public void SanitizeDicomLongStringTest()
{
var testCases = new List <(bool IsValidAlready, string Text, string Expected)>
{
(false, "12\\34", "12/34"),
(true, "abcd/efg", "abcd/efg"),
(true, null, null),
(false, new string('a', NiiToDicomHelpers.MaxDicomLongStringLength * 2), new string('a', NiiToDicomHelpers.MaxDicomLongStringLength))
};
foreach (var(isValidAlready, text, expected) in testCases)
{
Assert.AreEqual(isValidAlready, NiiToDicomHelpers.IsValidDicomLongString(text), $"Validity check before conversion on {text}");
var actual = NiiToDicomHelpers.SanitizeDicomLongString(text);
Assert.IsTrue(NiiToDicomHelpers.IsValidDicomLongString(actual), $"Should be valid after conversion on {text}");
Assert.AreEqual(expected, actual, "Conversion result does not match expected");
}
}
public void MaskToContourCheck(int trueForeground,
int renderedForeground,
int?maxAbsoluteDifference,
double?maxRelativeDifference,
bool isAccepted)
{
if (isAccepted)
{
NiiToDicomHelpers.CheckContourRendering(trueForeground, renderedForeground,
maxAbsoluteDifference, maxRelativeDifference, string.Empty);
}
else
{
var messagePrefix = "foo";
var exception = Assert.Throws <InvalidOperationException>(() =>
NiiToDicomHelpers.CheckContourRendering(trueForeground, renderedForeground,
maxAbsoluteDifference, maxRelativeDifference, messagePrefix));
Assert.IsTrue(exception.Message.Contains(messagePrefix));
}
}
public void VolumeToDicomAndBack()
{
var outputFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, "DicomOutput");
if (Directory.Exists(outputFolder))
{
Directory.Delete(outputFolder, recursive: true);
Thread.Sleep(1000);
}
Directory.CreateDirectory(outputFolder);
var scan = new Volume3D <short>(5, 5, 5);
foreach (var index in scan.Array.Indices())
{
scan.Array[index] = (short)index;
}
// Create 3 structures, each with a different color
var masks = new List <ContourRenderingInformation>();
var colors = new[]
{
new RGBColor(255, 0, 0),
new RGBColor(0, 255, 0),
new RGBColor(0, 0, 255),
};
foreach (var index in Enumerable.Range(0, 3))
{
var mask = scan.CreateSameSize <byte>();
mask[index + 1, index + 1, index + 1] = 1;
masks.Add(new ContourRenderingInformation($"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");
}
/// <summary>
/// Common code for planar Nifti to DICOM-RT tests.
/// </summary>
/// <param name="sourceMaskFilename">Source mask filename.</param>
/// <param name="expectedMaskFilename">Optional expected mask filename if not the same as source.</param>
/// <param name="fillHoles">Fill holes flag.</param>
/// <param name="debugFolderName">Optional folder name for debug images.</param>
public static void CommonTestNiftiToDicomFillHoles(string sourceMaskFilename, string expectedMaskFilename, bool?fillHoles, string debugFolderName)
{
// Create the Nifti file as a NxMx1 volume
var sourceMaskVolume2D = ExtractContourTests.LoadMask(sourceMaskFilename);
Assert.IsTrue(sourceMaskVolume2D.Array.Any(x => x == 0));
Assert.IsTrue(sourceMaskVolume2D.Array.Any(x => x == 1));
var dimZ = 2;
var sourceVolume3D = sourceMaskVolume2D.Extrude(dimZ, 1.0);
var niftiFile = TestHelpers.CreateTempNiftiName(NiftiCompression.GZip);
MedIO.SaveNifti(sourceVolume3D, niftiFile);
// Create the reference DICOM files.
var referenceDicomFolder = Path.Combine(TestContext.CurrentContext.TestDirectory, "ReferenceDicom");
if (Directory.Exists(referenceDicomFolder))
{
Directory.Delete(referenceDicomFolder, recursive: true);
Thread.Sleep(1000);
}
Directory.CreateDirectory(referenceDicomFolder);
var scan = new Volume3D <short>(sourceVolume3D.DimX, sourceVolume3D.DimY, sourceVolume3D.DimZ);
foreach (var index in scan.Array.Indices())
{
scan.Array[index] = (short)index;
}
var seriesDescription = "description";
var patientID = DicomUID.Generate().UID;
var studyInstanceID = DicomUID.Generate().UID;
var dicomFiles = NiiToDicomHelpers.ScanToDicomInMemory(scan, ImageModality.CT, seriesDescription, patientID, studyInstanceID, null);
var dicomFilesOnDisk = new List <string>();
foreach (var dicomFile in dicomFiles)
{
dicomFilesOnDisk.Add(dicomFile.SaveToFolder(referenceDicomFolder));
}
// Turn the expected mask into a volume.
var expectedNiftiFile = string.Empty;
if (!string.IsNullOrEmpty(expectedMaskFilename))
{
var expectedMask = ExtractContourTests.LoadMask(expectedMaskFilename);
var expectedVolume = expectedMask.Extrude(dimZ, 1.0);
expectedNiftiFile = TestHelpers.CreateTempNiftiName(NiftiCompression.GZip);
MedIO.SaveNifti(expectedVolume, expectedNiftiFile);
}
else
{
// Expected is the same as the source.
expectedNiftiFile = niftiFile;
}
DoTestNiftiToDicom(
niftiFile,
referenceDicomFolder,
new[] { "background", "foreground" },
new RGBColorOption?[] { new RGBColorOption(0xFF, 0x00, 0x00), new RGBColorOption(0x00, 0xFF, 0x00) },
new[] { fillHoles, fillHoles },
new[] { ROIInterpretedType.ORGAN, ROIInterpretedType.CTV },
debugFolderName,
true,
expectedNiftiFile);
}
