private SegmentationMenuInfo MenuInfoFromDocumentAndSeg(SegmentationDocument segmentationDocument, Seg seg, Sop sop)
{
if (seg.SegmentImageData != null &&
seg.SegmentImageData.SegmentFrameData != null &&
seg.SegmentImageData.SegmentFrameData.Count > 0)
{
return(new SegmentationMenuInfo
{
DisplayLabel = seg.DisplayLabel,
DisplayImageSeriesUid = seg.ImageSeriesUid,
SegmentationNumber = seg.SegmentationNumber,
SegmentationDocumentUid = segmentationDocument.SopInstanceUid,
SeriesNumber = segmentationDocument.SeriesNumber,
ImagePositionPatient = seg.SegmentImageData.SegmentFrameData[0].ImagePositionPatient,
ImageOrientationPatient =
seg.SegmentImageData.SegmentFrameData[0].ImageOrientationPatient,
FrameOfReferenceUid = seg.SegmentImageData.FrameOfReferenceUid,
PatientId = sop.PatientId,
PatientsName = sop.PatientsName,
StudyAccessionNumber = sop.AccessionNumber,
StudyDate = sop.StudyDate,
StudyTime = sop.StudyTime,
StudyDescription = sop.StudyDescription,
StudyInstanceUid = sop.StudyInstanceUid
});
}
return(null);
}
public static bool IsSegmentationDocumentGraphicLoaded(SegmentationDocument segmentationDocument, IDisplaySet displaySet)
{
Platform.CheckForNullReference(segmentationDocument, "segmentationDocument");
Platform.CheckForNullReference(displaySet, "displaySet");
return
(displaySet.PresentationImages.OfType <IOverlayGraphicsProvider>()
.SelectMany(overlayGraphicProvider => overlayGraphicProvider.OverlayGraphics.OfType <SegFrameImageGraphic>())
.Any(
segFrameImageGraphic =>
segFrameImageGraphic.SegmentationDocumentReference.SegmentationDocument.SopInstanceUid == segmentationDocument.SopInstanceUid));
}
private void AddSegmentationMenuInfo(SegmentationDocument segmentationDocument, Seg seg, Sop sop)
{
if (
!_segmentationMenuInfos.ContainsKey(
segmentationDocument.SopInstanceUid + seg.SegmentationNumber))
{
SegmentationMenuInfo info =
MenuInfoFromDocumentAndSeg(segmentationDocument, seg, sop);
if (info != null)
{
_segmentationMenuInfos.Add(
segmentationDocument.SopInstanceUid + seg.SegmentationNumber,
info);
}
}
}
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 SegmentationDocumentReference(SegmentationDocument segmentationDocument, int segmentNumber)
{
SegmentationDocument = segmentationDocument;
SegmentNumber = segmentNumber;
}
public SegmentationDocument DeserializeSegmenationDocument()
{
if (_segDocumentIod == null)
{
return(null);
}
var segDocument = new SegmentationDocument(_segDocumentIod);
segDocument.CreationDateTime = _segDocumentIod.CreationDateTime ?? DateTime.Now; // ??
segDocument.SeriesInstanceUid = _segDocumentIod.SeriesInstanceUid;
segDocument.SeriesDescription = _segDocumentIod.SeriesDescription;
segDocument.SeriesNumber = _segDocumentIod.SeriesNumber ?? 0; // ??
//segDocument.PreviousSegmentationUid = _segDocumentIod.PriorSegmentationUid;
segDocument.SopInstanceUid = _segDocumentIod.SopInstanceUid;
segDocument.ContentLabel = _segDocumentIod.SegmentationImageModuleIod.ContentLabel;
//var userName = _segDocumentIod.GeneralSeriesModuleIod.OperatorsName;
var userName = _segDocumentIod.SegmentationImageModuleIod.ContentCreatorsName;
if (!string.IsNullOrEmpty(userName))
{
segDocument.UserInfo = new UserInfo
{
Name = userName,
LoginName = userName // TODO - use _segDocumentIod.GeneralSeriesModuleIod.OperatorsName[1] when available
};
}
var hasErrors = false;
if (CanUnderstandSopInstance())
{
var segmentationImageModule = _segDocumentIod.SegmentationImageModuleIod;
if (segmentationImageModule != null)
{
for (int i = 0; i < segmentationImageModule.SegmentSequence.Length; i++)
{
var seg = InitializeSegFromIod(i);
if (seg == null)
{
hasErrors = true;
}
else
{
segDocument.Segs.Add(seg);
}
}
}
}
if (hasErrors || segDocument.Segs.Count == 0)
{
var invalidSeg = new Seg(false, null);
invalidSeg.Description = "Segmentation reading error(s) - see log for details";
invalidSeg.Label = "Errors/Not Supported";
segDocument.Segs.Add(invalidSeg);
}
return(segDocument);
}
public SegmentationDocumentReference(SegmentationDocument segmentationDocument, int segmentNumber)
{
SegmentationDocument = segmentationDocument;
SegmentNumber = segmentNumber;
}
