/// <summary>
/// Creates a new instance of the class, from a binary mask. The contour is extracted from the mask
/// using the default settings: Background 0, foreground 1, axial slices.
/// </summary>
/// <param name="name">The name of the anatomical structure that is represented by the contour.</param>
/// <param name="color">The color that should be used to render the contour.</param>
/// <param name="mask">The binary mask that represents the anatomical structure.</param>
/// <exception cref="ArgumentNullException">The contour name or mask was null.</exception>
public ContourRenderingInformation(string name, RGBColor color, Volume3D <byte> mask)
{
Name = name ?? throw new ArgumentNullException(nameof(name));
Color = color;
mask = mask ?? throw new ArgumentNullException(nameof(mask));
Contour = ExtractContours.ContoursWithHolesPerSlice(mask);
}
public void FillPolygonTests7()
{
var dimX = 5;
var dimY = 5;
var expectedArray = new byte[]
{
0, 1, 1, 0, 0,
1, 1, 1, 1, 0,
1, 1, 1, 1, 1,
1, 1, 0, 1, 0,
0, 0, 0, 0, 0,
};
var volume2D = new Volume2D <byte>(expectedArray, 5, 5, 1, 1, new Point2D(), new Matrix2());
var extractContour = ExtractContours.PolygonsFilled(volume2D);
var output1 = new byte[dimX * dimY];
var polygon = extractContour.First().Points.Select(x => CreatePoint(x.X + 0.00002, x.Y - 0.00001)).ToArray();
FillPolygon.Fill(polygon, output1, dimX, dimY, 0, 0, (byte)1);
for (var i = 0; i < output1.Length; i++)
{
Assert.AreEqual(expectedArray[i], output1[i]);
}
}
/// <summary>
/// Extracts contours from all slices of the given volume, searching for the given foreground value.
/// Contour extraction will take holes into account.
/// </summary>
/// <param name="volume"></param>
/// <param name="foregroundId">The voxel value that should be used in the contour search as foreground.</param>
/// <param name="axialSmoothingType">The smoothing that should be applied when going from a point polygon to
/// contours. This will only affect axial slice, for other slice types no smoothing will be applied.
/// <param name="sliceType">The type of slice that should be used for contour extraction.</param>
/// <param name="filterEmptyContours">If true, contours with no points are not extracted.</param>
/// <param name="regionOfInterest"></param>
/// <returns></returns>
public static ContoursPerSlice ContoursWithHolesPerSlice(
this Volume3D <byte> volume,
byte foregroundId = ModelConstants.MaskForegroundIntensity,
SliceType sliceType = SliceType.Axial,
bool filterEmptyContours = true,
Region3D <int> regionOfInterest = null,
ContourSmoothingType axialSmoothingType = ContourSmoothingType.Small)
=> ExtractContours.ContoursWithHolesPerSlice(volume, foregroundId, sliceType, filterEmptyContours, regionOfInterest, axialSmoothingType);
/// <summary>
/// Extracts axial contours for the foreground values in the given volume. After extracting the contours,
/// a check is conducted if the contours truthfully represent the actual volume. This will throw exceptions
/// for example if the incoming volume has "doughnut shape" structures.
/// </summary>
/// <param name="volume">The mask volume to extract contours from.</param>
/// <param name="maxAbsoluteDifference">The maximum allowed difference in foreground voxels when going
/// from mask to contours to mask.</param>
/// <param name="maxRelativeDifference">The maximum allowed relative in foreground voxels (true - rendered)/true
/// when going from mask to contours to mask.</param>
/// <returns></returns>
public static ContoursPerSlice ExtractContoursAndCheck(this Volume3D <byte> volume,
int?maxAbsoluteDifference = 10,
double?maxRelativeDifference = 0.15
)
{
var contours = ExtractContours.ContoursWithHolesPerSlice(
volume,
foregroundId: ModelConstants.MaskForegroundIntensity,
sliceType: SliceType.Axial,
filterEmptyContours: true,
regionOfInterest: null,
axialSmoothingType: ContourSmoothingType.Small);
var slice = new byte[volume.DimX * volume.DimY];
void ClearSlice()
{
for (var index = 0; index < slice.Length; index++)
{
slice[index] = ModelConstants.MaskBackgroundIntensity;
}
}
foreach (var contourPerSlice in contours)
{
var indexZ = contourPerSlice.Key;
var offsetZ = indexZ * volume.DimXY;
ClearSlice();
foreach (var contour in contourPerSlice.Value)
{
FillPolygon.Fill(contour.ContourPoints, slice,
volume.DimX, volume.DimY, 1, 0, ModelConstants.MaskForegroundIntensity);
}
var true1 = 0;
var rendered1 = 0;
for (var index = 0; index < slice.Length; index++)
{
if (volume[offsetZ + index] == ModelConstants.MaskForegroundIntensity)
{
true1++;
}
if (slice[index] == ModelConstants.MaskForegroundIntensity)
{
rendered1++;
}
}
CheckContourRendering(true1, rendered1, maxAbsoluteDifference, maxRelativeDifference, $"Slice z={indexZ}");
}
;
return(contours);
}
public void FillPolygonTestsRandomCheckTermination()
{
var dimX = 2000;
int seed = Guid.NewGuid().GetHashCode();
Console.WriteLine($"Seed {seed}");
var random = new Random(seed);
var byteArray = Enumerable.Range(0, dimX * dimX).Select(_ => (byte)random.Next(0, 2)).ToArray();
var volume2D = new Volume2D <byte>(byteArray, dimX, dimX, 1, 1, new Point2D(), new Matrix2());
var extractContour = ExtractContours.PolygonsFilled(volume2D);
Console.WriteLine($"Contours count {extractContour.Count}");
Assert.IsTrue(extractContour.Count > 0);
}
/// <summary>
/// Extracts the contours around all voxel values in the volume that have the given foreground value.
/// All other voxel values (zero and anything that is not the foreground value) is treated as background.
/// Contour extraction will not take account of holes, and hence only return the outermost
/// contour around a region of interest.
/// </summary>
/// <param name="volume"></param>
/// <param name="foregroundId">The voxel value that should be used as foreground in the contour search.</param>
/// <param name="smoothingType">The smoothing that should be applied when going from a point polygon to
/// a contour.</param>
/// <returns></returns>
public static IReadOnlyList <ContourPolygon> ContoursFilled(
this Volume2D <byte> volume,
byte foregroundId = 1,
ContourSmoothingType smoothingType = ContourSmoothingType.Small)
=> ExtractContours.ContoursFilled(volume, foregroundId, smoothingType);