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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
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