public void Encode(DicomUncompressedPixelData oldPixelData, DicomCompressedPixelData newPixelData, DicomCodecParameters parameters)
{
if (oldPixelData.UncompressedFrameSize % 2 == 1)
{
for (var n = 0; n < oldPixelData.NumberOfFrames; ++n)
{
using (var stream = new MemoryStream())
{
var data = oldPixelData.GetFrame(n);
stream.Write(data, 0, data.Length);
stream.WriteByte(0); // must pad fragments to even length
newPixelData.AddFrameFragment(stream.ToArray());
}
}
}
else
{
for (var n = 0; n < oldPixelData.NumberOfFrames; ++n)
{
newPixelData.AddFrameFragment(oldPixelData.GetFrame(n));
}
}
}
/// <summary>
/// Called by the base class to create a new byte buffer containing normalized pixel data
/// for this frame (8 or 16-bit grayscale, or 32-bit ARGB).
/// </summary>
/// <returns>A new byte buffer containing the normalized pixel data.</returns>
protected override byte[] CreateNormalizedPixelData()
{
DicomMessageBase message = this.Parent.SourceMessage;
CodeClock clock = new CodeClock();
clock.Start();
PhotometricInterpretation photometricInterpretation;
byte[] rawPixelData = null;
if (!message.TransferSyntax.Encapsulated)
{
DicomUncompressedPixelData pixelData = new DicomUncompressedPixelData(message);
// DICOM library uses zero-based frame numbers
MemoryManager.Execute(delegate { rawPixelData = pixelData.GetFrame(_frameIndex); });
ExtractOverlayFrames(rawPixelData, pixelData.BitsAllocated);
photometricInterpretation = PhotometricInterpretation.FromCodeString(message.DataSet[DicomTags.PhotometricInterpretation]);
}
else if (DicomCodecRegistry.GetCodec(message.TransferSyntax) != null)
{
DicomCompressedPixelData pixelData = new DicomCompressedPixelData(message);
string pi = null;
MemoryManager.Execute(delegate { rawPixelData = pixelData.GetFrame(_frameIndex, out pi); });
photometricInterpretation = PhotometricInterpretation.FromCodeString(pi);
}
else
{
throw new DicomCodecException("Unsupported transfer syntax");
}
if (photometricInterpretation.IsColor)
{
rawPixelData = ToArgb(message.DataSet, rawPixelData, photometricInterpretation);
}
else
{
NormalizeGrayscalePixels(message.DataSet, rawPixelData);
}
clock.Stop();
PerformanceReportBroker.PublishReport("DicomMessageSopDataSource", "CreateFrameNormalizedPixelData", clock.Seconds);
return(rawPixelData);
}
public void Encode(DicomUncompressedPixelData oldPixelData, DicomCompressedPixelData newPixelData, DicomCodecParameters parameters)
{
if (oldPixelData.UncompressedFrameSize%2 == 1)
{
for (var n = 0; n < oldPixelData.NumberOfFrames; ++n)
{
using (var stream = new MemoryStream())
{
var data = oldPixelData.GetFrame(n);
stream.Write(data, 0, data.Length);
stream.WriteByte(0); // must pad fragments to even length
newPixelData.AddFrameFragment(stream.ToArray());
}
}
}
else
{
for (var n = 0; n < oldPixelData.NumberOfFrames; ++n)
{
newPixelData.AddFrameFragment(oldPixelData.GetFrame(n));
}
}
}
public void TestAdvanced_FileOnDisk_16Bits_OW()
{
var filename = Path.GetTempFileName();
CreateDicomImage(rows: 20, columns: 30, numberOfFrames: 5).Save(filename);
var dcf = new DicomFile(filename);
dcf.Load(DicomReadOptions.StorePixelDataReferences);
try
{
var pd = new DicomUncompressedPixelData(dcf);
Assert.AreEqual(16, pd.BitsAllocated, "BitsAllocated");
Assert.AreEqual(16, pd.BitsStored, "BitsStored");
Assert.AreEqual(15, pd.HighBit, "HighBit");
Assert.AreEqual(20, pd.ImageHeight, "ImageHeight");
Assert.AreEqual(30, pd.ImageWidth, "ImageWidth");
Assert.AreEqual(5, pd.NumberOfFrames, "NumberOfFrames");
Assert.AreEqual("MONOCHROME2", pd.PhotometricInterpretation, "PhotometricInterpretation");
Assert.AreEqual(0, pd.PixelRepresentation, "PixelRepresentation");
Assert.AreEqual(1, pd.SamplesPerPixel, "SamplesPerPixel");
Assert.AreEqual(20 * 30 * 2, pd.UncompressedFrameSize, "UncompressedFrameSize");
var newFrameData = new byte[pd.UncompressedFrameSize];
for (var n = 0; n < newFrameData.Length; ++n)
{
newFrameData[n] = 0x7F;
}
pd.SetFrame(1, newFrameData);
pd.UpdateAttributeCollection(dcf.DataSet);
var pixelData = dcf.DataSet[DicomTags.PixelData].Values as byte[];
for (var frame = 0; frame < 5; ++frame)
{
var fd = pd.GetFrame(frame);
var expectedValue = frame == 1 ? (byte)0x7F : (byte)(0x80 + frame);
Assert.AreEqual(pd.UncompressedFrameSize, fd.Length, "PixelData(frame={0}).Length", frame);
AssertBytesEqual(expectedValue, fd, "PixelData(frame={0})", frame);
AssertBytesEqual(expectedValue, pixelData, frame * pd.UncompressedFrameSize, pd.UncompressedFrameSize, "AttributeValues(frame={0})", frame);
}
}
finally
{
File.Delete(filename);
}
}
public void GetPixelData(PrintScu.ImageBox imageBox, ColorMode colorMode, out ushort rows, out ushort columns, out byte[] pixelData)
{
try
{
LocalSopDataSource dataSource = _file.DataSource as LocalSopDataSource;
dataSource.File.Load(DicomReadOptions.Default | DicomReadOptions.StorePixelDataReferences);
rows = dataSource.File.DataSet[DicomTags.Rows].GetUInt16(0, 0);
columns = dataSource.File.DataSet[DicomTags.Columns].GetUInt16(0, 0);
DicomUncompressedPixelData uncompressedPixelData = new DicomUncompressedPixelData(dataSource.File);
pixelData = uncompressedPixelData.GetFrame(0);
}
catch (Exception e)
{
Platform.Log(LogLevel.Error, string.Format("获得像素数据失败：{0}", e.Message));
throw e;
}
}
protected override void Upload(DicomFile dicomObject, int frame, IStorageLocation storeLocation)
{
var frameIndex = frame - 1;
if (dicomObject.TransferSyntax == TransferSyntax.JpegBaselineProcess1)
{
DicomCompressedPixelData pd = DicomPixelData.CreateFrom(dicomObject) as DicomCompressedPixelData;
byte[] buffer = pd.GetFrameFragmentData(frameIndex);
storeLocation.Upload(buffer);
}
else if (false) //TODO: handle compressed images properly!
{
DicomFile dcmJpeg = new DicomFile( );
DicomUncompressedPixelData unCompressed = DicomPixelData.CreateFrom(dicomObject) as DicomUncompressedPixelData;
DicomCompressedPixelData compressed = new DicomCompressedPixelData(unCompressed);
//compressed.ImageWidth = unCompressed.ImageWidth;
//compressed.ImageHeight = unCompressed.HighBit;
compressed.BitsStored = 8;
compressed.BitsAllocated = 8;
//compressed.HighBit = 7;
compressed.SamplesPerPixel = 3;
//compressed.PlanarConfiguration = 0;
compressed.PhotometricInterpretation = "YBR_FULL_422";
compressed.TransferSyntax = TransferSyntax.JpegBaselineProcess1;
byte[] imageBuffer = unCompressed.GetFrame(frameIndex);
compressed.AddFrameFragment(imageBuffer);
compressed.UpdateMessage(dcmJpeg);
storeLocation.Upload(compressed.GetFrame(frameIndex));
//ClearCanvas.Dicom.Codec.Jpeg.Jpeg8Codec codec = new ClearCanvas.Dicom.Codec.Jpeg.Jpeg8Codec (ClearCanvas.Dicom.Codec.Jpeg.JpegMode.Baseline, 0, 0 ) ;
//ClearCanvas.Dicom.Codec.Jpeg.DicomJpegParameters jparam = new ClearCanvas.Dicom.Codec.Jpeg.DicomJpegParameters ( ) ;
//jparam.
//codec.
//codec.Encode ( )
}
}
public void Encode(DicomUncompressedPixelData oldPixelData, DicomCompressedPixelData newPixelData, DicomCodecParameters parameters)
{
for (var n = 0; n < oldPixelData.NumberOfFrames; ++n)
{
using (var output = new MemoryStream())
{
using (var gzipStream = new GZipStream(output, CompressionMode.Compress, true))
{
var data = oldPixelData.GetFrame(n);
gzipStream.Write(data, 0, data.Length);
}
// if the compressed stream is odd length, append an extra byte - gzip will know that it's padding during decompression
if (output.Length%2 == 1) output.WriteByte(0);
newPixelData.AddFrameFragment(output.ToArray());
}
}
}
public void TestBasic_FileOnDisk_8Bits_BigEndian_OddFrameLength()
{
var filename = Path.GetTempFileName();
CreateDicomImage(rows: 19, columns: 29, numberOfFrames: 5, bitsAllocated16: false, endian: Endian.Big).Save(filename);
var dcf = new DicomFile(filename);
dcf.Load(DicomReadOptions.StorePixelDataReferences);
try
{
var pd = new DicomUncompressedPixelData(dcf);
Assert.AreEqual(8, pd.BitsAllocated, "BitsAllocated");
Assert.AreEqual(8, pd.BitsStored, "BitsStored");
Assert.AreEqual(7, pd.HighBit, "HighBit");
Assert.AreEqual(19, pd.ImageHeight, "ImageHeight");
Assert.AreEqual(29, pd.ImageWidth, "ImageWidth");
Assert.AreEqual(5, pd.NumberOfFrames, "NumberOfFrames");
Assert.AreEqual("MONOCHROME2", pd.PhotometricInterpretation, "PhotometricInterpretation");
Assert.AreEqual(0, pd.PixelRepresentation, "PixelRepresentation");
Assert.AreEqual(1, pd.SamplesPerPixel, "SamplesPerPixel");
Assert.AreEqual(19 * 29, pd.UncompressedFrameSize, "UncompressedFrameSize");
for (var frame = 0; frame < 5; ++frame)
{
if (frame == 4)
{
Assert.Ignore("Skipping last frame validation due to bug #10749");
}
var fd = pd.GetFrame(frame);
Assert.AreEqual(pd.UncompressedFrameSize, fd.Length, "PixelData(frame={0}).Length", frame);
AssertBytesEqual((byte)(0x80 + frame), fd, "PixelData(frame={0})", frame);
}
}
finally
{
File.Delete(filename);
}
}
public void Encode(DicomUncompressedPixelData oldPixelData, DicomCompressedPixelData newPixelData, DicomCodecParameters parameters)
{
for (var n = 0; n < oldPixelData.NumberOfFrames; ++n)
{
using (var output = new MemoryStream())
{
using (var gzipStream = new GZipStream(output, CompressionMode.Compress, true))
{
var data = oldPixelData.GetFrame(n);
gzipStream.Write(data, 0, data.Length);
}
// if the compressed stream is odd length, append an extra byte - gzip will know that it's padding during decompression
if (output.Length % 2 == 1)
{
output.WriteByte(0);
}
newPixelData.AddFrameFragment(output.ToArray());
}
}
}
public void TestBasic_MessageInMemory_8Bits_OB()
{
var dcf = CreateDicomImage(rows : 20, columns : 30, numberOfFrames : 3, bitsAllocated16 : false, useOB : true);
var pd = new DicomUncompressedPixelData(dcf);
Assert.AreEqual(8, pd.BitsAllocated, "BitsAllocated");
Assert.AreEqual(8, pd.BitsStored, "BitsStored");
Assert.AreEqual(7, pd.HighBit, "HighBit");
Assert.AreEqual(20, pd.ImageHeight, "ImageHeight");
Assert.AreEqual(30, pd.ImageWidth, "ImageWidth");
Assert.AreEqual(3, pd.NumberOfFrames, "NumberOfFrames");
Assert.AreEqual("MONOCHROME2", pd.PhotometricInterpretation, "PhotometricInterpretation");
Assert.AreEqual(0, pd.PixelRepresentation, "PixelRepresentation");
Assert.AreEqual(1, pd.SamplesPerPixel, "SamplesPerPixel");
Assert.AreEqual(20*30, pd.UncompressedFrameSize, "UncompressedFrameSize");
for (var frame = 0; frame < 3; ++frame)
{
var fd = pd.GetFrame(frame);
Assert.AreEqual(pd.UncompressedFrameSize, fd.Length, "PixelData(frame={0}).Length", frame);
AssertBytesEqual((byte) (0x80 + frame), fd, "PixelData(frame={0})", frame);
}
}
private void CheckPixels(string filename)
{
DicomReadOptions readOptions = DicomReadOptions.StorePixelDataReferences;
DicomFile newFile = new DicomFile(filename);
newFile.Load(readOptions);
DicomUncompressedPixelData pd = new DicomUncompressedPixelData(newFile.DataSet);
for (int frame = 0; frame < pd.NumberOfFrames; frame++)
{
byte[] data = pd.GetFrame(frame);
uint pdVal = (uint)frame + 1;
for (int i = 0; i < pd.UncompressedFrameSize; i++, pdVal++)
{
if (data[i] != pdVal % 255)
{
string val = String.Format("Value bad: frame: {0}, pixel: {1}, val1: {2}, val2: {3}", frame, i, data[i], pdVal % 255);
Console.Write(val);
}
Assert.AreEqual(data[i], pdVal % 255);
}
}
}
public void TestBasic_DatasetInMemory_8Bits()
{
var dcf = CreateDicomImage(rows: 20, columns: 30, numberOfFrames: 3, bitsAllocated16: false, signed: true);
var pd = new DicomUncompressedPixelData(dcf.DataSet);
Assert.AreEqual(8, pd.BitsAllocated, "BitsAllocated");
Assert.AreEqual(8, pd.BitsStored, "BitsStored");
Assert.AreEqual(7, pd.HighBit, "HighBit");
Assert.AreEqual(20, pd.ImageHeight, "ImageHeight");
Assert.AreEqual(30, pd.ImageWidth, "ImageWidth");
Assert.AreEqual(3, pd.NumberOfFrames, "NumberOfFrames");
Assert.AreEqual("MONOCHROME2", pd.PhotometricInterpretation, "PhotometricInterpretation");
Assert.AreEqual(1, pd.PixelRepresentation, "PixelRepresentation");
Assert.AreEqual(1, pd.SamplesPerPixel, "SamplesPerPixel");
Assert.AreEqual(20 * 30, pd.UncompressedFrameSize, "UncompressedFrameSize");
for (var frame = 0; frame < 3; ++frame)
{
var fd = pd.GetFrame(frame);
Assert.AreEqual(pd.UncompressedFrameSize, fd.Length, "PixelData(frame={0}).Length", frame);
AssertBytesEqual((byte)(0x80 + frame), fd, "PixelData(frame={0})", frame);
}
}
public void TestBasic_FileOnDisk_16Bits_BigEndian()
{
var filename = Path.GetTempFileName();
CreateDicomImage(rows: 20, columns: 30, numberOfFrames: 3, endian: Endian.Big).Save(filename);
var dcf = new DicomFile(filename);
dcf.Load(DicomReadOptions.StorePixelDataReferences);
try
{
var pd = new DicomUncompressedPixelData(dcf);
Assert.AreEqual(16, pd.BitsAllocated, "BitsAllocated");
Assert.AreEqual(16, pd.BitsStored, "BitsStored");
Assert.AreEqual(15, pd.HighBit, "HighBit");
Assert.AreEqual(20, pd.ImageHeight, "ImageHeight");
Assert.AreEqual(30, pd.ImageWidth, "ImageWidth");
Assert.AreEqual(3, pd.NumberOfFrames, "NumberOfFrames");
Assert.AreEqual("MONOCHROME2", pd.PhotometricInterpretation, "PhotometricInterpretation");
Assert.AreEqual(0, pd.PixelRepresentation, "PixelRepresentation");
Assert.AreEqual(1, pd.SamplesPerPixel, "SamplesPerPixel");
Assert.AreEqual(20 * 30 * 2, pd.UncompressedFrameSize, "UncompressedFrameSize");
for (var frame = 0; frame < 3; ++frame)
{
var fd = pd.GetFrame(frame);
Assert.AreEqual(pd.UncompressedFrameSize, fd.Length, "PixelData(frame={0}).Length", frame);
AssertBytesEqual((byte)(0x80 + frame), fd, "PixelData(frame={0})", frame);
}
}
finally
{
File.Delete(filename);
}
}
public void Encode(DicomUncompressedPixelData oldPixelData, DicomCompressedPixelData newPixelData, DicomCodecParameters parameters)
{
DicomRleCodecParameters rleParams = parameters as DicomRleCodecParameters;
if (rleParams == null)
throw new DicomCodecException("Unexpected RLE Codec parameters");
// Convert to RGB
if (oldPixelData.HasPaletteColorLut && parameters.ConvertPaletteToRGB)
{
oldPixelData.ConvertPaletteColorToRgb();
newPixelData.HasPaletteColorLut = false;
newPixelData.SamplesPerPixel = oldPixelData.SamplesPerPixel;
newPixelData.PlanarConfiguration = oldPixelData.PlanarConfiguration;
newPixelData.PhotometricInterpretation = oldPixelData.PhotometricInterpretation;
}
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.GetFrame(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.AddFrameFragment(encoder.GetBuffer());
}
}
public void TestAdvanced_FileOnDisk_16Bits_OW()
{
var filename = Path.GetTempFileName();
CreateDicomImage(rows : 20, columns : 30, numberOfFrames : 5).Save(filename);
var dcf = new DicomFile(filename);
dcf.Load(DicomReadOptions.StorePixelDataReferences);
try
{
var pd = new DicomUncompressedPixelData(dcf);
Assert.AreEqual(16, pd.BitsAllocated, "BitsAllocated");
Assert.AreEqual(16, pd.BitsStored, "BitsStored");
Assert.AreEqual(15, pd.HighBit, "HighBit");
Assert.AreEqual(20, pd.ImageHeight, "ImageHeight");
Assert.AreEqual(30, pd.ImageWidth, "ImageWidth");
Assert.AreEqual(5, pd.NumberOfFrames, "NumberOfFrames");
Assert.AreEqual("MONOCHROME2", pd.PhotometricInterpretation, "PhotometricInterpretation");
Assert.AreEqual(0, pd.PixelRepresentation, "PixelRepresentation");
Assert.AreEqual(1, pd.SamplesPerPixel, "SamplesPerPixel");
Assert.AreEqual(20*30*2, pd.UncompressedFrameSize, "UncompressedFrameSize");
var newFrameData = new byte[pd.UncompressedFrameSize];
for (var n = 0; n < newFrameData.Length; ++n)
newFrameData[n] = 0x7F;
pd.SetFrame(1, newFrameData);
pd.UpdateAttributeCollection(dcf.DataSet);
var pixelData = dcf.DataSet[DicomTags.PixelData].Values as byte[];
for (var frame = 0; frame < 5; ++frame)
{
var fd = pd.GetFrame(frame);
var expectedValue = frame == 1 ? (byte) 0x7F : (byte) (0x80 + frame);
Assert.AreEqual(pd.UncompressedFrameSize, fd.Length, "PixelData(frame={0}).Length", frame);
AssertBytesEqual(expectedValue, fd, "PixelData(frame={0})", frame);
AssertBytesEqual(expectedValue, pixelData, frame*pd.UncompressedFrameSize, pd.UncompressedFrameSize, "AttributeValues(frame={0})", frame);
}
}
finally
{
File.Delete(filename);
}
}
public void TestBasic_FileOnDisk_16Bits_BigEndian_OddFrameLength()
{
var filename = Path.GetTempFileName();
CreateDicomImage(rows : 19, columns : 29, numberOfFrames : 5, endian : Endian.Big).Save(filename);
var dcf = new DicomFile(filename);
dcf.Load(DicomReadOptions.StorePixelDataReferences);
try
{
var pd = new DicomUncompressedPixelData(dcf);
Assert.AreEqual(16, pd.BitsAllocated, "BitsAllocated");
Assert.AreEqual(16, pd.BitsStored, "BitsStored");
Assert.AreEqual(15, pd.HighBit, "HighBit");
Assert.AreEqual(19, pd.ImageHeight, "ImageHeight");
Assert.AreEqual(29, pd.ImageWidth, "ImageWidth");
Assert.AreEqual(5, pd.NumberOfFrames, "NumberOfFrames");
Assert.AreEqual("MONOCHROME2", pd.PhotometricInterpretation, "PhotometricInterpretation");
Assert.AreEqual(0, pd.PixelRepresentation, "PixelRepresentation");
Assert.AreEqual(1, pd.SamplesPerPixel, "SamplesPerPixel");
Assert.AreEqual(19*29*2, pd.UncompressedFrameSize, "UncompressedFrameSize");
for (var frame = 0; frame < 5; ++frame)
{
var fd = pd.GetFrame(frame);
Assert.AreEqual(pd.UncompressedFrameSize, fd.Length, "PixelData(frame={0}).Length", frame);
AssertBytesEqual((byte) (0x80 + frame), fd, "PixelData(frame={0})", frame);
}
}
finally
{
File.Delete(filename);
}
}
public void TestBasic_FileOnDisk_8Bits_OB()
{
var filename = Path.GetTempFileName();
CreateDicomImage(rows : 20, columns : 30, numberOfFrames : 3, bitsAllocated16 : false, useOB : true).Save(filename);
var dcf = new DicomFile(filename);
dcf.Load(DicomReadOptions.StorePixelDataReferences);
try
{
var pd = new DicomUncompressedPixelData(dcf);
Assert.AreEqual(8, pd.BitsAllocated, "BitsAllocated");
Assert.AreEqual(8, pd.BitsStored, "BitsStored");
Assert.AreEqual(7, pd.HighBit, "HighBit");
Assert.AreEqual(20, pd.ImageHeight, "ImageHeight");
Assert.AreEqual(30, pd.ImageWidth, "ImageWidth");
Assert.AreEqual(3, pd.NumberOfFrames, "NumberOfFrames");
Assert.AreEqual("MONOCHROME2", pd.PhotometricInterpretation, "PhotometricInterpretation");
Assert.AreEqual(0, pd.PixelRepresentation, "PixelRepresentation");
Assert.AreEqual(1, pd.SamplesPerPixel, "SamplesPerPixel");
Assert.AreEqual(20*30, pd.UncompressedFrameSize, "UncompressedFrameSize");
for (var frame = 0; frame < 3; ++frame)
{
var fd = pd.GetFrame(frame);
Assert.AreEqual(pd.UncompressedFrameSize, fd.Length, "PixelData(frame={0}).Length", frame);
AssertBytesEqual((byte) (0x80 + frame), fd, "PixelData(frame={0})", frame);
}
}
finally
{
File.Delete(filename);
}
}
/// <summary>
/// Fills the <see cref="OverlayData"/> property with the overlay(s) that had been encoded
/// in the <see cref="DicomTags.PixelData"/> of the SOP Instance. If the image is a
/// multi-frame, overlay data is extracted from all the frames.
/// </summary>
/// <param name="pd">The pixel data that contains the encoded overlay(s).</param>
/// <exception cref="DicomException">Thrown if <paramref name="pd"/> is not a valid source of embedded overlay data.</exception>
/// <returns>True if the <see cref="OverlayData"/> was populated with data encoded in the pixel data; False if <see cref="OverlayData"/> is not empty.</returns>
public unsafe bool ExtractEmbeddedOverlay(DicomUncompressedPixelData pd)
{
byte[] overlayData = this.OverlayData;
if (overlayData != null && overlayData.Length > 0)
{
return(false);
}
// General sanity checks
if (pd.SamplesPerPixel > 1)
{
throw new DicomException("Unable to convert embedded overlays when Samples Per Pixel > 1");
}
if (pd.BitsStored == 8 && pd.BitsAllocated == 8)
{
throw new DicomException("Unable to remove overlay with 8 Bits Stored and 8 Bits Allocated");
}
if (pd.BitsStored == 16 && pd.BitsAllocated == 16)
{
throw new DicomException("Unable to remove overlay with 16 Bits Stored and 16 Bits Allocated");
}
if (OverlayBitPosition <= pd.HighBit && OverlayBitPosition >= pd.LowBit)
{
throw new DicomException(String.Format("Invalid overlay bit position ({0}); overlay would be in the middle of the pixel data.", OverlayBitPosition));
}
int frameSize = pd.UncompressedFrameSize;
int overlayDataLength = (int)Math.Ceiling((frameSize * pd.NumberOfFrames) / (pd.BitsAllocated * 1d));
int frameLength = frameSize / pd.BytesAllocated;
// Ensure even length overlay
if (overlayDataLength % 2 == 1)
{
overlayDataLength++;
}
overlayData = new byte[overlayDataLength];
int overlayOffset = 0;
byte overlayMask = 0x01;
if (pd.BitsAllocated <= 8)
{
var embeddedOverlayMask = ((byte)(0x1 << OverlayBitPosition));
// Embededded overlays must exist for all frames, they can't be for a subset
for (int i = 0; i < pd.NumberOfFrames; i++)
{
byte[] frameData = pd.GetFrame(i);
ExtractEmbeddedOverlay(frameData, frameLength, embeddedOverlayMask, overlayData, ref overlayOffset, ref overlayMask);
pd.SetFrame(i, frameData);
}
}
else
{
var embeddedOverlayMask = ((ushort)(0x1 << OverlayBitPosition));
// Embededded overlays must exist for all frames, they can't be for a subset
for (int i = 0; i < pd.NumberOfFrames; i++)
{
byte[] frameData = pd.GetFrame(i);
ExtractEmbeddedOverlay(frameData, frameLength, embeddedOverlayMask, overlayData, ref overlayOffset, ref overlayMask);
pd.SetFrame(i, frameData);
}
}
pd.UpdatePixelDataAttribute();
// Assign the new overlay tags
this.OverlayBitPosition = 0;
this.OverlayBitsAllocated = 1;
if (this.IsBigEndianOW)
{
// Just do a bulk swap, performance isn't much of an issue.
ByteBuffer buffer = new ByteBuffer(overlayData, Endian.Little);
buffer.Swap2();
this.OverlayData = buffer.ToBytes();
}
else
{
this.OverlayData = overlayData;
}
// Cleanup Rows/Columns if necessary
if (this.OverlayColumns == 0)
{
this.OverlayColumns = pd.ImageWidth;
}
if (this.OverlayRows == 0)
{
this.OverlayRows = pd.ImageHeight;
}
return(true);
}
public void Encode(DicomUncompressedPixelData oldPixelData, DicomCompressedPixelData newPixelData, DicomCodecParameters parameters)
{
DicomRleCodecParameters rleParams = parameters as DicomRleCodecParameters ?? new DicomRleCodecParameters();
// Convert to RGB
if (oldPixelData.HasPaletteColorLut && parameters.ConvertPaletteToRGB)
{
oldPixelData.ConvertPaletteColorToRgb();
newPixelData.HasPaletteColorLut = false;
newPixelData.SamplesPerPixel = oldPixelData.SamplesPerPixel;
newPixelData.PlanarConfiguration = oldPixelData.PlanarConfiguration;
newPixelData.PhotometricInterpretation = oldPixelData.PhotometricInterpretation;
}
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.GetFrame(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.AddFrameFragment(encoder.GetBuffer());
}
}
private void CheckPixels(string filename)
{
DicomReadOptions readOptions = DicomReadOptions.StorePixelDataReferences;
DicomFile newFile = new DicomFile(filename);
newFile.Load(readOptions);
DicomUncompressedPixelData pd = new DicomUncompressedPixelData(newFile.DataSet);
for (int frame = 0; frame < pd.NumberOfFrames; frame++)
{
byte[] data = pd.GetFrame(frame);
uint pdVal = (uint)frame + 1;
for (int i = 0; i < pd.UncompressedFrameSize; i++, pdVal++)
{
if (data[i] != pdVal%255)
{
string val = String.Format("Value bad: frame: {0}, pixel: {1}, val1: {2}, val2: {3}", frame, i, data[i], pdVal%255);
Console.Write(val);
}
Assert.AreEqual(data[i], pdVal%255);
}
}
}
/// <summary>
/// Fills the <see cref="OverlayData"/> property with the overlay that had been encoded
/// in the <see cref="DicomTags.PixelData"/> of the SOP Instance.
/// </summary>
/// <param name="pd">The pixel data that contains the encoded overlay.</param>
/// <exception cref="DicomException">Thrown if <paramref name="pd"/> is not a valid source of embedded overlay data.</exception>
/// <returns>True if the <see cref="OverlayData"/> was populated with data encoded in the pixel data; False if <see cref="OverlayData"/> is not empty.</returns>
public unsafe bool ConvertEmbeddedOverlay(DicomUncompressedPixelData pd)
{
byte[] oldOverlayData = this.OverlayData;
if (oldOverlayData != null && oldOverlayData.Length > 0)
{
return(false);
}
// General sanity checks
if (pd.SamplesPerPixel > 1)
{
throw new DicomException("Unable to convert embedded overlays when Samples Per Pixel > 1");
}
if (pd.BitsStored == 8 && pd.BitsAllocated == 8)
{
throw new DicomException("Unable to remove overlay with 8 Bits Stored and 8 Bits Allocated");
}
if (pd.BitsStored == 16 && pd.BitsAllocated == 16)
{
throw new DicomException("Unable to remove overlay with 16 Bits Stored and 16 Bits Allocated");
}
int frameSize = pd.UncompressedFrameSize;
int overlaySize = frameSize / pd.BitsAllocated;
if (frameSize % pd.BitsAllocated > 0)
{
overlaySize++;
}
int numValues = frameSize / pd.BytesAllocated;
byte[] overlay = new byte[overlaySize];
int overlayOffset = 0;
// Embededded overlays must exist for all frames, they can't be for a subset
for (int i = 0; i < pd.NumberOfFrames; i++)
{
byte[] frameData = pd.GetFrame(i);
if (pd.BitsAllocated <= 8)
{
byte pixelMask = ((byte)(0x1 << this.OverlayBitPosition));
byte overlayMask = 0x01;
fixed(byte *pFrameData = frameData)
{
byte *pixelData = pFrameData;
for (int p = 0; p < numValues; p++, pixelData++)
{
if ((*pixelData & pixelMask) != 0)
{
overlay[overlayOffset] |= overlayMask;
*pixelData &= (byte)~pixelMask;
}
if (overlayMask == 0x80)
{
overlayMask = 0x01;
overlayOffset++;
}
else
{
overlayMask <<= 1;
}
}
}
}
else
{
fixed(byte *pFrameData = frameData)
{
ushort pixelMask = ((ushort)(0x1 << OverlayBitPosition));
byte overlayMask = 0x01;
ushort *pixelData = (ushort *)pFrameData;
for (int p = 0; p < numValues; p++, pixelData++)
{
if ((*pixelData & pixelMask) != 0)
{
overlay[overlayOffset] |= overlayMask;
*pixelData &= (ushort)~pixelMask;
}
if (overlayMask == 0x80)
{
overlayMask = 0x01;
overlayOffset++;
}
else
{
overlayMask <<= 1;
}
}
}
}
}
// Assign the new overlay tags
this.OverlayBitPosition = 0;
this.OverlayBitsAllocated = 1;
if (this.IsBigEndianOW)
{
// Just do a bulk swap, performance isn't much of an issue.
ByteBuffer buffer = new ByteBuffer(overlay, Endian.Little);
buffer.Swap2();
this.OverlayData = buffer.ToBytes();
}
else
{
this.OverlayData = overlay;
}
// Cleanup Rows/Columns if necessary
if (this.OverlayColumns == 0)
{
this.OverlayColumns = pd.ImageWidth;
}
if (this.OverlayRows == 0)
{
this.OverlayRows = pd.ImageHeight;
}
return(true);
}
