% Small edits to the EEGLAB file
%
% reref() - convert common reference EEG data to some other common reference
%           or to average reference
% Usage:
%   >> Dataout = reref(data);  % convert all channels to average reference
%   >> [Dataout Chanlocs] = reref(data, refchan, 'key', 'val');
%                              % convert data to new reference with options
% Inputs:
%   data - 2-D or 3-D data matrix (chans,frames*epochs) 
%   refchan  - reference channel number(s). There are three possibilities:
%          1) [] -  compute average reference
%          2) [X]: re-reference to channel X 
%          2) [X Y Z ...]: re-reference to the average of channel X Y Z ... 
% 
% Optional inputs:
%   'exclude'    - [integer array] channel indices to exclude from re-referencing
%                  (e.g., event marker channels, etc.)
%   'keepref'    - ['on'|'off'] keep reference channel in output (only usable 
%                  when there are several references).
%   'elocs'      - Current data electrode location structure (e.g., EEG.chanlocs).
%   'refloc'     - Reference channel location single element structure or cell array
%                  {'label' theta radius} containing the name and polar coordinates 
%                  of the current channel. Including this entry means that
%                  this channel will be included (reconstructed) in the
%                  output.
%
% Outputs:
%   Dataout     - Input data converted to the new reference
%   Chanlocs    - Updated channel locations structure
%
% Notes: 1) The average reference calculation implements two methods 
%           (see www.egi.com/Technotes/AverageReference.pdf)
%            V'i = (Vi-Vref) - sum(Vi-Vref)/number_of_electrodes
%
% Authors: Arnaud Delorme, SCCN/INC/UCSD, La Jolla, 2009-
%          previous version: Arnaud Delorme & Scott Makeig, 1999-2002

% Deprecated inputs:
% These inputs are still accepted but not processed. The function returns
% accurate results irrespective of the entry of these options.
%   'refstate  ' - ['common'|'averef'|[indices]] Current reference condition,
%                  ('averef') = average reference; ('common' or 0) = common
%                  reference. [indices] designate the current reference channel 
%                  or channels if present in the data {default: 'common'}
%   'method'     - ['standard'|'withref'] Do not ('standard') or do ('withref') 
%                  include reference channel data in output {def: 'standard'}. 
%                  Note: Option 'withref' not possible when multiple ref channel 
%                  indices are given as argument to 'refstate' (below).
%
% ICA inputs:
% These inputs are still accepted but not the ICA conversion is now
% performed from within pop_reref()
%   'icaweights' - ICA weight matrix. Note: If this is ICA weights*sphere, 
%                  then the 'icasphere' input below should be [] or identity.
%   'icasphere'  - ICA sphere matrix (if any)
%   'icachansind' - Indices of the channels used in ICA decomposition
%
% Outputs:
%   Wout        - ICA weight matrix (former icaweights*icasphere)
%                 converted to new data reference
%   Sout        - ICA sphere matrix converted to an identity matrix
%   ICAinds     - New indices of channels used in ICA decomposition
%   meandata    - (1,dataframes) means removed from each data point
%
%        2) In conversion of the weight matrix to a new reference
%           where WS = Wts*Sph  and  ica_act = WS*data, then
%              data = inv(WS)*ica_act;
%           If R*data are the re-referenced data,
%              R*data= R*inv(WS)*ica_act;   
%           And Wout = inv(R*inv(WS));
%           Now, Sout = eye(length(ICAinds));
%           The re-referenced ICA component maps are now the 
%           columns of inv(Wout), and the icasphere matrix, Sout, 
%           is an identity matrix. Note: inv() -> pinv() when 
%           PCA dimension reduction is used during ICA decomposition.

%123456789012345678901234567890123456789012345678901234567890123456789012

% Copyright (C) 1999 Scott Makeig, SCCN/INC/UCSD, scott@sccn.ucsd.edu
%
% This program is free software; you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software Foundation; either version 2 of the License, or
% (at your option) any later version.
%
% This program is distributed in the hope that it will be useful,
% but WITHOUT ANY WARRANTY; without even the implied warranty of
% MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
% GNU General Public License for more details.
%
% You should have received a copy of the GNU General Public License
% along with this program; if not, write to the Free Software
% Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

% $Log: reref.m,v $
% Revision 1.38  2009/06/28 06:33:38  arno
% Fixing rereferencing futher
%
% Revision 1.37  2009/06/28 05:49:56  arno
% Adding reference and reprogramming pop_chanedit
%
% Revision 1.36  2007/05/22 13:57:36  arno
% double reference
%
% Revision 1.35  2007/02/16 20:12:16  scott
% added electrode(s) for completeness -sm
%
% Revision 1.34  2007/02/16 19:55:30  toby
% error message formatting
%
% Revision 1.33  2007/02/16 17:22:06  scott
% clarified help msg -- with major ??? remaining ! -sm
%
% Revision 1.32  2006/10/02 11:36:56  arno
% fix excluding channels
%
% Revision 1.30  2006/05/04 10:33:54  arno
% fixing last changes when not all channels are used for ICA
%
% Revision 1.28  2004/11/05 18:29:16  arno
% fixing channel label problem
%
% Revision 1.27  2003/12/11 17:55:22  arno
% remove debug msg
%
% Revision 1.26  2003/10/14 17:13:36  arno
% *** empty log message ***
%
% Revision 1.25  2003/10/14 17:12:07  arno
% *** empty log message ***
%
% Revision 1.24  2003/10/14 17:11:25  arno
% *** empty log message ***
%
% Revision 1.23  2003/07/29 18:39:59  arno
% debuging empty channel location structure
%
% Revision 1.22  2003/07/29 16:58:18  arno
% debuging exclude
%
% Revision 1.21  2003/07/28 16:44:26  arno
% allowing to include current ref channel
%
% Revision 1.20  2003/07/27 00:59:49  arno
% debuging re-referencing
%
% Revision 1.19  2003/07/26 01:13:56  arno
% debuging reref to several channels
%
% Revision 1.18  2003/07/26 00:01:32  arno
% brand new function
%
% Revision 1.17  2003/07/02 01:07:41  arno
% debug input check
%
% Revision 1.16  2003/06/11 00:10:27  arno
% debug multiple references
%
% Revision 1.15  2002/11/15 03:00:17  arno
% same
%
% Revision 1.14  2002/11/15 02:59:34  arno
% header for web
%
% Revision 1.13  2002/11/15 01:44:44  scott
% can not -> cannot
%
% Revision 1.12  2002/11/15 01:41:04  arno
% header for web
%
% Revision 1.11  2002/11/14 18:14:02  arno
% updating elocs parameter filter
%
% Revision 1.10  2002/11/13 23:04:41  arno
% removing extra electrode in average ref
%
% Revision 1.9  2002/11/13 22:28:57  arno
% removing the average reference with original common reference
%
% Revision 1.8  2002/11/13 20:29:41  arno
% debugging
%
% Revision 1.7  2002/11/13 15:12:21  scott
% help msg
%
% Revision 1.6  2002/11/13 15:08:40  scott
% help msg
%
% Revision 1.5  2002/11/12 23:32:59  arno
% debugging old ref channel potential
%
% Revision 1.4  2002/11/12 23:22:47  arno
% header typo
%
% Revision 1.3  2002/11/12 19:08:02  arno
% debugging
%
% Revision 1.2  2002/11/12 18:43:31  arno
% debug
%
% Revision 1.1  2002/11/12 17:58:08  arno
% Initial revision
%
% Revision 1.7  2002/09/05 00:30:23  scott
% added meandata output -sm
%
% Revision 1.6  2002/08/21 02:08:19  arno
% nothing
%
% Revision 1.5  2002/08/21 02:03:32  arno
% debugging ica reref
%
% Revision 1.4  2002/08/21 00:21:51  arno
% debugging
%
% Revision 1.3  2002/04/11 18:37:33  scott
% revised help msg
%
% Revision 1.2  2002/04/11 18:02:03  arno
% computing average reference of components
%
% Revision 1.1  2002/04/05 17:36:45  jorn
% Initial revision
%

% 12/16/99 Corrected denomiator on the suggestion of Ian Nimmo-Smith, Cambridge UK
% 01-25-02 reformated help & license -ad 

function [data, Elocs, morechans, W, S, icachansind, meandata] = h_reref(data, ref, varargin)

if nargin<1
  help reref
  return
end
if nargin < 2
    ref = [];
end;

% check inputs
% ------------
g = finputcheck(varargin, { 'icaweight'   'real'    []          [];
                            'icaweights'  'real'    []          [];
                            'icasphere'   'real'    []          [];
                            'icachansind' 'integer'    []       [];
                            'method'     'string'  { 'standard' 'withref' }  'standard';
                            'refstate'   { 'string' 'integer' } { { 'common' 'averef' } [1 size(data,1)] }     'common'; % ot used but kept for backward compatib.
                            'exclude'    'integer' [1 size(data,1)]          [];
                            'refloc'     { 'cell' 'struct' }  { [] [] }   {};
                            'keepref'    'string'  {'on' 'off' }             'off';
                            'elocs'      {'integer' 'struct'}  []            [] });
if isstr(g), error(g); end;
if ~isempty(g.icaweight)
    g.icaweights = g.icaweight;
end;
if ~isempty(g.icaweights)
    if isempty(g.icachansind), 
        g.icachansind = [1:size(g.icaweights,2)]; 
        disp('Warning: reref() output has changed slightly since EEGLAB 5.02');
        disp('         the 4th output argument is the indices of channels used for ICA instead');
        disp('         of the mean reference value (which is now output argument 5)');
    end;
end;

if ~isempty(ref)
    if ref > size(data,1)
        error('reference channel index out of range');
    end;
end;

[dim1 dim2 dim3] = size(data);
data = reshape(data, dim1, dim2*dim3);

% single reference not present in the data
% add it as blank data channel at the end
% ----------------------------------------
if ~isempty(g.refloc) == 1
    data(end+1,:) = 0;
    if ~isempty(g.elocs)
        if iscell(g.refloc)
            g.elocs(end+1).labels = g.refloc{1};
            g.elocs(end  ).theta  = g.refloc{2};
            g.elocs(end  ).radius = g.refloc{3};
        else
            g.elocs(end+1).labels = g.refloc.labels;
            fieldloc = fieldnames(g.refloc);
            for ind = 1:length(fieldloc)
                g.elocs(end) = setfield(g.elocs(end), fieldloc{ind}, getfield(g.refloc, fieldloc{ind}));
            end;
        end;
    end;
    [dim1 dim2 dim3] = size(data);
end;

% exclude some channels
% ---------------------
chansin   = setdiff([1:dim1], g.exclude);
nchansin  = length(chansin);

% return mean data
% ----------------
if nargout > 4
    meandata = sum(data(chansin,2))/nchansin;
end;

% generate rereferencing matrix
% -----------------------------
if ~isempty(ref) % not average reference   
    refmatrix = eye(nchansin); % begin with identity matrix
    for index = 1:length(ref)
        refmatrix(:,ref(index)) = refmatrix(:,ref(index))-1/length(ref);
    end;
else % compute average reference
    refmatrix = eye(nchansin)-ones(nchansin)*1/nchansin;
end;
chansout = chansin;
data(chansout,:) = refmatrix*data(chansin,:);

% change reference in elocs structure
% -----------------------------------
if ~isempty(g.elocs)
    if isempty(ref)
        for ind = chansin
            g.elocs(ind).ref = 'average';
        end;
    else
        reftxt = { g.elocs(ref).labels };
        if length(reftxt) == 1, reftxt = reftxt{1}; end;
        for ind = chansin
            g.elocs(ind).ref = reftxt;
        end;
    end;
end;

% remove reference
% ----------------
morechans = [];
if strcmpi(g.keepref, 'off')
    data(ref,:) = [];
    if ~isempty(g.elocs)
        morechans = g.elocs(ref);
        g.elocs(ref) = [];
    end;
end;

data = reshape(data, size(data,1), dim2, dim3);

% treat optional ica parameters
% -----------------------------
W = []; S = []; icachansind = [];
if ~isempty(g.icaweights) 
    disp('Warning: This function does not process ICA array anymore, use the pop_reref function instead');
end;
Elocs = g.elocs;