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function savesnirf(data, outfile, varargin)
%
% savesnirf(snirfdata, fname)
% or
% savesnirf(snirfdata, fname, 'Param1',value1, 'Param2',value2,...)
%
% Load an HDF5 based SNIRF file, and optionally convert it to a JSON
% file based on the JSNIRF specification:
% https://github.com/NeuroJSON/jsnirf
%
% author: Qianqian Fang (q.fang <at> neu.edu)
%
% input:
% snirfdata: a raw SNIRF data, preprocessed SNIRF data or JSNIRF
% data (root object must be SNIRFData)
% fname: the output SNIRF (.snirf) or JSNIRF data file name (.jnirs, .bnirs)
%
% output:
% data: a MATLAB structure with the grouped data fields
%
% example:
% data=loadsnirf('test.snirf');
% savesnirf(data,'newfile.snirf');
%
% 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 || ~ischar(outfile))
error('you must provide data and a file name');
end
opt = varargin2struct(varargin{:});
if (~isfield(opt, 'root'))
opt.rootname = '';
end
if (~isfield(opt, 'variablelengthstring'))
opt.variablelengthstring = 1;
end
if (~isfield(opt, 'rowas1d'))
opt.rowas1d = 1;
end
if (isfield(data, 'SNIRFData'))
data.nirs = data.SNIRFData;
data.formatVersion = data.SNIRFData.formatVersion;
data.nirs = rmfield(data.nirs, 'formatVersion');
data = rmfield(data, 'SNIRFData');
end
if (~isempty(outfile))
if (~isempty(regexp(outfile, '\.[Hh]5$', 'once')))
saveh5(data, outfile, opt);
elseif (~isempty(regexp(outfile, '\.[Ss][Nn][Ii][Rr][Ff]$', 'once')))
if (isfield(data.nirs.data, 'measurementList'))
forceint = {'sourceIndex', 'detectorIndex', 'wavelengthIndex', ...
'dataType', 'dataTypeIndex', 'moduleIndex', ...
'sourceModuleIndex', 'detectorModuleIndex'};
for i = 1:length(forceint)
if (isfield(data.nirs.data.measurementList, forceint{i}))
if (iscell(data.nirs.data.measurementList.(forceint{i})))
data.nirs.data.measurementList.(forceint{i}) = cell2mat(data.nirs.data.measurementList.(forceint{i}));
end
data.nirs.data.measurementList.(forceint{i}) = int32(data.nirs.data.measurementList.(forceint{i}));
end
end
if (length(data.nirs.data.measurementList) == 1 && ...
length(data.nirs.data.measurementList.sourceIndex) > 1)
data.nirs.data.measurementList = soa2aos(data.nirs.data.measurementList);
end
end
if (opt.rowas1d)
force1d.probe = {'wavelengths', 'wavelengthsEmission', 'frequencies', ...
'timeDelays', 'timeDelayWidths', 'momentOrders', 'correlationTimeDelays', ...
'correlationTimeDelayWidths'};
force1d.data = {'time'};
force1d.aux = {'time', 'timeOffset'};
fields = fieldnames(force1d);
for i = 1:length(fields)
for j = 1:length(force1d.(fields{i}))
if (isfield(data.nirs.(fields{i}), force1d.(fields{i}){j}))
if (iscell(data.nirs.(fields{i}).(force1d.(fields{i}){j})))
data.nirs.(fields{i}).(force1d.(fields{i}){j}) = cell2mat(data.nirs.(fields{i}).(force1d.(fields{i}){j}));
end
data.nirs.(fields{i}).(force1d.(fields{i}){j}) = timeseries(data.nirs.(fields{i}).(force1d.(fields{i}){j})(:).');
end
end
end
end
if (isfield(data.nirs, 'probe'))
forcestrarray.probe = {'sourceLabels', 'detectorLabels', 'landmarkLabels'};
forcestrarray.stim = {'dataLabels'};
fields = fieldnames(forcestrarray);
for i = 1:length(fields)
for j = 1:length(forcestrarray.(fields{i}))
if (isfield(data.nirs.(fields{i}), forcestrarray.(fields{i}){j}))
if (iscell(data.nirs.(fields{i}).(forcestrarray.(fields{i}){j})))
data.nirs.(fields{i}).(forcestrarray.(fields{i}){j}) = cell2mat(data.nirs.(fields{i}).(forcestrarray.(fields{i}){j}));
end
data.nirs.(fields{i}).(forcestrarray.(fields{i}){j}) = timeseries(string(data.nirs.(fields{i}).(forcestrarray.(fields{i}){j})(:).'));
end
end
end
end
if (~isempty(regexp(data.formatVersion, '^1\.', 'once')))
if (length(data.nirs.data.measurementList) == 1 && length(data.nirs.data.measurementList.sourceIndex) > 1)
data.nirs.data.measurementList = soa2aos(data.nirs.data.measurementList);
end
end
data.nirs.data = forceindex(data.nirs.data, 'measurementList');
data.nirs = forceindex(data.nirs, 'data');
data.nirs = forceindex(data.nirs, 'stim');
data.nirs = forceindex(data.nirs, 'aux');
saveh5(data, outfile, opt);
elseif (~isempty(regexp(outfile, '\.[Jj][Nn][Ii][Rr][Ss]$', 'once')) || ~isempty(regexp(outfile, '\.[Jj][Ss][Oo][Nn]$', 'once')))
savejson('SNIRFData', data, 'FileName', outfile, opt);
elseif (regexp(outfile, '\.[Mm][Aa][Tt]$'))
save(outfile, 'data');
elseif (regexp(outfile, '\.[Bb][Nn][Ii][Rr][Ss]$'))
savebj('SNIRFData', data, 'FileName', outfile, opt);
else
error('only support .snirf, .h5, .jnirs, .bnirs and .mat files');
end
end
% force adding index 1 to the group name for singular struct and cell
function newroot = forceindex(root, name)
newroot = root;
fields = fieldnames(newroot);
idx = find(ismember(fields, name));
if (~isempty(idx) && length(newroot.(name)) == 1)
newroot.(sprintf('%s1', name)) = newroot.(name);
newroot = rmfield(newroot, name);
fields{idx(1)} = sprintf('%s1', name);
newroot = orderfields(newroot, fields);
end
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