/// <summary>
/// Handle options, if no errors.
/// </summary>
/// <param name="opts">Command line options</param>
/// <returns>Exit code.</returns>
static int RunOptionsAndReturnExitCode(Options opts)
{
try
{
RTConverters.ConvertNiftiToDicom(opts.InFile, opts.ReferenceSeries, opts.StructureNames,
opts.StructureColors, opts.FillHoles, opts.ROIInterpretedTypes, opts.OutFile, opts.ModelNameAndVersion, opts.Manufacturer, opts.Interpreter);
Console.WriteLine($"Successfully written {opts.OutFile}");
}
catch (Exception e)
{
Console.Error.WriteLine($"Error while processing: {e}");
return(1);
}
return(0);
}
/// <summary>
/// Test Nifti file to DICOM-RT translation.
/// </summary>
/// <param name="niftiFilename">Source Nifti file.</param>
/// <param name="referenceSeries">Reference DICOM series folder.</param>
/// <param name="structureNames">List of structure names for DICOM-RT.</param>
/// <param name="structureColors">List of structure colours for DICOM-RT.</param>
/// <param name="fillHoles">List of fill hole flags for DICOM-RT.</param>
/// <param name="roiInterpretedType">List of roiInterpretedType for DICOM-RT.</param>
/// <param name="debugFolderName">If present, create a full set of debug images.</param>
/// <param name="testVolumesMatch">If true, check the volumes match.</param>
/// <param name="expectedNiftiFilename">Expect volume to match Nifti file.</param>
public static void DoTestNiftiToDicom(
string niftiFilename,
string referenceSeries,
string[] structureNames,
RGBColorOption?[] structureColors,
bool?[] fillHoles,
ROIInterpretedType[] roiInterpretedTypes,
string debugFolderName,
bool testVolumesMatch,
string expectedNiftiFilename)
{
var outputFileName = Path.GetRandomFileName() + ".dcm";
RTConverters.ConvertNiftiToDicom(
niftiFilename,
referenceSeries,
structureNames,
structureColors,
fillHoles,
roiInterpretedTypes,
outputFileName,
"modelX:1",
"manufacturer",
"interpreter");
// Open the newly created DICOM-RT file
var dicomRTFile = DicomFile.Open(outputFileName);
// Get the medical volume from the reference
var acceptanceTests = new ModerateGeometricAcceptanceTest(string.Empty, string.Empty);
var referenceMedicalVolumes = MedIO.LoadAllDicomSeriesInFolderAsync(referenceSeries, acceptanceTests).Result;
Assert.AreEqual(1, referenceMedicalVolumes.Count);
var referenceMedicalVolume = referenceMedicalVolumes.First().Volume;
var referenceIdentifiers = referenceMedicalVolume.Identifiers.First();
// Extract the RTStruct from the DICOM-RT file
var reloaded = RtStructReader.LoadContours(
dicomRTFile.Dataset,
referenceMedicalVolume.Volume.Transform.DicomToData,
referenceIdentifiers.Series.SeriesInstanceUid,
referenceIdentifiers.Study.StudyInstanceUid);
Assert.IsNotNull(reloaded);
var reloadedRTStruct = reloaded.Item1;
Assert.AreEqual(referenceIdentifiers.Patient.Id, reloadedRTStruct.Patient.Id);
Assert.AreEqual(referenceIdentifiers.Study.StudyInstanceUid, reloadedRTStruct.Study.StudyInstanceUid);
Assert.AreEqual(DicomRTSeries.RtModality, reloadedRTStruct.RTSeries.Modality);
// Load the nifti file
var sourceVolume = MedIO.LoadNiftiAsByte(expectedNiftiFilename);
// Split this volume from segment id to a set of mask volumes
var labels = VolumeMetadataMapper.MultiLabelMapping(sourceVolume, structureNames.Length);
// Make tuples of mask volume, color, names, fill holes.
var volumesWithMetadata = VolumeMetadataMapper.MapVolumeMetadata(labels, structureNames, structureColors, fillHoles, roiInterpretedTypes).ToArray();
Assert.AreEqual(structureNames.Length, reloadedRTStruct.Contours.Count);
for (int i = 0; i < reloadedRTStruct.Contours.Count; i++)
{
var contourVolumes = new Volume3D <byte>(
referenceMedicalVolume.Volume.DimX,
referenceMedicalVolume.Volume.DimY,
referenceMedicalVolume.Volume.DimZ,
referenceMedicalVolume.Volume.SpacingX,
referenceMedicalVolume.Volume.SpacingY,
referenceMedicalVolume.Volume.SpacingZ,
referenceMedicalVolume.Volume.Origin,
referenceMedicalVolume.Volume.Direction);
contourVolumes.Fill(reloadedRTStruct.Contours[i].Contours, (byte)1);
var v = volumesWithMetadata[i];
if (!string.IsNullOrWhiteSpace(debugFolderName))
{
for (var z = 0; z < referenceMedicalVolume.Volume.DimZ; z++)
{
var actualFileName = Path.Combine(debugFolderName, "actual", $"slice_{v.name}_{z}.png");
var actualSlice = contourVolumes.Slice(SliceType.Axial, z);
actualSlice.SaveBinaryMaskToPng(actualFileName);
var expectedFileName = Path.Combine(debugFolderName, "expected", $"slice_{v.name}_{z}.png");
var expectedSlice = v.volume.Slice(SliceType.Axial, z);
expectedSlice.SaveBinaryMaskToPng(expectedFileName);
}
}
if (testVolumesMatch)
{
VolumeAssert.AssertVolumesMatch(v.volume, contourVolumes, $"Loaded mask {i}");
}
Assert.AreEqual(v.name, reloadedRTStruct.Contours[i].StructureSetRoi.RoiName, $"Loaded mask name {i}");
var expectedColor = Tuple.Create(v.color.R, v.color.G, v.color.B);
Assert.AreEqual(expectedColor, reloadedRTStruct.Contours[i].DicomRtContour.RGBColor, $"Loaded color {i}");
}
}