/// <summary>
/// Read a Nifti file (or hdr/img pair).
/// </summary>
/// <param name="path"></param>
/// <returns></returns>
public static Nifti Read(string path, short forceType = NiftiHeader.DT_UNKNOWN)
{
Nifti result = new Nifti();
using (var stream = ReadStream(path))
{
var hdr = ReadHeader(stream);
result.Header = hdr;
if (FileType.NII == TypeOf(hdr))
{
result.Data = ReadData(stream, hdr, forceType);
}
}
if (FileType.HDR == TypeOf(result.Header))
{
var imgpath = path.ToLower().Replace(".hdr", ".img");
if (File.Exists(imgpath))
{
using (var stream = ReadStream(imgpath))
{
result.Data = ReadData(stream, result.Header, forceType);
}
}
}
if (TypeOf(result.Header) == FileType.UNKNOWN)
{
throw new InvalidDataException("Not a NIfTI file (no magic bytes)");
}
return(result);
}
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}");
}
/// <summary>
/// Write the Nifti file according to the path.
/// If the Header.magic[1] byte is 0x69 then the file will be split as hdr and img (we will assume the .hdr file is the path).
/// Otherwise the magic[1] should be 0x2B
/// </summary>
/// <param name="nifti"></param>
/// <param name="path"></param>
/// <param name="gzip"></param>
public static void Write(Nifti nifti, string path, bool gzip = false)
{
if (typeof(Color[]) == nifti.Data.GetType())
{
System.Console.WriteLine("Detected Color data. Converting to 24bit RBG representation.");
nifti = ConvertToRGB(nifti);
}
FileType type = TypeOf(nifti.Header);
if (gzip && !path.EndsWith(".gz"))
{
path += ".gz";
}
using (var stream = WriteStream(path, gzip))
{
Write(stream, nifti.Header);
// For a nifti file we can just keep on writing.
if (FileType.NII == type)
{
Write(stream, nifti.Data);
}
stream.Flush();
}
// If the file type is hdr/img we want to split the data.
if (FileType.HDR == type && nifti.Data != null)
{
var newPath = path.Replace(".hdr", ".img");
if (newPath.Equals(path))
{
newPath += ".img";
}
using (var stream = WriteStream(newPath, gzip))
{
Write(stream, nifti.Data);
stream.Flush();
}
}
}
private static Nifti ConvertToRGB(Nifti nifti)
{
// Handle 32bit RGBA data
if (nifti.Header.datatype == NiftiHeader.DT_RGBA32)
{
var bytedata = new byte[nifti.Data.Length * 4];
for (int i = 0; i < bytedata.Length; i += 4)
{
// Convert RGB to uint
bytedata[i] = nifti.Data[i / 4].R;
bytedata[i + 1] = nifti.Data[i / 4].G;
bytedata[i + 2] = nifti.Data[i / 4].B;
bytedata[i + 3] = nifti.Data[i / 4].A;
}
nifti.Data = bytedata;
}
else
{
// Setup the header info in case someone converted from non-color input
nifti.Header.dim[0] = 5; // RGB and RGBA both have 5 dimensions
nifti.Header.dim[4] = 1;
nifti.Header.dim[5] = 1;
nifti.Header.bitpix = 24;
nifti.Header.datatype = NiftiHeader.DT_RGB;
nifti.Header.intent_code = NiftiHeader.NIFTI_INTENT_RGB_VECTOR;
var bytedata = new byte[nifti.Data.Length * 3];
for (int i = 0; i < bytedata.Length; i += 3)
{
// Convert RGB to uint
bytedata[i] = nifti.Data[i / 3].R;
bytedata[i + 1] = nifti.Data[i / 3].G;
bytedata[i + 2] = nifti.Data[i / 3].B;
}
nifti.Data = bytedata;
}
return(nifti);
}
