/// <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>
/// Loads a medical volume from a Nifti file. The <see cref="MedicalVolume.Volume"/> property
/// will be set to the volume in the Nifti file, the RT structures will be empty, empty
/// Dicom identifiers.
/// </summary>
/// <param name="path"></param>
/// <returns></returns>
public static MedicalVolume LoadMedicalVolumeFromNifti(string path)
{
var volume = LoadNiftiAsShort(path);
return(new MedicalVolume(
volume,
new DicomIdentifiers[0],
new[] { path },
RadiotherapyStruct.CreateDefault(new[] { DicomIdentifiers.CreateEmpty() })));
}
/// <summary>
/// Attempt to load a volume from the given SeriesUID for the given DicomFolderContents
/// </summary>
/// <param name="dfc">A pre-built description of DICOM contents within a particular folder</param>
/// <param name="seriesUID">The DICOM seriesUID you wish to construct a volume for</param>
/// <param name="acceptanceTests">An implementation of IVolumeGeometricAcceptanceTest defining the geometric constraints of your application</param>
/// <param name="loadStructuresIfExists">True if rt-structures identified in the folder and referencing seriesUID should be loaded</param>
/// <param name="supportLossyCodecs">If you wish to accept lossy encodings of image pixel data</param>
/// <returns></returns>
private static VolumeLoaderResult LoadDicomSeries(
DicomFolderContents dfc, DicomUID seriesUID, IVolumeGeometricAcceptanceTest acceptanceTests, bool loadStructuresIfExists, bool supportLossyCodecs)
{
try
{
var dicomSeriesContent = dfc.Series.FirstOrDefault((s) => s.SeriesUID == seriesUID);
var warnings = new List <string>();
RadiotherapyStruct rtStruct = null;
if (dicomSeriesContent != null)
{
var volumeData = DicomSeriesReader.BuildVolume(dicomSeriesContent.Content.Select(x => x.File.Dataset), acceptanceTests, supportLossyCodecs);
if (volumeData != null && loadStructuresIfExists)
{
var rtStructData = dfc.RTStructs.FirstOrDefault(rt => rt.SeriesUID == seriesUID);
if (rtStructData != null)
{
if (rtStructData.Content.Count == 1)
{
var rtStructAndWarnings = RtStructReader.LoadContours(
rtStructData.Content.First().File.Dataset,
volumeData.Transform.DicomToData,
seriesUID.UID,
null,
false);
rtStruct = rtStructAndWarnings.Item1;
var warning = rtStructAndWarnings.Item2;
if (!string.IsNullOrEmpty(warning))
{
warnings.Add(warning);
}
}
else if (rtStructData.Content.Count > 1)
{
warnings.Add("There is more than 1 RT STRUCT referencing this series - skipping structure set load");
}
}
}
var dicomIdentifiers = dicomSeriesContent.Content.Select((v) => DicomIdentifiers.ReadDicomIdentifiers(v.File.Dataset)).ToArray();
if (rtStruct == null)
{
rtStruct = RadiotherapyStruct.CreateDefault(dicomIdentifiers);
}
var result = new MedicalVolume(
volumeData,
dicomIdentifiers,
dicomSeriesContent.Content.Select((d) => d.Path).ToArray(),
rtStruct);
return(new VolumeLoaderResult(seriesUID.UID, result, null, warnings));
}
throw new Exception("Could not find that series");
}
catch (Exception oops)
{
return(new VolumeLoaderResult(seriesUID.UID, null, oops, new List <string>()));
}
}