public void WritingInvalidExtension()
{
var file = @"C:\temp\nonsense.ni";
var ex = Assert.Catch(() => MedIO.SaveNifti(image, file));
Assert.IsTrue(ex.Message.Contains("filenames must end with"));
Assert.IsTrue(ex.Message.Contains(file));
}
public void WritingInvalidFile()
{
var file = "XYZ:/somegarbage.nii.gz";
var ex = Assert.Catch(() => MedIO.SaveNifti(image, file), "Writing to a nonsensical path should fail");
Assert.IsTrue(ex.Message.Contains(file));
Assert.IsTrue(ex.Message.Contains("writing to file"));
}
public void NiftiSaveShort(NiftiCompression niftiCompression)
{
var volume = TestHelpers.SingleSlice(Enumerable.Range(0, 9).Select(b => (short)b).ToArray());
var file = TestHelpers.CreateTempNiftiName(niftiCompression);
MedIO.SaveNifti(volume, file);
var loadedVolume = MedIO.LoadNiftiAsShort(file);
VolumeAssert.AssertVolumesMatch(volume, loadedVolume);
}
public void WritingToFileAndReading(string extension)
{
var file = Path.GetTempFileName() + extension;
MedIO.SaveNifti(image, file);
var image2 = MedIO.LoadNiftiAsByte(file);
Assert.AreEqual(image.DimX, image2.DimX);
Assert.AreEqual(image.DimY, image2.DimY);
Assert.AreEqual(image.DimZ, image2.DimZ);
File.Delete(file);
}
public void ReadniftiAndSave()
{
var tempRandomNiftyFilePath = GetTempNiftiFileName();
var medimage3D = MedIO.LoadNiftiAsFloat(TestData.GetFullImagesPath(@"vol_int16.nii.gz"));
Assert.IsNotNull(medimage3D);
Assert.AreEqual(3, medimage3D.Dimensions);
MedIO.SaveNifti(medimage3D, tempRandomNiftyFilePath);
var savedMedimage3D = MedIO.LoadNiftiAsFloat(tempRandomNiftyFilePath);
Assert.AreEqual(medimage3D.Origin, savedMedimage3D.Origin);
Assert.AreEqual(medimage3D.Array, savedMedimage3D.Array);
}
public void LoadingInvalidExtensions()
{
const string validExtension = ".nii";
const string invalidExtension = ".ni";
var basePath = Path.GetTempFileName();
var validPath = basePath + validExtension;
var invalidPath = basePath + invalidExtension;
// Can't save with invalid extension, so save with valid extension and rename.
MedIO.SaveNifti(image, validPath);
File.Move(validPath, invalidPath);
var ex = Assert.Catch(() => MedIO.LoadNiftiAsFloat(invalidPath));
Assert.IsTrue(ex.Message.Contains("filenames must end with"));
Assert.IsTrue(ex.Message.Contains(invalidPath));
}
/// <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);
}
