/// <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);
}
public static void CreateSeriesGraphicsForSeg(IPresentationImage presentationImage, Seg seg,
SegmentationDocument segmentationDocument,
IDicomMessageSopDataSource dicomMessageSopDataSourceSop)
{
Platform.CheckForNullReference(presentationImage, "presentationImage");
Platform.CheckForNullReference(seg, "seg");
Platform.CheckForNullReference(segmentationDocument, "segmentationDocument");
SegmentImageData segImageData = seg.SegmentImageData;
if (segImageData == null)
{
Platform.Log(LogLevel.Error,
"Cannot create segmentation graphics when no segmentation imaging data is provided");
return;
}
var imageSopProvider = presentationImage as IImageSopProvider;
if (imageSopProvider == null)
{
Platform.Log(LogLevel.Error,
"Failed to populate SegFrameGraphics collection. Image is not an ImageSopProvider");
return;
}
DicomPixelData segmentationPixelData = DicomPixelData.CreateFrom(dicomMessageSopDataSourceSop.SourceMessage);
var rawPixelData =
(byte[])dicomMessageSopDataSourceSop.SourceMessage.DataSet.GetAttribute(DicomTags.PixelData).Values;
var pixelDataGetter = new Func <int, byte[]>(frameIndex =>
{
if (segImageData.BitsStored == 1)
{
// Do unpacking
int frameLength = segImageData.Rows *
segImageData.Columns;
var overlayData =
new OverlayData(frameIndex * frameLength,
segImageData.Rows,
segImageData.Columns, false,
rawPixelData);
return(overlayData.Unpack());
}
if (segImageData.BitsStored == 8)
{
return(segmentationPixelData.GetFrame(frameIndex));
}
throw new InvalidDataException(
"Segmentation objects need to have BitsStored as either 1 or 8");
});
// NOTE: SegmentFrameData was already sorted
foreach (SegmentFrameData segmentFrameData in segImageData.SegmentFrameData)
{
IPresentationImage segPresentationImage = null;
// Get the presentation image if we have an image reference
string referencedSopInstanceUid = segmentFrameData.ReferencedSopInstanceUid;
int referencedImageFrameNumber = segmentFrameData.ReferencedFrameNumber ?? 1;
if (!string.IsNullOrEmpty(referencedSopInstanceUid))
{
segPresentationImage =
presentationImage.ParentDisplaySet.PresentationImages.OfType <IImageSopProvider>()
.FirstOrDefault(curImageSopProvider => curImageSopProvider != null &&
curImageSopProvider.ImageSop.SopInstanceUid ==
referencedSopInstanceUid &&
curImageSopProvider.Frame.FrameNumber ==
referencedImageFrameNumber) as IPresentationImage;
}
// Location defaults to 0, 0 unless determined otherwise from image position and image orientation
var segLocation = new PointF();
// Get the presentation image from the image position and orientation
if (segmentFrameData.ImagePositionPatient != null &&
segmentFrameData.ImagePositionPatient.Count() > 2 &&
segmentFrameData.ImageOrientationPatient != null &&
segmentFrameData.ImageOrientationPatient.Count() > 5)
{
var imagePositionPatient = new ImagePositionPatient(
segmentFrameData.ImagePositionPatient[0],
segmentFrameData.ImagePositionPatient[1],
segmentFrameData.ImagePositionPatient[2]);
var imageOrientationPatient = new ImageOrientationPatient(
segmentFrameData.ImageOrientationPatient[0],
segmentFrameData.ImageOrientationPatient[1],
segmentFrameData.ImageOrientationPatient[2],
segmentFrameData.ImageOrientationPatient[3],
segmentFrameData.ImageOrientationPatient[4],
segmentFrameData.ImageOrientationPatient[5]);
IDisplaySet displaySet = presentationImage.ParentDisplaySet;
if (segPresentationImage == null)
{
segPresentationImage = PresentationImageFromPositionOrientation(
imagePositionPatient,
imageOrientationPatient,
displaySet,
segImageData.FrameOfReferenceUid);
}
var imageSop = segPresentationImage as IImageSopProvider;
if (imageSop != null)
{
Vector3D segImageLocation =
imageSop.Frame.ImagePlaneHelper.ConvertToImagePlane(new Vector3D(
(float)imagePositionPatient.X,
(float)imagePositionPatient.Y,
(float)imagePositionPatient.Z));
PointF?segPixelLocation =
imageSop.Frame.ImagePlaneHelper.ConvertToImage(
new PointF(segImageLocation.X, segImageLocation.Y));
if (segPixelLocation.HasValue)
{
segLocation = segPixelLocation.Value;
}
}
}
if (segPresentationImage != null)
{
SegFrameImageGraphic newGraphic = AddSegFrameImageGraphicToPresentationImage(
segPresentationImage,
segImageData.Rows,
segImageData.Columns,
segLocation.X,
segLocation.Y,
seg.Color,
referencedImageFrameNumber,
seg.Label,
seg.Description,
pixelDataGetter.Invoke(segmentFrameData.FrameNumber - 1),
new SegmentationDocumentReference(segmentationDocument, seg.SegmentationNumber));
if (newGraphic != null &&
segPresentationImage == segPresentationImage.ParentDisplaySet.ImageBox.TopLeftPresentationImage)
{
newGraphic.Draw();
}
}
else
{
Platform.Log(LogLevel.Error, "Failed to find Presentation Image to display a segment on");
}
}
}
public static List <OverlayPlaneGraphic> CreateOverlayPlaneGraphics(Frame frame, OverlayPlaneModuleIod overlaysFromPresentationState)
{
ISopDataSource dataSource = frame.ParentImageSop.DataSource;
OverlayPlaneModuleIod overlaysIod = new OverlayPlaneModuleIod(dataSource);
List <OverlayPlaneGraphic> overlayPlaneGraphics = new List <OverlayPlaneGraphic>();
bool failedOverlays = false;
foreach (var overlayPlane in overlaysIod)
{
// DICOM 2009 PS 3.3 Section C.9.3.1.1 specifies the rule: NumberOfFramesInOverlay+ImageFrameOrigin-1 must be <= NumberOfFrames
if (!overlayPlane.IsValidMultiFrameOverlay(frame.ParentImageSop.NumberOfFrames))
{
failedOverlays = true;
Platform.Log(LogLevel.Warn, new DicomOverlayDeserializationException(overlayPlane.Group, OverlayPlaneSource.Image), "Encoding error encountered while reading overlay from image headers.");
continue;
}
try
{
byte[] overlayData = dataSource.GetFrameData(frame.FrameNumber).GetNormalizedOverlayData(overlayPlane.Index + 1);
overlayPlaneGraphics.Add(new OverlayPlaneGraphic(overlayPlane, overlayData, OverlayPlaneSource.Image));
// if overlay data is null, the data source failed to retrieve the overlay data for some reason, so we also treat it as an encoding error
// this is different from if the overlay data is zero-length, which indicates that the retrieval succeeded, but that the overlay data for the frame is empty
if (overlayData == null)
{
throw new NullReferenceException();
}
}
catch (Exception ex)
{
failedOverlays = true;
Platform.Log(LogLevel.Warn, new DicomOverlayDeserializationException(overlayPlane.Group, OverlayPlaneSource.Image, ex), "Failed to load overlay from the image header.");
}
}
if (overlaysFromPresentationState != null)
{
foreach (var overlayPlane in overlaysFromPresentationState)
{
// if overlay data is missing, treat as an encoding error
if (!overlayPlane.HasOverlayData)
{
failedOverlays = true;
Platform.Log(LogLevel.Warn, new DicomOverlayDeserializationException(overlayPlane.Group, OverlayPlaneSource.PresentationState), "Encoding error encountered while reading overlay from softcopy presentation state.");
continue;
}
try
{
byte[] overlayData;
// 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, bitOffset;
if (overlayPlane.TryGetRelevantOverlayFrame(frame.FrameNumber, frame.ParentImageSop.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 = od.Unpack();
}
else
{
// no relevant overlay frame found - i.e. the overlay for this image frame is blank
overlayData = new byte[0];
}
overlayPlaneGraphics.Add(new OverlayPlaneGraphic(overlayPlane, overlayData, OverlayPlaneSource.PresentationState));
}
catch (Exception ex)
{
failedOverlays = true;
Platform.Log(LogLevel.Warn, new DicomOverlayDeserializationException(overlayPlane.Group, OverlayPlaneSource.PresentationState, ex), "Failed to load overlay from softcopy presentation state.");
}
}
}
if (failedOverlays)
{
// add an error graphic if any overlays are not being displayed due to deserialization errors.
overlayPlaneGraphics.Add(new ErrorOverlayPlaneGraphic(SR.MessageErrorDisplayingOverlays));
}
return(overlayPlaneGraphics);
}