private static CompressionParameters ToCompressionParameters(DicomJpegParams parameters)
{
var compressionParams = new CompressionParameters();
if (parameters != null)
{
compressionParams.Quality = parameters.Quality;
compressionParams.SmoothingFactor = parameters.SmoothingFactor;
}
return(compressionParams);
}
internal static void Decode(
DicomPixelData oldPixelData,
DicomPixelData newPixelData,
DicomJpegParams parameters)
{
var pixelCount = oldPixelData.Height * oldPixelData.Width;
if (parameters.ConvertColorspaceToRGB)
{
if (oldPixelData.PixelRepresentation == PixelRepresentation.Signed)
{
throw new DicomCodecException(
"JPEG codec unable to perform colorspace conversion on signed pixel data");
}
newPixelData.PhotometricInterpretation = PhotometricInterpretation.Rgb;
newPixelData.PlanarConfiguration = PlanarConfiguration.Interleaved;
}
for (var frame = 0; frame < oldPixelData.NumberOfFrames; frame++)
{
var jpegData = oldPixelData.GetFrame(frame);
// Destination frame should be of even length
var frameSize = newPixelData.UncompressedFrameSize;
if ((frameSize & 1) == 1)
{
++frameSize;
}
var destArray = new byte[frameSize];
using (var stream = new MemoryStream(jpegData.Data))
{
var decoder = new JpegImage(stream);
var w = decoder.Width;
var h = decoder.Height;
for (var c = 0; c < decoder.ComponentsPerSample; c++)
{
var pos = newPixelData.PlanarConfiguration == PlanarConfiguration.Planar ? c * pixelCount : c;
var offset = newPixelData.PlanarConfiguration == PlanarConfiguration.Planar
? 1
: decoder.ComponentsPerSample;
if (newPixelData.BytesAllocated == 1)
{
for (var y = 0; y < h; ++y)
{
var row = decoder.GetRow(y);
for (var x = 0; x < w; ++x)
{
destArray[pos] = (byte)row[x][c];
pos += offset;
}
}
}
#if SUPPORT16BIT
else if (newPixelData.BytesAllocated == 2)
{
var destArray16 = new short[frameSize >> 1];
for (var y = 0; y < h; ++y)
{
var row = decoder.GetRow(y);
for (var x = 0; x < w; ++x)
{
destArray16[pos] = row[x][c];
pos += offset;
}
}
Buffer.BlockCopy(destArray16, 0, destArray, 0, frameSize);
}
#endif
else
{
throw new InvalidOperationException(
$"JPEG module does not support Bits Allocated == {newPixelData.BitsAllocated}!");
}
}
newPixelData.AddFrame(new MemoryByteBuffer(destArray));
}
}
}
/// <summary>
/// Loads the pixel data for specified frame and set the internal dataset
///
/// </summary>
/// <param name="dataset">dataset to load pixeldata from</param>
/// <param name="frame">The frame number to create pixeldata for</param>
private void Load(DicomDataset dataset, int frame)
{
Dataset = dataset;
if (PixelData == null) {
PixelData = DicomPixelData.Create(Dataset);
PhotometricInterpretation = PixelData.PhotometricInterpretation;
}
if (Dataset.InternalTransferSyntax.IsEncapsulated) {
// decompress single frame from source dataset
DicomCodecParams cparams = null;
if (Dataset.InternalTransferSyntax == DicomTransferSyntax.JPEGProcess1 || Dataset.InternalTransferSyntax == DicomTransferSyntax.JPEGProcess2_4) {
cparams = new DicomJpegParams {
ConvertColorspaceToRGB = true
};
}
var transcoder = new DicomTranscoder(Dataset.InternalTransferSyntax, DicomTransferSyntax.ExplicitVRLittleEndian);
transcoder.InputCodecParams = cparams;
transcoder.OutputCodecParams = cparams;
var buffer = transcoder.DecodeFrame(Dataset, frame);
// clone the dataset because modifying the pixel data modifies the dataset
var clone = Dataset.Clone();
clone.InternalTransferSyntax = DicomTransferSyntax.ExplicitVRLittleEndian;
var pixelData = DicomPixelData.Create(clone, true);
pixelData.AddFrame(buffer);
// temporary fix for JPEG compressed YBR images
if ((Dataset.InternalTransferSyntax == DicomTransferSyntax.JPEGProcess1 || Dataset.InternalTransferSyntax == DicomTransferSyntax.JPEGProcess2_4) && pixelData.SamplesPerPixel == 3)
pixelData.PhotometricInterpretation = PhotometricInterpretation.Rgb;
// temporary fix for JPEG 2000 Lossy images
if (pixelData.PhotometricInterpretation == PhotometricInterpretation.YbrIct || pixelData.PhotometricInterpretation == PhotometricInterpretation.YbrRct)
pixelData.PhotometricInterpretation = PhotometricInterpretation.Rgb;
_pixelData = PixelDataFactory.Create(pixelData, 0);
} else {
// pull uncompressed frame from source pixel data
_pixelData = PixelDataFactory.Create(PixelData, frame);
}
_pixelData = _pixelData.Rescale(_scale);
_overlays = DicomOverlayData.FromDataset(Dataset).Where(x => x.Type == DicomOverlayType.Graphics && x.Data != null).ToArray();
_currentFrame = frame;
CreatePipeline();
}
internal static void Encode(
DicomPixelData oldPixelData,
DicomPixelData newPixelData,
DicomJpegParams parameters)
{
if ((oldPixelData.PhotometricInterpretation == PhotometricInterpretation.YbrFull422) ||
(oldPixelData.PhotometricInterpretation == PhotometricInterpretation.YbrPartial422) ||
(oldPixelData.PhotometricInterpretation == PhotometricInterpretation.YbrPartial420))
{
throw new InvalidOperationException(
"Photometric Interpretation '" + oldPixelData.PhotometricInterpretation
+ "' not supported by JPEG encoder");
}
var w = oldPixelData.Width;
var h = oldPixelData.Height;
for (var frame = 0; frame < oldPixelData.NumberOfFrames; frame++)
{
var frameData = oldPixelData.GetFrame(frame);
var nc = oldPixelData.SamplesPerPixel;
var sgnd = oldPixelData.PixelRepresentation == PixelRepresentation.Signed;
var rows = Enumerable.Range(0, h).Select(i => new short[w, nc]).ToArray();
for (var c = 0; c < nc; c++)
{
var pos = oldPixelData.PlanarConfiguration == PlanarConfiguration.Planar ? (c * w * h) : c;
var offset = oldPixelData.PlanarConfiguration == PlanarConfiguration.Planar ? 1 : nc;
if (oldPixelData.BytesAllocated == 1)
{
var data = frameData.Data;
if (sgnd)
{
if (oldPixelData.BitsStored < 8)
{
var sign = (byte)(1 << oldPixelData.HighBit);
var mask = (byte)(0xff >> (oldPixelData.BitsAllocated - oldPixelData.BitsStored));
for (var y = 0; y < h; ++y)
{
for (var x = 0; x < w; ++x)
{
var pixel = (sbyte)data[pos];
rows[y][x, c] = (short)((pixel & sign) > 0 ? -(((-pixel) & mask) + 1) : pixel);
pos += offset;
}
}
}
else
{
for (var y = 0; y < h; ++y)
{
for (var x = 0; x < w; ++x)
{
rows[y][x, c] = (sbyte)data[pos];
pos += offset;
}
}
}
}
else
{
for (var y = 0; y < h; ++y)
{
for (var x = 0; x < w; ++x)
{
rows[y][x, c] = data[pos];
pos += offset;
}
}
}
}
#if SUPPORT16BIT
else if (oldPixelData.BytesAllocated == 2)
{
if (sgnd)
{
if (oldPixelData.BitsStored < 16)
{
var frameData16 = new ushort[w * h];
Buffer.BlockCopy(frameData.Data, 0, frameData16, 0, (int)frameData.Size);
var sign = (ushort)(1 << oldPixelData.HighBit);
var mask = (ushort)(0xffff >> (oldPixelData.BitsAllocated - oldPixelData.BitsStored));
for (var y = 0; y < h; ++y)
{
for (var x = 0; x < w; ++x)
{
var pixel = frameData16[pos];
rows[y][x, c] = (short)((pixel & sign) > 0 ? -(((-pixel) & mask) + 1) : pixel);
pos += offset;
}
}
}
else
{
var frameData16 = new short[w * h];
Buffer.BlockCopy(frameData.Data, 0, frameData16, 0, (int)frameData.Size);
for (var y = 0; y < h; ++y)
{
for (var x = 0; x < w; ++x)
{
rows[y][x, c] = frameData16[pos];
pos += offset;
}
}
}
}
else
{
var frameData16 = new ushort[w * h];
Buffer.BlockCopy(frameData.Data, 0, frameData16, 0, (int)frameData.Size);
for (var y = 0; y < h; ++y)
{
for (var x = 0; x < w; ++x)
{
rows[y][x, c] = (short)frameData16[pos];
pos += offset;
}
}
}
}
#endif
else
{
throw new InvalidOperationException(
$"JPEG codec does not support Bits Allocated == {oldPixelData.BitsAllocated}");
}
}
try
{
using (var stream = new MemoryStream())
{
var sampleRows =
rows.Select(
row =>
new SampleRow(
ToRawRow(row, oldPixelData.BitsAllocated),
w,
(byte)oldPixelData.BitsStored,
(byte)nc)).ToArray();
var colorSpace = GetColorSpace(oldPixelData.PhotometricInterpretation);
using (var encoder = new JpegImage(sampleRows, colorSpace))
{
encoder.WriteJpeg(stream, ToCompressionParameters(parameters));
}
newPixelData.AddFrame(new MemoryByteBuffer(stream.ToArray()));
newPixelData.PhotometricInterpretation =
(parameters != null && parameters.SampleFactor == DicomJpegSampleFactor.SF422)
? PhotometricInterpretation.YbrFull422 : PhotometricInterpretation.YbrFull;
}
}
catch (Exception e)
{
throw new InvalidOperationException("Unable to JPEG encode image", e);
}
}
if (oldPixelData.PhotometricInterpretation == PhotometricInterpretation.Rgb)
{
newPixelData.PlanarConfiguration = PlanarConfiguration.Interleaved;
}
}
protected abstract IJpegNativeCodec GetCodec(int bits, DicomJpegParams jparams);
protected abstract IJpegNativeCodec GetCodec(int bits, DicomJpegParams jparams);
private static CompressionParameters ToCompressionParameters(DicomJpegParams parameters)
{
var compressionParams = new CompressionParameters();
if (parameters != null)
{
compressionParams.Quality = parameters.Quality;
compressionParams.SmoothingFactor = parameters.SmoothingFactor;
}
return compressionParams;
}
internal static void Decode(
DicomPixelData oldPixelData,
DicomPixelData newPixelData,
DicomJpegParams parameters)
{
var pixelCount = oldPixelData.Height * oldPixelData.Width;
if (newPixelData.PhotometricInterpretation == PhotometricInterpretation.YbrIct
|| newPixelData.PhotometricInterpretation == PhotometricInterpretation.YbrRct)
{
newPixelData.PhotometricInterpretation = PhotometricInterpretation.Rgb;
}
if (newPixelData.PhotometricInterpretation == PhotometricInterpretation.YbrFull422
|| newPixelData.PhotometricInterpretation == PhotometricInterpretation.YbrPartial422)
{
newPixelData.PhotometricInterpretation = PhotometricInterpretation.YbrFull;
}
if (newPixelData.PhotometricInterpretation == PhotometricInterpretation.YbrFull)
{
newPixelData.PlanarConfiguration = PlanarConfiguration.Planar;
}
for (var frame = 0; frame < oldPixelData.NumberOfFrames; frame++)
{
var jpegData = oldPixelData.GetFrame(frame);
// Destination frame should be of even length
var frameSize = newPixelData.UncompressedFrameSize;
if ((frameSize & 1) == 1) ++frameSize;
var destArray = new byte[frameSize];
using (var stream = new MemoryStream(jpegData.Data))
{
var decoder = new JpegImage(stream);
var w = decoder.Width;
var h = decoder.Height;
for (var c = 0; c < decoder.ComponentsPerSample; c++)
{
var pos = newPixelData.PlanarConfiguration == PlanarConfiguration.Planar ? (c * pixelCount) : c;
var offset = newPixelData.PlanarConfiguration == PlanarConfiguration.Planar
? 1
: decoder.ComponentsPerSample;
if (newPixelData.BytesAllocated == 1)
{
for (var y = 0; y < h; ++y)
{
var row = decoder.GetRow(y);
for (var x = 0; x < w; ++x)
{
destArray[pos] = (byte)row[x][c];
pos += offset;
}
}
}
#if SUPPORT16BIT
else if (newPixelData.BytesAllocated == 2)
{
var destArray16 = new short[frameSize >> 1];
for (var y = 0; y < h; ++y)
{
var row = decoder.GetRow(y);
for (var x = 0; x < w; ++x)
{
destArray16[pos] = row[x][c];
pos += offset;
}
}
Buffer.BlockCopy(destArray16, 0, destArray, 0, frameSize);
}
#endif
else
{
throw new InvalidOperationException(
$"JPEG module does not support Bits Allocated == {newPixelData.BitsAllocated}!");
}
}
newPixelData.AddFrame(new MemoryByteBuffer(destArray));
}
}
}
internal static void Encode(
DicomPixelData oldPixelData,
DicomPixelData newPixelData,
DicomJpegParams parameters)
{
if ((oldPixelData.PhotometricInterpretation == PhotometricInterpretation.YbrFull422)
|| (oldPixelData.PhotometricInterpretation == PhotometricInterpretation.YbrPartial422)
|| (oldPixelData.PhotometricInterpretation == PhotometricInterpretation.YbrPartial420))
{
throw new InvalidOperationException(
"Photometric Interpretation '" + oldPixelData.PhotometricInterpretation
+ "' not supported by JPEG encoder");
}
var w = oldPixelData.Width;
var h = oldPixelData.Height;
for (var frame = 0; frame < oldPixelData.NumberOfFrames; frame++)
{
var frameData = oldPixelData.GetFrame(frame);
var nc = oldPixelData.SamplesPerPixel;
var sgnd = oldPixelData.PixelRepresentation == PixelRepresentation.Signed;
var rows = Enumerable.Range(0, h).Select(i => new short[w, nc]).ToArray();
for (var c = 0; c < nc; c++)
{
var pos = oldPixelData.PlanarConfiguration == PlanarConfiguration.Planar ? (c * w * h) : c;
var offset = oldPixelData.PlanarConfiguration == PlanarConfiguration.Planar ? 1 : nc;
if (oldPixelData.BytesAllocated == 1)
{
var data = frameData.Data;
if (sgnd)
{
if (oldPixelData.BitsStored < 8)
{
var sign = (byte)(1 << oldPixelData.HighBit);
var mask = (byte)(0xff >> (oldPixelData.BitsAllocated - oldPixelData.BitsStored));
for (var y = 0; y < h; ++y)
{
for (var x = 0; x < w; ++x)
{
var pixel = (sbyte)data[pos];
rows[y][x, c] = (short)((pixel & sign) > 0 ? -(((-pixel) & mask) + 1) : pixel);
pos += offset;
}
}
}
else
{
for (var y = 0; y < h; ++y)
{
for (var x = 0; x < w; ++x)
{
rows[y][x, c] = (sbyte)data[pos];
pos += offset;
}
}
}
}
else
{
for (var y = 0; y < h; ++y)
{
for (var x = 0; x < w; ++x)
{
rows[y][x, c] = data[pos];
pos += offset;
}
}
}
}
#if SUPPORT16BIT
else if (oldPixelData.BytesAllocated == 2)
{
if (sgnd)
{
if (oldPixelData.BitsStored < 16)
{
var frameData16 = new ushort[w * h];
Buffer.BlockCopy(frameData.Data, 0, frameData16, 0, (int)frameData.Size);
var sign = (ushort)(1 << oldPixelData.HighBit);
var mask = (ushort)(0xffff >> (oldPixelData.BitsAllocated - oldPixelData.BitsStored));
for (var y = 0; y < h; ++y)
{
for (var x = 0; x < w; ++x)
{
var pixel = frameData16[pos];
rows[y][x, c] = (short)((pixel & sign) > 0 ? -(((-pixel) & mask) + 1) : pixel);
pos += offset;
}
}
}
else
{
var frameData16 = new short[w * h];
Buffer.BlockCopy(frameData.Data, 0, frameData16, 0, (int)frameData.Size);
for (var y = 0; y < h; ++y)
{
for (var x = 0; x < w; ++x)
{
rows[y][x, c] = frameData16[pos];
pos += offset;
}
}
}
}
else
{
var frameData16 = new ushort[w * h];
Buffer.BlockCopy(frameData.Data, 0, frameData16, 0, (int)frameData.Size);
for (var y = 0; y < h; ++y)
{
for (var x = 0; x < w; ++x)
{
rows[y][x, c] = (short)frameData16[pos];
pos += offset;
}
}
}
}
#endif
else
{
throw new InvalidOperationException(
$"JPEG codec does not support Bits Allocated == {oldPixelData.BitsAllocated}");
}
}
try
{
using (var stream = new MemoryStream())
{
var sampleRows =
rows.Select(
row =>
new SampleRow(
ToRawRow(row, oldPixelData.BitsAllocated),
w,
(byte)oldPixelData.BitsStored,
(byte)nc)).ToArray();
var colorSpace = GetColorSpace(oldPixelData.PhotometricInterpretation);
using (var encoder = new JpegImage(sampleRows, colorSpace))
{
encoder.WriteJpeg(stream, ToCompressionParameters(parameters));
}
newPixelData.AddFrame(new MemoryByteBuffer(stream.ToArray()));
}
}
catch (Exception e)
{
throw new InvalidOperationException("Unable to JPEG encode image", e);
}
}
if (oldPixelData.PhotometricInterpretation == PhotometricInterpretation.Rgb)
{
newPixelData.PlanarConfiguration = PlanarConfiguration.Interleaved;
}
}
