/// <summary>
/// Creates a radiotherapy structure from a set of contours, including the given rendering
/// information (name of the contour, color to render in).
/// </summary>
/// <param name="contours">The contours and their rendering information.</param>
/// <param name="dicomIdentifiers">The Dicom identifiers for the scan to which the contours belong.</param>
/// <param name="volumeTransform">The Dicom-to-data transformation of the scan to which the contours belong.</param>
/// <returns></returns>
public static RadiotherapyStruct ContoursToRadiotherapyStruct(IEnumerable <ContourRenderingInformation> contours,
IReadOnlyList <DicomIdentifiers> dicomIdentifiers,
VolumeTransform volumeTransform)
{
var radiotherapyStruct = RadiotherapyStruct.CreateDefault(dicomIdentifiers);
int roiNumber = 0;
var nameConverter = new DicomPersonNameConverter("InnerEye", "CreateDataset", string.Empty, string.Empty, string.Empty);
foreach (var contour in contours)
{
// ROIs need to start at 1 by DICOM spec
roiNumber++;
// Create contours - mapping each contour into the volume.
var radiotherapyContour = RTStructCreator.CreateRadiotherapyContour(
contour.Contour,
dicomIdentifiers,
volumeTransform,
contour.Name,
(contour.Color.R, contour.Color.G, contour.Color.B),
roiNumber.ToString(),
nameConverter,
ROIInterpretedType.None
);
radiotherapyStruct.Contours.Add(radiotherapyContour);
}
return(radiotherapyStruct);
}
/// <summary>
/// Creates a single Dicom file that contains a radiotherapy structure,
/// derived from a set of contours and rendering information.
/// </summary>
/// <param name="contours">The contours and their rendering information.</param>
/// <param name="dicomIdentifiers">The Dicom identifiers for the scan to which the contours belong.</param>
/// <param name="volumeTransform">The Dicom-to-data transformation of the scan to which the contours belong.</param>
/// <returns></returns>
public static DicomFileAndPath ContoursToDicomRtFile(IEnumerable <ContourRenderingInformation> contours,
IReadOnlyList <DicomIdentifiers> dicomIdentifiers,
VolumeTransform volumeTransform)
{
var radiotherapyStruct = ContoursToRadiotherapyStruct(contours, dicomIdentifiers, volumeTransform);
return(new DicomFileAndPath(RtStructWriter.GetRtStructFile(radiotherapyStruct), "RTStruct.dcm"));
}
/// <summary>
/// Creates a new RadiotherapyContour for inclusion in a RadiotherapyStruct ready for serialization
/// </summary>
/// <typeparam name="T"></typeparam>
/// <param name="axialContours">The contours relative to the given volume you wish to map into the DICOM reference coordinate system</param>
/// <param name="identifiers"> The DICOM identifiers describing the origin of the volume</param>
/// <param name="volumeTransform">The volume transform.</param>
/// <param name="name">The DICOM structure name</param>
/// <param name="color">The color of this structure</param>
/// <param name="roiNumber">The roiNumber of this structure</param>
/// <returns></returns>
public static RadiotherapyContour CreateRadiotherapyContour(
ContoursPerSlice axialContours,
IReadOnlyList <DicomIdentifiers> identifiers,
VolumeTransform volumeTransform,
string name,
(byte R, byte G, byte B) color,
/// <summary>
/// Converts a set of application contours into DICOM RT objects ready for serialization
/// </summary>
/// <typeparam name="T"></typeparam>
/// <param name="axialContours">The axial contours you wish to convert</param>
/// <param name="identifiers">The set of identifiers, 1 for each slice in parentVolume</param>
/// <param name="volumeTransform">The volume transform.</param>
/// <returns></returns>
public static List <DicomRTContourItem> ToDicomRtContours(
this Microsoft.RTConvert.Contours.ContoursPerSlice axialContours, IReadOnlyList <DicomIdentifiers> identifiers, VolumeTransform volumeTransform)
{
if (identifiers == null || identifiers.Count == 0)
{
throw new ArgumentException(nameof(identifiers), "The identifiers cannot be null or empty");
}
if (volumeTransform == null)
{
throw new ArgumentException(nameof(volumeTransform), "The volume cannot be null or empty");
}
var resultList = new List <DicomRTContourItem>();
var tolerance = volumeTransform.SpacingZ / 2;
// Iterate through the sets of contours per slice
foreach (var tuple in axialContours)
{
// For this slice, compute the z-axis coordinate in the DICOM reference coordinate system
var z = tuple.Key;
var zAxisPhysicalCoordinate = (volumeTransform.DataToDicom * new Point3D(0, 0, z)).Z;
// Locate the DICOM identifier containing this slice. Note that for non-axial volumes this is not the right test
// but is sufficient for Axial volumes.
var identifier = identifiers.FirstOrDefault(x => Math.Abs(x.Image.ImagePositionPatient.Z - zAxisPhysicalCoordinate) < tolerance);
if (identifier == null)
{
throw new Exception("Invalid contour or image identifiers");
}
// Reference the slice containing these contours by SopInstance UID
var sopCommonInstance = identifier.Image.SopCommon;
var contourImageSeq = new List <DicomRTContourImageItem>()
{
new DicomRTContourImageItem(sopCommonInstance.SopClassUid, sopCommonInstance.SopInstanceUid)
};
// Iterate through the contour objects on this slice.
foreach (var contour in tuple.Value)
{
// Convert the pixel based contour into the DICOM reference coordinate system and flatten to an arry of doubles.
var allpoints = contour.ContourPoints.SelectMany(
p => (volumeTransform.DataToDicom * new Point3D(p.X, p.Y, z)).Data).ToArray();
resultList.Add(new DicomRTContourItem(
allpoints,
contour.Length,
ClosedPlanarString,
contourImageSeq));
}
}
return(resultList);
}
