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);
}
static void Main(string[] args)
{
var sw = new Stopwatch();
sw.Start();
if (args.Length < 2)
{
System.Console.WriteLine("Open-Vistarsier requires at least 2 NiftiFiles as input.");
System.Console.WriteLine("Usage: vt [prior nifti] [current nifti] [output-prefix](optional)");
return;
}
var prior = args[0];
var current = args[1];
var outputPrefix = "";
if (args.Length > 2)
{
outputPrefix = args[2];
}
if (!Path.IsPathRooted(prior))
{
prior = Path.GetFullPath(Path.Combine(AppDomain.CurrentDomain.BaseDirectory, prior));
}
if (!Path.IsPathRooted(current))
{
current = Path.GetFullPath(Path.Combine(AppDomain.CurrentDomain.BaseDirectory, current));
}
// Create an MS pipeline.
var pipeline = new MSPipeline(
current,
prior,
current,
true, true, true,
new string[] { outputPrefix + "vt-increase.nii", outputPrefix + "vt-decrease.nii" }, outputPrefix + "vt-prior.nii");
var metrics = pipeline.Process();
// Hack(ish), there's all sorts of to-ing and fro-ing with BMP encoding going on under the hood.
// If we don't do this step the nifti will blue itself.
var nii = new NiftiFloat32().ReadNifti(outputPrefix + "vt-increase.nii");
for (int i = 0; i < nii.Voxels.Length; ++i)
{
nii.Voxels[i] = ToBgr((int)nii.Voxels[i]);
}
nii.WriteNifti(outputPrefix + "vt-increase.nii");
System.Console.WriteLine("Complete:");
System.Console.WriteLine($"Initial brain match : {metrics.BrainMatch}");
System.Console.WriteLine($"Union brain match : {metrics.CorrectedBrainMatch}");
System.Console.WriteLine($"Successful : {metrics.Passed}");
System.Console.WriteLine($"Time to complete : {sw.Elapsed}");
}
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 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);
}
