public void ChangeTransferSyntax(DicomTransferSyntax newTransferSyntax, DcmCodecParameters parameters)
{
DicomTransferSyntax oldTransferSyntax = InternalTransferSyntax;
if (oldTransferSyntax == newTransferSyntax)
return;
if (oldTransferSyntax.IsEncapsulated && newTransferSyntax.IsEncapsulated) {
ChangeTransferSyntax(DicomTransferSyntax.ExplicitVRLittleEndian, parameters);
oldTransferSyntax = DicomTransferSyntax.ExplicitVRLittleEndian;
}
if (Contains(DicomTags.PixelData)) {
DcmPixelData oldPixelData = new DcmPixelData(this);
DcmPixelData newPixelData = new DcmPixelData(newTransferSyntax, oldPixelData);
if (oldTransferSyntax.IsEncapsulated) {
IDcmCodec codec = DicomCodec.GetCodec(oldTransferSyntax);
codec.Decode(this, oldPixelData, newPixelData, parameters);
}
else if (newTransferSyntax.IsEncapsulated) {
IDcmCodec codec = DicomCodec.GetCodec(newTransferSyntax);
codec.Encode(this, oldPixelData, newPixelData, parameters);
}
else {
for (int i = 0; i < oldPixelData.NumberOfFrames; i++) {
byte[] data = oldPixelData.GetFrameDataU8(i);
newPixelData.AddFrame(data);
}
}
newPixelData.UpdateDataset(this);
}
SetInternalTransferSyntax(newTransferSyntax);
}
public void Decode(DcmDataset dataset, DcmPixelData oldPixelData, DcmPixelData newPixelData, DcmCodecParameters parameters)
{
DcmRleCodecParameters rleParams = parameters as DcmRleCodecParameters;
if (rleParams == null)
rleParams = GetDefaultParameters() as DcmRleCodecParameters;
int pixelCount = oldPixelData.ImageWidth * oldPixelData.ImageHeight;
int numberOfSegments = oldPixelData.BytesAllocated * oldPixelData.SamplesPerPixel;
byte[] frameData = new byte[newPixelData.UncompressedFrameSize];
for (int i = 0; i < oldPixelData.NumberOfFrames; i++)
{
IList<ByteBuffer> rleData = oldPixelData.GetFrameFragments(i);
RLEDecoder decoder = new RLEDecoder(rleData);
if (decoder.NumberOfSegments != numberOfSegments)
throw new DicomCodecException("Unexpected number of RLE segments!");
for (int s = 0; s < numberOfSegments; s++)
{
int sample = s / newPixelData.BytesAllocated;
int sabyte = s % newPixelData.BytesAllocated;
int pos, offset;
if (newPixelData.PlanarConfiguration == 0)
{
pos = sample * newPixelData.BytesAllocated;
offset = newPixelData.SamplesPerPixel * newPixelData.BytesAllocated;
}
else
{
pos = sample * newPixelData.BytesAllocated * pixelCount;
offset = newPixelData.BytesAllocated;
}
if (rleParams.ReverseByteOrder)
pos += sabyte;
else
pos += newPixelData.BytesAllocated - sabyte - 1;
decoder.DecodeSegment(s, frameData, pos, offset);
}
newPixelData.AddFrame(frameData);
}
}
public void Decode(DcmDataset dataset, DcmPixelData oldPixelData, DcmPixelData newPixelData, DcmCodecParameters parameters)
{
if (oldPixelData.NumberOfFrames == 0) return;
// Determine JPEG image precision and assert that the implemented codec supports this precision
int precision;
try
{
precision = JpegHelper.ScanHeaderForBitDepth(oldPixelData);
}
catch (DicomCodecException)
{
precision = oldPixelData.BitsStored;
}
AssertImagePrecision(precision);
// Ensure consistency in the new pixel data header
if (precision > 8)
newPixelData.BitsAllocated = 16;
else if (newPixelData.BitsStored <= 8)
newPixelData.BitsAllocated = 8;
// Set up new pixel data specifics
newPixelData.PhotometricInterpretation = newPixelData.PhotometricInterpretation.Equals("YBR_FULL_422") ||
newPixelData.PhotometricInterpretation.Equals("YBR_PARTIAL_422")
? "YBR_FULL"
: oldPixelData.PhotometricInterpretation;
if (newPixelData.PhotometricInterpretation.Equals("YBR_FULL")) newPixelData.PlanarConfiguration = 1;
try
{
for (int j = 0; j < oldPixelData.NumberOfFrames; ++j)
{
var frameData = new byte[newPixelData.UncompressedFrameSize];
var jpegStream = new MemoryStream(oldPixelData.GetFrameDataU8(j));
// Decode JPEG from stream
var decoder = new JpegDecoder(jpegStream);
var jpegDecoded = decoder.Decode();
var img = jpegDecoded.Image;
// Init Buffer
int w = img.Width;
int h = img.Height;
var pixelsFromJpeg = img.Raster;
// Copy FluxJpeg buffer into frame data array
/*
int comps = pixelsFromJpeg.GetLength(0);
int preIncr = newPixelData.BytesAllocated - comps;
if (preIncr < 0)
throw new InvalidOperationException(
String.Format("Number of JPEG components: {0} exceeds number of bytes allocated: {1}",
comps, newPixelData.BytesAllocated));
*/
int i = 0;
for (int y = 0; y < h; ++y)
{
for (int x = 0; x < w; ++x)
{
var pixel = pixelsFromJpeg[0][x, y];
frameData[i++] = (byte)((pixel >> 8) & 0xff);
frameData[i++] = (byte)(pixel & 0xff);
// for (int k = 0; k < preIncr; ++k) frameData[i++] = 0xff;
// for (int k = 0; k < comps; ++k) frameData[i++] = pixelsFromJpeg[k][x, y];
}
}
oldPixelData.Unload();
if (newPixelData.IsPlanar)
DcmCodecHelper.ChangePlanarConfiguration(frameData,
frameData.Length / newPixelData.BytesAllocated,
newPixelData.BitsAllocated,
newPixelData.SamplesPerPixel, 0);
newPixelData.AddFrame(frameData);
}
}
catch (Exception e)
{
Debug.Log.Error("Failed to decode JPEG image: {0}, reason: {1}", e.StackTrace, e.Message);
}
}
public void Encode(DcmDataset dataset, DcmPixelData oldPixelData, DcmPixelData newPixelData, DcmCodecParameters parameters)
{
DcmRleCodecParameters rleParams = parameters as DcmRleCodecParameters;
if (rleParams == null)
rleParams = GetDefaultParameters() as DcmRleCodecParameters;
int pixelCount = oldPixelData.ImageWidth * oldPixelData.ImageHeight;
int numberOfSegments = oldPixelData.BytesAllocated * oldPixelData.SamplesPerPixel;
for (int i = 0; i < oldPixelData.NumberOfFrames; i++)
{
RLEEncoder encoder = new RLEEncoder();
byte[] frameData = oldPixelData.GetFrameDataU8(i);
for (int s = 0; s < numberOfSegments; s++)
{
encoder.NextSegment();
int sample = s / oldPixelData.BytesAllocated;
int sabyte = s % oldPixelData.BytesAllocated;
int pos;
int offset;
if (newPixelData.PlanarConfiguration == 0)
{
pos = sample * oldPixelData.BytesAllocated;
offset = numberOfSegments;
}
else
{
pos = sample * oldPixelData.BytesAllocated * pixelCount;
offset = oldPixelData.BytesAllocated;
}
if (rleParams.ReverseByteOrder)
pos += sabyte;
else
pos += oldPixelData.BytesAllocated - sabyte - 1;
for (int p = 0; p < pixelCount; p++)
{
if (pos >= frameData.Length)
throw new DicomCodecException("");
encoder.Encode(frameData[pos]);
pos += offset;
}
encoder.Flush();
}
encoder.MakeEvenLength();
newPixelData.AddFrame(encoder.GetBuffer());
}
}
public string MakeGreyDicom(byte[] greybytes, ushort imgwidth, ushort imgheight)
{
DcmUID studyUid = DcmUID.Generate();
DcmUID seriesUid = DcmUID.Generate(studyUid, 1);
DcmUID instUid = DcmUID.Generate(seriesUid, 1);
DcmDataset data = new DcmDataset(DcmTS.ExplicitVRBigEndian);//.ImplicitVRLittleEndian ok
data.AddElementWithValue(DcmTags.SOPClassUID, DcmUIDs.CTImageStorage);//ComputedRadiographyImageStorage ok
//data.AddElementWithValue(DcmTags.SOPClassUID, DcmUIDs .SecondaryCapture);
data.AddElementWithValue(DcmTags.StudyInstanceUID, studyUid);
data.AddElementWithValue(DcmTags.SeriesInstanceUID, seriesUid);
data.AddElementWithValue(DcmTags.SOPInstanceUID, instUid);//"1.3.6.1.4.1.30071.6.635719267134010719.1.1"
//data.AddElementWithValue(DcmTags.MediaStorageSOPClassUID, DcmUIDs.ImplicitVRLittleEndian);
//data.AddElementWithValueString(DcmTags.MediaStorageSOPClassUID, DcmUIDs.ComputedRadiographyImageStorage.ToString());
//type 2 attributes
////data.AddElement(DcmTags.PrinterStatus);
if (tags.ContainsKey("0010,0020"))
data.AddElementWithValueString(DcmTags.PatientID, tags["0010,0020"].Substring(5));
if (tags.ContainsKey("0010,0010"))
data.AddElementWithValueString(DcmTags.PatientsName, tags["0010,0010"].Substring(5));
if (tags.ContainsKey("0010,0030"))
data.AddElementWithValueString(DcmTags.PatientsBirthDate, tags["0010,0030"].Substring(5));
if (tags.ContainsKey("0010,0040"))
data.AddElementWithValueString(DcmTags.PatientsSex, tags["0010,0040"].Substring(5));
if (tags.ContainsKey("0010,1010"))
data.AddElementWithValueString(DcmTags.PatientsAge, tags["0010,1010"].Substring(5));
if (tags.ContainsKey("0008,0005"))
data.AddElementWithValueString(DcmTags.SpecificCharacterSet, tags["0008,0005"].Substring(5));
if (tags.ContainsKey("0008,0008"))
data.AddElementWithValueString(DcmTags.ImageType, tags["0008,0008"].Substring(5));
//if (tags.ContainsKey("0008,0016"))
// data.AddElementWithValueString(DcmTags.ContentTime, DateTime.Now.ToString());
//if (tags.ContainsKey("0008,0018"))
// data.AddElementWithValueString(DcmTags.ContentTime, DateTime.Now.ToString());
if (tags.ContainsKey("0008,0020"))
data.AddElementWithValueString(DcmTags.StudyDate, tags["0008,0020"].Substring(5));
if (tags.ContainsKey("0008,0021"))
data.AddElementWithValueString(DcmTags.SeriesDate, tags["0008,0021"].Substring(5));
if (tags.ContainsKey("0008,0022"))
data.AddElementWithValueString(DcmTags.AcquisitionDate, tags["0008,0022"].Substring(5));
if (tags.ContainsKey("0008,0023"))
data.AddElementWithValueString(DcmTags.ContentDate, tags["0008,0023"].Substring(5));
if (tags.ContainsKey("0008,002a"))
data.AddElementWithValueString(DcmTags.AcquisitionDateTime, tags["0008,002a"].Substring(5));
if (tags.ContainsKey("0008,0030"))
data.AddElementWithValueString(DcmTags.StudyTime, tags["0008,0030"].Substring(5));
if (tags.ContainsKey("0008,0031"))
data.AddElementWithValueString(DcmTags.SeriesTime, tags["0008,0031"].Substring(5));
if (tags.ContainsKey("0008,0032"))
data.AddElementWithValueString(DcmTags.AcquisitionTime, tags["0008,0032"].Substring(5));
if (tags.ContainsKey("0008,0033"))
data.AddElementWithValueString(DcmTags.ContentTime, tags["0008,0033"].Substring(5));
if (tags.ContainsKey("0008,0050"))
data.AddElementWithValueString(DcmTags.AcquisitionNumber, tags["0008,0050"].Substring(5));
if (tags.ContainsKey("0008,0060"))
data.AddElementWithValueString(DcmTags.Modality, tags["0008,0060"].Substring(5));
if (tags.ContainsKey("0008,0070"))
data.AddElementWithValueString(DcmTags.Manufacturer, tags["0008,0070"].Substring(5));
if (tags.ContainsKey("0008,0080"))
data.AddElementWithValueString(DcmTags.InstitutionName, tags["0008,0080"].Substring(5));
if (tags.ContainsKey("0008,0081"))
data.AddElementWithValueString(DcmTags.InstitutionAddress, tags["0008,0081"].Substring(5));
if (tags.ContainsKey("0008,0090"))
data.AddElementWithValueString(DcmTags.ReferringPhysiciansName, tags["0008,0090"].Substring(5));
if (tags.ContainsKey("0008,1010"))
data.AddElementWithValueString(DcmTags.StationName, tags["0008,1010"].Substring(5));
if (tags.ContainsKey("0008,1030"))
data.AddElementWithValueString(DcmTags.StudyDescription, tags["0008,1030"].Substring(5));
if (tags.ContainsKey("0008,103e"))
data.AddElementWithValueString(DcmTags.SeriesDescription, tags["0008,103e"].Substring(5));
if (tags.ContainsKey("0008,1090"))
data.AddElementWithValueString(DcmTags.ManufacturersModelName, tags["0008,1090"].Substring(5));
if (tags.ContainsKey("0018,0010"))
data.AddElementWithValueString(DcmTags.ContrastBolusAgent, tags["0018,0010"].Substring(5));
if (tags.ContainsKey("0018,0015"))
data.AddElementWithValueString(DcmTags.BodyPartExamined, tags["0018,0015"].Substring(5));
if (tags.ContainsKey("0018,0050"))
data.AddElementWithValueString(DcmTags.SliceThickness, tags["0018,0050"].Substring(5));
if (tags.ContainsKey("0018,0060"))
data.AddElementWithValueString(DcmTags.KVP, tags["0018,0060"].Substring(5));
if (tags.ContainsKey("0018,0090"))
data.AddElementWithValueString(DcmTags.DataCollectionDiameter, tags["0018,0090"].Substring(5));
if (tags.ContainsKey("0018,1000"))
data.AddElementWithValueString(DcmTags.DeviceSerialNumber, tags["0018,1000"].Substring(5));
if (tags.ContainsKey("0018,1020"))
data.AddElementWithValueString(DcmTags.SoftwareVersions, tags["0018,1020"].Substring(5));
if (tags.ContainsKey("0018,1030"))
data.AddElementWithValueString(DcmTags.ProtocolName, tags["0018,1030"].Substring(5));
if (tags.ContainsKey("0018,1041"))
data.AddElementWithValueString(DcmTags.ContrastBolusVolume, tags["0018,1041"].Substring(5));
if (tags.ContainsKey("0018,1042"))
data.AddElementWithValueString(DcmTags.ContrastBolusStartTime, tags["0018,1042"].Substring(5));
if (tags.ContainsKey("0018,1043"))
data.AddElementWithValueString(DcmTags.ContrastBolusStopTime, tags["0018,1043"].Substring(5));
if (tags.ContainsKey("0018,1044"))
data.AddElementWithValueString(DcmTags.ContrastBolusTotalDose, tags["0018,1044"].Substring(5));
if (tags.ContainsKey("0018,1046"))
data.AddElementWithValueString(DcmTags.ContrastFlowRate, tags["0018,1046"].Substring(5));
if (tags.ContainsKey("0018,1047"))
data.AddElementWithValueString(DcmTags.ContrastFlowDuration, tags["0018,1047"].Substring(5));
if (tags.ContainsKey("0018,1049"))
data.AddElementWithValueString(DcmTags.ContrastBolusIngredientConcentration, tags["0018,1049"].Substring(5));
if (tags.ContainsKey("0018,1100"))
data.AddElementWithValueString(DcmTags.ReconstructionDiameter, tags["0018,1100"].Substring(5));
if (tags.ContainsKey("0018,1110"))
data.AddElementWithValueString(DcmTags.DistanceSourceToDetector, tags["0018,1110"].Substring(5));
if (tags.ContainsKey("0018,1111"))
data.AddElementWithValueString(DcmTags.DistanceSourceToPatient, tags["0018,1111"].Substring(5));
if (tags.ContainsKey("0018,1120"))
data.AddElementWithValueString(DcmTags.GantryDetectorTilt, tags["0018,1120"].Substring(5));
if (tags.ContainsKey("0018,1130"))
data.AddElementWithValueString(DcmTags.TableHeight, tags["0018,1130"].Substring(5));
if (tags.ContainsKey("0018,1140"))
data.AddElementWithValueString(DcmTags.RotationDirection, tags["0018,1140"].Substring(5));
if (tags.ContainsKey("0018,1150"))
data.AddElementWithValueString(DcmTags.ExposureTime, tags["0018,1150"].Substring(5));
if (tags.ContainsKey("0018,1151"))
data.AddElementWithValueString(DcmTags.XRayTubeCurrent, tags["0018,1151"].Substring(5));
if (tags.ContainsKey("0018,1152"))
data.AddElementWithValueString(DcmTags.Exposure, tags["0018,1152"].Substring(5));
if (tags.ContainsKey("0018,1160"))
data.AddElementWithValueString(DcmTags.FilterType, tags["0018,1160"].Substring(5));
if (tags.ContainsKey("0018,1170"))
data.AddElementWithValueString(DcmTags.GeneratorPower, tags["0018,1170"].Substring(5));
if (tags.ContainsKey("0018,1190"))
data.AddElementWithValueString(DcmTags.FocalSpots, tags["0018,1190"].Substring(5));
if (tags.ContainsKey("0018,1200"))
data.AddElementWithValueString(DcmTags.DateOfLastCalibration, tags["0018,1200"].Substring(5));
if (tags.ContainsKey("0018,1201"))
data.AddElementWithValueString(DcmTags.TimeOfLastCalibration, tags["0018,1201"].Substring(5));
if (tags.ContainsKey("0018,1210"))
data.AddElementWithValueString(DcmTags.ConvolutionKernel, tags["0018,1210"].Substring(5));
if (tags.ContainsKey("0018,5100"))
data.AddElementWithValueString(DcmTags.PatientPosition, tags["0018,5100"].Substring(5));
//if (tags.ContainsKey("0020,000D"))
// data.AddElementWithValueString(DcmTags.ContrastBolusStopTime, DateTime.Now.ToString());
//if (tags.ContainsKey("0020,000E"))
// data.AddElementWithValueString(DcmTags.ContrastBolusStopTime, DateTime.Now.ToString());
if (tags.ContainsKey("0020,0010"))
data.AddElementWithValueString(DcmTags.StudyID, tags["0020,0010"].Substring(5));
if (tags.ContainsKey("0020,0011"))
data.AddElementWithValueString(DcmTags.SeriesNumber, tags["0020,0011"].Substring(5));
if (tags.ContainsKey("0020,0012"))
data.AddElementWithValueString(DcmTags.AccessionNumber, tags["0020,0012"].Substring(5));
if (tags.ContainsKey("0020,0013"))
data.AddElementWithValueString(DcmTags.InstanceNumber, tags["0020,0013"].Substring(5));
if (tags.ContainsKey("0020,0032"))
data.AddElementWithValueString(DcmTags.ImagePositionPatient, tags["0020,0032"].Substring(5));
if (tags.ContainsKey("0020,0037"))
data.AddElementWithValueString(DcmTags.ImageOrientationPatient, tags["0020,0037"].Substring(5));
if (tags.ContainsKey("0020,0052"))
data.AddElementWithValueString(DcmTags.FrameOfReferenceUID, tags["0020,0052"].Substring(5));
if (tags.ContainsKey("0020,1040"))
data.AddElementWithValueString(DcmTags.PositionReferenceIndicator, tags["0020,1040"].Substring(5));
if (tags.ContainsKey("0020,1041"))
data.AddElementWithValueString(DcmTags.SliceLocation, tags["0020,1041"].Substring(5));
if (tags.ContainsKey("0020,4000"))
data.AddElementWithValueString(DcmTags.ImageComments, tags["0020,4000"].Substring(5));
//data.AddElementWithValueString(DcmTags.StudyTime, DateTime.Now.ToString());
//data.AddElementWithValueString(DcmTags.AccessionNumber, "");
//data.AddElementWithValueString(DcmTags.ReferringPhysiciansName, "");
//data.AddElementWithValueString(DcmTags.StudyID, "1");
//data.AddElementWithValueString(DcmTags.SeriesNumber, "1");
//data.AddElementWithValueString(DcmTags.ModalitiesInStudy, "CT");//CR
//data.AddElementWithValueString(DcmTags.Modality, "CT");//CR
//data.AddElementWithValueString(DcmTags.NumberOfStudyRelatedInstances, "1");
//data.AddElementWithValueString(DcmTags.NumberOfStudyRelatedSeries, "1");
//data.AddElementWithValueString(DcmTags.NumberOfSeriesRelatedInstances, "1");
//data.AddElementWithValueString(DcmTags.PatientOrientation, "HFS");//F/A
//data.AddElementWithValueString(DcmTags.ImageLaterality, "U");
if (tags.ContainsKey("0028,1050"))
data.AddElementWithValueString(DcmTags.WindowCenter, "1113");
if (tags.ContainsKey("0028,1051"))
data.AddElementWithValueString(DcmTags.WindowWidth, "749");
//data.AddElementWithValueString(DcmTags.WindowCenterWidthExplanation, "WINDOW1\\WINDOW2");
data.AddElementWithValueString(DcmTags.PixelRepresentation, "0");
data.AddElementWithValueString(DcmTags.RescaleIntercept, "0");//0
data.AddElementWithValueString(DcmTags.RescaleSlope, "1");
//data.AddElementWithValueString(DcmTags.RotationDirection, "CW");
//ushort bitdepth = 2;未使用过
DcmPixelData pixelData = new DcmPixelData(DcmTS.ImplicitVRLittleEndian);
pixelData.PixelRepresentation = 0;//ok
pixelData.ImageWidth = imgwidth;
pixelData.ImageHeight = imgheight;
pixelData.SamplesPerPixel = 1;//ok
pixelData.HighBit = 15;//ok
pixelData.BitsStored = 16;//ok
pixelData.BitsAllocated = 16;//ok
//pixelData.SamplesPerPixel = 1;
//pixelData.HighBit = 7;
//pixelData.BitsStored = 8;
//pixelData.BitsAllocated = 8;
pixelData.ImageType = "ORIGINAL\\PRIMARY\\AXIAL";
pixelData.PhotometricInterpretation = "MONOCHROME2";//2 byte gray? //ok
//pixelData.FragmentSize
//pixelData.IsLossy = true;
//pixelData.LossyCompressionMethod = "01";
pixelData.PixelDataElement = DcmElement.Create(DcmTags.PixelData, DcmVR.OW); //OB: Other Byte, OW: Other Word
//pixelData.AddFrame(bmpBytes);
pixelData.AddFrame(greybytes);
pixelData.UpdateDataset(data);
DicomFileFormat ff = new DicomFileFormat(data);
//string fileout = System.IO.Path.Combine(Directory.GetCurrentDirectory(), "greyimg_test.dcm");
ff.Save(fileout, Dicom.DicomWriteOptions.Default);//Default
ff = null;
return fileout;
}
