringValue(DateParser.ToDicomString(studyTime));
theSet[DicomTags.SeriesTime].SetStringValue(TimeParser.ToDicomString(studyTime));
theSet[DicomTags.AccessionNumber].SetStringValue("A1234");
theSet[DicomTags.Modality].SetStringValue("MR");
theSet[DicomTags.Manufacturer].SetStringValue("ClearCanvas");
theSet[DicomTags.ManufacturersModelName].SetNullValue();
theSet[DicomTags.InstitutionName].SetStringValue("Mount Sinai Hospital");
theSet[DicomTags.ReferringPhysiciansName].SetStringValue("Last^First");
theSet[DicomTags.StudyDescription].SetStringValue("HEART");
theSet[DicomTags.SeriesDescription].SetStringValue("Heart 2D EPI BH TRA");
theSet[DicomTags.PatientsName].SetStringValue("Patient^Test");
theSet[DicomTags.PatientId].SetStringValue("ID123-45-9999");
theSet[DicomTags.PatientsBirthDate].SetStringValue("19600101");
theSet[DicomTags.PatientsSex].SetStringValue("M");
theSet[DicomTags.PatientsWeight].SetStringValue("70");
theSet[DicomTags.PatientsSize].SetStringValue("10.000244140625");
theSet[DicomTags.PatientsAge].SetStringValue("035Y");
theSet[DicomTags.SequenceVariant].SetStringValue("OTHER");
theSet[DicomTags.ScanOptions].SetStringValue("CG");
theSet[DicomTags.MrAcquisitionType].SetStringValue("2D");
theSet[DicomTags.SliceThickness].SetStringValue("10.000000");
theSet[DicomTags.RepetitionTime].SetStringValue("857.142883");
theSet[DicomTags.EchoTime].SetStringValue("8.712100");
theSet[DicomTags.NumberOfAverages].SetStringValue("1");
theSet[DicomTags.ImagingFrequency].SetStringValue("63.901150");
theSet[DicomTags.ImagedNucleus].SetStringValue("1H");
theSet[DicomTags.EchoNumbers].SetStringValue("1");
theSet[DicomTags.MagneticFieldStrength].SetStringValue("1.500000");
theSet[DicomTags.SpacingBetweenSlices].SetStringValue("10.00000");
theSet[DicomTags.NumberOfPhaseEncodingSteps].SetStringValue("81");
theSet[DicomTags.EchoTrainLength].SetStringValue("0");
theSet[DicomTags.PercentSampling].SetStringValue("63.281250");
theSet[DicomTags.PercentPhaseFieldOfView].SetStringValue("68.75000");
theSet[DicomTags.DeviceSerialNumber].SetStringValue("1234");
theSet[DicomTags.SoftwareVersions].SetStringValue("V1.0");
theSet[DicomTags.ProtocolName].SetStringValue("2D EPI BH");
theSet[DicomTags.TriggerTime].SetStringValue("14.000000");
theSet[DicomTags.LowRRValue].SetStringValue("948");
theSet[DicomTags.HighRRValue].SetStringValue("1178");
theSet[DicomTags.IntervalsAcquired].SetStringValue("102");
theSet[DicomTags.IntervalsRejected].SetStringValue("0");
theSet[DicomTags.HeartRate].SetStringValue("56");
theSet[DicomTags.ReceiveCoilName].SetStringValue("B");
theSet[DicomTags.TransmitCoilName].SetStringValue("B");
theSet[DicomTags.InPlanePhaseEncodingDirection].SetStringValue("COL");
theSet[DicomTags.FlipAngle].SetStringValue("50.000000");
theSet[DicomTags.PatientPosition].SetStringValue("HFS");
theSet[DicomTags.StudyInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.SeriesInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.StudyId].SetStringValue("1933");
theSet[DicomTags.SeriesNumber].SetStringValue("1");
theSet[DicomTags.AcquisitionNumber].SetStringValue("7");
theSet[DicomTags.InstanceNumber].SetStringValue("1");
theSet[DicomTags.ImagePositionPatient].SetStringValue("-61.7564\\-212.04848\\-99.6208");
theSet[DicomTags.ImageOrientationPatient].SetStringValue("0.861\\0.492\\0.126\\-0.2965");
theSet[DicomTags.FrameOfReferenceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.PositionReferenceIndicator].SetStringValue(null);
theSet[DicomTags.ImageComments].SetStringValue("Test MR Image");
theSet[DicomTags.SamplesPerPixel].SetStringValue("1");
theSet[DicomTags.PhotometricInterpretation].SetStringValue("MONOCHROME2");
theSet[DicomTags.Rows].SetStringValue("256");
theSet[DicomTags.Columns].SetStringValue("256");
theSet[DicomTags.PixelSpacing].SetStringValue("1.367188");
theSet[DicomTags.BitsAllocated].SetStringValue("16");
theSet[DicomTags.BitsStored].SetStringValue("12");
theSet[DicomTags.HighBit].SetStringValue("11");
theSet[DicomTags.PixelRepresentation].SetStringValue("0");
theSet[DicomTags.WindowCenter].SetStringValue("238");
theSet[DicomTags.WindowWidth].SetStringValue("471");
theSet[DicomTags.RescaleSlope].SetStringValue("1.1234567890123");
theSet[DicomTags.RescaleIntercept].SetStringValue("0.0123456789012");
uint length = 256 * 256 * 2;
DicomAttributeOW pixels = new DicomAttributeOW(DicomTags.PixelData);
byte[] pixelArray = new byte[length];
for (uint i = 0; i < length; i += 2)
pixelArray[i] = (byte)(i % 255);
pixels.Values = pixelArray;
theSet[DicomTags.PixelData] = pixels;
DicomSequenceItem item = new DicomSequenceItem();
theSet[DicomTags.RequestAttributesSequence].AddSequenceItem(item);
item[DicomTags.RequestedProcedureId].SetStringValue("MRR1234");
item[DicomTags.ScheduledProcedureStepId].SetStringValue("MRS1234");
item = new DicomSequenceItem();
theSet[DicomTags.RequestAttributesSequence].AddSequenceItem(item);
item[DicomTags.RequestedProcedureId].SetStringValue("MR2R1234");
item[DicomTags.ScheduledProcedureStepId].SetStringValue("MR2S1234");
DicomSequenceItem studyItem = new DicomSequenceItem();
item[DicomTags.ReferencedStudySequence].AddSequenceItem(studyItem);
studyItem[DicomTags.ReferencedSopClassUid].SetStringValue(SopClass.MrImageStorageUid);
studyItem[DicomTags.ReferencedSopInstanceUid].SetStringValue("1.2.3.4.5.6.7.8.9");
}
public void SetupMultiframeXA(DicomAttributeCollection theSet, uint rows, uint columns, uint frames)
{
DateTime studyTime = DateTime.Now;
theSet[DicomTags.SpecificCharacterSet].SetStringValue("ISO_IR 100");
theSet[DicomTags.ImageType].SetStringValue("DERIVED\\SECONDARY\\SINGLE PLANE\\SINGLE A");
theSet[DicomTags.InstanceCreationDate].SetStringValue(DateParser.ToDicomString(DateTime.Now));
theSet[DicomTags.InstanceCreationTime].SetStringValue(TimeParser.ToDicomString(DateTime.Now));
theSet[DicomTags.SopClassUid].SetStringValue(SopClass.XRayAngiographicImageStorageUid);
theSet[DicomTags.SopInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.StudyDate].SetStringValue(DateParser.ToDicomString(studyTime));
theSet[DicomTags.StudyTime].SetStringValue(TimeParser.ToDicomString(studyTime));
theSet[DicomTags.SeriesDate].SetStringValue(DateParser.ToDicomString(studyTime));
theSet[DicomTags.SeriesTime].SetStringValue(TimeParser.ToDicomString(studyTime));
theSet[DicomTags.AccessionNumber].SetStringValue("A4567");
theSet[DicomTags.Modality].SetStringValue("XA");
theSet[DicomTags.Manufacturer].SetStringValue("ClearCanvas");
theSet[DicomTags.InstitutionName].SetStringValue("KardiologieUniklinikHeidelberg");
theSet[DicomTags.ReferringPhysiciansName].SetStringValue("Last^First");
theSet[DicomTags.StudyDescription].SetStringValue("HEART");
theSet[DicomTags.SeriesDescription].SetStringValue("Heart 2D EPI BH TRA");
theSet[DicomTags.PatientsName].SetStringValue("Patient^Test");
theSet[DicomTags.PatientId].SetStringValue("ID123-45-9999");
theSet[DicomTags.PatientsBirthDate].SetStringValue("19600101");
theSet[DicomTags.PatientsSex].SetStringValue("M");
theSet[DicomTags.PatientsWeight].SetStringValue("80");
theSet[DicomTags.PatientsSize].SetStringValue("10.000244140625");
theSet[DicomTags.Kvp].SetStringValue("80");
theSet[DicomTags.ProtocolName].SetStringValue("25 FPS Koronarien");
theSet[DicomTags.FrameTime].SetStringValue("40");
theSet[DicomTags.FrameDelay].SetStringValue("0");
theSet[DicomTags.DistanceSourceToDetector].SetStringValue("1018");
theSet[DicomTags.ExposureTime].SetStringValue("7");
theSet[DicomTags.XRayTubeCurrent].SetStringValue("815");
theSet[DicomTags.RadiationSetting].SetStringValue("GR");
theSet[DicomTags.IntensifierSize].SetStringValue("169.99998");
theSet[DicomTags.PositionerMotion].SetStringValue("STATIC");
theSet[DicomTags.PositionerPrimaryAngle].SetStringValue("-40.2999999");
theSet[DicomTags.PositionerSecondaryAngle].SetStringValue("-15.5");
theSet[DicomTags.DeviceSerialNumber].SetStringValue("1234");
theSet[DicomTags.SoftwareVersions].SetStringValue("V1.0");
theSet[DicomTags.StudyInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.SeriesInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.StudyId].SetStringValue("20021208125233");
theSet[DicomTags.SeriesNumber].SetStringValue("1");
theSet[DicomTags.AcquisitionNumber].SetStringValue("3");
theSet[DicomTags.InstanceNumber].SetStringValue("13");
theSet[DicomTags.PatientOrientation].SetNullValue();
theSet[DicomTags.ImagesInAcquisition].SetStringValue("1");
theSet[DicomTags.SamplesPerPixel].SetStringValue("1");
theSet[DicomTags.PhotometricInterpretation].SetStringValue("MONOCHROME2");
theSet[DicomTags.NumberOfFrames].SetUInt32(0, frames);
theSet[DicomTags.Rows].SetUInt32(0, rows);
theSet[DicomTags.Columns].SetUInt32(0, columns);
theSet[DicomTags.FrameIncrementPointer].SetUInt32(0, DicomTags.FrameTime);
theSet[DicomTags.BitsAllocated].SetStringValue("8");
theSet[DicomTags.BitsStored].SetStringValue("8");
theSet[DicomTags.HighBit].SetStringValue("7");
theSet[DicomTags.PixelRepresentation].SetStringValue("0");
theSet[DicomTags.WindowCenter].SetStringValue("128");
theSet[DicomTags.WindowWidth].SetStringValue("204.8");
theSet[DicomTags.PerformedProcedureStepStartDate].SetStringValue("20080219");
theSet[DicomTags.PerformedProcedureStepStartTime].SetStringValue("143600");
theSet[DicomTags.PerformedProcedureStepId].SetStringValue("UNKNOWN");
// Null SQ Test
theSet[DicomTags.ReferencedStudySequence].SetNullValue();
// FL & FD tags for testing
theSet[DicomTags.SlabThickness].SetFloat64(0, 0.1234567d);
theSet[DicomTags.CalciumScoringMassFactorPatient].SetFloat32(0, 0.7654321f);
uint length = rows * columns * frames;
if (length % 2 == 1)
{
length++;
}
DicomAttributeOW pixels = new DicomAttributeOW(DicomTags.PixelData);
byte[] pixelArray = new byte[length];
pixelArray[length - 1] = 0x00; // Padding char
for (uint frameCount = 0; frameCount < frames; frameCount++)
{
for (uint i = frameCount * rows * columns, val = frameCount + 1; i < (frameCount + 1) * rows * columns; i++, val++)
{
pixelArray[i] = (byte)(val % 255);
}
}
pixels.Values = pixelArray;
theSet[DicomTags.PixelData] = pixels;
DicomSequenceItem item = new DicomSequenceItem();
theSet[DicomTags.RequestAttributesSequence].AddSequenceItem(item);
item[DicomTags.RequestedProcedureId].SetStringValue("XA123");
item[DicomTags.ScheduledProcedureStepId].SetStringValue("XA1234");
item = new DicomSequenceItem();
theSet[DicomTags.RequestAttributesSequence].AddSequenceItem(item);
item[DicomTags.RequestedProcedureId].SetStringValue("XA567");
item[DicomTags.ScheduledProcedureStepId].SetStringValue("XA5678");
}
public void SetupSecondaryCapture(DicomAttributeCollection theSet)
{
DateTime studyTime = DateTime.Now;
theSet[DicomTags.SpecificCharacterSet].SetStringValue("ISO_IR 100");
theSet[DicomTags.ImageType].SetStringValue("ORIGINAL\\PRIMARY\\OTHER\\");
theSet[DicomTags.InstanceCreationDate].SetStringValue(DateParser.ToDicomString(DateTime.Now));
theSet[DicomTags.InstanceCreationTime].SetStringValue(TimeParser.ToDicomString(DateTime.Now));
theSet[DicomTags.SopClassUid].SetStringValue(SopClass.SecondaryCaptureImageStorageUid);
theSet[DicomTags.SopInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.StudyDate].SetStringValue(DateParser.ToDicomString(studyTime));
theSet[DicomTags.StudyTime].SetStringValue(TimeParser.ToDicomString(studyTime));
theSet[DicomTags.SeriesDate].SetStringValue(DateParser.ToDicomString(studyTime));
theSet[DicomTags.SeriesTime].SetStringValue(TimeParser.ToDicomString(studyTime));
theSet[DicomTags.AccessionNumber].SetStringValue("A1234");
theSet[DicomTags.Modality].SetStringValue("MR");
theSet[DicomTags.Manufacturer].SetStringValue("ClearCanvas");
theSet[DicomTags.ManufacturersModelName].SetNullValue();
theSet[DicomTags.InstitutionName].SetStringValue("Toronto General Hospital");
theSet[DicomTags.ReferringPhysiciansName].SetStringValue("Last^First");
theSet[DicomTags.StudyDescription].SetStringValue("TEST");
theSet[DicomTags.SeriesDescription].SetStringValue("TEST");
theSet[DicomTags.PatientsName].SetStringValue("Patient^Test");
theSet[DicomTags.PatientId].SetStringValue("ID123-45-9999");
theSet[DicomTags.PatientsBirthDate].SetStringValue("19600102");
theSet[DicomTags.PatientsSize].SetStringValue("10.000244140625");
theSet[DicomTags.SequenceVariant].SetStringValue("OTHER");
theSet[DicomTags.DeviceSerialNumber].SetStringValue("1234");
theSet[DicomTags.SoftwareVersions].SetStringValue("V1.0");
theSet[DicomTags.PatientPosition].SetStringValue("HFS");
theSet[DicomTags.StudyInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.SeriesInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.StudyId].SetStringValue("1933");
theSet[DicomTags.SeriesNumber].SetStringValue("1");
theSet[DicomTags.InstanceNumber].SetStringValue("1");
theSet[DicomTags.ImageComments].SetStringValue("Test SC Image");
theSet[DicomTags.SamplesPerPixel].SetStringValue("1");
theSet[DicomTags.PhotometricInterpretation].SetStringValue("MONOCHROME2");
theSet[DicomTags.Rows].SetStringValue("256");
theSet[DicomTags.Columns].SetStringValue("256");
theSet[DicomTags.BitsAllocated].SetStringValue("16");
theSet[DicomTags.BitsStored].SetStringValue("12");
theSet[DicomTags.HighBit].SetStringValue("11");
theSet[DicomTags.PixelRepresentation].SetStringValue("0");
uint length = 256 * 256 * 2;
DicomAttributeOW pixels = new DicomAttributeOW(DicomTags.PixelData);
byte[] pixelArray = new byte[length];
for (uint i = 0; i < length; i += 2)
{
pixelArray[i] = (byte)(i % 255);
}
pixels.Values = pixelArray;
theSet[DicomTags.PixelData] = pixels;
DicomSequenceItem item = new DicomSequenceItem();
theSet[DicomTags.RequestAttributesSequence].AddSequenceItem(item);
item[DicomTags.RequestedProcedureId].SetStringValue("MRR1234");
item[DicomTags.ScheduledProcedureStepId].SetStringValue("MRS1234");
item = new DicomSequenceItem();
theSet[DicomTags.RequestAttributesSequence].AddSequenceItem(item);
item[DicomTags.RequestedProcedureId].SetStringValue("MR2R1234");
item[DicomTags.ScheduledProcedureStepId].SetStringValue("MR2S1234");
DicomSequenceItem studyItem = new DicomSequenceItem();
item[DicomTags.ReferencedStudySequence].AddSequenceItem(studyItem);
studyItem[DicomTags.ReferencedSopClassUid].SetStringValue(SopClass.SecondaryCaptureImageStorageUid);
studyItem[DicomTags.ReferencedSopInstanceUid].SetStringValue("1.2.3.4.5.6.7.8.9");
}
public void SetupMR(DicomAttributeCollection theSet)
{
DateTime studyTime = DateTime.Now;
theSet[DicomTags.SpecificCharacterSet].SetStringValue("ISO_IR 100");
theSet[DicomTags.ImageType].SetStringValue("ORIGINAL\\PRIMARY\\OTHER\\M\\FFE");
theSet[DicomTags.InstanceCreationDate].SetStringValue(DateParser.ToDicomString(DateTime.Now));
theSet[DicomTags.InstanceCreationTime].SetStringValue(TimeParser.ToDicomString(DateTime.Now));
theSet[DicomTags.AcquisitionDatetime].SetDateTime(0, DateTime.Now);
theSet[DicomTags.SopClassUid].SetStringValue(SopClass.MrImageStorageUid);
theSet[DicomTags.SopInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.StudyDate].SetStringValue(DateParser.ToDicomString(studyTime));
theSet[DicomTags.StudyTime].SetStringValue(TimeParser.ToDicomString(studyTime));
theSet[DicomTags.SeriesDate].SetStringValue(DateParser.ToDicomString(studyTime));
theSet[DicomTags.SeriesTime].SetStringValue(TimeParser.ToDicomString(studyTime));
theSet[DicomTags.AccessionNumber].SetStringValue("A1234");
theSet[DicomTags.Modality].SetStringValue("MR");
theSet[DicomTags.Manufacturer].SetStringValue("ClearCanvas");
theSet[DicomTags.ManufacturersModelName].SetNullValue();
theSet[DicomTags.InstitutionName].SetStringValue("Mount Sinai Hospital");
theSet[DicomTags.ReferringPhysiciansName].SetStringValue("Last^First");
theSet[DicomTags.StudyDescription].SetStringValue("HEART");
theSet[DicomTags.SeriesDescription].SetStringValue("Heart 2D EPI BH TRA");
theSet[DicomTags.PatientsName].SetStringValue("Patient^Test");
theSet[DicomTags.PatientId].SetStringValue("ID123-45-9999");
theSet[DicomTags.PatientsBirthDate].SetStringValue("19600101");
theSet[DicomTags.PatientsSex].SetStringValue("M");
theSet[DicomTags.PatientsWeight].SetStringValue("70");
theSet[DicomTags.PatientsSize].SetStringValue("10.000244140625");
theSet[DicomTags.PatientsAge].SetStringValue("035Y");
theSet[DicomTags.SequenceVariant].SetStringValue("OTHER");
theSet[DicomTags.ScanOptions].SetStringValue("CG");
theSet[DicomTags.MrAcquisitionType].SetStringValue("2D");
theSet[DicomTags.SliceThickness].SetStringValue("10.000000");
theSet[DicomTags.RepetitionTime].SetStringValue("857.142883");
theSet[DicomTags.EchoTime].SetStringValue("8.712100");
theSet[DicomTags.NumberOfAverages].SetStringValue("1");
theSet[DicomTags.ImagingFrequency].SetStringValue("63.901150");
theSet[DicomTags.ImagedNucleus].SetStringValue("1H");
theSet[DicomTags.EchoNumbers].SetStringValue("1");
theSet[DicomTags.MagneticFieldStrength].SetStringValue("1.500000");
theSet[DicomTags.SpacingBetweenSlices].SetStringValue("10.00000");
theSet[DicomTags.NumberOfPhaseEncodingSteps].SetStringValue("81");
theSet[DicomTags.EchoTrainLength].SetStringValue("0");
theSet[DicomTags.PercentSampling].SetStringValue("63.281250");
theSet[DicomTags.PercentPhaseFieldOfView].SetStringValue("68.75000");
theSet[DicomTags.DeviceSerialNumber].SetStringValue("1234");
theSet[DicomTags.SoftwareVersions].SetStringValue("V1.0");
theSet[DicomTags.ProtocolName].SetStringValue("2D EPI BH");
theSet[DicomTags.TriggerTime].SetStringValue("14.000000");
theSet[DicomTags.LowRRValue].SetStringValue("948");
theSet[DicomTags.HighRRValue].SetStringValue("1178");
theSet[DicomTags.IntervalsAcquired].SetStringValue("102");
theSet[DicomTags.IntervalsRejected].SetStringValue("0");
theSet[DicomTags.HeartRate].SetStringValue("56");
theSet[DicomTags.ReceiveCoilName].SetStringValue("B");
theSet[DicomTags.TransmitCoilName].SetStringValue("B");
theSet[DicomTags.InPlanePhaseEncodingDirection].SetStringValue("COL");
theSet[DicomTags.FlipAngle].SetStringValue("50.000000");
theSet[DicomTags.PatientPosition].SetStringValue("HFS");
theSet[DicomTags.StudyInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.SeriesInstanceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.StudyId].SetStringValue("1933");
theSet[DicomTags.SeriesNumber].SetStringValue("1");
theSet[DicomTags.AcquisitionNumber].SetStringValue("7");
theSet[DicomTags.InstanceNumber].SetStringValue("1");
theSet[DicomTags.ImagePositionPatient].SetStringValue("-61.7564\\-212.04848\\-99.6208");
theSet[DicomTags.ImageOrientationPatient].SetStringValue("0.861\\0.492\\0.126\\-0.2965");
theSet[DicomTags.FrameOfReferenceUid].SetStringValue(DicomUid.GenerateUid().UID);
theSet[DicomTags.PositionReferenceIndicator].SetStringValue(null);
theSet[DicomTags.ImageComments].SetStringValue("Test MR Image");
theSet[DicomTags.SamplesPerPixel].SetStringValue("1");
theSet[DicomTags.PhotometricInterpretation].SetStringValue("MONOCHROME2");
theSet[DicomTags.Rows].SetStringValue("256");
theSet[DicomTags.Columns].SetStringValue("256");
theSet[DicomTags.PixelSpacing].SetStringValue("1.367188\\1.367188");
theSet[DicomTags.BitsAllocated].SetStringValue("16");
theSet[DicomTags.BitsStored].SetStringValue("12");
theSet[DicomTags.HighBit].SetStringValue("11");
theSet[DicomTags.PixelRepresentation].SetStringValue("0");
theSet[DicomTags.WindowCenter].SetStringValue("238");
theSet[DicomTags.WindowWidth].SetStringValue("471");
theSet[DicomTags.RescaleSlope].SetStringValue("1.1234567890123");
theSet[DicomTags.RescaleIntercept].SetStringValue("0.0123456789012");
uint length = 256 * 256 * 2;
DicomAttributeOW pixels = new DicomAttributeOW(DicomTags.PixelData);
byte[] pixelArray = new byte[length];
for (uint i = 0; i < length; i += 2)
{
pixelArray[i] = (byte)(i % 255);
}
pixels.Values = pixelArray;
theSet[DicomTags.PixelData] = pixels;
DicomSequenceItem item = new DicomSequenceItem();
theSet[DicomTags.RequestAttributesSequence].AddSequenceItem(item);
item[DicomTags.RequestedProcedureId].SetStringValue("MRR1234");
item[DicomTags.ScheduledProcedureStepId].SetStringValue("MRS1234");
item = new DicomSequenceItem();
theSet[DicomTags.RequestAttributesSequence].AddSequenceItem(item);
item[DicomTags.RequestedProcedureId].SetStringValue("MR2R1234");
item[DicomTags.ScheduledProcedureStepId].SetStringValue("MR2S1234");
DicomSequenceItem studyItem = new DicomSequenceItem();
item[DicomTags.ReferencedStudySequence].AddSequenceItem(studyItem);
studyItem[DicomTags.ReferencedSopClassUid].SetStringValue(SopClass.MrImageStorageUid);
studyItem[DicomTags.ReferencedSopInstanceUid].SetStringValue("1.2.3.4.5.6.7.8.9");
}
public DicomReadStatus Read(DicomTag stopAtTag, DicomReadOptions options)
{
if (stopAtTag == null)
stopAtTag = new DicomTag(0xFFFFFFFF, "Bogus Tag", "BogusTag", DicomVr.UNvr, false, 1, 1, false);
// Counters:
// _remain - bytes remaining in stream
// _bytes - estimates bytes to end of dataset
// _read - number of bytes read from stream
try
{
BytesNeeded = 0;
_remain = _stream.Length - _stream.Position;
while (_remain > 0)
{
if (_inGroup2 && BytesRead >= _endGroup2)
{
_inGroup2 = false;
// Only change if we're still reading the meta info
if (Dataset.StartTagValue < DicomTags.TransferSyntaxUid)
{
TransferSyntax group2Syntax =
TransferSyntax.GetTransferSyntax(
Dataset[DicomTags.TransferSyntaxUid].GetString(0, String.Empty));
if (group2Syntax == null)
throw new DicomException("Unsupported transfer syntax in group 2 elements");
TransferSyntax = group2Syntax;
}
}
uint tagValue;
if (LastTagRead == null)
{
if (_remain < 4)
return NeedMoreData(4);
_pos = _stream.Position;
ushort g = _reader.ReadUInt16();
ushort e = _reader.ReadUInt16();
tagValue = DicomTag.GetTagValue(g, e);
if (DicomTag.IsPrivateGroup(g) && e > 0x00ff)
{
SaveTagRead = LastTagRead = DicomTagDictionary.GetDicomTag(g, e) ??
new DicomTag((uint) g << 16 | e, "Private Tag", "PrivateTag", DicomVr.UNvr, false, 1, uint.MaxValue, false);
}
else
{
if (e == 0x0000)
SaveTagRead = LastTagRead = new DicomTag((uint)g << 16 | e, "Group Length", "GroupLength", DicomVr.ULvr, false, 1, 1, false);
else
{
SaveTagRead = LastTagRead = DicomTagDictionary.GetDicomTag(g, e) ??
new DicomTag((uint) g << 16 | e, "Private Tag", "PrivateTag", DicomVr.UNvr, false, 1, uint.MaxValue, false);
}
}
_remain -= 4;
BytesEstimated += 4;
BytesRead += 4;
}
else
tagValue = LastTagRead.TagValue;
if ((tagValue >= stopAtTag.TagValue)
&& (_sqrs.Count == 0)) // only exit in root message when after stop tag
return DicomReadStatus.Success;
bool twoByteLength;
if (_vr == null)
{
if (_syntax.ExplicitVr)
{
if (LastTagRead == DicomTag.Item ||
LastTagRead == DicomTag.ItemDelimitationItem ||
LastTagRead == DicomTag.SequenceDelimitationItem)
{
_vr = DicomVr.NONE;
twoByteLength = _vr.Is16BitLengthField;
}
else
{
if (_remain < 2)
return NeedMoreData(2);
string vr = new string(_reader.ReadChars(2));
_vr = DicomVr.GetVR(vr);
twoByteLength = _vr.Is16BitLengthField;
_remain -= 2;
BytesEstimated += 2;
BytesRead += 2;
if (LastTagRead.VR.Equals(DicomVr.UNvr))
{
LastTagRead = new DicomTag(LastTagRead.TagValue, "Private Tag", "PrivateTag", _vr, false, 1, uint.MaxValue, false);
if (vr.Equals("??"))
twoByteLength = true;
}
else if (!LastTagRead.VR.Equals(_vr))
{
if (!vr.Equals(" "))
{
DicomTag tag =
new DicomTag(LastTagRead.TagValue, LastTagRead.Name, LastTagRead.VariableName, _vr, LastTagRead.MultiVR,
LastTagRead.VMLow, LastTagRead.VMHigh,
LastTagRead.Retired);
LastTagRead = tag;
; // TODO, log something
}
}
}
}
else
{
_vr = LastTagRead.VR;
twoByteLength = _vr.Is16BitLengthField;
}
if (_vr == DicomVr.UNvr)
{
if (LastTagRead.IsPrivate)
{
if (LastTagRead.Element <= 0x00ff && LastTagRead.Element >= 0x0010)
{
// Reset the tag with the right VR and a more descriptive name.
LastTagRead = new DicomTag(LastTagRead.TagValue, "Private Creator Code", "PrivateCreatorCode", DicomVr.LOvr, false, 1, uint.MaxValue, false);
// private creator id
// Only set the VR to LO for Implicit VR, if we do it for
// Explicit VR syntaxes, we would incorrectly read the tag
// length below.
if (!_syntax.ExplicitVr)
_vr = DicomVr.LOvr;
}
else if (_stream.CanSeek && Flags.IsSet(options, DicomReadOptions.AllowSeekingForContext))
{
// attempt to identify private sequence by checking if the tag has
// an undefined length
long pos = _stream.Position;
int bytesToCheck = _syntax.ExplicitVr ? 6 : 4;
if (_remain >= bytesToCheck)
{
if (_syntax.ExplicitVr)
_reader.ReadUInt16();
uint l = _reader.ReadUInt32();
if (l == UndefinedLength)
_vr = DicomVr.SQvr;
}
_stream.Position = pos;
}
}
}
}
else
twoByteLength = _vr.Is16BitLengthField;
// Read the value length
if (_len == UndefinedLength)
{
if (_syntax.ExplicitVr)
{
if (LastTagRead == DicomTag.Item ||
LastTagRead == DicomTag.ItemDelimitationItem ||
LastTagRead == DicomTag.SequenceDelimitationItem)
{
if (_remain < 4)
return NeedMoreData(4);
_len = _reader.ReadUInt32();
_remain -= 4;
BytesEstimated += 4;
BytesRead += 4;
}
else
{
if (twoByteLength)
{
if (_remain < 2)
return NeedMoreData(2);
_len = _reader.ReadUInt16();
_remain -= 2;
BytesEstimated += 2;
BytesRead += 2;
}
else
{
if (_remain < 6)
return NeedMoreData(6);
_reader.ReadByte();
_reader.ReadByte();
_len = _reader.ReadUInt32();
_remain -= 6;
BytesEstimated += 6;
BytesRead += 6;
}
}
}
else
{
if (_remain < 4)
return NeedMoreData(4);
_len = _reader.ReadUInt32();
_remain -= 4;
BytesEstimated += 4;
BytesRead += 4;
}
if ((_len != UndefinedLength)
&& !_vr.Equals(DicomVr.SQvr)
&& !(LastTagRead.Equals(DicomTag.Item)
&& _fragment == null))
BytesEstimated += _len;
}
// If we have a private creator code, set the VR to LO, because
// that is what it is. We must do this after we read the length
// so that the 32 bit length is read properly.
if ((LastTagRead.IsPrivate)
&& (_vr.Equals(DicomVr.UNvr))
&& (LastTagRead.Element <= 0x00ff))
_vr = DicomVr.LOvr;
if (_fragment != null)
{
// In the middle of parsing pixels
if (LastTagRead == DicomTag.Item)
{
if (_remain < _len)
return NeedMoreData(_remain - _len);
if (Flags.IsSet(options, DicomReadOptions.StorePixelDataReferences)
&& _fragment.HasOffsetTable)
{
FileReference reference = new FileReference(Filename, _stream.Position, _len, _endian, DicomVr.OBvr);
DicomFragment fragment =
new DicomFragment(reference);
_fragment.AddFragment(fragment);
_stream.Seek(_len, SeekOrigin.Current);
}
else
{
ByteBuffer data = new ByteBuffer(_endian, _len);
data.CopyFrom(_stream, (int) _len);
if (!_fragment.HasOffsetTable)
_fragment.SetOffsetTable(data);
else
{
DicomFragment fragment = new DicomFragment(data);
_fragment.AddFragment(fragment);
}
}
_remain -= _len;
BytesRead += _len;
}
else if (LastTagRead == DicomTag.SequenceDelimitationItem)
{
Dataset[_fragment.Tag] = _fragment;
_fragment = null;
}
else
{
Platform.Log(LogLevel.Error, "Encountered unexpected tag in stream: {0}", LastTagRead.ToString());
// unexpected tag
return DicomReadStatus.UnknownError;
}
}
else if (_sqrs.Count > 0 &&
(LastTagRead == DicomTag.Item ||
LastTagRead == DicomTag.ItemDelimitationItem ||
LastTagRead == DicomTag.SequenceDelimitationItem))
{
SequenceRecord rec = _sqrs.Peek();
if (LastTagRead.Equals(DicomTag.Item))
{
if (_len != UndefinedLength)
{
if (_len > _remain)
return NeedMoreData(_remain - _len);
}
DicomSequenceItem ds;
if (rec.Tag.TagValue.Equals(DicomTags.DirectoryRecordSequence))
{
DirectoryRecordSequenceItem dr = new DirectoryRecordSequenceItem
{
Offset = (uint) _pos
};
ds = dr;
}
else
ds = new DicomSequenceItem();
rec.Current = ds;
if (rec.Tag.VR.Equals(DicomVr.UNvr))
{
DicomTag tag = new DicomTag(rec.Tag.TagValue, rec.Tag.Name,
rec.Tag.VariableName, DicomVr.SQvr, rec.Tag.MultiVR, rec.Tag.VMLow,
rec.Tag.VMHigh, rec.Tag.Retired);
rec.Parent[tag].AddSequenceItem(ds);
}
else
rec.Parent[rec.Tag].AddSequenceItem(ds);
// Specific character set is inherited, save it. It will be overwritten
// if a new value of the tag is encountered in the sequence.
rec.Current.SpecificCharacterSet = rec.Parent.SpecificCharacterSet;
// save the sequence length
rec.Curpos = _pos + 8;
rec.Curlen = _len;
_sqrs.Pop();
_sqrs.Push(rec);
if (_len != UndefinedLength)
{
ByteBuffer data = new ByteBuffer(_endian, _len);
data.CopyFrom(_stream, (int)_len);
data.Stream.Position = 0;
_remain -= _len;
BytesRead += _len;
DicomStreamReader idsr = new DicomStreamReader(data.Stream)
{
Dataset = ds,
TransferSyntax = rec.Tag.VR.Equals(DicomVr.UNvr)
? TransferSyntax.ImplicitVrLittleEndian
: _syntax,
Filename = Filename
};
DicomReadStatus stat = idsr.Read(null, options);
if (stat != DicomReadStatus.Success)
{
Platform.Log(LogLevel.Error, "Unexpected parsing error ({0}) when reading sequence attribute: {1}.", stat, rec.Tag.ToString());
return stat;
}
}
}
else if (LastTagRead == DicomTag.ItemDelimitationItem)
{
}
else if (LastTagRead == DicomTag.SequenceDelimitationItem)
{
SequenceRecord rec2 = _sqrs.Pop();
if (rec2.Current==null)
rec2.Parent[rec.Tag].SetNullValue();
}
if (rec.Len != UndefinedLength)
{
long end = rec.Pos + 8 + rec.Len;
if (_syntax.ExplicitVr)
end += 2 + 2;
if (_stream.Position >= end)
{
_sqrs.Pop();
}
}
}
else
{
if (_len == UndefinedLength)
{
if (_vr.Equals(DicomVr.UNvr))
{
if (!_syntax.ExplicitVr)
{
_vr = DicomVr.SQvr;
LastTagRead = LastTagRead.IsPrivate
? new DicomTag(LastTagRead.TagValue, "Private Tag", "PrivateTag", DicomVr.SQvr, false, 1, uint.MaxValue, false)
: new DicomTag(LastTagRead.TagValue, "Unknown Tag", "UnknownTag", DicomVr.SQvr, false, 1, uint.MaxValue, false);
}
else
{
// To handle this case, we'd have to add a new mechanism to transition the parser to implicit VR parsing,
// and then return back to implicit once the parsing of the SQ is complete.
Platform.Log(LogLevel.Error,
"Encountered unknown tag {0}, encoded as undefined length in an Explicit VR transfer syntax at offset {1}. Unable to parse.",
LastTagRead, _stream.Position);
return DicomReadStatus.UnknownError;
}
}
if (_vr.Equals(DicomVr.SQvr))
{
SequenceRecord rec = new SequenceRecord
{
Parent = _sqrs.Count > 0
? _sqrs.Peek().Current
: Dataset,
Current = null,
Tag = LastTagRead,
Len = UndefinedLength
};
_sqrs.Push(rec);
}
else
{
_fragment = new DicomFragmentSequence(LastTagRead);
Dataset.LoadDicomFields(_fragment);
}
}
else
{
if (_vr.Equals(DicomVr.SQvr))
{
if (_len == 0)
{
DicomAttributeCollection ds;
if (_sqrs.Count > 0)
{
SequenceRecord rec = _sqrs.Peek();
ds = rec.Current;
}
else
ds = Dataset;
ds[LastTagRead].SetNullValue();
}
else
{
SequenceRecord rec = new SequenceRecord
{
Len = _len,
Pos = _pos,
Tag = LastTagRead,
Parent = _sqrs.Count > 0
? _sqrs.Peek().Current
: Dataset
};
_sqrs.Push(rec);
}
}
else
{
if (_remain < _len)
return NeedMoreData(_len - _remain);
if ((LastTagRead.TagValue == DicomTags.PixelData)
&& Flags.IsSet(options, DicomReadOptions.DoNotStorePixelDataInDataSet))
{
// Skip PixelData !!
_stream.Seek((int) _len, SeekOrigin.Current);
_remain -= _len;
BytesRead += _len;
}
else if ((LastTagRead.TagValue == DicomTags.PixelData) &&
Flags.IsSet(options, DicomReadOptions.StorePixelDataReferences))
{
FileReference reference =
new FileReference(Filename, _stream.Position, _len, _endian,
LastTagRead.VR);
_stream.Seek((int) _len, SeekOrigin.Current);
if (LastTagRead.VR.Equals(DicomVr.OWvr))
{
DicomAttributeOW elem = new DicomAttributeOW(LastTagRead, reference);
Dataset[LastTagRead] = elem;
}
else if (LastTagRead.VR.Equals(DicomVr.OBvr))
{
DicomAttributeOB elem = new DicomAttributeOB(LastTagRead, reference);
Dataset[LastTagRead] = elem;
}
else
{
DicomAttributeOF elem = new DicomAttributeOF(LastTagRead, reference);
Dataset[LastTagRead] = elem;
}
_remain -= _len;
BytesRead += _len;
}
else
{
ByteBuffer bb = new ByteBuffer(_len);
// If the tag is impacted by specific character set,
// set the encoding properly.
if (LastTagRead.VR.SpecificCharacterSet)
{
if (_sqrs.Count > 0)
{
SequenceRecord rec = _sqrs.Peek();
bb.SpecificCharacterSet = rec.Current.SpecificCharacterSet;
}
else
{
bb.SpecificCharacterSet = Dataset.SpecificCharacterSet;
}
}
if (LastTagRead.VR.Equals(DicomVr.UNvr)
&& !SaveTagRead.VR.Equals(DicomVr.UNvr)
&& !SaveTagRead.VR.Equals(DicomVr.SQvr)
&& Flags.IsSet(options, DicomReadOptions.UseDictionaryForExplicitUN))
{
LastTagRead = SaveTagRead;
bb.Endian = Endian.Little;
}
else
{
bb.Endian = _endian;
}
bb.CopyFrom(_stream, (int) _len);
DicomAttribute elem = LastTagRead.CreateDicomAttribute(bb);
_remain -= _len;
BytesRead += _len;
if (_sqrs.Count > 0)
{
SequenceRecord rec = _sqrs.Peek();
DicomAttributeCollection ds = rec.Current;
if (elem.Tag.TagValue == DicomTags.SpecificCharacterSet)
{
ds.SpecificCharacterSet = elem.ToString();
}
if (LastTagRead.Element == 0x0000)
{
if (Flags.IsSet(options, DicomReadOptions.KeepGroupLengths))
ds[LastTagRead] = elem;
}
else
ds[LastTagRead] = elem;
if (rec.Curlen != UndefinedLength)
{
long end = rec.Curpos + rec.Curlen;
if (_stream.Position >= end)
{
rec.Current = null;
}
}
}
else
{
if (LastTagRead.TagValue == DicomTags.FileMetaInformationGroupLength)
{
// Save the end of the group 2 elements, so that we can automatically
// check and change our transfer syntax when needed.
_inGroup2 = true;
uint group2Len;
elem.TryGetUInt32(0, out group2Len);
_endGroup2 = BytesRead + group2Len;
}
else if (LastTagRead.TagValue == DicomTags.SpecificCharacterSet)
{
Dataset.SpecificCharacterSet = elem.ToString();
}
if (LastTagRead.Element == 0x0000)
{
if (Flags.IsSet(options, DicomReadOptions.KeepGroupLengths))
Dataset[LastTagRead] = elem;
}
else
Dataset[LastTagRead] = elem;
}
}
}
}
}
LastTagRead = null;
_vr = null;
_len = UndefinedLength;
}
return DicomReadStatus.Success;
}
catch (EndOfStreamException e)
{
// should never happen
Platform.Log(LogLevel.Error, "Unexpected exception when reading file: {0}", e.ToString());
return DicomReadStatus.UnknownError;
}
}
//public void SaveEfilm(string efilmFullPath, ref string efilmOriginalSopInstanceUID)
//{
// efilmOriginalSopInstanceUID = string.Empty;
//}
public void SaveEfilm(string efilmFullPath, ref string efilmOriginalSopInstanceUID, ref string efilmOriginalStudyInstanceUid, bool ifSaveEFilm)
{
efilmOriginalSopInstanceUID = string.Empty;
try
{
Logger.LogFuncUp();
if (_dicomDataHeader == null)
{
return;
}
var wrtBmp = RenderControlWriteableBitmap();
if (wrtBmp == null)
{
throw new ApplicationException("ViewerControl Writeable Bitmap Render failed.");
}
byte[] data = ProcessImage(wrtBmp);
Console.WriteLine(Convert.ToString(wrtBmp.PixelWidth) + " ,,,,," + Convert.ToString(wrtBmp.PixelHeight));
////MedViewerLayoutCell layoutCell = medViewerControl.LayoutManager.RootCell;
////MedViewerControlCell cell = GetControlCell(layoutCell);
var pixelHeightTag = new DicomAttributeUS(new DicomTag(Pipeline.Dictionary.Tag.Rows));
pixelHeightTag.SetUInt16(0, Convert.ToUInt16(wrtBmp.PixelHeight));
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.Rows);
_dicomDataHeader.AddDicomAttribute(pixelHeightTag);
var pixelWidthTag = new DicomAttributeUS(new DicomTag(Pipeline.Dictionary.Tag.Columns));
pixelWidthTag.SetUInt16(0, Convert.ToUInt16(wrtBmp.PixelWidth));
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.Columns);
_dicomDataHeader.AddDicomAttribute(pixelWidthTag);
var bitStoredTag = new DicomAttributeUS(new DicomTag(Pipeline.Dictionary.Tag.BitsStored));
bitStoredTag.SetUInt16(0, 8);
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.BitsStored);
_dicomDataHeader.AddDicomAttribute(bitStoredTag);
var bitAllocatedTag = new DicomAttributeUS(new DicomTag(Pipeline.Dictionary.Tag.BitsAllocated));
bitAllocatedTag.SetUInt16(0, 8);
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.BitsAllocated);
_dicomDataHeader.AddDicomAttribute(bitAllocatedTag);
var hightBitTag = new DicomAttributeUS(new DicomTag(Pipeline.Dictionary.Tag.HighBit));
hightBitTag.SetUInt16(0, 7);
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.HighBit);
_dicomDataHeader.AddDicomAttribute(hightBitTag);
var pixelRepresentationTag = new DicomAttributeUS(new DicomTag(Pipeline.Dictionary.Tag.PixelRepresentation));
pixelRepresentationTag.SetUInt16(0, 0);
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.PixelRepresentation);
_dicomDataHeader.AddDicomAttribute(pixelRepresentationTag);
var rescaleSlopeTag = new DicomAttributeDS(new DicomTag(Pipeline.Dictionary.Tag.RescaleSlope));
rescaleSlopeTag.SetString(0, "1");
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.RescaleSlope);
_dicomDataHeader.AddDicomAttribute(rescaleSlopeTag);
var rescaleInterceptTag = new DicomAttributeDS(new DicomTag(Pipeline.Dictionary.Tag.RescaleIntercept));
rescaleInterceptTag.SetString(0, "0");;
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.RescaleIntercept);
_dicomDataHeader.AddDicomAttribute(rescaleInterceptTag);
////insert Photometric Interpretation //maybe can fix inverse problem
//var photometricInterpretationTag = new DicomAttributeUS(new DicomTag(Pipeline.Dictionary.Tag.PhotometricInterpretation));
//rescaleInterceptTag.SetString(0, "MONOCHROME2");
////_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.PhotometricInterpretation);
//_dicomDataHeader.AddDicomAttribute(photometricInterpretationTag);
//insert Photometric Interpretation
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.PhotometricInterpretation);
var photometricInterpretationTag = DicomAttribute.CreateAttribute(Pipeline.Dictionary.Tag.PhotometricInterpretation);
if (!photometricInterpretationTag.SetString(0, "MONOCHROME2"))
{
throw new Exception("Failed to Insert Columns to Data header");
}
_dicomDataHeader.AddDicomAttribute(photometricInterpretationTag);
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.WindowWidth);
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.WindowCenter);
var windowWidthTag = new DicomAttributeDS(new DicomTag(Pipeline.Dictionary.Tag.WindowWidth));
//var windowWidthTag = DicomAttribute.CreateAttribute(Pipeline.Dictionary.Tag.WindowWidth);
windowWidthTag.SetString(0, "256");
_dicomDataHeader.AddDicomAttribute(windowWidthTag);
var windowCenterTag = new DicomAttributeDS(new DicomTag(Pipeline.Dictionary.Tag.WindowCenter));
//var windowCenterTag = DicomAttribute.CreateAttribute(Pipeline.Dictionary.Tag.WindowCenter);
windowCenterTag.SetString(0, "127");
_dicomDataHeader.AddDicomAttribute(windowCenterTag);
if (_dicomDataHeader.Contains(Pipeline.Dictionary.Tag.PixelData))
{
_dicomDataHeader[Pipeline.Dictionary.Tag.PixelData].SetBytes(0, data);
}
else
{
var pixelTag = new DicomAttributeOW(new DicomTag(Pipeline.Dictionary.Tag.PixelData));
pixelTag.SetBytes(0, data);
_dicomDataHeader.AddDicomAttribute(pixelTag);
}
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.ShutterShape);
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.ShutterLowerHorizontalEdge);
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.ShutterRightVerticalEdge);
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.ShutterLeftVerticalEdge);
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.ShutterUpperHorizontalEdge);
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.ImageHorizontalFlip);
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.ImageRotation);
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.SeriesNumber);
//_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.);
//AssembleTag();
var uidManager = McsfDatabaseDicomUIDManagerFactory.Instance().CreateUIDManager();
var seriesInstanceUid = uidManager.CreateSeriesUID("1", "2", ""); //seriesUID; //
var imageUid = uidManager.CreateImageUID("");
//_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.SeriesInstanceUid);
//var seriesInstanceUidTag = new DicomAttributeUI(new DicomTag(Pipeline.Dictionary.Tag.SeriesInstanceUid));
//seriesInstanceUidTag.SetString(0, seriesInstanceUid);
//_dicomDataHeader.AddDicomAttribute(seriesInstanceUidTag);
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.SOPInstanceUID);
var sopInstanceUidTag = new DicomAttributeUI(new DicomTag(Pipeline.Dictionary.Tag.SOPInstanceUID));
sopInstanceUidTag.SetString(0, imageUid);
_dicomDataHeader.AddDicomAttribute(sopInstanceUidTag);
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.ImageType);
var imageTypeCollection = ("DERIVED\\SECONDARY\\DISPLAY\\FILMING\\EFILM").Split('\\');
InsertStringArrayDicomElement(_dicomDataHeader, Pipeline.Dictionary.Tag.ImageType, imageTypeCollection);
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.ConversionType);
var cTypeTag = new DicomAttributeCS(new DicomTag(Pipeline.Dictionary.Tag.ConversionType));
cTypeTag.SetString(0, "WSD");
_dicomDataHeader.AddDicomAttribute(cTypeTag);
_dicomDataHeader.RemoveDicomAttribute(Pipeline.Dictionary.Tag.SeriesDescription);
var seriesDescriptionTag = new DicomAttributeLO(new DicomTag(Pipeline.Dictionary.Tag.SeriesDescription));
seriesDescriptionTag.SetString(0, "Electronic film_" + DateTime.Now.ToString());
_dicomDataHeader.AddDicomAttribute(seriesDescriptionTag);
_dicomConvertorProxy.SaveFile(_dicomDataHeader, efilmFullPath, _proxy);
var medViewerControlCell = medViewerControl.LayoutManager.ControlCells.FirstOrDefault();
if (medViewerControlCell != null)
{
var currentPage = medViewerControlCell.Image.CurrentPage;
efilmOriginalSopInstanceUID = currentPage.SOPInstanceUID;
var dicomHeader = currentPage.ImageHeader.DicomHeader;
if (dicomHeader.ContainsKey(ServiceTagName.StudyInstanceUID))
{
efilmOriginalStudyInstanceUid = dicomHeader[ServiceTagName.StudyInstanceUID];
}
}
if (!ifSaveEFilm)
{
return;
}
CreateSeries(efilmOriginalStudyInstanceUid, seriesInstanceUid);
SaveEFilmInCommonSave(seriesInstanceUid);
Logger.LogFuncDown();
}
catch (Exception ex)
{
Logger.LogFuncException(ex.Message + ex.StackTrace);
}
finally
{
medViewerControl.RemoveAll();
}
}
