/// <summary>
/// Read the structure set from a DICOM dataset.
/// </summary>
/// <param name="ds"></param>
/// <returns></returns>
public static RadiotherapyStruct Read(DicomDataset ds)
{
var patient = DicomPatient.Read(ds);
var study = DicomStudy.Read(ds);
var series = DicomRTSeries.Read(ds);
var equipment = DicomEquipment.Read(ds);
var structureSet = DicomRTStructureSet.Read(ds);
// DicomRTStructureSetROI.RoiNumber is the primary key. We try and locate the first observation and roiContour data for eaach
// RoiNumber encountered.
var structures = DicomRTStructureSetROI.Read(ds);
var contoursData = DicomRTContour.Read(ds);
var observations = DicomRTObservation.Read(ds);
var allContours = new List <RadiotherapyContour>();
foreach (var s in structures)
{
var roiContours = contoursData.FirstOrDefault(c => c.ReferencedRoiNumber == s.Key);
var roiObservation = observations.FirstOrDefault(o => o.ReferencedRoiNumber == s.Key);
// we insist both must exist
if (roiContours != null && roiObservation != null)
{
allContours.Add(new RadiotherapyContour(roiContours, s.Value, roiObservation));
}
}
return(new RadiotherapyStruct(structureSet, patient, equipment, study, series, allContours));
}
/// <summary>
/// Serialize the structure set to a DICOM dataset.
/// </summary>
/// <param name="ds"></param>
/// <param name="s"></param>
public static void Write(DicomDataset ds, RadiotherapyStruct s)
{
DicomPatient.Write(ds, s.Patient);
DicomStudy.Write(ds, s.Study);
DicomRTSeries.Write(ds, s.RTSeries);
DicomEquipment.Write(ds, s.Equipment);
DicomRTStructureSet.Write(ds, s.StructureSet);
// For each ROI, gather the contours, observations and roi details into seperate arrays and serialize
var rois = s.Contours.Select(c => c.StructureSetRoi);
var contours = s.Contours.Select(c => c.DicomRtContour);
var observations = s.Contours.Select(c => c.DicomRtObservation);
DicomRTStructureSetROI.Write(ds, rois);
DicomRTContour.Write(ds, contours);
DicomRTObservation.Write(ds, observations);
}
public RadiotherapyContour(DicomRTContour dicomRtContour, DicomRTStructureSetROI structure, DicomRTObservation dicomRtObservation)
{
DicomRtContour = dicomRtContour;
StructureSetRoi = structure;
DicomRtObservation = dicomRtObservation;
}
public void LoadAndSaveMedicalVolumeTest()
{
var directory = TestData.GetFullImagesPath("sample_dicom");
var acceptanceTests = new StrictGeometricAcceptanceTest(string.Empty, string.Empty);
var medicalVolume = MedIO.LoadAllDicomSeriesInFolderAsync(directory, acceptanceTests).Result.First().Volume;
Directory.CreateDirectory(_tempFolder);
Console.WriteLine($"Directory created {_tempFolder}");
Volume3D <byte>[] contourVolumes = new Volume3D <byte> [medicalVolume.Struct.Contours.Count];
for (int i = 0; i < medicalVolume.Struct.Contours.Count; i++)
{
contourVolumes[i] = new Volume3D <byte>(
medicalVolume.Volume.DimX,
medicalVolume.Volume.DimY,
medicalVolume.Volume.DimZ,
medicalVolume.Volume.SpacingX,
medicalVolume.Volume.SpacingY,
medicalVolume.Volume.SpacingZ,
medicalVolume.Volume.Origin,
medicalVolume.Volume.Direction);
contourVolumes[i].Fill(medicalVolume.Struct.Contours[i].Contours, (byte)1);
}
// Calculate contours based on masks
var rtContours = new List <RadiotherapyContour>();
for (int i = 0; i < medicalVolume.Struct.Contours.Count; i++)
{
var contour = medicalVolume.Struct.Contours[i];
var contourForAllSlices = GetContoursForAllSlices(contourVolumes[i]);
var rtcontour = new DicomRTContour(
contour.DicomRtContour.ReferencedRoiNumber,
contour.DicomRtContour.RGBColor,
contourForAllSlices);
DicomRTStructureSetROI rtROIstructure = new DicomRTStructureSetROI(
contour.StructureSetRoi.RoiNumber,
contour.StructureSetRoi.RoiName,
string.Empty,
ERoiGenerationAlgorithm.Semiautomatic);
DicomRTObservation observation = new DicomRTObservation(
contour.DicomRtObservation.ReferencedRoiNumber, new DicomPersonNameConverter("Left^Richard^^Dr"), ROIInterpretedType.EXTERNAL);
rtContours.Add(new RadiotherapyContour(rtcontour, rtROIstructure, observation));
}
var rtStructureSet = new RadiotherapyStruct(
medicalVolume.Struct.StructureSet,
medicalVolume.Struct.Patient,
medicalVolume.Struct.Equipment,
medicalVolume.Struct.Study,
medicalVolume.Struct.RTSeries,
rtContours);
MedIO.SaveMedicalVolumeAsync(_tempFolder, new MedicalVolume(
medicalVolume.Volume,
medicalVolume.Identifiers,
medicalVolume.FilePaths,
rtStructureSet)).Wait();
var medicalVolume2 = MedIO.LoadAllDicomSeriesInFolderAsync(_tempFolder, acceptanceTests).Result.First().Volume;
foreach (var radiotherapyContour in medicalVolume2.Struct.Contours.Where(x => x.DicomRtContour.DicomRtContourItems.First().GeometricType == "CLOSED_PLANAR"))
{
var savedContour =
medicalVolume2.Struct.Contours.First(x => x.StructureSetRoi.RoiName == radiotherapyContour.StructureSetRoi.RoiName);
foreach (var contour in radiotherapyContour.Contours)
{
Assert.AreEqual(radiotherapyContour.DicomRtObservation.ROIInterpretedType, ROIInterpretedType.EXTERNAL);
for (int i = 0; i < contour.Value.Count; i++)
{
if (!contour.Value[i].Equals(savedContour.Contours.ContoursForSlice(contour.Key)[i]))
{
Console.WriteLine(radiotherapyContour.StructureSetRoi.RoiName);
Assert.Fail();
}
}
}
}
}
