jnifticreate.m

function jnii = jnifticreate(varargin)
%
%    jnii=jnifticreate
%       or
%    jnii=jnifticreate('header1', value1, 'header2', value2, ...)
%    jnii=jnifticreate(img, 'header1', value1, ...)
%
%    Create a default JNIfTI structure with default header and image volume
%
%    author: Qianqian Fang (q.fang <at> neu.edu)
%
%    input:
%        img: set the jnii.NIFTIData section
%        'header_i': the header subfield name defined in the JNIfTI
%                    specification, see https://github.com/NeuroJSON/jnifti
%        value_i: set the value for the specified JNIfTI header field
%
%    output:
%        jnii: without any input, jnii gives the default jnii header
%              if img is given, jnii also includes the NIFTIData field
%
%
%    this file is part of JNIfTI specification: https://github.com/NeuroJSON/jnifti
%
%    License: Apache 2.0, see https://github.com/NeuroJSON/jnifti for details
%

jnii = struct(encodevarname('_DataInfo_'), struct(), 'NIFTIHeader', struct(), 'NIFTIData', []);

% jnii.NIFTIHeader.NIIHeaderSize=  0;
% jnii.NIFTIHeader.A75DataTypeName=   'uint8';
% jnii.NIFTIHeader.A75DBName=      '';
% jnii.NIFTIHeader.A75Extends=     0;
% jnii.NIFTIHeader.A75SessionError='';
% jnii.NIFTIHeader.A75Regular=     0;
jnii.NIFTIHeader.DimInfo.Freq =   0;
jnii.NIFTIHeader.DimInfo.Phase =  0;
jnii.NIFTIHeader.DimInfo.Slice =  0;
jnii.NIFTIHeader.Dim =            [];
jnii.NIFTIHeader.Param1 =         0;
jnii.NIFTIHeader.Param2 =         0;
jnii.NIFTIHeader.Param3 =         0;
jnii.NIFTIHeader.Intent =         '';
jnii.NIFTIHeader.DataType =       'uint8';
jnii.NIFTIHeader.BitDepth =       8;
jnii.NIFTIHeader.FirstSliceID =   1;
jnii.NIFTIHeader.VoxelSize =      [1, 1, 1, 1];
jnii.NIFTIHeader.Orientation =    struct('x', 'r', 'y', 'a', 'z', 's');
% jnii.NIFTIHeader.NIIByteOffset=  0;
jnii.NIFTIHeader.ScaleSlope =     0;
jnii.NIFTIHeader.ScaleOffset =    0;
jnii.NIFTIHeader.LastSliceID =    1;
jnii.NIFTIHeader.SliceType =      '';
jnii.NIFTIHeader.Unit =           struct('L', 'mm', 'T', 's');
jnii.NIFTIHeader.MaxIntensity =   255;
jnii.NIFTIHeader.MinIntensity =   0;
jnii.NIFTIHeader.SliceTime =      1;
jnii.NIFTIHeader.TimeOffset =     0;
% jnii.NIFTIHeader.A75GlobalMax=  255;
% jnii.NIFTIHeader.A75GlobalMin=   0;
jnii.NIFTIHeader.Description =    '';
% jnii.NIFTIHeader.AuxFile=        '';
jnii.NIFTIHeader.QForm =          0;
jnii.NIFTIHeader.SForm =          1;
jnii.NIFTIHeader.Quatern.b =      0;
jnii.NIFTIHeader.Quatern.c =      0;
jnii.NIFTIHeader.Quatern.d =      0;
jnii.NIFTIHeader.QuaternOffset.x = 0;
jnii.NIFTIHeader.QuaternOffset.y = 0;
jnii.NIFTIHeader.QuaternOffset.z = 0;
jnii.NIFTIHeader.Affine(1, :) =    [1 0 0 0];
jnii.NIFTIHeader.Affine(2, :) =    [0 1 0 0];
jnii.NIFTIHeader.Affine(3, :) =    [0 0 1 0];
jnii.NIFTIHeader.Name =           'default';
jnii.NIFTIHeader.NIIFormat =      'jnifti';
% jnii.NIFTIHeader.NIIExtender=    [0,0,0,0];

datainfo.JNIFTIVersion = '0.5';
datainfo.Comment = 'Created by JNIFTY Toolbox (https://github.com/NeuroJSON/jnifty)';
datainfo.AnnotationFormat = 'https://github.com/NeuroJSON/jnifti/blob/master/JNIfTI_specification.md';
datainfo.SerialFormat = 'http://json.org';
datainfo.Parser = struct('Python', [], ...
                         'MATLAB', [], ...
                         'JavaScript', 'https://github.com/NeuroJSON/jsdata', ...
                         'CPP', 'https://github.com/NeuroJSON/json', ...
                         'C', 'https://github.com/NeuroJSON/ubj');
datainfo.Parser.Python = {'https://pypi.org/project/jdata', 'https://pypi.org/project/bjdata'};
datainfo.Parser.MATLAB = {'https://github.com/NeuroJSON/jnifty', 'https://github.com/NeuroJSON/jsonlab'};
jnii.(encodevarname('_DataInfo_')) = datainfo;

if (nargin == 0)
    return
end

img = [];
pid = 1;
if (~ischar(varargin{1}))
    img = varargin{1};
    pid = 2;
end

if (~isempty(varargin))
    for i = pid:2:length(varargin)
        jnii.NIFTIHeader.(varargin{i}) = varargin{i + 1};
    end
end

if (~isnumeric(img) && ~islogical(img))
    error('img input must be a numerical or logical array');
end

jnii.NIFTIHeader.Dim = size(img);
jnii.NIFTIHeader.DataType = class(img);
info = whos('img');
jnii.NIFTIHeader.BitDepth = info.bytes / numel(img) * 8;
jnii.NIFTIHeader.MinIntensity = min(img(:));
jnii.NIFTIHeader.MaxIntensity = max(img(:));

jnii.NIFTIData = img;