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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;
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