public void Write()
{
// Read our minimal Nifti file
var nifti = new NiftiFloat32();
nifti.ReadNifti(_minimalNiftiPath);
// Write the minimal Nifti file.
nifti.WriteNifti(_outfile);
// Check that we've written something.
Assert.IsTrue(File.Exists(_outfile), "Nifti file does not exist");
// Read our nifti file back in.
var nifti2 = new NiftiFloat32();
nifti2.ReadNifti(_outfile);
// Delete the old file.
File.Delete(_outfile);
Assert.IsFalse(File.Exists(_outfile), "Nifti file could not be deleted.");
// Check that the dimensions match the expected Nifti file.
nifti.GetDimensions(SliceType.Axial, out var width, out var height, out var nSlices);
Assert.AreEqual(height, 64);
Assert.AreEqual(width, 64);
Assert.AreEqual(nSlices, 10);
}
private void TestForChanges(Func <string, DataReceivedEventHandler, string> func, Func <INifti <float>, DataReceivedEventHandler, INifti <float> > funcNii, string niftiPath)
{
// If anything's gone horribly wrong we'll probably get an exception here.
var nii = func(niftiPath, (d, e) => Console.WriteLine(e.Data));
var nifti = new NiftiFloat32().ReadNifti(nii);
nifti.RecalcHeaderMinMax();
// Quick check to see if the file exists and is sane.
Assert.IsFalse(nifti.Header.cal_min == nifti.Header.cal_max);
// Remove the temp file
File.Delete(nii);
// Read the input nifti file and run the nifti->nifti version.
nifti.ReadNifti(niftiPath);
var outnifti = funcNii(nifti, (d, e) => Console.WriteLine(e.Data));
// Check that there has been some change made to the voxels.
var diff = 0f;
for (int i = 0; i < outnifti.Voxels.Length; ++i)
{
diff += Math.Abs(nifti.Voxels[i] - outnifti.Voxels[i]);
}
// Some change has happened.
Assert.IsFalse(diff == 0);
}
public void Reorient()
{
var nifti = new NiftiFloat32();
nifti.ReadNifti(_minimalNiftiPath);
nifti.Reorient(nifti.Header.dim[2], nifti.Header.dim[3], nifti.Header.dim[1]);
nifti.GetDimensions(SliceType.Axial, out var width, out var height, out var nSlices);
// TODO: Check that this is the expected result.
Assert.AreEqual(height, 10);
Assert.AreEqual(width, 64);
Assert.AreEqual(nSlices, 64);
}
public void WriteRgb()
{
if (File.Exists(_rgbfile))
{
File.Delete(_rgbfile);
}
var nifti = new NiftiFloat32();
nifti.ReadNifti(_minimalNiftiPath);
// Read pixdim from sample file
nifti.ReadNiftiHeader(_minimalNiftiHdrPath);
// set dimensions for new file
nifti.ConvertHeaderToRgb();
nifti.Header.cal_min = 0;
nifti.Header.cal_max = uint.MaxValue * (3 / 4);
// write voxels
//var voxelsSize = nifti.Header.dim[1] * nifti.Header.dim[2] * nifti.Header.dim[3];
//var bytepix = nifti.Header.bitpix / 8;
//nifti.VoxelsBytes = new byte[voxelsSize * bytepix];
const int r = 255;
const int g = 51;
const int b = 204;
for (var x = 0; x < nifti.Header.dim[1]; x++)
{
for (var y = 0; y < nifti.Header.dim[2]; y++)
{
for (var z = 0; z < nifti.Header.dim[3]; z++)
{
nifti.SetPixelRgb(x, y, z, SliceType.Axial, r, g, b);
}
}
}
if (File.Exists(_rgbfile))
{
File.Delete(_rgbfile);
}
nifti.WriteNifti(_rgbfile);
Assert.IsTrue(File.Exists(_rgbfile)); //TODO: More meaningful asserts
File.Delete(_rgbfile);
}
public void RegistrationTest()
{
if (!RuntimeInformation.IsOSPlatform(OSPlatform.Windows))
{
Assert.Inconclusive("Currently uses Windows Binaries");
}
var NiftiA = new NiftiFloat32().ReadNifti(_lrMaskNiftiPath);
var NiftiB = new NiftiFloat32().ReadNifti(_lrNiftiPath);
// Only doing a couple of asserts here. If something horrible goes wrong, we're expecting an exception.
// You can also check the console output to see what the tools reckon.
_ = Registration.ANTSRegistration(NiftiA, NiftiB, (d, e) => Console.WriteLine(e.Data));
var outFile = Registration.ANTSApplyTransforms(_lrMaskNiftiPath, _lrNiftiPath, (d, e) => Console.WriteLine(e.Data));
Assert.IsTrue(File.Exists(outFile), "No out file for ANTSApplyTransforms");
_ = new NiftiFloat32().ReadNifti(outFile);
_ = Registration.CMTKRegistration(NiftiA, NiftiB, (d, e) => Console.WriteLine(e.Data));
outFile = Registration.CMTKResliceUsingPrevious(_lrMaskNiftiPath, _lrNiftiPath, (d, e) => Console.WriteLine(e.Data));
Assert.IsTrue(File.Exists(outFile), "No out file for CMTKResliceUsingPrevious rego");
NiftiA.ReadNifti(outFile);
}
public void WriteRgba()
// TODO: This is currently unsupported (technically RGBA doesn't seem to be part
// of the NifTI 1.1 format, so it will throw an error on the datatype
{
var nifti = new NiftiFloat32();
nifti.ReadNifti(_minimalNiftiPath);
nifti.ConvertHeaderToRgba();
// Read pixdim from sample file
// set dimensions for new file
nifti.Header.dim[1] = 100;
nifti.Header.dim[2] = 80;
nifti.Header.dim[3] = 50;
nifti.Header.cal_min = 0;
nifti.Header.cal_max = uint.MaxValue;
// write voxels
var voxelsSize = nifti.Header.dim[1] * nifti.Header.dim[2] * nifti.Header.dim[3];
nifti.Voxels = new float[voxelsSize];
for (var i = 0; i < voxelsSize; i++)
{
nifti.Voxels[i] = 255;
}
if (File.Exists(_rgbafile))
{
File.Delete(_rgbafile);
}
nifti.WriteNifti(_rgbafile);
Assert.IsTrue(File.Exists(_rgbafile)); //TODO more meaningful asserts.
File.Delete(_rgbafile);
}
public void ReadNifti()
{
// Read the minimal nifti file.
var nifti = new NiftiFloat32();
nifti.ReadNifti(_minimalNiftiPath);
// Check that the dimensions are correct.
nifti.GetDimensions(SliceType.Axial, out var width, out var height, out var nSlices);
Assert.AreEqual(height, 64);
Assert.AreEqual(width, 64);
Assert.AreEqual(nSlices, 10);
//// Read the minimal nifti file.
//var nifti2 = new NiftiRgb48();
//nifti2.ReadNifti(_minimalNiftiPath);
//// Check that the dimensions are correct.
//nifti2.GetDimensions(SliceType.Axial, out var width2, out var height2, out var nSlices2);
//Assert.AreEqual(height2, 64);
//Assert.AreEqual(width2, 64);
//Assert.AreEqual(nSlices2, 10);
//Assert.IsFalse(nifti2.Voxels[10] == 0);
}
