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function data = savejsnirf(jnirs, filename, varargin)
%
% savejsnirf(jnirs, outputfile)
% or
% savejsnirf(jnirs, outputfile, 'Param1',value1, 'Param2',value2,...)
%
% Save an in-memory JSNIRF structure into a JSNIRF file with format
% defined in JSNIRF specification: https://github.com/NeuroJSON/jsnirf
%
% author: Qianqian Fang (q.fang <at> neu.edu)
%
% input:
% jnirs: a structure (array) or cell (array). The data structure can
% be completely generic or auxilary data without any JSNIRF
% constructs. However, if a JSNIRF object is included, it shall
% contain the below subfields (can appear within any depth of the
% structure)
% jnirs.SNIRFData - the main image data array
% outputfile: the output file name to the JSNIRF file
% *.bnirs for binary JSNIRF file
% *.jnirs for text JSNIRF file
% *.snirf or *.h5 for HDF5-based SNIRF file
% options: (optional) if saving to a .bnirs file, please see the options for
% savebj.m (part of JSONLab); if saving to .jnirs, please see the
% supported options for savejson.m (part of JSONLab).
%
% dependency:
% - the savejson and savebj functions are provided by the JSONLab
% toolbox at http://github.com/NeuroJSON/jsonlab
% - if data compression is specified by 'compression','zlib' param/value
% pairs, ZMat toolbox will be needed, http://github.com/fangq/zmat
% - the saveh5 function is provided by the eazyh5 toolbox at
% http://github.com/fangq/eazyh5
%
% example:
% jnirs=jsnirfcreate('aux',struct('name','pO2','dataTimeSeries',1:10,'time',1:10));
% savejsnirf(jnirs, 'test.jnirs');
% savejsnirf(jnirs, 'test.bnirs','compression','zlib');
%
% 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
%
if (nargin < 2)
error('you must provide data and output file name');
end
if (~exist('savejson', 'file'))
error('you must first install JSONLab from http://github.com/NeuroJSON/jsonlab/');
end
data = '';
if (regexp(filename, '\.[Jj][Nn][Ii][Rr][Ss]$'))
data = savejson('', jnirs, 'filename', filename, varargin{:});
elseif (regexp(filename, '\.[Bb][Nn][Ii][Rr][Ss]$'))
data = savebj('', jnirs, 'filename', filename, varargin{:});
elseif (~isempty(regexp(filename, '\.[Ss][Nn][Ii][Rr][Ff]$', 'once')) || ~isempty(regexp(outfile, '\.[Hh]5$', 'once')))
saveh5(jnirs, filename, varargin{:});
else
error('file suffix must be .jnirs for text JSNIRF or .bnirs for binary JSNIRF');
end
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