snirfdecode.m

function data=snirfdecode(root, varargin)
%
%    data=snirfdecode(root)
%       or
%    data=snirfdecode(root,type)
%    data=snirfdecode(root,{'nameA','nameB',...})
%
%    Processing an HDF5 based SNIRF data and group indexed datasets into a
%    cell array
%
%    author: Qianqian Fang (q.fang <at> neu.edu)
%
%    input:
%        root: the raw input snirf data structure (loaded from loadh5.m)
%        type: if type is set as a cell array of strings, it restrict the
%              grouping only to the subset of field names in this list;
%              if type is a string as 'snirf', it is the same as setting 
%              type as {'aux','data','nirs','stim','measurementList'}.
%
%    output:
%        data: a reorganized matlab structure. Each SNIRF data chunk is
%              enclosed inside a 'SNIRFData' subfield or cell array.
%
%    example:
%        rawdata=loadh5('mydata.snirf');
%        data=snirfdecode(rawdata);
%
%    this file is part of JSNIRF specification: https://github.com/NeuroJSON/jsnirf
%
%    License: Apache 2.0, see https://github.com/NeuroJSON/jsnirf for details
%

if(nargin<1)
    help snirfdecode;
    return;
end

data=regrouph5(root, varargin{:});

issnirf=1;

if(~isempty(varargin))
    if(ischar(varargin{1}) && strcmpi(varargin{1},'jsnirf'))
        issnirf=0;
    end
end

if(issnirf==0 && isfield(data,'nirs') && isfield(data,'formatVersion') && ~isfield(data,'SNIRFData'))
    data.SNIRFData=data.nirs;
    if(isfield(data.SNIRFData,'data') && isfield(data.SNIRFData.data,'measurementList'))
        data.SNIRFData.data.measurementList=aos2soa(data.nirs.data.measurementList);
    end
    if(iscell(data.nirs))
        for i=1:length(data.nirs)
            data.SNIRFData{i}.formatVersion=data.formatVersion;
            len=length(fieldnames(data.SNIRFData{i}));
            data.SNIRFData{i}=orderfields(data.SNIRFData{i},[len,1:len-1]);
        end
    else
        data.SNIRFData.formatVersion=data.formatVersion;
        len=length(fieldnames(data.SNIRFData));
        data.SNIRFData=orderfields(data.SNIRFData,[len,1:len-1]);
    end
    data=rmfield(data,{'nirs','formatVersion'});
end