public static StructureSetMeta ParseDICOM(string file)
{
var sm = new StructureSetMeta();
var dcm = DICOMObject.Read(file);
var sel = dcm.GetSelector();
var metas = sel.StructureSetROISequence.Items.Select(i =>
{
var meta = new StructureMeta();
meta.StructureId = i.GetSelector().ROIName?.Data;
meta.ROINumber = i.GetSelector().ROINumber.Data;
return(meta);
});
foreach (var meta in metas)
{
try
{
var comatch = sel.ROIContourSequence.Items.FirstOrDefault(i => i.GetSelector().ReferencedROINumber.Data == meta.ROINumber);
var romatch = sel.RTROIObservationsSequence.Items.FirstOrDefault(i => i.GetSelector().ReferencedROINumber.Data == meta.ROINumber);
var colorValues = comatch.GetSelector().ROIDisplayColor.Data_;
var color = new Vec3b((byte)colorValues[0], (byte)colorValues[1], (byte)colorValues[2]);
var dicomType = romatch.GetSelector().RTROIInterpretedType.Data;
var name = romatch.GetSelector().ROIObservationLabel.Data;
meta.StructureName = name;
meta.Color = new Scalar(colorValues[0], colorValues[1], colorValues[2]);
var hasContours = comatch.GetSelector().ContourSequence != null;
if (!hasContours)
{
continue;
}
//HAS CONTOURS - SET COLOR BYTES IN MATRIX
foreach (var slice in comatch.GetSelector().ContourSequence.Items)
{
var contours = slice.GetSelector().ContourData.Data_;
if (contours.Count % 3 != 0)
{
_logger.LogWarning($"Slice for structure {meta.StructureId} has {contours.Count} contour points. Not divisible by 3! Can't process."); continue;
}
try
{
var contour = new SliceContourMeta();
for (int i = 0; i < contours.Count; i += 3)
{
var contourPt = new OpenCvSharp.Point3f((float)contours[i + 0], (float)contours[i + 1], (float)contours[i + 2]);
contour.AddPoint(contourPt);
}
meta.SliceContours.Add(contour);
meta.DICOMType = dicomType;
}
catch (Exception e)
{
_logger.LogError(e.ToString());
}
}
//OrganizeContours - contours containing other contours (holes and fills) will be organized
//into children. All other contours are outermost contours and not children of any other
var slices = meta.SliceContours.GroupBy(s => s.Z).ToList();
foreach (var slice in slices)
{
var sliceContours = slice.OrderByDescending(s => s.CalculateArea()).ToList();
ContourHelper.OrganizeIntoChildren(sliceContours[0], sliceContours.Skip(1));
}
sm.Structures.Add(meta.StructureId, meta);
}
catch (Exception e)
{
_logger.LogError(e, $"Could not add structure {meta.StructureId}");
}
}
return(sm);
}
