public static Tuple <RadiotherapyStruct, string> LoadContours(
string filePath, Transform3 dicomToData, string seriesUID = null, string studyUID = null, bool warningsAsErrors = true)
{
var file = DicomFile.Open(filePath);
return(LoadContours(file.Dataset, dicomToData, seriesUID, studyUID, warningsAsErrors));
}
/// <summary>
/// Map an array of doubles are read from DICOM into the coordinate space of the given volume3D
/// </summary>
/// <param name="dicomToData">The dicom to data transform.</param>
/// <param name="contourData"></param>
/// <returns></returns>
private static Tuple <int, ContourPolygon> ToContour(Transform3 dicomToData, IReadOnlyList <double> contourData)
{
var array = new PointF[contourData.Count / 3];
var first3DPoint = new Point3D(contourData[0], contourData[1], contourData[2]);
var firstPixel = dicomToData * first3DPoint;
var z = Convert.ToInt32(firstPixel.Z);
Parallel.For(
0,
array.Length,
i =>
{
var j = i * 3;
var physicalPoint = new Point3D(
contourData[j],
contourData[j + 1],
contourData[j + 2]);
var pixelPoint = dicomToData * physicalPoint;
if (Convert.ToInt32(pixelPoint.Z) != z)
{
throw new ArgumentException(
"Invalid data: this contour contains points that are not in the same plane");
}
array[i] = new PointF((float)pixelPoint.X, (float)pixelPoint.Y);
});
return(Tuple.Create(z, new ContourPolygon(array, 0)));
}
/// <summary>
/// Load a RadiotherapyStruct from the given dicom dataset and map into the coordinate of the given Volume3D
/// </summary>
/// <param name="ds">Dataset to read the structure set from</param>
/// <param name="dicomToData">The transform from going between dicom and voxel points.</param>
/// <param name="seriesUID">SeriesUID that must match the referenced seriesUID inside the structure set</param>
/// <param name="studyUID">The structure set must belong to the same study</param>
/// <param name="warningsAsErrors">true if warnings should be treated as errors and thrown from this method.</param>
/// <returns>A new RadiotherapyStruct with any warnings collated into a string</returns>
public static Tuple <RadiotherapyStruct, string> LoadContours(
DicomDataset ds, Transform3 dicomToData, string seriesUID = null, string studyUID = null, bool warningsAsErrors = true)
{
RadiotherapyStruct rtStruct = RadiotherapyStruct.Read(ds);
if (studyUID != null && studyUID != rtStruct.Study.StudyInstanceUid)
{
var warningText = $"The RT STRUCTURE Set does not belong to this Study";
if (warningsAsErrors)
{
throw new ArgumentException(warningText);
}
return(Tuple.Create <RadiotherapyStruct, string>(null, warningText));
}
// ReferencedFramesOfRef must contain at least 1 study/series reference
if (CheckUnreferencedSeries(rtStruct.StructureSet, seriesUID))
{
var warningText = $"The RT STRUCTURE does not reference this Series";
if (warningsAsErrors)
{
throw new ArgumentException(warningText);
}
return(Tuple.Create <RadiotherapyStruct, string>(null, warningText));
}
var contoursData = rtStruct.Contours;
// Do not warn if all structures are empty
if (contoursData.Count != 0 && !contoursData.Any(c => CanUseStructData(c.DicomRtContour)))
{
var warningText = $"The RT STRUCTURE does not contain CLOSED PLANAR contours";
if (warningsAsErrors)
{
throw new ArgumentException(warningText);
}
return(Tuple.Create <RadiotherapyStruct, string>(null, warningText));
}
var warningTypeText = string.Empty;
if (CheckUnsupportedData(rtStruct))
{
var badTypes = UnsupportedTypes(rtStruct);
warningTypeText = $"The RT STRUCTURE contains unsupported Contour Types: {string.Join(",",badTypes)}";
// remove the parent structures
RemoveUnsupportedTypes(rtStruct);
}
Parallel.ForEach(contoursData, c => CreateStructureContoursBySlice(dicomToData, c));
return(Tuple.Create(rtStruct, warningTypeText));
}
public OpticalSurface(int id,
Vector3Pair p,
Transform3 transform,
Curve curve,
Shape shape,
Medium left,
Medium right) : base(id, p, transform, curve, shape)
{
_mat[0] = left;
_mat[1] = right;
}
public static Tuple <RadiotherapyStruct, string> LoadStruct(string rtfile, Transform3 dicomToData, string studyUId, string seriesUId)
{
try
{
var file = DicomFile.Open(rtfile);
return(RtStructReader.LoadContours(file.Dataset, dicomToData, seriesUId, studyUId, true));
}
catch (Exception ex)
{
throw new ArgumentException($"RT file {rtfile} cannot be loaded - {ex.Message}");
}
}
public MainViewModel()
{
EffectsManager = new DefaultEffectsManager();
Title = "Material Demo";
this.Camera = new PerspectiveCamera {
Position = new Point3D(-30, 30, -30), LookDirection = new Vector3D(30, -30, 30), UpDirection = new Vector3D(0, 1, 0)
};
var builder = new MeshBuilder();
builder.AddBox(new Vector3(0, -6, 0), 200, 2, 100);
Floor = builder.ToMesh();
builder = new MeshBuilder();
builder.AddSphere(Vector3.Zero, 2);
LoadObj(@"shaderBall\shaderBall.obj");
EnvironmentMap = LoadFileToMemory("Cubemap_Grandcanyon.dds");
ColorStripeMaterial.ColorStripeX = GetGradients(new Color4(1, 0, 0, 1), new Color4(0, 1, 0, 1), new Color4(0, 0, 1, 1), 48).ToList();
ColorStripeMaterial.ColorStripeY = GetGradients(new Color4(1, 1, 0, 1), new Color4(0, 1, 1, 1), new Color4(1, 0, 1, 1), 48).ToList();
MeshTitles = new BillboardText3D();
MeshTitles.TextInfo.Add(new TextInfo("Blinn", Transform1.ToVector3())
{
Scale = 0.08f, Background = new Color4(1, 1, 1, 1)
});
MeshTitles.TextInfo.Add(new TextInfo("Normal", Transform2.ToVector3())
{
Scale = 0.08f, Background = new Color4(1, 1, 1, 1)
});
MeshTitles.TextInfo.Add(new TextInfo("Diffuse", Transform3.ToVector3())
{
Scale = 0.08f, Background = new Color4(1, 1, 1, 1)
});
MeshTitles.TextInfo.Add(new TextInfo("Position", Transform4.ToVector3())
{
Scale = 0.08f, Background = new Color4(1, 1, 1, 1)
});
MeshTitles.TextInfo.Add(new TextInfo("VertexColor", Transform5.ToVector3())
{
Scale = 0.08f, Background = new Color4(1, 1, 1, 1)
});
MeshTitles.TextInfo.Add(new TextInfo("ColorStripe", Transform6.ToVector3())
{
Scale = 0.08f, Background = new Color4(1, 1, 1, 1)
});
(FloorMaterial as PhongMaterial).RenderShadowMap = true;
}
public List <byte> Write()
{
List <byte> bytes = new List <byte>();
bytes.AddRange(Transform1.Write());
bytes.AddRange(Transform2.Write());
bytes.AddRange(Transform3.Write());
bytes.AddRange(Transform4.Write());
bytes.AddRange(Transform5.Write());
if (bytes.Count != 320)
{
throw new InvalidDataException("FPF_SubEntry is an invalid size.");
}
return(bytes);
}
/// <summary>
/// Map the given structure into the coordinate space of the Volume3D specified creating the
/// ContoursBySlice instance
/// </summary>
/// <param name="dicomToData">The dicom to data transform.</param>
/// <param name="c"></param>
private static void CreateStructureContoursBySlice(Transform3 dicomToData, RadiotherapyContour c)
{
var structContours = c.DicomRtContour.DicomRtContourItems;
var contourPoints = new List <Tuple <int, ContourPolygon> >();
foreach (var contour in structContours)
{
var pointsOnSlice = ToContour(dicomToData, contour.Data);
contourPoints.Add(pointsOnSlice);
}
var sliceDict =
contourPoints.GroupBy(x => x.Item1).
ToDictionary(x => x.Key, g => (IReadOnlyList <ContourPolygon>)g.Select(x => x.Item2).
ToList());
c.Contours = new ContoursPerSlice(sliceDict);
}
public Camera(Point3 pos, Point3 lookat, Vector3 up, int width, int height, double fov = 45.0)
{
this.campos = pos;
Vector3 lookdir = (lookat - pos).Normalized;
Vector3 camside = up.Normalized.Cross(lookdir);
Vector3 camup = camside.Cross(lookdir);
camtrans = new Transform3(camside, camup, lookdir);
this.Width = width;
this.Height = height;
double fovx = Coral.MathUtil.DegToRad(fov);
double fovy = ((double)height / (double)width) * fovx;
tan_fovx = Math.Tan(fovx);
tan_fovy = -Math.Tan(fovy);
}
private double r; //tube radius
public TrTorus(Point3 center, double majrad, double tuberad, Material mat) : base(Transform3.Scale(majrad), mat)
{
this.R = 1.0;
this.r = tuberad / majrad;
this.center = center;
}
public static TexMat ToTexMat(this Transform3 transform)
{
return(new TexMat(transform.ToMatrixd()));
}
public TracerObject(Transform3 pos, Material mat)
{
this.Position = pos;
this.Material = mat;
this.InvPosition = Position.Inverse;
}
public Stop(int id, Vector3Pair p, Transform3 transform, Curve curve, Shape shape) :
base(id, p, transform, curve, shape)
{
_external_radius = shape.max_radius() * 2.0;
}
//x^4+5x^2+y^4-5y^2+z^4-5z^2+11.8=0
public TrTangleCube(Point3 center, double size, Material mat) : base(Transform3.Scale(100.0), mat)
{
}
public MirrorSurface(int id, Vector3Pair p, Transform3 transform, Curve curve, Shape shape, Medium left,
Medium right) : base(id, p, transform, curve, shape, left, right)
{
}
internal TransformVolume(Volume root)
{
Root = root;
transformStack = Transform3.NewTransformStack();
}
public TrSphere(Point3 center, double rad, Material mat) : base(Transform3.Translate(center.X, center.Y, center.Z), mat)
{
this.rad = rad;
}
public Image(int id, Vector3Pair p, Transform3 transform, Curve curve, Shape shape) : base(id, p, transform,
curve, shape)
{
}
