/// <summary>
/// Converts a multi-label map to a set of binary volumes. If a voxel has value v in the
/// input image, v >= 1, then the (v-1)th result volume will have set that voxel to 1.
/// Put another way: The i.th result volume will have voxels non-zero wherever the input
/// volume had value (i+1).
/// </summary>
/// <param name="image">A multi-label input volume.</param>
/// <param name="numOutputMasks">The number of result volumes that will be generated.
/// This value must be at least equal to the maximum voxel value in the input volume.</param>
/// <returns></returns>
public static Volume3D <byte>[] MultiLabelMapping(Volume3D <byte> image, int numOutputMasks)
{
var result = new Volume3D <byte> [numOutputMasks];
for (var i = 0; i < numOutputMasks; i++)
{
result[i] = image.CreateSameSize <byte>();
}
for (var i = 0; i < image.Length; ++i)
{
if (image[i] != 0 && image[i] <= numOutputMasks)
{
result[image[i] - 1][i] = 1;
}
}
return(result);
}
public void VolumeToDicomAndBack()
{
var outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, "DicomOutput");
if (Directory.Exists(outputFolder))
{
Directory.Delete(outputFolder, recursive: true);
Thread.Sleep(1000);
}
Directory.CreateDirectory(outputFolder);
var scan = new Volume3D <short>(5, 5, 5);
foreach (var index in scan.Array.Indices())
{
scan.Array[index] = (short)index;
}
// Create 3 structures, each with a different color
var masks = new List <ContourRenderingInformation>();
var colors = new[]
{
new RGBColor(255, 0, 0),
new RGBColor(0, 255, 0),
new RGBColor(0, 0, 255),
};
foreach (var index in Enumerable.Range(0, 3))
{
var mask = scan.CreateSameSize <byte>();
mask[index + 1, index + 1, index + 1] = 1;
masks.Add(new ContourRenderingInformation($"structure_{index}", colors[index], mask));
}
var seriesDescription = "description";
var patientId = DicomUID.Generate().UID;
var studyId = DicomUID.Generate().UID;
var dicomFiles = NiiToDicomHelpers.ScanAndContoursToDicom(scan, ImageModality.CT, masks,
seriesDescription, patientId, studyId);
// Write to disk, so that we can load it into the App as well
var dicomFilesOnDisk = new List <string>();
foreach (var dicomFile in dicomFiles)
{
dicomFilesOnDisk.Add(dicomFile.SaveToFolder(outputFolder));
}
// Test if the first returned Dicom file is really the RTStruct
var rtStructFromFile = RtStructReader.LoadContours(dicomFilesOnDisk[0], scan.Transform.DicomToData);
Assert.IsNotNull(rtStructFromFile);
Assert.AreEqual(masks.Count, rtStructFromFile.Item1.Contours.Count);
var fromDisk = NiiToDicomHelpers.MedicalVolumeFromDicomFolder(outputFolder);
VolumeAssert.AssertVolumesMatch(scan, fromDisk.Volume, "Loaded scan does not match");
Assert.AreEqual(seriesDescription, fromDisk.Identifiers.First().Series.SeriesDescription);
Assert.AreEqual(patientId, fromDisk.Identifiers.First().Patient.Id);
Assert.AreEqual(studyId, fromDisk.Identifiers.First().Study.StudyInstanceUid);
foreach (var index in Enumerable.Range(0, fromDisk.Struct.Contours.Count))
{
var loadedMask = fromDisk.Struct.Contours[index].Contours.ToVolume3D(scan);
VolumeAssert.AssertVolumesMatch(masks[index].Contour.ToVolume3D(scan), loadedMask, $"Loaded mask {index}");
Assert.AreEqual(masks[index].Name, fromDisk.Struct.Contours[index].StructureSetRoi.RoiName, $"Loaded mask name {index}");
}
// Now test if we can ZIP up all the Dicom files, and read them back in.
var zippedDicom = ZippedDicom.DicomFilesToZipArchive(dicomFiles);
var dicomFromZip = ZippedDicom.DicomFilesFromZipArchive(zippedDicom);
var volumeFromZip = NiiToDicomHelpers.MedicalVolumeFromDicom(dicomFromZip.ToList());
VolumeAssert.AssertVolumesMatch(scan, volumeFromZip.Volume, "Scan from Zip archive does not match");
Assert.AreEqual(masks.Count, volumeFromZip.Struct.Contours.Count, "RtStructs from Zip do not match");
}