public void LoadImageAndContours()
{
var acceptanceTests = new ModerateGeometricAcceptanceTest(string.Empty, string.Empty);
var medicalVolume = MedIO.LoadAllDicomSeriesInFolderAsync(TestData.GetFullImagesPath(@"sample_dicom"), acceptanceTests).Result.First().Volume;
var volumes = new Dictionary <string, ContourStatistics>()
{
{ "Bladder", new ContourStatistics(95.87, -1000.0, 0) },
{ "Femur_L", new ContourStatistics(205.04, -1000.0, 0) },
};
var readOnlyVolume = new ReadOnlyVolume3D <short>(medicalVolume.Volume);
for (int i = 0; i < medicalVolume.Struct.Contours.Count; i++)
{
var contour = medicalVolume.Struct.Contours[i];
var name = contour.StructureSetRoi.RoiName;
var contourVolume = contour.Contours.ToVolume3D(medicalVolume.Volume);
Console.WriteLine($"Starting checks for contour {name}");
var contourStatistics = ContourStatistics.FromVolumeAndMask(readOnlyVolume, contourVolume);
Assert.AreEqual(volumes[contour.StructureSetRoi.RoiName].SizeInCubicCentimeters, contourStatistics.SizeInCubicCentimeters, 1e-1, $"Size for contour {name}");
Assert.AreEqual(volumes[contour.StructureSetRoi.RoiName].VoxelValueMean, contourStatistics.VoxelValueMean, 1e-1, $"Mean for contour {name}");
Assert.AreEqual(volumes[contour.StructureSetRoi.RoiName].VoxelValueStandardDeviation, contourStatistics.VoxelValueStandardDeviation, 1e-1, $"Std for contour {name}");
}
}
/// <summary>
/// Computes an instance of contour statistics, <see cref="ContourStatistics"/>, from those voxels
/// of the <paramref name="originalVolume"/> where the mask volume attains the foreground value.
/// </summary>
/// <param name="image"></param>
/// <param name="mask"></param>
/// <param name="foreground"></param>
/// <returns></returns>
public static ContourStatistics FromVolumeAndMask(ReadOnlyVolume3D <short> image, Volume3D <byte> mask, byte foreground = 1)
{
image = image ?? throw new ArgumentNullException(nameof(image));
mask = mask ?? throw new ArgumentNullException(nameof(mask));
if (mask.Length != image.Length)
{
throw new ArgumentException("Image and mask must have the same length", nameof(image));
}
double mean = 0;
double variance = 0;
double sum = 0;
ulong count = 0;
// StreamingStatistics.MeanVariance
for (int i = 0; i < image.Length; i++)
{
if (mask[i] == foreground)
{
count++;
double xi = image[i];
sum += xi;
var diff = (count * xi) - sum;
if (count > 1)
{
variance += (diff * diff) / (count * (count - 1));
}
mean += (xi - mean) / count;
}
}
var volumeSizeInCC = count * image.VoxelVolume / 1000d;
var standardDeviation = count == 0 ? 0 : Math.Sqrt(variance / count);
return(new ContourStatistics(volumeSizeInCC, mean, standardDeviation));
}