public static SliceContourMeta FindZeroLevelContours(this Mat mat, Func <Vector3, Vector3> imageToPatientFunc, int z)
{
var zPos = imageToPatientFunc(new Vector3(0, 0, z)).Z;
var meta = new SliceContourMeta();
var child = new SliceContourMeta();
var level = new IsodoseLevel()
{
Value = 0, Color = new Scalar(255)
};
Point[][] ctrs;
HierarchyIndex[] hi;
var thresh = mat.Threshold(level.Value, 255, ThresholdTypes.Binary);
thresh = thresh.WindowAndLevel(128, 256);
thresh.FindContours(out ctrs, out hi, RetrievalModes.CComp, ContourApproximationModes.ApproxSimple);
for (int i = 0; i < hi.Length; i++)
{
var contour = ctrs[i];
if (hi[i].Parent == -1)
{
contour.ToList().ForEach(c =>
{
var pos = imageToPatientFunc(new Vector3(c.X, c.Y, 1));
pos.Z = zPos;
meta.AddPoint(new Point3f((float)pos.X, (float)pos.Y, (float)pos.Z));
});
}
if (hi[i].Parent != -1)
{
contour.ToList().ForEach(c =>
{
var pos = imageToPatientFunc(new Vector3(c.X, c.Y, 1));
pos.Z = zPos;
child.AddPoint(new Point3f((float)pos.X, (float)pos.Y, (float)pos.Z));
});
}
}
if (child.ContourPoints.Any())
{
meta.Children.Add(child);
}
thresh.Dispose();
return(meta);
}
/// <summary>
/// Finds contours on StructureMeta model (1 inside, -1 outsize, 0 boundry)
/// </summary>
/// <param name="mat"></param>
/// <returns></returns>
public static SliceContourMeta FindStructureContour(this Matrix model, double zPos)
{
var contourSlice = model.GetZPlane(zPos);
var meta = new SliceContourMeta();
var child = new SliceContourMeta();
Point[][] ctrs;
HierarchyIndex[] hi;
var thresh = contourSlice.Threshold(0, 255, ThresholdTypes.Binary).WindowAndLevel(128, 255);
//Cv2.ImShow("Threshold", thresh);
//Cv2.WaitKey();
thresh.FindContours(out ctrs, out hi, RetrievalModes.CComp, ContourApproximationModes.ApproxNone);
for (int i = 0; i < hi.Length; i++)
{
var contour = ctrs[i];
if (hi[i].Parent == -1)
{
contour.ToList().ForEach(c =>
{
var pos = model.ImageToPatientTx(new Vector3(c.X, c.Y, 1));
pos.Z = zPos;
meta.AddPoint(new Point3f((float)pos.X, (float)pos.Y, (float)pos.Z));
});
}
if (hi[i].Parent != -1)
{
contour.ToList().ForEach(c =>
{
var pos = model.ImageToPatientTx(new Vector3(c.X, c.Y, 1));
pos.Z = zPos;
child.AddPoint(new Point3f((float)pos.X, (float)pos.Y, (float)pos.Z));
});
}
}
if (child.ContourPoints.Any())
{
meta.Children.Add(child);
}
contourSlice.Dispose();
thresh.Dispose();
return(meta);
}
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);
}
