protected override byte[] CreateNormalizedPixelData()
{
string photometricInterpretation;
byte[] pixelData = _framePixelData.GetUncompressedPixelData(out photometricInterpretation);
string photometricInterpretationCode = photometricInterpretation ?? Parent[DicomTags.PhotometricInterpretation].ToString();
PhotometricInterpretation pi = PhotometricInterpretation.FromCodeString(photometricInterpretationCode);
if (pi.IsColor)
{
pixelData = ToArgb(this.Parent, pixelData, pi);
}
else
{
var overlayPlaneModuleIod = new OverlayPlaneModuleIod(Parent);
foreach (var overlayPlane in overlayPlaneModuleIod)
{
if (!overlayPlane.HasOverlayData && _overlayData[overlayPlane.Index] == null)
{
// if the overlay is embedded in pixel data and we haven't cached it yet, extract it now before we normalize the frame pixel data
var overlayData = OverlayData.UnpackFromPixelData(overlayPlane.OverlayBitPosition, Parent[DicomTags.BitsAllocated].GetInt32(0, 0), false, pixelData);
_overlayData[overlayPlane.Index] = overlayData;
}
}
NormalizeGrayscalePixels(this.Parent, pixelData);
}
return(pixelData);
}
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");
}
}
public void TestIsValidMultiFrameOverlay()
{
const int size = 3;
var dataset = new DicomAttributeCollection();
SetOverlay(dataset, 0, new bool[size*size], OverlayType.R, new Point(0, 0), size, size, null, false, false);
SetOverlay(dataset, 1, new bool[size*size], OverlayType.R, new Point(0, 0), size, size, 1, false, false);
SetOverlay(dataset, 2, new bool[size*size*5], OverlayType.R, new Point(0, 0), size, size, 5, false, false);
SetOverlay(dataset, 3, new bool[size*size], OverlayType.R, new Point(0, 0), size, size, 1, 3, false, false);
SetOverlay(dataset, 4, new bool[size*size*5], OverlayType.R, new Point(0, 0), size, size, 5, 2, false, false);
var module = new OverlayPlaneModuleIod(dataset);
Assert.IsTrue(module[0].IsValidMultiFrameOverlay(1), "Single Frame Overlay / 1 Frame in Image");
Assert.IsTrue(module[0].IsValidMultiFrameOverlay(2), "Single Frame Overlay / 2 Frames in Image");
Assert.IsTrue(module[1].IsValidMultiFrameOverlay(1), "1 Frame in Overlay (origin null==1) / 1 Frame in Image");
Assert.IsTrue(module[1].IsValidMultiFrameOverlay(2), "1 Frame in Overlay (origin null==1) / 2 Frames in Image");
Assert.IsFalse(module[2].IsValidMultiFrameOverlay(4), "5 Frames in Overlay (origin null==1) / 4 Frames in Image");
Assert.IsTrue(module[2].IsValidMultiFrameOverlay(5), "5 Frames in Overlay (origin null==1) / 5 Frames in Image");
Assert.IsTrue(module[2].IsValidMultiFrameOverlay(6), "5 Frames in Overlay (origin null==1) / 6 Frames in Image");
Assert.IsFalse(module[3].IsValidMultiFrameOverlay(2), "1 Frames in Overlay (origin 3) / 2 Frames in Image");
Assert.IsTrue(module[3].IsValidMultiFrameOverlay(3), "1 Frames in Overlay (origin 3) / 3 Frames in Image");
Assert.IsTrue(module[3].IsValidMultiFrameOverlay(4), "1 Frames in Overlay (origin 3) / 4 Frames in Image");
Assert.IsFalse(module[4].IsValidMultiFrameOverlay(5), "5 Frames in Overlay (origin 2) / 5 Frames in Image");
Assert.IsTrue(module[4].IsValidMultiFrameOverlay(6), "5 Frames in Overlay (origin 2) / 6 Frames in Image");
Assert.IsTrue(module[4].IsValidMultiFrameOverlay(7), "5 Frames in Overlay (origin 2) / 7 Frames in Image");
}
/// <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);
}
private void ExtractOverlayFrames(byte[] rawPixelData, int bitsAllocated)
{
// if any overlays have embedded pixel data, extract them now or forever hold your peace
var overlayPlaneModuleIod = new OverlayPlaneModuleIod(Parent);
foreach (var overlayPlane in overlayPlaneModuleIod)
{
if (!overlayPlane.HasOverlayData && _overlayCache[overlayPlane.Index] == null)
{
// if the overlay is embedded in pixel data and we haven't cached it yet, extract it now before we normalize the frame pixel data
var overlayData = OverlayData.UnpackFromPixelData(overlayPlane.OverlayBitPosition, bitsAllocated, false, rawPixelData);
_overlayCache[overlayPlane.Index] = overlayData;
}
}
}
public void SetupMRWithOverlay(DicomAttributeCollection theSet)
{
SetupMR(theSet);
OverlayPlaneModuleIod overlayIod = new OverlayPlaneModuleIod(theSet);
DicomUncompressedPixelData pd = new DicomUncompressedPixelData(theSet);
OverlayPlane overlay = overlayIod[0];
// Embedded overlays are retired in dicom, just doing it for testing purposes
theSet[DicomTags.OverlayBitPosition].SetInt32(0, pd.HighBit + 1);
overlay.OverlayBitsAllocated = 1;
overlay.OverlayColumns = pd.ImageWidth;
overlay.OverlayRows = pd.ImageHeight;
overlay.OverlayOrigin = new Point(0, 0);
overlay.OverlayType = OverlayType.R;
}
public void SetupMRWithOverlay(DicomAttributeCollection theSet)
{
SetupMR(theSet);
OverlayPlaneModuleIod overlayIod = new OverlayPlaneModuleIod(theSet);
DicomUncompressedPixelData pd = new DicomUncompressedPixelData(theSet);
OverlayPlane overlay = overlayIod[0];
// Embedded overlays are retired in dicom, just doing it for testing purposes
theSet[DicomTags.OverlayBitPosition].SetInt32(0, pd.HighBit + 1);
overlay.OverlayBitsAllocated = 1;
overlay.OverlayColumns = pd.ImageWidth;
overlay.OverlayRows = pd.ImageHeight;
overlay.OverlayOrigin = new Point(0, 0);
overlay.OverlayType = OverlayType.R;
}
public void RleOverlayTest()
{
DicomFile file = new DicomFile("RleCodecOverlayTest.dcm");
SetupMRWithOverlay(file.DataSet);
SetupMetaInfo(file);
// Save a copy
file.Save();
// Load the file into new DicomFile object
DicomFile newFile = new DicomFile(file.Filename);
newFile.Load();
OverlayPlaneModuleIod overlayIod = new OverlayPlaneModuleIod(newFile.DataSet);
OverlayPlane overlay = overlayIod[0];
// SHould be no OverlayData tag
Assert.IsNull(overlay.OverlayData, "Overlay should be in pixel data");
// Overlay should be extracted out of pixel data here
newFile.ChangeTransferSyntax(TransferSyntax.RleLossless);
Assert.IsNotNull(overlay.OverlayData, "Overlay Data is not null");
newFile.Save();
// Load a new copy
newFile = new DicomFile(file.Filename);
newFile.Load();
newFile.ChangeTransferSyntax(TransferSyntax.ExplicitVrLittleEndian);
newFile.Filename = "Output" + file.Filename;
newFile.Save();
List <DicomAttributeComparisonResult> results = new List <DicomAttributeComparisonResult>();
bool compare = file.DataSet.Equals(newFile.DataSet, ref results);
// Shouldn't be the same, OverlayData tag should have been added
Assert.IsFalse(compare, results.Count > 0 ? CollectionUtils.FirstElement(results).Details : string.Empty);
}
protected override byte[] CreateNormalizedPixelData()
{
byte[] pixelData = _framePixelData.GetUncompressedPixelData();
string photometricInterpretationCode = this.Parent[DicomTags.PhotometricInterpretation].ToString();
PhotometricInterpretation pi = PhotometricInterpretation.FromCodeString(photometricInterpretationCode);
TransferSyntax ts = TransferSyntax.GetTransferSyntax(this.Parent.TransferSyntaxUid);
if (pi.IsColor)
{
if (ts == TransferSyntax.Jpeg2000ImageCompression ||
ts == TransferSyntax.Jpeg2000ImageCompressionLosslessOnly ||
ts == TransferSyntax.JpegExtendedProcess24 ||
ts == TransferSyntax.JpegBaselineProcess1)
{
pi = PhotometricInterpretation.Rgb;
}
pixelData = ToArgb(this.Parent, pixelData, pi);
}
else
{
OverlayPlaneModuleIod opmi = new OverlayPlaneModuleIod(this.Parent);
foreach (OverlayPlane overlayPlane in opmi)
{
if (IsOverlayEmbedded(overlayPlane) && _overlayData[overlayPlane.Index] == null)
{
byte[] overlayData = OverlayData.UnpackFromPixelData(overlayPlane.OverlayBitPosition, this.Parent[DicomTags.BitsAllocated].GetInt32(0, 0), false, pixelData);
_overlayData[overlayPlane.Index] = overlayData;
}
else if (!overlayPlane.HasOverlayData)
{
Platform.Log(LogLevel.Warn, "The image {0} appears to be missing OverlayData for group 0x{1:X4}.", this.Parent.SopInstanceUid, overlayPlane.Group);
}
}
NormalizeGrayscalePixels(this.Parent, pixelData);
}
return(pixelData);
}
protected void DeserializeOverlayPlane(OverlayPlaneModuleIod overlayPlaneModule, T image)
{
DicomGraphicsPlane dicomGraphicsPlane = DicomGraphicsPlane.GetDicomGraphicsPlane(image, true);
foreach (OverlayPlaneGraphic overlay in DicomGraphicsFactory.CreateOverlayPlaneGraphics(image.Frame, overlayPlaneModule))
{
// the results are a mix of overlays from the image itself and the presentation state
if (overlay.Source == OverlayPlaneSource.Image)
{
dicomGraphicsPlane.ImageOverlays.Add(overlay);
}
else
{
dicomGraphicsPlane.PresentationOverlays.Add(overlay);
}
// the above lines will automatically add the overlays to the inactive layer
}
_overlayPlanesDeserialized = true;
}
protected override byte[] CreateNormalizedPixelData()
{
byte[] pixelData = _framePixelData.GetUncompressedPixelData();
string photometricInterpretationCode = this.Parent[DicomTags.PhotometricInterpretation].ToString();
PhotometricInterpretation pi = PhotometricInterpretation.FromCodeString(photometricInterpretationCode);
TransferSyntax ts = TransferSyntax.GetTransferSyntax(this.Parent.TransferSyntaxUid);
if (pi.IsColor)
{
if (ts == TransferSyntax.Jpeg2000ImageCompression ||
ts == TransferSyntax.Jpeg2000ImageCompressionLosslessOnly ||
ts == TransferSyntax.JpegExtendedProcess24 ||
ts == TransferSyntax.JpegBaselineProcess1)
{
pi = PhotometricInterpretation.Rgb;
}
pixelData = ToArgb(this.Parent, pixelData, pi);
}
else
{
var overlayPlaneModuleIod = new OverlayPlaneModuleIod(Parent);
foreach (var overlayPlane in overlayPlaneModuleIod)
{
if (!overlayPlane.HasOverlayData && _overlayData[overlayPlane.Index] == null)
{
// if the overlay is embedded in pixel data and we haven't cached it yet, extract it now before we normalize the frame pixel data
var overlayData = OverlayData.UnpackFromPixelData(overlayPlane.OverlayBitPosition, Parent[DicomTags.BitsAllocated].GetInt32(0, 0), false, pixelData);
_overlayData[overlayPlane.Index] = overlayData;
}
}
NormalizeGrayscalePixels(this.Parent, pixelData);
}
return(pixelData);
}
/// <summary>
/// Initializes a new instance of the <see cref="ScImageIod"/> class.
/// </summary>
/// <param name="dicomAttributeProvider">The DICOM attribute provider.</param>
public ScImageIod(IDicomAttributeProvider dicomAttributeProvider)
{
_dicomAttributeProvider = dicomAttributeProvider;
_patientModule = new PatientModuleIod(_dicomAttributeProvider);
_clinicalTrialSubjectModule = new ClinicalTrialSubjectModuleIod(_dicomAttributeProvider);
_generalStudyModule = new GeneralStudyModuleIod(_dicomAttributeProvider);
_patientStudyModule = new PatientStudyModuleIod(_dicomAttributeProvider);
_clinicalTrialStudyModule = new ClinicalTrialStudyModuleIod(_dicomAttributeProvider);
_generalSeriesModule = new GeneralSeriesModuleIod(_dicomAttributeProvider);
_clinicalTrialSeriesModule = new ClinicalTrialSeriesModuleIod(_dicomAttributeProvider);
_generalEquipmentModule = new GeneralEquipmentModuleIod(_dicomAttributeProvider);
_scEquipmentModule = new ScEquipmentModuleIod(_dicomAttributeProvider);
_generalImageModule = new GeneralImageModuleIod(_dicomAttributeProvider);
_imagePixelModule = new ImagePixelMacroIod(_dicomAttributeProvider);
_deviceModule = new DeviceModuleIod(_dicomAttributeProvider);
_scImageModule = new ScImageModuleIod(_dicomAttributeProvider);
_overlayPlaneModule = new OverlayPlaneModuleIod(_dicomAttributeProvider);
_modalityLutModule = new ModalityLutModuleIod(_dicomAttributeProvider);
_voiLutModule = new VoiLutModuleIod(_dicomAttributeProvider);
_iccProfileModule = new IccProfileModuleIod(_dicomAttributeProvider);
_sopCommonModule = new SopCommonModuleIod(_dicomAttributeProvider);
}
/// <summary>
/// Initializes a new instance of the <see cref="ScImageIod"/> class.
/// </summary>
/// <param name="dicomAttributeProvider">The DICOM attribute provider.</param>
public ScImageIod(IDicomAttributeProvider dicomAttributeProvider)
{
_dicomAttributeProvider = dicomAttributeProvider;
_patientModule = new PatientModuleIod(_dicomAttributeProvider);
_clinicalTrialSubjectModule = new ClinicalTrialSubjectModuleIod(_dicomAttributeProvider);
_generalStudyModule = new GeneralStudyModuleIod(_dicomAttributeProvider);
_patientStudyModule = new PatientStudyModuleIod(_dicomAttributeProvider);
_clinicalTrialStudyModule = new ClinicalTrialStudyModuleIod(_dicomAttributeProvider);
_generalSeriesModule = new GeneralSeriesModuleIod(_dicomAttributeProvider);
_clinicalTrialSeriesModule = new ClinicalTrialSeriesModuleIod(_dicomAttributeProvider);
_generalEquipmentModule = new GeneralEquipmentModuleIod(_dicomAttributeProvider);
_scEquipmentModule = new ScEquipmentModuleIod(_dicomAttributeProvider);
_generalImageModule = new GeneralImageModuleIod(_dicomAttributeProvider);
_imagePixelModule = new ImagePixelMacroIod(_dicomAttributeProvider);
_deviceModule = new DeviceModuleIod(_dicomAttributeProvider);
_scImageModule = new ScImageModuleIod(_dicomAttributeProvider);
_overlayPlaneModule = new OverlayPlaneModuleIod(_dicomAttributeProvider);
_modalityLutModule = new ModalityLutModuleIod(_dicomAttributeProvider);
_voiLutModule = new VoiLutModuleIod(_dicomAttributeProvider);
_iccProfileModule = new IccProfileModuleIod(_dicomAttributeProvider);
_sopCommonModule = new SopCommonModuleIod(_dicomAttributeProvider);
}
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 void TestComputeOverlayDataBitOffset_SingleFrameEmbedded()
{
const bool bigEndian = false;
// these parameters should be kept prime numbers so that we can exercise the overlay handling for rows/frames that cross byte boundaries
const int rows = 97;
const int columns = 101;
const int overlayIndex = 0;
var dataset = new DicomAttributeCollection();
SetImage(dataset, new byte[rows*columns*2], rows, columns, 1, 16, 12, 14, false);
SetOverlay(dataset, overlayIndex, new bool[rows*columns], OverlayType.G, new Point(1, 1), 15, bigEndian);
var module = new OverlayPlaneModuleIod(dataset);
var overlayPlane = module[overlayIndex];
int actualBitOffset;
// bit offset doesn't make any sense for embedded data
Assert.IsFalse(overlayPlane.TryComputeOverlayDataBitOffset(-1, out actualBitOffset), "Should not be able to compute bit offset for frame number -1");
Assert.IsFalse(overlayPlane.TryComputeOverlayDataBitOffset(0, out actualBitOffset), "Should not be able to compute bit offset for frame number 0");
Assert.IsFalse(overlayPlane.TryComputeOverlayDataBitOffset(1, out actualBitOffset), "Should not be able to compute bit offset for frame number 1");
Assert.IsFalse(overlayPlane.TryComputeOverlayDataBitOffset(2, out actualBitOffset), "Should not be able to compute bit offset for frame number 2");
}
/// <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 TestComputeOverlayDataBitOffset_MultiframeOverlayDataWithOrigin()
{
const bool bigEndian = false;
// these parameters should be kept prime numbers so that we can exercise the overlay handling for rows/frames that cross byte boundaries
const int rows = 97;
const int columns = 101;
const int frames = 7;
// just because you're getting overlay frame #2 for image frame #4 doesn't change the offset where overlay frame #2 can be found!!
const int imageFrameOrigin = 3;
const int overlayIndex = 0;
var dataset = new DicomAttributeCollection();
SetOverlay(dataset, overlayIndex, new bool[rows*columns*frames], OverlayType.G, new Point(1, 1), rows, columns, frames, imageFrameOrigin, bigEndian, false);
var module = new OverlayPlaneModuleIod(dataset);
var overlayPlane = module[overlayIndex];
int actualBitOffset;
Assert.IsFalse(overlayPlane.TryComputeOverlayDataBitOffset(-1, out actualBitOffset), "Should not be able to compute bit offset for frame number -1");
Assert.IsFalse(overlayPlane.TryComputeOverlayDataBitOffset(0, out actualBitOffset), "Should not be able to compute bit offset for frame number 0");
Assert.IsFalse(overlayPlane.TryComputeOverlayDataBitOffset(8, out actualBitOffset), "Should not be able to compute bit offset for frame number 8");
Assert.IsTrue(overlayPlane.TryComputeOverlayDataBitOffset(1, out actualBitOffset), "Should be able to compute bit offset for frame number 1");
Assert.AreEqual(0*rows*columns, actualBitOffset, "Wrong offset computed for frame number 1");
Assert.IsTrue(overlayPlane.TryComputeOverlayDataBitOffset(2, out actualBitOffset), "Should be able to compute bit offset for frame number 2");
Assert.AreEqual(1*rows*columns, actualBitOffset, "Wrong offset computed for frame number 2");
Assert.IsTrue(overlayPlane.TryComputeOverlayDataBitOffset(3, out actualBitOffset), "Should be able to compute bit offset for frame number 3");
Assert.AreEqual(2*rows*columns, actualBitOffset, "Wrong offset computed for frame number 3");
Assert.IsTrue(overlayPlane.TryComputeOverlayDataBitOffset(4, out actualBitOffset), "Should be able to compute bit offset for frame number 4");
Assert.AreEqual(3*rows*columns, actualBitOffset, "Wrong offset computed for frame number 4");
Assert.IsTrue(overlayPlane.TryComputeOverlayDataBitOffset(5, out actualBitOffset), "Should be able to compute bit offset for frame number 5");
Assert.AreEqual(4*rows*columns, actualBitOffset, "Wrong offset computed for frame number 5");
Assert.IsTrue(overlayPlane.TryComputeOverlayDataBitOffset(6, out actualBitOffset), "Should be able to compute bit offset for frame number 6");
Assert.AreEqual(5*rows*columns, actualBitOffset, "Wrong offset computed for frame number 6");
Assert.IsTrue(overlayPlane.TryComputeOverlayDataBitOffset(7, out actualBitOffset), "Should be able to compute bit offset for frame number 7");
Assert.AreEqual(6*rows*columns, actualBitOffset, "Wrong offset computed for frame number 7");
}
public void TestComputeOverlayDataBitOffset_SingleFrameOverlayData()
{
const bool bigEndian = false;
// these parameters should be kept prime numbers so that we can exercise the overlay handling for rows/frames that cross byte boundaries
const int rows = 97;
const int columns = 101;
const int overlayIndex = 0;
var dataset = new DicomAttributeCollection();
SetOverlay(dataset, overlayIndex, new bool[rows*columns], OverlayType.G, new Point(1, 1), rows, columns, null, null, bigEndian, false);
var module = new OverlayPlaneModuleIod(dataset);
var overlayPlane = module[overlayIndex];
int actualBitOffset;
Assert.IsFalse(overlayPlane.TryComputeOverlayDataBitOffset(-1, out actualBitOffset), "Should not be able to compute bit offset for frame number -1");
Assert.IsFalse(overlayPlane.TryComputeOverlayDataBitOffset(0, out actualBitOffset), "Should not be able to compute bit offset for frame number 0");
Assert.IsFalse(overlayPlane.TryComputeOverlayDataBitOffset(2, out actualBitOffset), "Should not be able to compute bit offset for frame number 2");
Assert.IsTrue(overlayPlane.TryComputeOverlayDataBitOffset(1, out actualBitOffset), "Should be able to compute bit offset for frame number 1");
Assert.AreEqual(0, actualBitOffset, "Wrong offset computed for frame number 1");
}
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);
}
public void RleOverlayTest()
{
DicomFile file = new DicomFile("RleCodecOverlayTest.dcm");
SetupMRWithOverlay(file.DataSet);
SetupMetaInfo(file);
// Save a copy
file.Save();
// Load the file into new DicomFile object
DicomFile newFile = new DicomFile(file.Filename);
newFile.Load();
OverlayPlaneModuleIod overlayIod = new OverlayPlaneModuleIod(newFile.DataSet);
OverlayPlane overlay = overlayIod[0];
// SHould be no OverlayData tag
Assert.IsNull(overlay.OverlayData, "Overlay should be in pixel data");
// Overlay should be extracted out of pixel data here
newFile.ChangeTransferSyntax(TransferSyntax.RleLossless);
Assert.IsNotNull(overlay.OverlayData,"Overlay Data is not null");
newFile.Save();
// Load a new copy
newFile = new DicomFile(file.Filename);
newFile.Load();
newFile.ChangeTransferSyntax(TransferSyntax.ExplicitVrLittleEndian);
newFile.Filename = "Output" + file.Filename;
newFile.Save();
List<DicomAttributeComparisonResult> results = new List<DicomAttributeComparisonResult>();
bool compare = file.DataSet.Equals(newFile.DataSet, ref results);
// Shouldn't be the same, OverlayData tag should have been added
Assert.IsFalse(compare, results.Count > 0 ? CollectionUtils.FirstElement(results).Details : string.Empty);
}
protected void SerializeOverlayPlane(OverlayPlaneModuleIod overlayPlaneModule, out IOverlayMapping overlayMapping, DicomPresentationImageCollection <T> images)
{
// Doesn't support multiframe or whatever case it is when we get more than one image serialized to one state
List <OverlayPlaneGraphic> visibleOverlays = new List <OverlayPlaneGraphic>();
foreach (T image in images)
{
DicomGraphicsPlane dicomGraphics = DicomGraphicsPlane.GetDicomGraphicsPlane(image, false);
if (dicomGraphics != null)
{
// identify visible bitmap shutter if exists
OverlayPlaneGraphic bitmapShutter = dicomGraphics.Shutters.ActiveShutter as OverlayPlaneGraphic;
if (bitmapShutter != null)
{
visibleOverlays.Add(bitmapShutter);
}
// identify any visible overlays
visibleOverlays.AddRange(((IEnumerable <ILayer>)dicomGraphics.Layers).Where(l => l.Visible).SelectMany(l => l.Graphics).OfType <OverlayPlaneGraphic>().Where(g => g.Visible));
}
}
OverlayMapping overlayMap = new OverlayMapping();
Queue <OverlayPlaneGraphic> overlaysToRemap = new Queue <OverlayPlaneGraphic>();
// user and presentation state overlays are high priority items to remap
foreach (OverlayPlaneGraphic overlay in CollectionUtils.Select(visibleOverlays, delegate(OverlayPlaneGraphic t) { return(t.Source != OverlayPlaneSource.Image); }))
{
overlaysToRemap.Enqueue(overlay);
}
foreach (OverlayPlaneGraphic overlay in CollectionUtils.Select(visibleOverlays, delegate(OverlayPlaneGraphic t) { return(t.Source == OverlayPlaneSource.Image); }))
{
if (overlayMap[overlay.Index] == null)
{
overlayMap[overlay.Index] = overlay;
}
else
{
overlaysToRemap.Enqueue(overlay); // image overlays are lower priority items to remap, since they will be included in the header anyway
}
}
// seed the overlays to remap into the remaining available overlay groups
for (int n = 0; n < 16 && overlaysToRemap.Count > 0; n++)
{
if (overlayMap[n] == null)
{
overlayMap[n] = overlaysToRemap.Dequeue();
}
}
// serialize the overlays
for (int n = 0; n < 16; n++)
{
OverlayPlaneGraphic overlay = overlayMap[n];
if (overlay != null)
{
if (overlay.Source != OverlayPlaneSource.Image || overlay.Index != n)
{
// only record this overlay in the presentation state if it is being remapped to another group or is not already in the image.
OverlayPlane overlayIod = overlayPlaneModule[n];
overlayIod.OverlayData = overlay.CreateOverlayData(overlayIod.IsBigEndianOW).Raw;
overlayIod.OverlayBitPosition = 0;
overlayIod.OverlayBitsAllocated = 1;
overlayIod.OverlayColumns = overlay.Columns;
overlayIod.OverlayDescription = overlay.Description;
overlayIod.OverlayLabel = overlay.Label;
overlayIod.OverlayOrigin = Point.Round(overlay.Origin);
overlayIod.OverlayRows = overlay.Rows;
overlayIod.OverlaySubtype = overlay.Subtype;
overlayIod.OverlayType = overlay.Type;
overlayIod.RoiArea = null;
overlayIod.RoiMean = null;
overlayIod.RoiStandardDeviation = null;
}
else
{
overlayPlaneModule.Delete(n);
}
}
}
if (overlaysToRemap.Count > 0)
{
Platform.Log(LogLevel.Warn, "Attempt to serialize presentation state with more than 16 visible overlays - some information may be lost.");
}
overlayMapping = overlayMap;
}
private void ExtractOverlayFrames(byte[] rawPixelData, int bitsAllocated)
{
// if any overlays have embedded pixel data, extract them now or forever hold your peace
var overlayPlaneModuleIod = new OverlayPlaneModuleIod(Parent);
foreach (var overlayPlane in overlayPlaneModuleIod)
{
if (!overlayPlane.HasOverlayData && _overlayCache[overlayPlane.Index] == null)
{
// if the overlay is embedded in pixel data and we haven't cached it yet, extract it now before we normalize the frame pixel data
var overlayData = OverlayData.UnpackFromPixelData(overlayPlane.OverlayBitPosition, bitsAllocated, false, rawPixelData);
_overlayCache[overlayPlane.Index] = overlayData;
}
}
}
protected override byte[] CreateNormalizedPixelData()
{
byte[] pixelData = _framePixelData.GetUncompressedPixelData();
string photometricInterpretationCode = this.Parent[DicomTags.PhotometricInterpretation].ToString();
PhotometricInterpretation pi = PhotometricInterpretation.FromCodeString(photometricInterpretationCode);
TransferSyntax ts = TransferSyntax.GetTransferSyntax(this.Parent.TransferSyntaxUid);
if (pi.IsColor)
{
if (ts == TransferSyntax.Jpeg2000ImageCompression ||
ts == TransferSyntax.Jpeg2000ImageCompressionLosslessOnly ||
ts == TransferSyntax.JpegExtendedProcess24 ||
ts == TransferSyntax.JpegBaselineProcess1)
pi = PhotometricInterpretation.Rgb;
pixelData = ToArgb(this.Parent, pixelData, pi);
}
else
{
var overlayPlaneModuleIod = new OverlayPlaneModuleIod(Parent);
foreach (var overlayPlane in overlayPlaneModuleIod)
{
if (!overlayPlane.HasOverlayData && _overlayData[overlayPlane.Index] == null)
{
// if the overlay is embedded in pixel data and we haven't cached it yet, extract it now before we normalize the frame pixel data
var overlayData = OverlayData.UnpackFromPixelData(overlayPlane.OverlayBitPosition, Parent[DicomTags.BitsAllocated].GetInt32(0, 0), false, pixelData);
_overlayData[overlayPlane.Index] = overlayData;
}
}
NormalizeGrayscalePixels(this.Parent, pixelData);
}
return pixelData;
}
/// <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;
}
public void TestGetRelevantOverlayFrame_MultiframeEmbedded()
{
const bool bigEndian = false;
// these parameters should be kept prime numbers so that we can exercise the overlay handling for rows/frames that cross byte boundaries
const int rows = 97;
const int columns = 101;
const int frames = 7;
const int overlayIndex = 0;
var dataset = new DicomAttributeCollection();
SetImage(dataset, new byte[rows*columns*2*frames], rows, columns, frames, 16, 12, 11, false);
SetOverlay(dataset, overlayIndex, new bool[rows*columns*frames], OverlayType.G, new Point(1, 1), 12, bigEndian);
var module = new OverlayPlaneModuleIod(dataset);
var overlayPlane = module[overlayIndex];
int actualOverlayFrame;
Assert.IsFalse(overlayPlane.TryGetRelevantOverlayFrame(-1, frames, out actualOverlayFrame), "Should not any matching overlay frame for image frame #-1");
Assert.IsFalse(overlayPlane.TryGetRelevantOverlayFrame(0, frames, out actualOverlayFrame), "Should not any matching overlay frame for image frame #0");
Assert.IsFalse(overlayPlane.TryGetRelevantOverlayFrame(8, frames, out actualOverlayFrame), "Should not any matching overlay frame for image frame #8");
// all valid image frame inputs should map 1-to-1 with the same numbered overlay frame
Assert.IsTrue(overlayPlane.TryGetRelevantOverlayFrame(1, frames, out actualOverlayFrame), "Should be able to match an overlay frame to image frame #1");
Assert.AreEqual(1, actualOverlayFrame, "Wrong overlay frame matched to image frame #1");
Assert.IsTrue(overlayPlane.TryGetRelevantOverlayFrame(2, frames, out actualOverlayFrame), "Should be able to match an overlay frame to image frame #2");
Assert.AreEqual(2, actualOverlayFrame, "Wrong overlay frame matched to image frame #2");
Assert.IsTrue(overlayPlane.TryGetRelevantOverlayFrame(3, frames, out actualOverlayFrame), "Should be able to match an overlay frame to image frame #3");
Assert.AreEqual(3, actualOverlayFrame, "Wrong overlay frame matched to image frame #3");
Assert.IsTrue(overlayPlane.TryGetRelevantOverlayFrame(4, frames, out actualOverlayFrame), "Should be able to match an overlay frame to image frame #4");
Assert.AreEqual(4, actualOverlayFrame, "Wrong overlay frame matched to image frame #4");
Assert.IsTrue(overlayPlane.TryGetRelevantOverlayFrame(5, frames, out actualOverlayFrame), "Should be able to match an overlay frame to image frame #5");
Assert.AreEqual(5, actualOverlayFrame, "Wrong overlay frame matched to image frame #5");
Assert.IsTrue(overlayPlane.TryGetRelevantOverlayFrame(6, frames, out actualOverlayFrame), "Should be able to match an overlay frame to image frame #6");
Assert.AreEqual(6, actualOverlayFrame, "Wrong overlay frame matched to image frame #6");
Assert.IsTrue(overlayPlane.TryGetRelevantOverlayFrame(7, frames, out actualOverlayFrame), "Should be able to match an overlay frame to image frame #7");
Assert.AreEqual(7, actualOverlayFrame, "Wrong overlay frame matched to image frame #7");
}
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;
}
public void TestGetRelevantOverlayFrame_SingleFrameEmbedded()
{
const bool bigEndian = false;
// these parameters should be kept prime numbers so that we can exercise the overlay handling for rows/frames that cross byte boundaries
const int rows = 97;
const int columns = 101;
const int overlayIndex = 0;
var dataset = new DicomAttributeCollection();
SetImage(dataset, new byte[rows*columns*2], rows, columns, 1, 16, 12, 11, false);
SetOverlay(dataset, overlayIndex, new bool[rows*columns], OverlayType.G, new Point(1, 1), 12, bigEndian);
var module = new OverlayPlaneModuleIod(dataset);
var overlayPlane = module[overlayIndex];
int actualOverlayFrame;
Assert.IsFalse(overlayPlane.TryGetRelevantOverlayFrame(-1, 1, out actualOverlayFrame), "Should not any matching overlay frame for image frame #-1");
Assert.IsFalse(overlayPlane.TryGetRelevantOverlayFrame(0, 1, out actualOverlayFrame), "Should not any matching overlay frame for image frame #0");
Assert.IsFalse(overlayPlane.TryGetRelevantOverlayFrame(8, 1, out actualOverlayFrame), "Should not any matching overlay frame for image frame #8");
// in the single frame case, there's only one pairing
Assert.IsTrue(overlayPlane.TryGetRelevantOverlayFrame(1, 1, out actualOverlayFrame), "Should be able to match an overlay frame to image frame #1");
Assert.AreEqual(1, actualOverlayFrame, "Wrong overlay frame matched to image frame #1");
}
protected override byte[] CreateNormalizedPixelData()
{
string photometricInterpretation;
byte[] pixelData = _framePixelData.GetUncompressedPixelData(out photometricInterpretation);
string photometricInterpretationCode = photometricInterpretation ?? Parent[DicomTags.PhotometricInterpretation].ToString();
PhotometricInterpretation pi = PhotometricInterpretation.FromCodeString(photometricInterpretationCode);
if (pi.IsColor)
{
pixelData = ToArgb(this.Parent, pixelData, pi);
}
else
{
var overlayPlaneModuleIod = new OverlayPlaneModuleIod(Parent);
foreach (var overlayPlane in overlayPlaneModuleIod)
{
if (!overlayPlane.HasOverlayData && _overlayData[overlayPlane.Index] == null)
{
// if the overlay is embedded in pixel data and we haven't cached it yet, extract it now before we normalize the frame pixel data
var overlayData = OverlayData.UnpackFromPixelData(overlayPlane.OverlayBitPosition, Parent[DicomTags.BitsAllocated].GetInt32(0, 0), false, pixelData);
_overlayData[overlayPlane.Index] = overlayData;
}
}
NormalizeGrayscalePixels(this.Parent, pixelData);
}
return pixelData;
}
public void TestGetRelevantOverlayFrame_SingleFrameOverlayData()
{
const bool bigEndian = false;
// these parameters should be kept prime numbers so that we can exercise the overlay handling for rows/frames that cross byte boundaries
const int rows = 97;
const int columns = 101;
const int imageFrames = 7;
const int overlayIndex = 0;
var dataset = new DicomAttributeCollection();
SetOverlay(dataset, overlayIndex, new bool[rows*columns], OverlayType.G, new Point(1, 1), rows, columns, null, null, bigEndian, false);
var module = new OverlayPlaneModuleIod(dataset);
var overlayPlane = module[overlayIndex];
int actualOverlayFrame;
Assert.IsFalse(overlayPlane.TryGetRelevantOverlayFrame(-1, imageFrames, out actualOverlayFrame), "Should not any matching overlay frame for image frame #-1");
Assert.IsFalse(overlayPlane.TryGetRelevantOverlayFrame(0, imageFrames, out actualOverlayFrame), "Should not any matching overlay frame for image frame #0");
Assert.IsFalse(overlayPlane.TryGetRelevantOverlayFrame(8, imageFrames, out actualOverlayFrame), "Should not any matching overlay frame for image frame #8");
// in the single frame case, all valid image frame inputs should map to overlay frame #1
Assert.IsTrue(overlayPlane.TryGetRelevantOverlayFrame(1, imageFrames, out actualOverlayFrame), "Should be able to match an overlay frame to image frame #1");
Assert.AreEqual(1, actualOverlayFrame, "Wrong overlay frame matched to image frame #1");
Assert.IsTrue(overlayPlane.TryGetRelevantOverlayFrame(2, imageFrames, out actualOverlayFrame), "Should be able to match an overlay frame to image frame #2");
Assert.AreEqual(1, actualOverlayFrame, "Wrong overlay frame matched to image frame #2");
Assert.IsTrue(overlayPlane.TryGetRelevantOverlayFrame(3, imageFrames, out actualOverlayFrame), "Should be able to match an overlay frame to image frame #3");
Assert.AreEqual(1, actualOverlayFrame, "Wrong overlay frame matched to image frame #3");
Assert.IsTrue(overlayPlane.TryGetRelevantOverlayFrame(4, imageFrames, out actualOverlayFrame), "Should be able to match an overlay frame to image frame #4");
Assert.AreEqual(1, actualOverlayFrame, "Wrong overlay frame matched to image frame #4");
Assert.IsTrue(overlayPlane.TryGetRelevantOverlayFrame(5, imageFrames, out actualOverlayFrame), "Should be able to match an overlay frame to image frame #5");
Assert.AreEqual(1, actualOverlayFrame, "Wrong overlay frame matched to image frame #5");
Assert.IsTrue(overlayPlane.TryGetRelevantOverlayFrame(6, imageFrames, out actualOverlayFrame), "Should be able to match an overlay frame to image frame #6");
Assert.AreEqual(1, actualOverlayFrame, "Wrong overlay frame matched to image frame #6");
Assert.IsTrue(overlayPlane.TryGetRelevantOverlayFrame(7, imageFrames, out actualOverlayFrame), "Should be able to match an overlay frame to image frame #7");
Assert.AreEqual(1, actualOverlayFrame, "Wrong overlay frame matched to image frame #7");
}
public void TestOverlayPlaneModuleIod_SingleFrame()
{
const bool bigEndian = false;
// these parameters should be kept prime numbers so that we can exercise the overlay handling for rows/frames that cross byte boundaries
const int imageRows = 97;
const int imageColumns = 101;
const int overlay1Rows = 103;
const int overlay1Columns = 89;
const int overlay2Rows = 67;
const int overlay2Columns = 71;
var dataset = new DicomAttributeCollection();
SetImage(dataset, new byte[imageRows*imageColumns*2], imageRows, imageColumns, 1, 16, 13, 12, false);
SetOverlay(dataset, 0, new bool[overlay1Rows*overlay1Columns], OverlayType.G, new Point(1, 1), overlay1Rows, overlay1Columns, bigEndian, false);
SetOverlay(dataset, 1, new bool[imageRows*imageColumns], OverlayType.G, new Point(2, 3), 15, bigEndian);
SetOverlay(dataset, 2, new bool[overlay2Rows*overlay2Columns], OverlayType.R, new Point(4, 5), overlay2Rows, overlay2Columns, bigEndian, true);
SetOverlay(dataset, 13, new bool[imageRows*imageColumns], OverlayType.R, new Point(6, 7), 14, bigEndian);
var module = new OverlayPlaneModuleIod(dataset);
// test overlay group 6000
{
const int overlayIndex = 0;
var overlayPlane = module[overlayIndex];
// assert overlay plane identification
Assert.AreEqual(0x6000, overlayPlane.Group, "Wrong overlay group for plane #{0}", overlayIndex);
Assert.AreEqual(0, overlayPlane.Index, "Wrong overlay index for plane #{0}", overlayIndex);
Assert.AreEqual(0x000000, overlayPlane.TagOffset, "Wrong tag offset for plane #{0}", overlayIndex);
// assert overlay plane encoding detection
Assert.AreEqual(true, overlayPlane.HasOverlayData, "Incorrect OverlayData detection for plane #{0}", overlayIndex);
Assert.AreEqual(false, overlayPlane.IsBigEndianOW, "Incorrect OW/OB detection for plane #{0}", overlayIndex);
Assert.AreEqual(false, overlayPlane.IsMultiFrame, "Incorrect multiframe detection for plane #{0}", overlayIndex);
Assert.AreEqual(103*89, overlayPlane.GetOverlayFrameLength(), "Incorrect frame size computation for plane #{0}", overlayIndex);
// assert overlay plane basic attribute values
Assert.AreEqual(103, overlayPlane.OverlayRows, "Wrong overlay rows for plane #{0}", overlayIndex);
Assert.AreEqual(89, overlayPlane.OverlayColumns, "Wrong overlay columns for plane #{0}", overlayIndex);
Assert.AreEqual(0, overlayPlane.OverlayBitPosition, "Wrong overlay bit position for plane #{0}", overlayIndex);
Assert.AreEqual(1, overlayPlane.OverlayBitsAllocated, "Wrong overlay bits allocated for plane #{0}", overlayIndex);
Assert.AreEqual(OverlayType.G, overlayPlane.OverlayType, "Wrong overlay type for plane #{0}", overlayIndex);
Assert.AreEqual(new Point(1, 1), overlayPlane.OverlayOrigin, "Wrong overlay origin for plane #{0}", overlayIndex);
// assert overlay plane multiframe attribute values
Assert.AreEqual(null, overlayPlane.ImageFrameOrigin, "Wrong image frame origin for plane #{0}", overlayIndex);
Assert.AreEqual(null, overlayPlane.NumberOfFramesInOverlay, "Wrong number of frames in overlay for plane #{0}", overlayIndex);
}
// test overlay group 6002
{
const int overlayIndex = 1;
var overlayPlane = module[overlayIndex];
// assert overlay plane identification
Assert.AreEqual(0x6002, overlayPlane.Group, "Wrong overlay group for plane #{0}", overlayIndex);
Assert.AreEqual(1, overlayPlane.Index, "Wrong overlay index for plane #{0}", overlayIndex);
Assert.AreEqual(0x020000, overlayPlane.TagOffset, "Wrong tag offset for plane #{0}", overlayIndex);
// assert overlay plane encoding detection
Assert.AreEqual(false, overlayPlane.HasOverlayData, "Incorrect OverlayData detection for plane #{0}", overlayIndex);
Assert.AreEqual(false, overlayPlane.IsBigEndianOW, "Incorrect OW/OB detection for plane #{0}", overlayIndex);
Assert.AreEqual(false, overlayPlane.IsMultiFrame, "Incorrect multiframe detection for plane #{0}", overlayIndex);
Assert.AreEqual(97*101, overlayPlane.GetOverlayFrameLength(), "Incorrect frame size computation for plane #{0}", overlayIndex);
// assert overlay plane basic attribute values
Assert.AreEqual(97, overlayPlane.OverlayRows, "Wrong overlay rows for plane #{0}", overlayIndex);
Assert.AreEqual(101, overlayPlane.OverlayColumns, "Wrong overlay columns for plane #{0}", overlayIndex);
Assert.AreEqual(15, overlayPlane.OverlayBitPosition, "Wrong overlay bit position for plane #{0}", overlayIndex);
Assert.AreEqual(16, overlayPlane.OverlayBitsAllocated, "Wrong overlay bits allocated for plane #{0}", overlayIndex);
Assert.AreEqual(OverlayType.G, overlayPlane.OverlayType, "Wrong overlay type for plane #{0}", overlayIndex);
Assert.AreEqual(new Point(2, 3), overlayPlane.OverlayOrigin, "Wrong overlay origin for plane #{0}", overlayIndex);
// assert overlay plane multiframe attribute values
Assert.AreEqual(null, overlayPlane.ImageFrameOrigin, "Wrong image frame origin for plane #{0}", overlayIndex);
Assert.AreEqual(null, overlayPlane.NumberOfFramesInOverlay, "Wrong number of frames in overlay for plane #{0}", overlayIndex);
}
// test overlay group 6004
{
const int overlayIndex = 2;
var overlayPlane = module[overlayIndex];
// assert overlay plane identification
Assert.AreEqual(0x6004, overlayPlane.Group, "Wrong overlay group for plane #{0}", overlayIndex);
Assert.AreEqual(2, overlayPlane.Index, "Wrong overlay index for plane #{0}", overlayIndex);
Assert.AreEqual(0x040000, overlayPlane.TagOffset, "Wrong tag offset for plane #{0}", overlayIndex);
// assert overlay plane encoding detection
Assert.AreEqual(true, overlayPlane.HasOverlayData, "Incorrect OverlayData detection for plane #{0}", overlayIndex);
Assert.AreEqual(false, overlayPlane.IsBigEndianOW, "Incorrect OW/OB detection for plane #{0}", overlayIndex);
Assert.AreEqual(false, overlayPlane.IsMultiFrame, "Incorrect multiframe detection for plane #{0}", overlayIndex);
Assert.AreEqual(67*71, overlayPlane.GetOverlayFrameLength(), "Incorrect frame size computation for plane #{0}", overlayIndex);
// assert overlay plane basic attribute values
Assert.AreEqual(67, overlayPlane.OverlayRows, "Wrong overlay rows for plane #{0}", overlayIndex);
Assert.AreEqual(71, overlayPlane.OverlayColumns, "Wrong overlay columns for plane #{0}", overlayIndex);
Assert.AreEqual(0, overlayPlane.OverlayBitPosition, "Wrong overlay bit position for plane #{0}", overlayIndex);
Assert.AreEqual(1, overlayPlane.OverlayBitsAllocated, "Wrong overlay bits allocated for plane #{0}", overlayIndex);
Assert.AreEqual(OverlayType.R, overlayPlane.OverlayType, "Wrong overlay type for plane #{0}", overlayIndex);
Assert.AreEqual(new Point(4, 5), overlayPlane.OverlayOrigin, "Wrong overlay origin for plane #{0}", overlayIndex);
// assert overlay plane multiframe attribute values
Assert.AreEqual(null, overlayPlane.ImageFrameOrigin, "Wrong image frame origin for plane #{0}", overlayIndex);
Assert.AreEqual(null, overlayPlane.NumberOfFramesInOverlay, "Wrong number of frames in overlay for plane #{0}", overlayIndex);
}
// test overlay group 601A
{
const int overlayIndex = 13;
var overlayPlane = module[overlayIndex];
// assert overlay plane identification
Assert.AreEqual(0x601A, overlayPlane.Group, "Wrong overlay group for plane #{0}", overlayIndex);
Assert.AreEqual(13, overlayPlane.Index, "Wrong overlay index for plane #{0}", overlayIndex);
Assert.AreEqual(0x1A0000, overlayPlane.TagOffset, "Wrong tag offset for plane #{0}", overlayIndex);
// assert overlay plane encoding detection
Assert.AreEqual(false, overlayPlane.HasOverlayData, "Incorrect OverlayData detection for plane #{0}", overlayIndex);
Assert.AreEqual(false, overlayPlane.IsBigEndianOW, "Incorrect OW/OB detection for plane #{0}", overlayIndex);
Assert.AreEqual(false, overlayPlane.IsMultiFrame, "Incorrect multiframe detection for plane #{0}", overlayIndex);
Assert.AreEqual(97*101, overlayPlane.GetOverlayFrameLength(), "Incorrect frame size computation for plane #{0}", overlayIndex);
// assert overlay plane basic attribute values
Assert.AreEqual(97, overlayPlane.OverlayRows, "Wrong overlay rows for plane #{0}", overlayIndex);
Assert.AreEqual(101, overlayPlane.OverlayColumns, "Wrong overlay columns for plane #{0}", overlayIndex);
Assert.AreEqual(14, overlayPlane.OverlayBitPosition, "Wrong overlay bit position for plane #{0}", overlayIndex);
Assert.AreEqual(16, overlayPlane.OverlayBitsAllocated, "Wrong overlay bits allocated for plane #{0}", overlayIndex);
Assert.AreEqual(OverlayType.R, overlayPlane.OverlayType, "Wrong overlay type for plane #{0}", overlayIndex);
Assert.AreEqual(new Point(6, 7), overlayPlane.OverlayOrigin, "Wrong overlay origin for plane #{0}", overlayIndex);
// assert overlay plane multiframe attribute values
Assert.AreEqual(null, overlayPlane.ImageFrameOrigin, "Wrong image frame origin for plane #{0}", overlayIndex);
Assert.AreEqual(null, overlayPlane.NumberOfFramesInOverlay, "Wrong number of frames in overlay for plane #{0}", overlayIndex);
}
}
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;
}
}
}
