private void InitializeFrameData(DicomUncompressedPixelData owner, DicomAttribute pixelDataAttribute)
{
var obAttrib = pixelDataAttribute as DicomAttributeOB;
if (obAttrib != null && obAttrib.StreamLength > 0)
{
for (var n = 0; n < NumberOfFrames; ++n)
_fd.Add(new FrameDataOB(owner, obAttrib, n));
}
var owAttrib = pixelDataAttribute as DicomAttributeOW;
if (owAttrib != null && owAttrib.StreamLength > 0)
{
for (var n = 0; n < NumberOfFrames; ++n)
_fd.Add(new FrameDataOW(owner, owAttrib, n));
}
}
/// <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;
}
/// <summary>
/// Initializes the frame data container from the specified byte buffer.
/// </summary>
public FrameDataBytes(DicomUncompressedPixelData owner, byte[] frameData, bool copyRequired = true)
: base(owner)
{
if (copyRequired)
{
var buffer = new byte[frameData.Length];
Array.Copy(frameData, buffer, buffer.Length);
_buffer = buffer;
}
else
{
_buffer = frameData;
}
}
/// <summary>
/// Initializes the frame data container.
/// </summary>
protected FrameData(DicomUncompressedPixelData owner)
{
_owner = owner;
}
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>
/// Constructor from a <see cref="DicomUncompressedPixelData"/> instance.
/// </summary>
/// <param name="pd">The uuncompressed pixel data attribute to initialize the object from.</param>
public DicomCompressedPixelData(DicomUncompressedPixelData pd) : base(pd)
{
_sq = new DicomFragmentSequence(DicomTags.PixelData);
}
/// <summary>
/// Get a specific frame's data in uncompressed format.
/// </summary>
/// <remarks>
/// <para>
/// If a DICOM file is loaded with the <see cref="DicomReadOptions.StorePixelDataReferences"/>
/// option set, this method will only load the specific frame's data from the source file to
/// do the decompress, thus reducing memory usage to only the frame being decompressed.
/// </para>
/// </remarks>
/// <param name="frame">A zero offset frame to request.</param>
/// <param name="photometricInterpretation">The photometric interpretation of the output data</param>
/// <returns>A byte array containing the frame.</returns>
public override byte[] GetFrame(int frame, out string photometricInterpretation)
{
DicomUncompressedPixelData pd = new DicomUncompressedPixelData(this);
IDicomCodec 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);
}
DicomCodecParameters parameters = DicomCodecRegistry.GetCodecParameters(TransferSyntax, null);
codec.DecodeFrame(frame, this, pd, parameters);
pd.TransferSyntax = TransferSyntax.ExplicitVrLittleEndian;
photometricInterpretation = pd.PhotometricInterpretation;
return pd.GetData();
}