public void GZipTest()
{
string hdr1 = Path.Combine("resources", "avg152T1_LR_nifti.hdr");
string hdr2 = Path.Combine("resources", "avg152T1_LR_nifti.hdr.gz");
Assert.IsFalse(NiftiFile.IsCompressed(hdr1));
Assert.IsTrue(NiftiFile.IsCompressed(hdr2));
string nii1 = Path.Combine("resources", "avg152T1_LR_nifti.nii");
string nii2 = Path.Combine("resources", "avg152T1_LR_nifti.nii.gz");
var nifti1 = NiftiFile.Read(nii1);
var nifti2 = NiftiFile.Read(nii2);
Assert.IsTrue(nifti1.Data.Length == nifti2.Data.Length);
Assert.IsTrue(nifti1.Data[100] == nifti2.Data[100]);
Assert.IsTrue(nifti1.Header.sizeof_hdr == nifti2.Header.sizeof_hdr);
Assert.IsTrue(nifti1.Header.slice_start == nifti2.Header.slice_start);
var tmp = "tmp.nii.gz";
NiftiFile.Write(nifti1, tmp, gzip: true);
Assert.IsTrue(File.Exists(tmp));
File.Delete(tmp);
}
public void TestBadFormat()
{
string path = Path.Combine("resources", "gato.nii");
Assert.IsFalse(NiftiFile.IsCompressed(path));
try
{
_ = NiftiFile.ReadHeader(path);
Assert.Fail("Failed to fail.");
}
catch (InvalidDataException) {}
catch (Exception e)
{
Assert.Fail("Hmmm... " + e.Message);
}
try
{
_ = NiftiFile.Read(path);
Assert.Fail("Failed to fail.");
}
catch (InvalidDataException) { }
catch (Exception e)
{
Assert.Fail("Hmmm..." + e.Message);
}
}
public void ReadHdr()
{
string file = Path.Combine("resources", "avg152T1_LR_nifti.hdr");
var hdr = NiftiFile.ReadHeader(file);
Assert.IsTrue((hdr.sizeof_hdr == 348 && !hdr.SourceIsBigEndian()) || hdr.SourceIsBigEndian());
}
public void ReadNii()
{
string file = Path.Combine("resources", "avg152T1_LR_nifti.nii");
var nifti = NiftiFile.Read(file);
Assert.IsTrue(nifti.Header.sizeof_hdr == 348 || nifti.Header.SourceIsBigEndian());
}
public void ColorConversion()
{
var niiFile = Path.Combine("resources", "minimal.nii.gz");
var tmp = "color_pattern.nii";
var nifti = NiftiFile.Read(niiFile);
var colors = new Color[nifti.Data.Length];
for (int i = 0; i < colors.Length; ++i)
{
colors[i] = Color.FromArgb(i % 256, (i / 2) % 256, (i / 4) % 256);
}
nifti.Data = colors;
System.Console.WriteLine(nifti.Header.datatype);
System.Console.WriteLine(nifti.Header.data_type);
// Write color data
NiftiFile.Write(nifti, tmp);
var tmp2 = tmp + ".2.nii";
// Copy and check that size hasn't changed
NiftiFile.Write(NiftiFile.Read(tmp), tmp2);
Assert.AreEqual(new System.IO.FileInfo(tmp).Length, new System.IO.FileInfo(tmp2).Length);
// Remove these lines to check output files
File.Delete(tmp);
File.Delete(tmp2);
}
public void ReadHdrImg()
{
var file = Path.Combine("resources", "minimal.hdr.gz");
var nifti1 = NiftiFile.Read(file);
var niiFile = Path.Combine("resources", "minimal.nii.gz");
var nifti2 = NiftiFile.Read(niiFile);
Assert.IsTrue(nifti1.Data.Length == nifti2.Data.Length);
Assert.IsTrue(nifti1.Data[100] == nifti2.Data[100]);
Assert.IsTrue(nifti1.Header.sizeof_hdr == nifti2.Header.sizeof_hdr);
Assert.IsTrue(nifti1.Header.slice_start == nifti2.Header.slice_start);
}
static void Main(string[] args)
{
string inPath;
if (args.Length > 0)
{
inPath = args[0];
}
else
{
Console.WriteLine("Please give path to nii file");
return;
}
Console.WriteLine($"Reading... From {inPath}");
Nifti.NET.Nifti nifti = null;
if (!inPath.EndsWith("ole"))
{
nifti = NiftiFile.Read(inPath);
}
Console.WriteLine($"Completed Nifti generation from {inPath}");
var outPath = string.Empty;
if (args.Length >= 2)
{
outPath = args[1];
}
var filetype = inPath.Split(".")
.Skip(1) // First part is not filetype
.Where(s => !int.TryParse(s, out _)) // ".01." is subversion and should be part of filename
.Aggregate((acc, s) => $"{acc}.{s}");
var filename = inPath.Split("\\/".ToCharArray()).Last().Replace("." + filetype, "");
var jsonPath = $"{outPath}{filename}.json";
if (outPath.EndsWith("json", StringComparison.InvariantCultureIgnoreCase))
{
jsonPath = outPath;
}
Console.WriteLine($"Serializing... To JSON at {jsonPath}");
if (!inPath.EndsWith("ole"))
{
JsonSerialize(nifti, jsonPath);
}
Console.WriteLine($"Done! JSON file at {jsonPath}");
}
public void TestWriteNii()
{
var niiFile = Path.Combine("resources", "minimal.nii.gz");
var tmp = "tmp.nii";
var nifti = NiftiFile.Read(niiFile);
NiftiFile.Write(nifti, tmp);
var nifti2 = NiftiFile.Read(tmp);
Assert.IsTrue(nifti.Header.magic[2] == nifti2.Header.magic[2]);
Assert.IsTrue(nifti.Header.cal_max == nifti2.Header.cal_max);
File.Delete(tmp);
}
public void TestWriteHeader()
{
var niiFile = Path.Combine("resources", "minimal.nii.gz");
var tmp = "tmp.hdr";
var nifti = NiftiFile.Read(niiFile);
NiftiFile.Write(nifti.Header, tmp);
var niftiHdr = NiftiFile.ReadHeader(tmp);
// Maybe we could play with the bits at some point.
// At the moment this will fail.
//Assert.IsTrue(niftiHdr.magic[1] == 0x69);
//Assert.IsTrue(nifti.Header.magic[1] == 0X2B);
Assert.IsTrue(nifti.Header.cal_max == niftiHdr.cal_max);
File.Delete(tmp);
}
public void Index()
{
string fileLR = Path.Combine("resources", "avg152T1_LR_nifti.nii");
var niiLR = NiftiFile.Read(fileLR);
var pos = 0;
for (int k = 0; k < niiLR.Dimensions[2]; ++k)
{
for (int j = 0; j < niiLR.Dimensions[1]; ++j)
{
for (int i = 0; i < niiLR.Dimensions[0]; ++i)
{
var val = niiLR[i, j, k];
pos++;
}
}
}
// TODO: Add more exhastive checks.
Assert.IsTrue(pos == niiLR.Data.Length);
}
public void TestWriteHdrImg()
{
var niiFile = Path.Combine("resources", "minimal.nii.gz");
var tmp = "tmp.hdr";
var nifti = NiftiFile.Read(niiFile);
nifti.Header.magic[1] = 0x69;
NiftiFile.Write(nifti, tmp);
Assert.IsTrue(File.Exists(tmp));
Assert.IsTrue(File.Exists("tmp.img"));
var nifti2 = NiftiFile.Read(tmp);
Assert.IsTrue(nifti.Header.magic[2] == nifti2.Header.magic[2]);
Assert.IsTrue(nifti.Header.cal_max == nifti2.Header.cal_max);
File.Delete(tmp);
File.Delete("tmp.img");
}
