pop_newtimef.m

% POP_NEWTIMEF - Returns estimates and plots of event-related (log) spectral
%           perturbation (ERSP) and inter-trial coherence (ITC) phenomena 
%           timelocked to a set of single-channel input epochs 
%
% Usage:
%   >> pop_newtimef(EEG, typeplot);          % pop_up window
%   >> pop_newtimef(EEG, typeplot, lastcom); % pop_up window
%   >> pop_newtimef(EEG, typeplot, channel); % do not pop-up window
%   >> pop_newtimef(EEG, typeproc, num, tlimits,cycles,
%                        'key1',value1,'key2',value2, ... );   
%     
% Graphical interface:
%   "Channel/component number" - [edit box] this is the index of the data 
%              channel or the index of the component for which to plot the
%              time-frequency decomposition.
%   "Sub-epoch time limits" - [edit box] sub epochs may be extracted (note that
%              this function aims at plotting data epochs not continuous data).
%              You may select the new epoch limits in this edit box.
%   "Use n time points" - [multiple choice list] this is the number of time
%              points to use for the time-frequency decomposition. The more
%              time points, the longer the time-frequency decomposition
%              takes to compute.
%   "Frequency limits" - [edit box] these are the lower and upper
%              frequency limit of the time-frequency decomposition. Instead
%              of limits, you may also enter a sequence of frequencies. For
%              example to compute the time-frequency decomposition at all
%              frequency between 5 and 50 hertz with 1 Hz increment, enter "1:50"
%   "Use limits, padding n" - [multiple choice list] "using limits" means
%              to use the upper and lower limits in "Frequency limits" with
%              a specific padding ratio (padratio argument of newtimef).
%              The last option "use actual frequencies" forces newtimef to
%              ignore the padratio argument and use the vector of frequencies  
%              given as input in the "Frequency limits" edit box.
%   "Log spaced" - [checkbox] you may check this box to compute log-spaced
%              frequencies. Note that this is only relevant if you specify
%              frequency limits (in case you specify actual frequencies,
%              this parameter is ignored).
%   "Use divisive baseline" - [multiple choice list] there are two types of
%              baseline correction, additive (the baseline is subtracted)
%              or divisive (the data is divided by the baseline values).
%              The choice is yours. There is also the option to perform 
%              baseline correction in single trials. See the 'trialbase' "full"
%              option in the newtimef.m documentation for more information.
%   "No baseline" - [checkbox] check this box to compute the raw time-frequency
%              decomposition with no baseline removal.
%   "Wavelet cycles" - [edit box] specify the number of cycle at the lowest 
%              and highest frequency. Instead of specifying the number of cycle 
%              at the highest frequency, you may also specify a wavelet
%              "factor" (see newtimef help message). In addition, it is
%              possible to specify actual wavelet cycles for each frequency
%              by entering a sequence of numbers.
%   "Use FFT" - [checkbox] check this checkbox to use FFT instead of
%              wavelet decomposition.
%   "ERSP color limits" - [edit box] set the upper and lower limit for the
%              ERSP image. 
%   "see log power" - [checkbox] the log power values (in dB) are plotted. 
%              Uncheck this box to plot the absolute power values.
%   "ITC color limits" - [edit box] set the upper and lower limit for the
%              ITC image. 
%   "plot ITC phase" - [checkbox] check this box plot plot (overlaid on
%              the ITC amplitude) the polarity of the ITC complex value.
%   "Bootstrap significance level" - [edit box] use this edit box to enter
%              the p-value threshold for masking both the ERSP and the ITC
%              image for significance (masked values appear as light green)
%   "FDR correct" - [checkbox] this correct the p-value for multiple comparisons
%              (across all time and frequencies) using the False Discovery
%              Rate method. See the fdr.m function for more details.
%   "Optional newtimef arguments" - [edit box] addition argument for the
%              newtimef function may be entered here in the 'key', value
%              format.
%   "Plot Event Related Spectral Power" - [checkbox] plot the ERSP image
%              showing event related spectral stimulus induced changes
%   "Plot Inter Trial Coherence" - [checkbox] plot the ITC image.
%   "Plot Curve at each frequency" - [checkbox] instead of plotting images,
%              it is also possible to display curves at each frequency.
%              This functionality is beta and might not work in all cases.
% 
% Inputs:            
%   INEEG    - input EEG dataset
%   typeproc - type of processing: 1 process the raw channel data 
%                                  0 process the ICA component data
%   num      - component or channel number
%   tlimits  - [mintime maxtime] (ms) sub-epoch time limits to plot
%   cycles   -  > 0 --> Number of cycles in each analysis wavelet 
%               = 0 --> Use FFTs (with constant window length 
%                       at all frequencies)
%
% Optional inputs:
%    See the NEWTIMEF function.
%    
% Outputs: Same as NEWTIMEF; no outputs are returned when a
%          window pops-up to ask for additional arguments
%
% Saving the ERSP and ITC output values:
%    Simply look up the history using the eegh function (type eegh).
%    Then copy and paste the POP_NEWTIMEF command and add output args.
%    See the NEWTIMEF function for a list of outputs. For instance,
% >> [ersp itc powbase times frequencies] = pop_newtimef( EEG, ....);
%
% Author: Arnaud Delorme, CNL / Salk Institute, 2001 
%
% See also: NEWTIMEF, EEGLAB 

% Copyright (C) 2002 University of California San Diego
%
% 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.

% 01-25-02 reformated help & license -ad 
% 03-08-02 add eeglab option & optimize variable sizes -ad
% 03-10-02 change newtimef call -ad
% 03-18-02 added title -ad & sm
% 04-04-02 added outputs -ad & sm

function varargout = pop_newtimef(EEG, typeproc, num, tlimits, cycles, varargin );

varargout{1} = '';
% display help if not enough arguments
% ------------------------------------
if nargin < 2
	help pop_newtimef;
	return;
end
lastcom = [];
if nargin < 3
	popup = 1;
else
	popup = ischar(num) | isempty(num);
	if ischar(num)
		lastcom = num;
	end
end

% pop up window
% -------------
if popup
	[txt, vars] = gethelpvar('newtimef.m');
    commandchan = 'tmpEEG = get(gcbf, ''userdata''); tmpchanlocs = tmpEEG(1).chanlocs; [tmp tmpval] = pop_chansel({tmpchanlocs.labels}, ''withindex'', ''on'', ''selectionmode'', ''single''); set(findobj(gcbf, ''tag'', ''chan''), ''string'',tmpval); clear tmpEEG tmp tmpchanlocs tmpval'; 
	
    g = [1 0.3 0.6 0.4];
    g2 = [1 0.3 0.25 0.75];
	geometry = { g2 g g g g g g g [0.975 1.27] [1] [1.2 1 1.2]};
    uilist = { ...
               { 'Style', 'text', 'string', fastif(typeproc, 'Channel number', 'Component number'), 'fontweight', 'bold'  } ...
			   { 'Style', 'edit', 'string', getkeyval(lastcom,3,[],'1') 'tag' 'chan'} ...
               { 'style' 'pushbutton' 'string'  '...', 'enable' fastif(~isempty(EEG(1).chanlocs) && typeproc, 'on', 'off') 'callback' commandchan } ...               
               {} ...
               ...
			   { 'Style', 'text', 'string', 'Sub epoch time limits [min max] (msec)', 'fontweight', 'bold' } ...
			   { 'Style', 'edit', 'string', getkeyval(lastcom,4,[],[ int2str(EEG.xmin*1000) ' ' int2str(EEG.xmax*1000) ]) 'tag' 'tlimits' } ...
               { 'Style', 'popupmenu', 'string', 'Use 50 time points|Use 100 time points|Use 150 time points|Use 200 time points|Use 300 time points|Use 400 time points' 'tag' 'ntimesout' 'value' 4} { } ...
			   ...
			   { 'Style', 'text', 'string', 'Frequency limits [min max] (Hz) or sequence', 'fontweight', 'bold' } ...
			   { 'Style', 'edit', 'string', '' 'tag' 'freqs'  } ...
               { 'Style', 'popupmenu', 'string', 'Use limits, padding 1|Use limits, padding 2|Use limits, padding 4|Use actual freqs.' 'tag' 'nfreqs' }  ...
               { 'Style', 'checkbox', 'string' 'Log spaced' 'value' 0 'tag' 'freqscale' } ...
			   ...
			   { 'Style', 'text', 'string', 'Baseline limits [min max] (msec) (0->pre-stim.)', 'fontweight', 'bold' } ...
			   { 'Style', 'edit', 'string', '0' 'tag' 'baseline' } ...
			   { 'Style', 'popupmenu',  'string', 'Use divisive baseline (DIV)|Use standard deviation (STD)|Use single trial DIV baseline|Use single trial STD baseline' 'tag' 'basenorm' } ...
               { 'Style', 'checkbox', 'string' 'No baseline' 'tag' 'nobase' } ...
               ...
               { 'Style', 'text', 'string', 'Wavelet cycles [min max/fact] or sequence', 'fontweight', 'bold' } ...
               { 'Style', 'edit', 'string', getkeyval(lastcom,5,[],'3 0.8') 'tag' 'cycle' } ...
               { 'Style', 'checkbox', 'string' 'Use FFT' 'value' 0 'tag' 'fft' } ...
               { } ...
			   ...
			   { 'Style', 'text', 'string', 'ERSP color limits [max] (min=-max)', 'fontweight', 'bold' } ...
               { 'Style', 'edit', 'string', '' 'tag' 'erspmax'} ...
               { 'Style', 'checkbox', 'string' 'see log power (set)' 'tag' 'scale' 'value' 1} {} ...
			   ...
			   { 'Style', 'text', 'string', 'ITC color limits [max]', 'fontweight', 'bold' } ...
               { 'Style', 'edit', 'string', '' 'tag' 'itcmax'} ...
               { 'Style', 'checkbox', 'string' 'plot ITC phase (set)' 'tag' 'plotphase' } {} ...
			   ...
			   { 'Style', 'text', 'string', 'Bootstrap significance level (Ex: 0.01 -> 1%)', 'fontweight', 'bold' } ...
               { 'Style', 'edit', 'string', getkeyval(lastcom,'alpha') 'tag' 'alpha'} ...
               { 'Style', 'checkbox', 'string' 'FDR correct (set)' 'tag' 'fdr' } {} ...
			   ...
			   { 'Style', 'text', 'string', 'Optional newtimef() arguments (see Help)', 'fontweight', 'bold', ...
				 'tooltipstring', 'See newtimef() help via the Help button on the right...' } ...
			   { 'Style', 'edit', 'string', '' 'tag' 'options' } ...
			   {} ...
			   { 'Style', 'checkbox', 'value', ~getkeyval(lastcom,'plotersp','present',0), 'string', ...
				 'Plot Event Related Spectral Power', 'tooltipstring', ...
				 'Plot log spectral perturbation image in the upper panel' 'tag' 'plotersp' } ...
			   { 'Style', 'checkbox', 'value', ~getkeyval(lastcom,'plotitc','present',0), 'string', ...
				 'Plot Inter Trial Coherence', 'tooltipstring', ...
				 'Plot the inter-trial coherence image in the lower panel' 'tag' 'plotitc' } ...
			   { 'Style', 'checkbox', 'value', 0, 'string', ...
				 'Plot curve at each frequency' 'tag' 'plotcurve' } ...
			 };
      % { 'Style', 'edit', 'string', '''padratio'', 4, ''plotphase'', ''off''' } ...
			   %{ 'Style', 'text', 'string',  '[set] -> Plot ITC phase sign', 'fontweight', 'bold', ...
			%	 'tooltipstring', ['Plot the sign (+/-) of inter-trial coherence phase' 10 ...
			%		'as red (+) or blue (-)'] } ...
			%   { 'Style', 'checkbox', 'value', ~getkeyval(lastcom,'plotphase','present',1) } { } ...

	[ tmp1, tmp2, strhalt, result ] = inputgui( 'geometry', geometry, 'uilist', uilist, 'helpcom', 'pophelp(''pop_newtimef'');', ...
					   'title', fastif(typeproc, 'Plot channel time frequency -- pop_newtimef()', ...
							  'Plot component time frequency -- pop_newtimef()'), 'userdata', EEG);
	if isempty( tmp1 ) 
        return; 
    end

	if result.fft,      result.cycle = '0'; end
	if result.nobase,   result.baseline = 'NaN'; end
    
    num   = eeg_decodechan(EEG.chanlocs, result.chan );
	tlimits	 = eval( [ '[' result.tlimits ']' ] ); 
	cycles	 = eval( [ '[' result.cycle   ']' ] );
    freqs    = eval( [ '[' result.freqs   ']' ] );
    %result.ncycles == 2 is ignored
    
    % add topoplot
    % ------------
    options = [];
    if isfield(EEG.chanlocs, 'theta') && ~isempty(EEG.chanlocs(num).theta)
        if ~isfield(EEG, 'chaninfo'), EEG.chaninfo = []; end
        if typeproc == 1
            if isempty(EEG.chanlocs), caption = [ 'Channel ' int2str(num) ]; else caption = EEG.chanlocs(num).labels; end
            options = [options ', ''topovec'', ' int2str(num) ...
                        ', ''elocs'', EEG.chanlocs, ''chaninfo'', EEG.chaninfo, ''caption'', ''' caption '''' ];
        else
            options = [options ', ''topovec'', EEG.icawinv(:,' int2str(num) ...
                       '), ''elocs'', EEG.chanlocs, ''chaninfo'', EEG.chaninfo, ''caption'', [''IC ' num2str(num) ''']' ];
      end
    end
    
	if ~isempty( result.baseline ),  options = [ options ', ''baseline'',[' result.baseline ']' ]; end
    if ~isempty( result.alpha ),     options = [ options ', ''alpha'',' result.alpha ];   end
	if ~isempty( result.options ),   options = [ options ',' result.options ];            end
	if ~isempty( result.freqs ),     options = [ options ', ''freqs'', [' result.freqs ']'   ]; end
	if ~isempty( result.erspmax ),   options = [ options ', ''erspmax'', [' result.erspmax ']' ]; end
	if ~isempty( result.itcmax ),    options = [ options ', ''itcmax'','  result.itcmax ];      end
	if ~result.plotersp,             options = [ options ', ''plotersp'', ''off''' ];     end
	if ~result.plotitc,              options = [ options ', ''plotitc'' , ''off''' ];     end
	if result.plotcurve,             options = [ options ', ''plottype'', ''curve''' ];   end
	if result.fdr,                   options = [ options ', ''mcorrect'', ''fdr''' ];     end
	if result.freqscale,             options = [ options ', ''freqscale'', ''log''' ];    end
	if ~result.plotphase,            options = [ options ', ''plotphase'', ''off''' ];    end
	if ~result.scale,                options = [ options ', ''scale'', ''abs''' ];        end
    if result.ntimesout == 1,        options = [ options ', ''ntimesout'', 50' ];         end
    if result.ntimesout == 2,        options = [ options ', ''ntimesout'', 100' ];        end
    if result.ntimesout == 3,        options = [ options ', ''ntimesout'', 150' ];        end
    if result.ntimesout == 5,        options = [ options ', ''ntimesout'', 300' ];        end
    if result.ntimesout == 6,        options = [ options ', ''ntimesout'', 400' ];        end
    if result.nfreqs == 1,           options = [ options ', ''padratio'', 1' ];           end  
    if result.nfreqs == 2,           options = [ options ', ''padratio'', 2' ];           end   
    if result.nfreqs == 3,           options = [ options ', ''padratio'', 4' ];           end
    if result.nfreqs == 4,           options = [ options ', ''nfreqs'', ' int2str(length(freqs)) ]; end
    if result.basenorm == 2,         options = [ options ', ''basenorm'', ''on''' ];      end
    if result.basenorm == 4,         options = [ options ', ''basenorm'', ''on''' ];      end
    if result.basenorm >= 3,         options = [ options ', ''trialbase'', ''full''' ];      end

    % add title
    % ---------
	if isempty( findstr(  '''title''', result.options))
        if ~isempty(EEG.chanlocs) && typeproc
            chanlabel = EEG.chanlocs(num).labels;
        else
            chanlabel = int2str(num);
        end
	end
    
    % compute default winsize
    % -----------------------
    if EEG.xmin < 0 && isempty(findstr( '''winsize''', result.options)) && isempty( result.freqs )
        fprintf('Computing window size in pop_newtimef based on half of the length of the baseline period');
        options = [ options ', ''winsize'', ' int2str(-EEG.xmin*EEG.srate) ];
    end
    
	figure; try, icadefs; set(gcf, 'color', BACKCOLOR); catch, end
else
    options = [ ',' vararg2str(varargin) ];
end

% compute epoch limits
% --------------------
if isempty(tlimits)
	tlimits = [EEG.xmin, EEG.xmax]*1000;
end
pointrange1 = round(max((tlimits(1)/1000-EEG.xmin)*EEG.srate, 1));
pointrange2 = round(min((tlimits(2)/1000-EEG.xmin)*EEG.srate+1, EEG.pnts));
pointrange = [pointrange1:pointrange2];

% call function sample either on raw data or ICA data
% ---------------------------------------------------
if typeproc == 1
	tmpsig = EEG.data(num,pointrange,:);
else
	if ~isempty( EEG.icasphere )
        if ~isempty(EEG.icaact)
    		tmpsig = EEG.icaact(num,pointrange,:);
 	    else
            tmpsig = (EEG.icaweights(num,:)*EEG.icasphere)*reshape(EEG.data(:,pointrange,:), EEG.nbchan, EEG.trials*length(pointrange));
        end
	else
		error('You must run ICA first');
	end;	
end;	 
tmpsig = reshape( tmpsig, length(num), size(tmpsig,2)*size(tmpsig,3));

% outputs
% -------
outstr = '';
if ~popup
    for io = 1:nargout, outstr = [outstr 'varargout{' int2str(io) '},' ]; end
    if ~isempty(outstr), outstr = [ '[' outstr(1:end-1) '] =' ]; end
end

% plot the datas and generate output command
% --------------------------------------------
if length( options ) < 2
    options = '';
end
if nargin < 4
    varargout{1} = sprintf('figure; pop_newtimef( EEG, %d, %d, [%s], [%s] %s);', typeproc, num, ...
			int2str(tlimits), num2str(cycles), options);
end
com = sprintf('%s newtimef( tmpsig(:, :), length(pointrange), [tlimits(1) tlimits(2)], EEG.srate, cycles %s);', outstr, options);
eval(com)	    

return;

% get contextual help
% -------------------
function txt = context(var, allvars, alltext);
	loc = strmatch( var, allvars);
	if ~isempty(loc)
		txt= alltext{loc(1)};
	else
		disp([ 'warning: variable ''' var ''' not found']);
		txt = '';
	end