/// <summary>
/// Contructor from a <see cref="DicomCompressedPixelData"/> instance.
/// </summary>
/// <param name="compressedPixelData"></param>
public DicomUncompressedPixelData(DicomCompressedPixelData compressedPixelData)
: base(compressedPixelData)
{
if (BitsAllocated > 8)
{
_pd = new DicomAttributeOW(DicomTags.PixelData);
}
else
{
var pdTag = DicomTagDictionary.GetDicomTag(DicomTags.PixelData);
var obTag = new DicomTag(DicomTags.PixelData, pdTag.Name, pdTag.VariableName, DicomVr.OBvr, pdTag.MultiVR, pdTag.VMLow, pdTag.VMHigh, pdTag.Retired);
_pd = new DicomAttributeOB(obTag);
}
InitializeFrameData(this, _pd);
}
/// <summary>
/// Contructor from a <see cref="DicomCompressedPixelData"/> instance.
/// </summary>
/// <param name="compressedPixelData"></param>
public DicomUncompressedPixelData(DicomCompressedPixelData compressedPixelData)
: base(compressedPixelData)
{
if (BitsAllocated > 8)
{
_pd = new DicomAttributeOW(DicomTags.PixelData);
}
else
{
var pdTag = DicomTagDictionary.GetDicomTag(DicomTags.PixelData);
var obTag = new DicomTag(DicomTags.PixelData, pdTag.Name, pdTag.VariableName, DicomVr.OBvr, pdTag.MultiVR, pdTag.VMLow, pdTag.VMHigh, pdTag.Retired);
_pd = new DicomAttributeOB(obTag);
}
InitializeFrameData(this, _pd);
}
/// <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 = Parent.SourceMessage;
#if DEBUG
CodeClock clock = new CodeClock();
clock.Start();
#endif
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);
#if DEBUG
clock.Stop();
PerformanceReportBroker.PublishReport("DicomMessageSopDataSource", "CreateFrameNormalizedPixelData", clock.Seconds);
#endif
return rawPixelData;
}
public void ChangeTransferSyntax(TransferSyntax newTransferSyntax, IDicomCodec inputCodec, DicomCodecParameters inputParameters)
{
IDicomCodec codec = inputCodec;
DicomCodecParameters parameters = inputParameters;
if (newTransferSyntax.Encapsulated && TransferSyntax.Encapsulated)
throw new DicomCodecException("Source and destination transfer syntaxes encapsulated");
if (newTransferSyntax.Encapsulated)
{
if (codec == null)
{
codec = DicomCodecRegistry.GetCodec(newTransferSyntax);
if (codec == null)
{
Platform.Log(LogLevel.Error, "Unable to get registered codec for {0}", newTransferSyntax);
throw new DicomCodecException("No registered codec for: " + newTransferSyntax.Name);
}
}
if (parameters == null)
parameters = DicomCodecRegistry.GetCodecParameters(newTransferSyntax, DataSet);
DicomAttribute pixelData;
if (DataSet.TryGetAttribute(DicomTags.PixelData, out pixelData))
{
if (pixelData.IsNull)
throw new DicomCodecException("Sop pixel data has no valid value and cannot be compressed.");
DicomUncompressedPixelData pd = new DicomUncompressedPixelData(DataSet);
DicomCompressedPixelData fragments = new DicomCompressedPixelData(pd);
// Set before compression, the codecs need it.
fragments.TransferSyntax = newTransferSyntax;
codec.Encode(pd, fragments, parameters);
fragments.UpdateMessage(this);
//TODO: should we validate the number of frames in the compressed data?
if (!DataSet.TryGetAttribute(DicomTags.PixelData, out pixelData) || pixelData.IsNull)
throw new DicomCodecException("Sop has no pixel data after compression.");
}
else
{
//A bit cheap, but check for basic image attributes - if any exist
// and are non-empty, there should probably be pixel data too.
DicomAttribute attribute;
if (DataSet.TryGetAttribute(DicomTags.Rows, out attribute) && !attribute.IsNull)
throw new DicomCodecException("Suspect Sop appears to be an image (Rows is non-empty), but has no pixel data.");
if (DataSet.TryGetAttribute(DicomTags.Columns, out attribute) && !attribute.IsNull)
throw new DicomCodecException("Suspect Sop appears to be an image (Columns is non-empty), but has no pixel data.");
TransferSyntax = newTransferSyntax;
}
}
else
{
if (codec == null)
{
codec = DicomCodecRegistry.GetCodec(TransferSyntax);
if (codec == null)
{
Platform.Log(LogLevel.Error, "Unable to get registered codec for {0}", TransferSyntax);
throw new DicomCodecException("No registered codec for: " + TransferSyntax.Name);
}
if (parameters == null)
parameters = DicomCodecRegistry.GetCodecParameters(TransferSyntax, DataSet);
}
DicomAttribute pixelData;
if (DataSet.TryGetAttribute(DicomTags.PixelData, out pixelData))
{
if (pixelData.IsNull)
throw new DicomCodecException("Sop pixel data has no valid value and cannot be decompressed.");
DicomCompressedPixelData fragments = new DicomCompressedPixelData(DataSet);
DicomUncompressedPixelData pd = new DicomUncompressedPixelData(fragments);
codec.Decode(fragments, pd, parameters);
pd.TransferSyntax = TransferSyntax.ExplicitVrLittleEndian;
pd.UpdateMessage(this);
//TODO: should we validate the number of frames in the decompressed data?
if (!DataSet.TryGetAttribute(DicomTags.PixelData, out pixelData) || pixelData.IsNull)
throw new DicomCodecException("Sop has no pixel data after decompression.");
}
else
{
//NOTE: doing this for consistency, really.
DicomAttribute attribute;
if (DataSet.TryGetAttribute(DicomTags.Rows, out attribute) && !attribute.IsNull)
throw new DicomCodecException("Suspect Sop appears to be an image (Rows is non-empty), but has no pixel data.");
if (DataSet.TryGetAttribute(DicomTags.Columns, out attribute) && !attribute.IsNull)
throw new DicomCodecException("Suspect Sop appears to be an image (Columns is non-empty), but has no pixel data.");
TransferSyntax = TransferSyntax.ExplicitVrLittleEndian;
}
}
}
public void ChangeTransferSyntax(TransferSyntax newTransferSyntax, IDicomCodec inputCodec, DicomCodecParameters inputParameters)
{
IDicomCodec codec = inputCodec;
DicomCodecParameters parameters = inputParameters;
if (newTransferSyntax.Encapsulated && TransferSyntax.Encapsulated)
{
throw new DicomCodecException("Source and destination transfer syntaxes encapsulated");
}
if (newTransferSyntax.Encapsulated)
{
if (codec == null)
{
codec = DicomCodecRegistry.GetCodec(newTransferSyntax);
if (codec == null)
{
Platform.Log(LogLevel.Error, "Unable to get registered codec for {0}", newTransferSyntax);
throw new DicomCodecException("No registered codec for: " + newTransferSyntax.Name);
}
}
if (parameters == null)
{
parameters = DicomCodecRegistry.GetCodecParameters(newTransferSyntax, DataSet);
}
DicomAttribute pixelData;
if (DataSet.TryGetAttribute(DicomTags.PixelData, out pixelData))
{
if (pixelData.IsNull)
{
throw new DicomCodecException("Sop pixel data has no valid value and cannot be compressed.");
}
new OverlayPlaneModuleIod(DataSet).ExtractEmbeddedOverlays();
var pd = new DicomUncompressedPixelData(DataSet);
var rawPixelData = (byte[])pixelData.Values;
//Before compression, make the pixel data more "typical", so it's harder to mess up the codecs.
//NOTE: Could combine mask and align into one method so we're not iterating twice, but I prefer having the methods separate.
if (DicomUncompressedPixelData.RightAlign(rawPixelData, pd.BitsAllocated, pd.BitsStored, pd.HighBit))
{
var newHighBit = (ushort)(pd.HighBit - pd.LowBit);
Platform.Log(LogLevel.Debug, "Right aligned pixel data (High Bit: {0}->{1}).", pd.HighBit, newHighBit);
pd.HighBit = newHighBit; //correct high bit after right-aligning.
DataSet[DicomTags.HighBit].SetUInt16(0, newHighBit);
}
if (DicomUncompressedPixelData.ZeroUnusedBits(rawPixelData, pd.BitsAllocated, pd.BitsStored, pd.HighBit))
{
Platform.Log(LogLevel.Debug, "Zeroed some unused bits before compression.");
}
// Set transfer syntax before compression, the codecs need it.
var fragments = new DicomCompressedPixelData(pd)
{
TransferSyntax = newTransferSyntax
};
codec.Encode(pd, fragments, parameters);
fragments.UpdateMessage(this);
//TODO: should we validate the number of frames in the compressed data?
if (!DataSet.TryGetAttribute(DicomTags.PixelData, out pixelData) || pixelData.IsNull)
{
throw new DicomCodecException("Sop has no pixel data after compression.");
}
}
else
{
//A bit cheap, but check for basic image attributes - if any exist
// and are non-empty, there should probably be pixel data too.
DicomAttribute attribute;
if (DataSet.TryGetAttribute(DicomTags.Rows, out attribute) && !attribute.IsNull)
{
throw new DicomCodecException("Suspect Sop appears to be an image (Rows is non-empty), but has no pixel data.");
}
if (DataSet.TryGetAttribute(DicomTags.Columns, out attribute) && !attribute.IsNull)
{
throw new DicomCodecException("Suspect Sop appears to be an image (Columns is non-empty), but has no pixel data.");
}
TransferSyntax = newTransferSyntax;
}
}
else
{
if (codec == null)
{
codec = DicomCodecRegistry.GetCodec(TransferSyntax);
if (codec == null)
{
Platform.Log(LogLevel.Error, "Unable to get registered codec for {0}", TransferSyntax);
throw new DicomCodecException("No registered codec for: " + TransferSyntax.Name);
}
if (parameters == null)
{
parameters = DicomCodecRegistry.GetCodecParameters(TransferSyntax, DataSet);
}
}
DicomAttribute pixelData;
if (DataSet.TryGetAttribute(DicomTags.PixelData, out pixelData))
{
if (pixelData.IsNull)
{
throw new DicomCodecException("Sop pixel data has no valid value and cannot be decompressed.");
}
var fragments = new DicomCompressedPixelData(DataSet);
var pd = new DicomUncompressedPixelData(fragments);
codec.Decode(fragments, pd, parameters);
pd.TransferSyntax = TransferSyntax.ExplicitVrLittleEndian;
TransferSyntax = TransferSyntax.ExplicitVrLittleEndian;
pd.UpdateMessage(this);
//TODO: should we validate the number of frames in the decompressed data?
if (!DataSet.TryGetAttribute(DicomTags.PixelData, out pixelData) || pixelData.IsNull)
{
throw new DicomCodecException("Sop has no pixel data after decompression.");
}
}
else
{
//NOTE: doing this for consistency, really.
DicomAttribute attribute;
if (DataSet.TryGetAttribute(DicomTags.Rows, out attribute) && !attribute.IsNull)
{
throw new DicomCodecException("Suspect Sop appears to be an image (Rows is non-empty), but has no pixel data.");
}
if (DataSet.TryGetAttribute(DicomTags.Columns, out attribute) && !attribute.IsNull)
{
throw new DicomCodecException("Suspect Sop appears to be an image (Columns is non-empty), but has no pixel data.");
}
TransferSyntax = TransferSyntax.ExplicitVrLittleEndian;
}
}
}
public void ChangeTransferSyntax(TransferSyntax newTransferSyntax, IDicomCodec inputCodec, DicomCodecParameters inputParameters)
{
IDicomCodec codec = inputCodec;
DicomCodecParameters parameters = inputParameters;
if (newTransferSyntax.Encapsulated && TransferSyntax.Encapsulated)
throw new DicomCodecException("Source and destination transfer syntaxes encapsulated");
if (newTransferSyntax.Encapsulated)
{
if (codec == null)
{
codec = DicomCodecRegistry.GetCodec(newTransferSyntax);
if (codec == null)
{
Platform.Log(LogLevel.Error, "Unable to get registered codec for {0}", newTransferSyntax);
throw new DicomCodecException("No registered codec for: " + newTransferSyntax.Name);
}
}
if (parameters == null)
parameters = DicomCodecRegistry.GetCodecParameters(newTransferSyntax, DataSet);
DicomAttribute pixelData;
if (DataSet.TryGetAttribute(DicomTags.PixelData, out pixelData))
{
if (pixelData.IsNull)
throw new DicomCodecException("Sop pixel data has no valid value and cannot be compressed.");
new OverlayPlaneModuleIod(DataSet).ExtractEmbeddedOverlays();
var pd = new DicomUncompressedPixelData(DataSet);
using (var pixelStream = ((DicomAttributeBinary) pixelData).AsStream())
{
//Before compression, make the pixel data more "typical", so it's harder to mess up the codecs.
//NOTE: Could combine mask and align into one method so we're not iterating twice, but I prefer having the methods separate.
if (DicomUncompressedPixelData.RightAlign(pixelStream, pd.BitsAllocated, pd.BitsStored, pd.HighBit))
{
var newHighBit = (ushort) (pd.HighBit - pd.LowBit);
Platform.Log(LogLevel.Debug, "Right aligned pixel data (High Bit: {0}->{1}).", pd.HighBit, newHighBit);
pd.HighBit = newHighBit; //correct high bit after right-aligning.
DataSet[DicomTags.HighBit].SetUInt16(0, newHighBit);
}
if (DicomUncompressedPixelData.ZeroUnusedBits(pixelStream, pd.BitsAllocated, pd.BitsStored, pd.HighBit))
{
Platform.Log(LogLevel.Debug, "Zeroed some unused bits before compression.");
}
}
// Set transfer syntax before compression, the codecs need it.
var fragments = new DicomCompressedPixelData(pd) { TransferSyntax = newTransferSyntax };
codec.Encode(pd, fragments, parameters);
fragments.UpdateMessage(this);
//TODO: should we validate the number of frames in the compressed data?
if (!DataSet.TryGetAttribute(DicomTags.PixelData, out pixelData) || pixelData.IsNull)
throw new DicomCodecException("Sop has no pixel data after compression.");
}
else
{
//A bit cheap, but check for basic image attributes - if any exist
// and are non-empty, there should probably be pixel data too.
DicomAttribute attribute;
if (DataSet.TryGetAttribute(DicomTags.Rows, out attribute) && !attribute.IsNull)
throw new DicomCodecException("Suspect Sop appears to be an image (Rows is non-empty), but has no pixel data.");
if (DataSet.TryGetAttribute(DicomTags.Columns, out attribute) && !attribute.IsNull)
throw new DicomCodecException("Suspect Sop appears to be an image (Columns is non-empty), but has no pixel data.");
TransferSyntax = newTransferSyntax;
}
}
else
{
if (codec == null)
{
codec = DicomCodecRegistry.GetCodec(TransferSyntax);
if (codec == null)
{
Platform.Log(LogLevel.Error, "Unable to get registered codec for {0}", TransferSyntax);
throw new DicomCodecException("No registered codec for: " + TransferSyntax.Name);
}
if (parameters == null)
parameters = DicomCodecRegistry.GetCodecParameters(TransferSyntax, DataSet);
}
DicomAttribute pixelData;
if (DataSet.TryGetAttribute(DicomTags.PixelData, out pixelData))
{
if (pixelData.IsNull)
throw new DicomCodecException("Sop pixel data has no valid value and cannot be decompressed.");
var fragments = new DicomCompressedPixelData(DataSet);
var pd = new DicomUncompressedPixelData(fragments);
codec.Decode(fragments, pd, parameters);
pd.TransferSyntax = TransferSyntax.ExplicitVrLittleEndian;
TransferSyntax = TransferSyntax.ExplicitVrLittleEndian;
pd.UpdateMessage(this);
//TODO: should we validate the number of frames in the decompressed data?
if (!DataSet.TryGetAttribute(DicomTags.PixelData, out pixelData) || pixelData.IsNull)
throw new DicomCodecException("Sop has no pixel data after decompression.");
}
else
{
//NOTE: doing this for consistency, really.
DicomAttribute attribute;
if (DataSet.TryGetAttribute(DicomTags.Rows, out attribute) && !attribute.IsNull)
throw new DicomCodecException("Suspect Sop appears to be an image (Rows is non-empty), but has no pixel data.");
if (DataSet.TryGetAttribute(DicomTags.Columns, out attribute) && !attribute.IsNull)
throw new DicomCodecException("Suspect Sop appears to be an image (Columns is non-empty), but has no pixel data.");
TransferSyntax = TransferSyntax.ExplicitVrLittleEndian;
}
}
}
/// <summary>
/// Contructor from a <see cref="DicomCompressedPixelData"/> instance.
/// </summary>
/// <param name="pd"></param>
public DicomUncompressedPixelData(DicomCompressedPixelData pd) : base(pd)
{
if (BitsAllocated > 8)
_pd = new DicomAttributeOW(DicomTags.PixelData);
else
{
DicomTag pdTag = DicomTagDictionary.GetDicomTag(DicomTags.PixelData);
_pd =
new DicomAttributeOB(
new DicomTag(DicomTags.PixelData, pdTag.Name, pdTag.VariableName, DicomVr.OBvr, pdTag.MultiVR,
pdTag.VMLow, pdTag.VMHigh, pdTag.Retired));
}
}
public void ChangeTransferSyntax(TransferSyntax newTransferSyntax, IDicomCodec inputCodec, DicomCodecParameters inputParameters)
{
IDicomCodec codec = inputCodec;
DicomCodecParameters parameters = inputParameters;
if (newTransferSyntax.Encapsulated && TransferSyntax.Encapsulated)
{
throw new DicomCodecException("Source and destination transfer syntaxes encapsulated");
}
if (newTransferSyntax.Encapsulated)
{
if (codec == null)
{
codec = DicomCodecRegistry.GetCodec(newTransferSyntax);
if (codec == null)
{
Platform.Log(LogLevel.Error, "Unable to get registered codec for {0}", newTransferSyntax);
throw new DicomCodecException("No registered codec for: " + newTransferSyntax.Name);
}
}
if (parameters == null)
{
parameters = DicomCodecRegistry.GetCodecParameters(newTransferSyntax, DataSet);
}
DicomAttribute pixelData;
if (DataSet.TryGetAttribute(DicomTags.PixelData, out pixelData))
{
if (pixelData.IsNull)
{
throw new DicomCodecException("Sop pixel data has no valid value and cannot be compressed.");
}
DicomUncompressedPixelData pd = new DicomUncompressedPixelData(DataSet);
DicomCompressedPixelData fragments = new DicomCompressedPixelData(pd);
// Set before compression, the codecs need it.
fragments.TransferSyntax = newTransferSyntax;
codec.Encode(pd, fragments, parameters);
fragments.UpdateMessage(this);
//TODO: should we validate the number of frames in the compressed data?
if (!DataSet.TryGetAttribute(DicomTags.PixelData, out pixelData) || pixelData.IsNull)
{
throw new DicomCodecException("Sop has no pixel data after compression.");
}
}
else
{
//A bit cheap, but check for basic image attributes - if any exist
// and are non-empty, there should probably be pixel data too.
DicomAttribute attribute;
if (DataSet.TryGetAttribute(DicomTags.Rows, out attribute) && !attribute.IsNull)
{
throw new DicomCodecException("Suspect Sop appears to be an image (Rows is non-empty), but has no pixel data.");
}
if (DataSet.TryGetAttribute(DicomTags.Columns, out attribute) && !attribute.IsNull)
{
throw new DicomCodecException("Suspect Sop appears to be an image (Columns is non-empty), but has no pixel data.");
}
TransferSyntax = newTransferSyntax;
}
}
else
{
if (codec == null)
{
codec = DicomCodecRegistry.GetCodec(TransferSyntax);
if (codec == null)
{
Platform.Log(LogLevel.Error, "Unable to get registered codec for {0}", TransferSyntax);
throw new DicomCodecException("No registered codec for: " + TransferSyntax.Name);
}
if (parameters == null)
{
parameters = DicomCodecRegistry.GetCodecParameters(TransferSyntax, DataSet);
}
}
DicomAttribute pixelData;
if (DataSet.TryGetAttribute(DicomTags.PixelData, out pixelData))
{
if (pixelData.IsNull)
{
throw new DicomCodecException("Sop pixel data has no valid value and cannot be decompressed.");
}
DicomCompressedPixelData fragments = new DicomCompressedPixelData(DataSet);
DicomUncompressedPixelData pd = new DicomUncompressedPixelData(fragments);
codec.Decode(fragments, pd, parameters);
pd.TransferSyntax = TransferSyntax.ExplicitVrLittleEndian;
pd.UpdateMessage(this);
//TODO: should we validate the number of frames in the decompressed data?
if (!DataSet.TryGetAttribute(DicomTags.PixelData, out pixelData) || pixelData.IsNull)
{
throw new DicomCodecException("Sop has no pixel data after decompression.");
}
}
else
{
//NOTE: doing this for consistency, really.
DicomAttribute attribute;
if (DataSet.TryGetAttribute(DicomTags.Rows, out attribute) && !attribute.IsNull)
{
throw new DicomCodecException("Suspect Sop appears to be an image (Rows is non-empty), but has no pixel data.");
}
if (DataSet.TryGetAttribute(DicomTags.Columns, out attribute) && !attribute.IsNull)
{
throw new DicomCodecException("Suspect Sop appears to be an image (Columns is non-empty), but has no pixel data.");
}
TransferSyntax = TransferSyntax.ExplicitVrLittleEndian;
}
}
}
