jsnirfcreate.m

function jsn=jsnirfcreate(varargin)
%
%    jsn=jsnirfcreate
%       or
%    jsn=jsnirfcreate(option)
%    jsn=jsnirfcreate('Format',format,'Param1',value1, 'Param2',value2,...)
%
%    Create an empty JSNIRF data structure defined in the JSNIRF 
%    specification: https://github.com/NeuroJSON/jsnirf or a SNIRF data structure
%    based on https://github.com/fNIRS/snirf
%
%    author: Qianqian Fang (q.fang <at> neu.edu)
%
%    input:
%        option (optional): option can be ignored. If it is a string with a
%             value 'snirf', this creates a default SNIRF data structure;
%             otherwise, a JSNIRF data structure is created.
%        format: same as option.
%        param/value:   a list of name/value pairs specify
%             additional subfields to be stored under the /nirs object.
%
%    output:
%        jsn: a default SNIRF or JSNIRF data structure.
%
%    example:
%        jsn=jsnirfcreate('data',mydata,'aux',myauxdata,'comment','test');
%
%    this file is part of JSNIRF specification: https://github.com/NeuroJSON/jsnirf
%
%    License: GPLv3 or Apache 2.0, see https://github.com/NeuroJSON/jsnirf for details
%

% define empty SNIRF data structure with all required fields

defaultmeta=struct('SubjectID','default','MeasurementDate',datestr(now,29),...
                'MeasurementTime',datestr(now,'hh:mm:ss'),'LengthUnit','mm', ...
                'TimeUnit','s', 'FrequencyUnit','Hz');
defaultsrcmap=struct('sourceIndex',[],'detectorIndex',[],...
              'wavelengthIndex',[],'dataType',1,'dataTypeIndex',1); 
defaultdata=struct('dataTimeSeries',[],'time',[],'measurementList',defaultsrcmap);
defaultaux=struct('name','','dataTimeSeries',[],'time',[],'timeOffset',0);
defaultstim=struct('name','','data',[]);
defaultprobe=struct('wavelengths',[],'sourcePos2D',[],'detectorPos2D',[]);

nirsdata=struct('metaDataTags',defaultmeta,...
                'data',defaultdata,...
                'aux',defaultaux,...
                'stim',defaultstim,...
                'probe',defaultprobe);

% read user specified data fields - will validate format in future updates

if(nargin>1 && bitand(nargin,1)==0)
    for i=1:nargin*0.5
        key=varargin{2*i-1};
        if(strcmpi(key,'format'))
            key='format';
        end
        nirsdata.(key)=varargin{2*i};
    end
end

jsn=struct();

% return either a SNIRF data structure, or JSNIRF data (enclosed in SNIRFData tag)

if((nargin==1 && strcmpi(varargin{1},'snirf')) || ...
   (isfield(nirsdata,'format') && strcmpi(nirsdata.format,'snirf')))
    if(isfield(nirsdata,'format'))
        nirsdata=rmfield(nirsdata,'format');
    end
    jsn=struct('formatVersion','1.0','nirs', nirsdata);
else
    nirsdata.formatVersion='1.0';
    len=length(fieldnames(nirsdata));
    nirsdata=orderfields(nirsdata,[len,1:len-1]);
    jsn=struct('SNIRFData', nirsdata);
end