/// <summary>
/// Masks an image of the same voxel count as the input doseGrid. Voxels inside the
/// contour are filled with the specified color. Intent is white (0x255) on inside and outside
/// areas/holes are left black (0x00)
/// </summary>
/// <param name="mask">the mask to fill or modify (recursively)</param>
/// <param name="txMatrix">the patient transform matrix from the imagematrix/dosematrix</param>
/// <param name="color">the color to fill the contour</param>
/// <param name="scale">the scale of the image (in case the image has been resampled)</param>
public void MaskImageFast(Mat mask, Mat txMatrix, byte color = 255, double scale = 1)
{
if (ContourPoints.Count == 0)
{
mask.SetArray(new byte[mask.Cols * mask.Rows]); return;
}
var allPoints = new Vec4f[ContourPoints.Count];
var points = ContourPoints.Select(c => new Vec4f(c.X, c.Y, Z, 1));
using (var pointMat = new Mat <float>(new[] { ContourPoints.Count }, points.ToArray()))
{
var txPointMat = pointMat.Transform(txMatrix.Inv());
txPointMat.GetArray(out allPoints);
}
var points2D = allPoints.Select(a => new Point(a.Item0 * scale, a.Item1 * scale)).ToList();
Cv2.FillPoly(mask, new[] { points2D }, new Scalar(color), LineTypes.Link8);
var grandchildren = Children.SelectMany(c => c.Children);
var outermostChildren = Children.Where(c => !grandchildren.Any(gc => gc == c));
foreach (var child in outermostChildren)
{
//Recursively alternates black white to account for holes and fills of children contours
child.MaskImageFast(mask, txMatrix, color == 255 ? (byte)0 : (byte)255);
}
}
public static List <Point3f> AsPoint3fs(this Mat mat)
{
if (mat.Channels() == 4)
{
var vals = new Vec4f[mat.Total()];
mat.GetArray(0, 0, vals);
return(vals.Select(v => new Point3f(v.Item0, v.Item1, v.Item2)).ToList());
}
else
{
var vals = new Point3f[mat.Total()];
mat.GetArray(0, 0, vals);
return(vals.ToList());
}
}
public static StructureMeta[] Find2DIsodoseLines(this Matrix matrix, params IsodoseLevel[] levels)
{
List <StructureMeta> metas = new List <StructureMeta>();
foreach (var level in levels)
{
var meta = new StructureMeta()
{
StructureId = level.Value.ToString(),
StructureName = level.Value.ToString()
};
meta.Color = level.Color;
for (int z = 0; z < matrix.DimensionZ; z++)
{
using (var mat = matrix.GetZPlaneBySlice(z))
{
var ctrs = mat.Find2DIsodoseLine(level);
if (ctrs.Any())
{
foreach (var contour in ctrs)
{
var allPoints = new Vec4f[contour.Length];
var points = contour.Select(c => new Vec4f(c.X, c.Y, z, 1));
using (var pointMat = new Mat <float>(new[] { contour.Length }, points.ToArray()))
{
var txPointMat = pointMat.Transform(matrix.PatientTransformMatrix);
txPointMat.GetArray(out allPoints);
}
var sliceContour = new SliceContourMeta();
var points3D = allPoints.Select(a => new Point3f(a.Item0, a.Item1, a.Item2)).ToList();
points3D.ForEach(sliceContour.AddPoint);
meta.SliceContours.Add(sliceContour);
}
}
}
}
metas.Add(meta);
}
return(metas.ToArray());
}
public static CameraSpacePoint[] ToCamSpacePoints(this Mat mat)
{
if (mat.Channels() == 4)
{
var vals = new Vec4f[mat.Total()];
mat.GetArray(0, 0, vals);
return(vals.Select(v => new CameraSpacePoint()
{
X = v.Item0, Y = v.Item1, Z = v.Item2
}).ToArray());
}
else
{
var vals = new Point3f[mat.Total()];
mat.GetArray(0, 0, vals);
return(vals.Select(v => new CameraSpacePoint()
{
X = v.X, Y = v.Y, Z = v.Z
}).ToArray());
}
}
public Mat DrawOnSlice(Mat txMatrix, Mat slice, double scale = 1)
{
var allPoints = new Vec4f[ContourPoints.Count];
var points = ContourPoints.Select(c => new Vec4f(c.X, c.Y, Z, 1));
using (var pointMat = new Mat <float>(new[] { ContourPoints.Count }, points.ToArray()))
{
var txPointMat = pointMat.Transform(txMatrix.Inv());
txPointMat.GetArray(out allPoints);
}
var points2D = allPoints.Select(a => new Point(a.Item0 * scale, a.Item1 * scale)).ToList();
double min, max;
slice.MinMaxIdx(out min, out max);
var color = slice.Type() == MatType.CV_8UC3? slice: slice.WindowAndLevel((max - min) / 2, max - min);
Cv2.DrawContours(color, new[] { points2D }, 0, new Scalar(255, 255, 0));
var grandchildren = Children.SelectMany(c => c.Children);
var outermostChildren = Children.Where(c => !grandchildren.Any(gc => gc == c));
return(color);
}
