public void ChangeSyntax(TransferSyntax syntax)
{
try
{
if (!_dicomFile.TransferSyntax.Encapsulated)
{
// Check if Overlay is embedded in pixels
OverlayPlaneModuleIod overlayIod = new OverlayPlaneModuleIod(_dicomFile.DataSet);
for (int i = 0; i < 16; i++)
{
if (overlayIod.HasOverlayPlane(i))
{
OverlayPlane overlay = overlayIod[i];
if (overlay.OverlayData == null)
{
DicomUncompressedPixelData pd = new DicomUncompressedPixelData(_dicomFile);
overlay.ConvertEmbeddedOverlay(pd);
}
}
}
}
else if (syntax.Encapsulated)
{
// Must decompress first.
_dicomFile.ChangeTransferSyntax(TransferSyntax.ExplicitVrLittleEndian);
}
_dicomFile.ChangeTransferSyntax(syntax);
}
catch (Exception e)
{
Platform.Log(LogLevel.Error, e, "Unexpected exception compressing/decompressing DICOM file");
}
}
public void ChangeSyntax(TransferSyntax syntax)
{
try
{
if (!_dicomFile.TransferSyntax.Encapsulated)
{
// Check if Overlay is embedded in pixels
OverlayPlaneModuleIod overlayIod = new OverlayPlaneModuleIod(_dicomFile.DataSet);
for (int i = 0; i < 16; i++)
{
if (overlayIod.HasOverlayPlane(i))
{
OverlayPlane overlay = overlayIod[i];
if (overlay.OverlayData == null)
{
DicomUncompressedPixelData pd = new DicomUncompressedPixelData(_dicomFile);
overlay.ConvertEmbeddedOverlay(pd);
}
}
}
}
else if (syntax.Encapsulated)
{
// Must decompress first.
_dicomFile.ChangeTransferSyntax(TransferSyntax.ExplicitVrLittleEndian);
}
_dicomFile.ChangeTransferSyntax(syntax);
}
catch (Exception e)
{
Platform.Log(LogLevel.Error, e, "Unexpected exception compressing/decompressing DICOM file");
}
}
/// <summary>
/// Called by <see cref="StandardSopFrameData.GetNormalizedOverlayData"/> to create a new byte buffer containing normalized
/// overlay pixel data for a particular overlay plane.
/// </summary>
/// <remarks>
/// See <see cref="StandardSopFrameData.GetNormalizedOverlayData"/> for details on the expected format of the byte buffer.
/// </remarks>
/// <param name="overlayNumber">The 1-based overlay plane number.</param>
/// <returns>A new byte buffer containing the normalized overlay pixel data.</returns>
protected override byte[] CreateNormalizedOverlayData(int overlayNumber)
{
//TODO (CR December 2010): make this a helper method somewhere, since it's now identical to the one in StreamingSopFrameData?
var overlayIndex = overlayNumber - 1;
byte[] overlayData = null;
var clock = new CodeClock();
clock.Start();
// check whether or not the overlay plane exists before attempting to ascertain
// whether or not the overlay is embedded in the pixel data
var overlayPlaneModuleIod = new OverlayPlaneModuleIod(Parent);
if (overlayPlaneModuleIod.HasOverlayPlane(overlayIndex))
{
if (_overlayCache[overlayIndex] == null)
{
var overlayPlane = overlayPlaneModuleIod[overlayIndex];
if (!overlayPlane.HasOverlayData)
{
// if the overlay is embedded, trigger retrieval of pixel data which will populate the cache for us
GetNormalizedPixelData();
}
else
{
// try to compute the offset in the OverlayData bit stream where we can find the overlay frame that applies to this image frame
int overlayFrame;
int bitOffset;
if (overlayPlane.TryGetRelevantOverlayFrame(FrameNumber, Parent.NumberOfFrames, out overlayFrame) &&
overlayPlane.TryComputeOverlayDataBitOffset(overlayFrame, out bitOffset))
{
// offset found - unpack only that overlay frame
var od = new OverlayData(bitOffset,
overlayPlane.OverlayRows,
overlayPlane.OverlayColumns,
overlayPlane.IsBigEndianOW,
overlayPlane.OverlayData);
_overlayCache[overlayIndex] = od.Unpack();
}
else
{
// no relevant overlay frame found - i.e. the overlay for this image frame is blank
_overlayCache[overlayIndex] = new byte[0];
}
}
}
overlayData = _overlayCache[overlayIndex];
}
clock.Stop();
PerformanceReportBroker.PublishReport("DicomMessageSopDataSource", "CreateNormalizedOverlayData", clock.Seconds);
return(overlayData);
}
/// <summary>
/// Called by <see cref="StandardSopFrameData.GetNormalizedOverlayData"/> to create a new byte buffer containing normalized
/// overlay pixel data for a particular overlay plane.
/// </summary>
/// <remarks>
/// See <see cref="StandardSopFrameData.GetNormalizedOverlayData"/> for details on the expected format of the byte buffer.
/// </remarks>
/// <param name="overlayNumber">The 1-based overlay plane number.</param>
/// <returns>A new byte buffer containing the normalized overlay pixel data.</returns>
protected override byte[] CreateNormalizedOverlayData(int overlayNumber)
{
var overlayIndex = overlayNumber - 1;
byte[] overlayData = null;
// check whether or not the overlay plane exists before attempting to ascertain
// whether or not the overlay is embedded in the pixel data
var overlayPlaneModuleIod = new OverlayPlaneModuleIod(Parent);
if (overlayPlaneModuleIod.HasOverlayPlane(overlayIndex))
{
if (_overlayData[overlayIndex] == null)
{
var overlayPlane = overlayPlaneModuleIod[overlayIndex];
if (!overlayPlane.HasOverlayData)
{
// if the overlay is embedded, trigger retrieval of pixel data which will populate the cache for us
GetNormalizedPixelData();
}
else
{
// try to compute the offset in the OverlayData bit stream where we can find the overlay frame that applies to this image frame
int overlayFrame;
int bitOffset;
if (overlayPlane.TryGetRelevantOverlayFrame(FrameNumber, Parent.NumberOfFrames, out overlayFrame) &&
overlayPlane.TryComputeOverlayDataBitOffset(overlayFrame, out bitOffset))
{
// offset found - unpack only that overlay frame
var od = new OverlayData(bitOffset,
overlayPlane.OverlayRows,
overlayPlane.OverlayColumns,
overlayPlane.IsBigEndianOW,
overlayPlane.OverlayData);
_overlayData[overlayIndex] = od.Unpack();
}
else
{
// no relevant overlay frame found - i.e. the overlay for this image frame is blank
_overlayData[overlayIndex] = new byte[0];
}
}
}
overlayData = _overlayData[overlayIndex];
}
return(overlayData);
}
protected override byte[] CreateNormalizedOverlayData(int overlayGroupNumber, int overlayFrameNumber)
{
int frameIndex = overlayFrameNumber - 1;
int overlayIndex = overlayGroupNumber - 1;
byte[] overlayData = null;
OverlayPlaneModuleIod opmi = new OverlayPlaneModuleIod(this.Parent);
if (opmi.HasOverlayPlane(overlayIndex))
{
OverlayPlane overlayPlane = opmi[overlayIndex];
if (_overlayData[overlayIndex] == null)
{
if (IsOverlayEmbedded(overlayPlane))
{
this.GetNormalizedPixelData();
}
else
{
int bitOffset;
overlayPlane.TryComputeOverlayDataBitOffset(frameIndex, out bitOffset);
OverlayData od = new OverlayData(bitOffset,
overlayPlane.OverlayRows,
overlayPlane.OverlayColumns,
overlayPlane.IsBigEndianOW,
overlayPlane.OverlayData);
_overlayData[overlayIndex] = od.Unpack();
}
}
overlayData = _overlayData[overlayIndex];
}
return(overlayData);
}
/// <summary>
/// Called by <see cref="StandardSopFrameData.GetNormalizedOverlayData"/> to create a new byte buffer containing normalized
/// overlay pixel data for a particular overlay plane.
/// </summary>
/// <remarks>
/// See <see cref="StandardSopFrameData.GetNormalizedOverlayData"/> for details on the expected format of the byte buffer.
/// </remarks>
/// <param name="overlayNumber">The 1-based overlay plane number.</param>
/// <returns>A new byte buffer containing the normalized overlay pixel data.</returns>
protected override byte[] CreateNormalizedOverlayData(int overlayNumber)
{
//TODO (CR December 2010): make this a helper method somewhere, since it's now identical to the one in StreamingSopFrameData?
var overlayIndex = overlayNumber - 1;
byte[] overlayData = null;
var clock = new CodeClock();
clock.Start();
// check whether or not the overlay plane exists before attempting to ascertain
// whether or not the overlay is embedded in the pixel data
var overlayPlaneModuleIod = new OverlayPlaneModuleIod(Parent);
if (overlayPlaneModuleIod.HasOverlayPlane(overlayIndex))
{
if (_overlayCache[overlayIndex] == null)
{
var overlayPlane = overlayPlaneModuleIod[overlayIndex];
if (!overlayPlane.HasOverlayData)
{
// if the overlay is embedded, trigger retrieval of pixel data which will populate the cache for us
GetNormalizedPixelData();
}
else
{
// try to compute the offset in the OverlayData bit stream where we can find the overlay frame that applies to this image frame
int overlayFrame;
int bitOffset;
if (overlayPlane.TryGetRelevantOverlayFrame(FrameNumber, Parent.NumberOfFrames, out overlayFrame) &&
overlayPlane.TryComputeOverlayDataBitOffset(overlayFrame, out bitOffset))
{
// offset found - unpack only that overlay frame
var od = new OverlayData(bitOffset,
overlayPlane.OverlayRows,
overlayPlane.OverlayColumns,
overlayPlane.IsBigEndianOW,
overlayPlane.OverlayData);
_overlayCache[overlayIndex] = od.Unpack();
}
else
{
// no relevant overlay frame found - i.e. the overlay for this image frame is blank
_overlayCache[overlayIndex] = new byte[0];
}
}
}
overlayData = _overlayCache[overlayIndex];
}
clock.Stop();
PerformanceReportBroker.PublishReport("DicomMessageSopDataSource", "CreateNormalizedOverlayData", clock.Seconds);
return overlayData;
}
/// <summary>
/// Called by <see cref="StandardSopFrameData.GetNormalizedOverlayData"/> to create a new byte buffer containing normalized
/// overlay pixel data for a particular overlay plane.
/// </summary>
/// <remarks>
/// See <see cref="StandardSopFrameData.GetNormalizedOverlayData"/> for details on the expected format of the byte buffer.
/// </remarks>
/// <param name="overlayNumber">The 1-based overlay plane number.</param>
/// <returns>A new byte buffer containing the normalized overlay pixel data.</returns>
protected override byte[] CreateNormalizedOverlayData(int overlayNumber)
{
var overlayIndex = overlayNumber - 1;
byte[] overlayData = null;
// check whether or not the overlay plane exists before attempting to ascertain
// whether or not the overlay is embedded in the pixel data
var overlayPlaneModuleIod = new OverlayPlaneModuleIod(Parent);
if (overlayPlaneModuleIod.HasOverlayPlane(overlayIndex))
{
if (_overlayData[overlayIndex] == null)
{
var overlayPlane = overlayPlaneModuleIod[overlayIndex];
if (!overlayPlane.HasOverlayData)
{
// if the overlay is embedded, trigger retrieval of pixel data which will populate the cache for us
GetNormalizedPixelData();
}
else
{
// try to compute the offset in the OverlayData bit stream where we can find the overlay frame that applies to this image frame
int overlayFrame;
int bitOffset;
if (overlayPlane.TryGetRelevantOverlayFrame(FrameNumber, Parent.NumberOfFrames, out overlayFrame) &&
overlayPlane.TryComputeOverlayDataBitOffset(overlayFrame, out bitOffset))
{
// offset found - unpack only that overlay frame
var od = new OverlayData(bitOffset,
overlayPlane.OverlayRows,
overlayPlane.OverlayColumns,
overlayPlane.IsBigEndianOW,
overlayPlane.OverlayData);
_overlayData[overlayIndex] = od.Unpack();
}
else
{
// no relevant overlay frame found - i.e. the overlay for this image frame is blank
_overlayData[overlayIndex] = new byte[0];
}
}
}
overlayData = _overlayData[overlayIndex];
}
return overlayData;
}
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);
// Check if Overlay is embedded in pixels
OverlayPlaneModuleIod overlayIod = new OverlayPlaneModuleIod(DataSet);
for (int i = 0; i < 16; i++)
{
if (overlayIod.HasOverlayPlane(i))
{
OverlayPlane overlay = overlayIod[i];
if (overlay.OverlayData == null)
{
Platform.Log(LogLevel.Debug,
"SOP Instance has embedded overlay in pixel data, extracting");
overlay.ConvertEmbeddedOverlay(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;
}
}
}
