/// <summary>
/// Save all images and the rt struct to the given folder.
/// </summary>
/// <param name="folderPath"></param>
/// <param name="medicalVolume"></param>
/// <returns></returns>
public static async Task SaveMedicalVolumeAsync(
string folderPath, MedicalVolume medicalVolume)
{
await Task.WhenAll(
SaveDicomImageAsync(folderPath, medicalVolume),
SaveRtStructAsync(Path.Combine(folderPath, "rtstruct.dcm"), medicalVolume.Struct));
}
public VolumeLoaderResult(string seriesId, MedicalVolume volume, Exception error, IReadOnlyList <string> warnings)
{
SeriesUid = seriesId;
Volume = volume;
Error = error;
Warnings = warnings;
}
/// <summary>
/// Converts a medical volume, scan files and a set of binary masks, into a Dicom representation.
/// The returned set of Dicom files will have files for all slices of the scan, and an RtStruct
/// file containing the contours that were derived from the masks. The RtStruct file will be the first
/// entry in the returned list of Dicom files.
/// Use with extreme care - many Dicom elements have to be halluzinated here, and there's no
/// guarantee that the resulting Dicom will be usable beyond what is needed in InnerEye.
/// </summary>
/// <param name="medicalVolume">The medical scan.</param>
/// <param name="scanFiles">The image modality through which the scan was acquired.</param>
/// <param name="contours">A list of contours for individual anatomical structures, alongside
/// <returns></returns>
public static List <DicomFileAndPath> ScanAndContoursToDicom(
MedicalVolume medicalVolume,
IReadOnlyList <DicomFileAndPath> scanFiles,
IReadOnlyList <ContourRenderingInformation> contours)
{
var rtFile = ContoursToDicomRtFile(contours, medicalVolume.Identifiers, medicalVolume.Volume.Transform);
var dicomFiles = new List <DicomFileAndPath> {
rtFile
};
dicomFiles.AddRange(scanFiles);
return(dicomFiles);
}
/// <summary>
/// Returns a task that saves a copy of the original DICOM files forming a medical volume.
/// </summary>
/// <param name="folderPath"></param>
/// <param name="medicalVolume"></param>
/// <returns></returns>
private static async Task SaveDicomImageAsync(string folderPath, MedicalVolume medicalVolume)
{
await Task.Run(() =>
Parallel.ForEach(
medicalVolume.FilePaths,
file =>
{
if (!File.Exists(file))
{
throw new FileNotFoundException(
$"The original dicom directory was modified while using this image. File {file} is missing");
}
// ReSharper disable once AssignNullToNotNullAttribute
var destFile = Path.Combine(folderPath, Path.GetFileName(file));
File.Copy(file, destFile);
}));
}
/// <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>()));
}
}
