% NEWTIMEFTRIALBASELN - Remove baseline power values for single trials in 
%        newtimef. This only remove single trial baseline (not the average
%        baseline). 
%
% Usage:
%   >>  tf = newtimefbaseln(tf, tvals, 'key', val);
%
% Inputs:
%   tf       - [3-D or 4-D array] single-trial spectral estimates
%           [freqs x times x trials] or [channels x freqs x times x trials)
%           The function may also process cell arrays of such inputs.
%   tvals    - [array] time values
%
% Optional inputs: 'baseline', 'basenorm' and 'trialbase'. Same definition 
%  as for newtimef. If trialbase is 'off' this function does nothing.
%
% Outputs:
%   tf        - Baseline correct power (same size as input)
%
% Authors: Arnaud Delorme, SCCN, INC, UCSD, August 2016

% Copyright (C) Arnaud Delorme, SCCN, INC, UCSD, 2016, arno@sccn.ucsd.edu
%
% This file is part of EEGLAB, see http://www.eeglab.org
% for the documentation and details.
%
% Redistribution and use in source and binary forms, with or without
% modification, are permitted provided that the following conditions are met:
%
% 1. Redistributions of source code must retain the above copyright notice,
% this list of conditions and the following disclaimer.
%
% 2. Redistributions in binary form must reproduce the above copyright notice,
% this list of conditions and the following disclaimer in the documentation
% and/or other materials provided with the distribution.
%
% THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
% AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
% IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
% ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
% LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
% CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
% SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
% INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
% CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
% ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF
% THE POSSIBILITY OF SUCH DAMAGE.

function PP = newtimeftrialbaseln(PPori, timesout, varargin)

if nargin < 3
    help newtimefbaseln;
    return;
end

[g timefreqopts ] = finputcheck(varargin, ...
    {'basenorm'      'string'    {'on','off'} 'off';
    'baseline'      'real'      []          0;
    'trialbase'     'string'    {'on','off','full'} 'off';
    'verbose'       'string'    {'on','off'} 'on';
    }, 'newtimeftrialbaseln', 'ignore');
if ischar(g) error(g); return; end
PP = PPori; if ~iscell(PP), PP = { PP }; end

% ---------------
% baseline length
% ---------------
if size(g.baseline,2) == 2
    baseln = [];
    for index = 1:size(g.baseline,1)
        tmptime   = find(timesout >= g.baseline(index,1) & timesout <= g.baseline(index,2));
        baseln = union_bc(baseln, tmptime);
    end
    if length(baseln)==0
        error( [ 'There are no sample points found in the default baseline.' 10 ...
            'This may happen even though data time limits overlap with' 10 ...
            'the baseline period (because of the time-freq. window width).' 10 ...
            'Either disable the baseline, change the baseline limits.' ] );
    end
else
    if ~isempty(find(timesout < g.baseline))
         baseln = find(timesout < g.baseline); % subtract means of pre-0 (centered) windows
    else baseln = 1:length(timesout); % use all times as baseline
    end
end

for ind = 1:length(PP(:))
    
    P = PP{ind};
    
    % -----------------------------------------
    % remove baseline on a trial by trial basis
    % -----------------------------------------
    if strcmpi(g.trialbase, 'on'), tmpbase = baseln;
    else                           tmpbase = 1:size(P,2); % full baseline
    end
    if ~strcmpi(g.trialbase, 'off')
        if ndims(P) == 4
            mbase = mean(P(:,:,tmpbase,:),3);
            if strcmpi(g.basenorm, 'on')
                mstd = std(P(:,:,tmpbase,:),[],3);
                P = bsxfun(@rdivide, bsxfun(@minus, P, mbase), mstd);
            else P = bsxfun(@rdivide, P, mbase);
            end
        else
            mbase = mean(P(:,tmpbase,:),2);
            if strcmpi(g.basenorm, 'on')
                mstd = std(P(:,tmpbase,:),[],2);
                P = (P-repmat(mbase,[1 size(P,2) 1]))./repmat(mstd,[1 size(P,2) 1]); % convert to log then back to normal
            else
                P = P./repmat(mbase,[1 size(P,2) 1]);
                %P = 10 .^ (log10(P) - repmat(log10(mbase),[1 size(P,2) 1])); % same as above
            end
        end
    end
    
    PP{ind} = P;
end
if ~iscell(PPori) PP = PP{1}; end
