end;    if (~isnumeric(g.shuffle))   error('Shuffle argument type must be numeric');end;switch g.memory   case { 'low', 'high' },;   otherwise error('memory must be either ''low'' or ''high''');end;if strcmp(g.memory, 'low') & ~strcmp(g.boottype, 'times')   error(['Bootstrap type ''' g.boottype ''' cannot be used in low memory mode']);end;switch g.compute   case { 'matlab', 'c' },;   otherwise error('compute must be either ''matlab'' or ''c''');end;%%%%%%%%%%%%%%%%%%%%%%%%%%%% Compare 2 conditions %%%%%%%%%%%%%%%%%%%%%%%%%%%if iscell(X)	if length(X) ~= 2 | length(Y) ~= 2		error('crossf: to compare conditions, X and Y input must be 2-elements cell arrays');	end;	if ~strcmp(g.boottype, 'times')		disp('crossf warning: The significance bootstrap type is irrelevant when comparing conditions');	end;	for index = 1:2:length(vararginori)		if index<=length(vararginori) % needed: if elemenets are deleted			%if strcmp(vararginori{index}, 'alpha'), vararginori(index:index+1) = [];			if strcmp(vararginori{index}, 'title'), vararginori(index:index+1) = []; 			end;		end;	end;	if iscell(g.title) 		if length(g.title) <= 2,			g.title{3} = 'Condition 2 - condition 1';		end;	else		g.title = { 'Condition 1', 'Condition 2', 'Condition 2 - condition 1' };	end;		fprintf('Running crossf on condition 1 *********************\n');	fprintf('Note: If an out-of-memory error occurs, try reducing the\n');	fprintf('      number of time points or number of frequencies\n');	if ~strcmp(g.type, 'coher')	   fprintf('Note: Type ''coher'' takes 3 times as much memory as other options!)\n');        end	figure; 	subplot(1,3,1); title(g.title{1});	if ~strcmp(g.type, 'coher')		[R1,mbase,times,freqs,Rbootout1,Rangle1, savecoher1] = crossf(X{1}, Y{1}, ...								frame, tlimits, Fs, varwin, 'savecoher', 1, 'title', ' ',vararginori{:});	else		[R1,mbase,times,freqs,Rbootout1,Rangle1, savecoher1, Tfx1, Tfy1] = crossf(X{1}, Y{1}, ...								frame, tlimits, Fs, varwin, 'savecoher', 1,'title', ' ',vararginori{:});	end;	R1 = R1.*exp(j*Rangle1); % output Rangle is in radians		% Asking user for memory limitations	% if ~strcmp(g.noinput, 'yes')	%	  tmp = whos('Tfx1');	%	  fprintf('This function will require an additional %d bytes, do you wish\n', ...    %     tmp.bytes*6+size(savecoher1,1)*size(savecoher1,2)*g.naccu*8);	%	  res = input('to continue (y/n) (use the ''noinput'' option to disable this message):', 's');	%  	if res == 'n', return; end;	% end;	fprintf('\nRunning crossf on condition 2 *********************\n');	subplot(1,3,2); title(g.title{2});	if ~strcmp(g.type, 'coher')		  [R2,mbase,times,freqs,Rbootout2,Rangle2, savecoher2] = crossf(X{2}, Y{2}, ...								frame, tlimits, Fs, varwin,'savecoher', 1, 'title', ' ',vararginori{:});	else		  [R2,mbase,times,freqs,Rbootout2,Rangle2, savecoher2, Tfx2, Tfy2] = crossf(X{2}, Y{2}, ...								frame, tlimits, Fs, varwin,'savecoher', 1, 'title', ' ',vararginori{:});	end;	R2 = R2.*exp(j*Rangle2); % output Rangle is in radians	subplot(1,3,3); title(g.title{3});	if isnan(g.alpha)		plotall(R2-R1, [], [], times, freqs, mbase,  find(freqs <= g.maxfreq), g);	else 		% accumulate coherence images (all arrays [nb_points * timesout * trials])		% ---------------------------		allsavedcoher = zeros(size(savecoher1,1), ...                          size(savecoher1,2), ...                          size(savecoher1,3)+size(savecoher2,3));		allsavedcoher(:,:,1:size(savecoher1,3))     = savecoher1;		allsavedcoher(:,:,size(savecoher1,3)+1:end) = savecoher2;		clear savecoher1 savecoher2;				if strcmp(g.type, 'coher')			alltfx = zeros(size(Tfx1,1), size(Tfx2,2), size(Tfx1,3)+size(Tfx2,3));			alltfx(:,:,1:size(Tfx1,3))     = Tfx1;			alltfx(:,:,size(Tfx1,3)+1:end) = Tfx2;			clear Tfx1 Tfx2;						alltfy = zeros(size(Tfy1,1), size(Tfy2,2), size(Tfy1,3)+size(Tfy2,3));			alltfy(:,:,1:size(Tfy1,3))   = Tfy1;			alltfy(:,:,size(Tfy1,3)+1:end) = Tfy2;			clear Tfy1 Tfy2;		end;				coherimages = zeros(size(allsavedcoher,1), size(allsavedcoher,2), g.naccu);		cond1trials = length(X{1})/g.frame;		cond2trials = length(X{2})/g.frame;		alltrials = [1:cond1trials+cond2trials];		fprintf('Accumulating bootstrap:');				% preprocess data		% ---------------		switch g.type		 case 'coher', % take the square of alltfx and alltfy		  alltfx = alltfx.^2;		  alltfy = alltfy.^2;		 case 'phasecoher', % normalize		  allsavedcoher = allsavedcoher ./ abs(allsavedcoher);		 case 'phasecoher2', % don't do anything		end;				if strcmp(g.type, 'coher')			[coherdiff coher1 coher2] = coher2conddiff( allsavedcoher, alltrials, ...                                                        cond1trials, g.type, alltfx, alltfy);		else			[coherdiff coher1 coher2] = coher2conddiff( allsavedcoher, alltrials, ...                                                        cond1trials, g.type);		end;		%figure; g.alpha = NaN; & to check that the new images are the same as the original		%subplot(1,3,1); plotall(coher1, [], [], times, freqs, mbase, find(freqs <= g.maxfreq), g);		%subplot(1,3,2); plotall(coher2, [], [], times, freqs, mbase, find(freqs <= g.maxfreq), g);		%return;		for index=1:g.naccu			if rem(index,10) == 0,  fprintf(' %d',index); end			if rem(index,120) == 0, fprintf('\n'); end						if strcmp(g.type, 'coher')				coherimages(:,:,index) = coher2conddiff( allsavedcoher, shuffle(alltrials), ...                                                        cond1trials, g.type, alltfx, alltfy);			else				coherimages(:,:,index) = coher2conddiff( allsavedcoher, shuffle(alltrials), ...                                                        cond1trials, g.type);			end;		end;		fprintf('\n');		% create articially a Bootstrap object to compute significance		Boot = bootinit( [], size(allsavedcoher,1), g.timesout, g.naccu, 0, g.baseboot, ...														'noboottype', g.alpha, g.rboot);		Boot.Coherboot.R = coherimages;		Boot = bootcomppost(Boot, [], [], []);		g.title = '';		plotall(coherdiff, Boot.Coherboot.R, Boot.Rsignif, times, freqs, mbase, ...														find(freqs <= g.maxfreq), g);	end;	return; % ********************************** END PROCESSING TWO CONDITIONSend;%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% shuffle trials if necessary%%%%%%%%%%%%%%%%%%%%%%%%%%%%%if g.shuffle ~= 0   fprintf('x and y data trials being shuffled %d times\n',g.shuffle);   XX = reshape(X, 1, frame, length(X)/g.frame);   YY = Y;   X = [];   Y = [];   for index = 1:g.shuffle      XX = shuffle(XX,3);      X = [X XX(:,:)];      Y = [Y YY];   end;end;% detrend over epochs (trials) if requested% -----------------------------------------switch g.detrepcase 'on'   X = reshape(X, g.frame, length(X)/g.frame);   X = X - mean(X,2)*ones(1, length(X(:))/g.frame);   Y = reshape(Y, g.frame, length(Y)/g.frame);   Y = Y - mean(Y,2)*ones(1, length(Y(:))/g.frame);end;        % time limitswintime = 500*g.winsize/g.srate;times = [g.tlimits(1)+wintime:(g.tlimits(2)-g.tlimits(1)-2*wintime)/(g.timesout-1):g.tlimits(2)-wintime];%%%%%%%%%%% baseline%%%%%%%%%%if ~isnan(g.baseline)   baseln = find(times < g.baseline); % subtract means of pre-0 (centered) windows   if isempty(baseln)      baseln = 1:length(times); % use all times as baseline      disp('Bootstrap baseline empty, using the whole epoch.');   end;   baselength = length(baseln);else   baseln = 1:length(times); % use all times as baseline   baselength = length(times); % used for bootstrapend;%%%%%%%%%%%%%%%%%%%%% Initialize objects%%%%%%%%%%%%%%%%%%%%tmpsaveall = (~isnan(g.alpha) & isnan(g.rboot) & strcmp(g.memory, 'high')) ...                 | (strcmp(g.subitc, 'on') & strcmp(g.memory, 'high'));trials = length(X)/g.frame;if ~strcmp(lower(g.compute), 'c')   Tfx = tfinit(X, g.timesout, g.winsize, g.cycles, g.frame, g.padratio, g.detret, ...									g.srate, g.maxfreq, g.subitc, g.type, g.cyclesfact, tmpsaveall);   Tfy = tfinit(Y, g.timesout, g.winsize, g.cycles, g.frame, g.padratio, g.detret, ...									g.srate, g.maxfreq, g.subitc, g.type, g.cyclesfact, tmpsaveall);   Coher     = coherinit(Tfx.nb_points, trials, g.timesout, g.type);   Coherboot = coherinit(Tfx.nb_points, trials, g.naccu   , g.type);   Boot      = bootinit( Coherboot, Tfx.nb_points, g.timesout, g.naccu, baselength, ...									g.baseboot, g.boottype, g.alpha, g.rboot);   freqs = Tfx.freqs;   dispf = find(freqs <= g.maxfreq);   freqs = freqs(dispf);else   freqs = g.srate*g.cycles/g.winsize*[2:2/g.padratio:g.winsize]/2;end;dispf     = find(Tfx.freqs <= g.maxfreq);%-------------% Reserve space%-------------% R  = zeros(tfx.nb_points,g.timesout);       % mean coherence% RR = repmat(nan,tfx.nb_points,g.timesout); % initialize with nans% Rboot = zeros(tfx.nb_points,g.naccu);  % summed bootstrap coher% switch g.type% case 'coher',%    cumulXY = zeros(tfx.nb_points,g.timesout);%    cumulXYboot = zeros(tfx.nb_points,g.naccu);% end;        % if g.bootsub > 0%    Rboottrial = zeros(tfx.nb_points, g.timesout, g.bootsub); % summed bootstrap coher%    cumulXYboottrial = zeros(tfx.nb_points, g.timesout, g.bootsub);% end;% if ~isnan(g.alpha) & isnan(g.rboot)%    tf.tmpalltimes = repmat(nan,tfx.nb_points,g.timesout);% end   % --------------------% Display text to user% --------------------fprintf('\nComputing Event-Related ');switch g.type    case 'phasecoher',  fprintf('Phase Coherence (ITC) images for %d trials.\n',length(X)/g.frame);    case 'phasecoher2', fprintf('Phase Coherence 2 (ITC) images for %d trials.\n',length(X)/g.frame);    case 'coher',       fprintf('Linear Coherence (ITC) images for %d trials.\n',length(X)/g.frame);end;fprintf('The trial latency range is from %4.5g ms before to %4.5g ms after\n     the time-locking event.\n', 1000*g.tlimits(1),1000*g.tlimits(2));fprintf('The frequency range displayed will be %g-%g Hz.\n',min(freqs),g.maxfreq);if ~isnan(g.baseline)   if length(baseln) == length(times)      fprintf('Using the full trial latency range as baseline.\n');   else      fprintf('Using trial latencies from %4.5g ms to %4.5g ms as baseline.\n', 1000*g.tlimits,g.baseline);   end;else    fprintf('No baseline time range was specified.\n');	end;if g.cycles==0   fprintf('The data window size will be %d samples (%g ms).\n',g.winsize,2*wintime);   fprintf('The FFT length will be %d samples\n',g.winsize*g.padratio);else   fprintf('The window size will be %2.3g cycles.\n',g.cycles);   fprintf('The maximum window size will be %d samples (%g ms).\n',g.winsize,2*wintime);endfprintf('The window will be applied %d times\n',g.timesout);fprintf('     with an average step size of %2.2g samples (%2.4g ms).\n', Tfx.stp,1000*Tfx.stp/g.srate);fprintf('Results will be oversampled %d times.\n',g.padratio);if ~isnan(g.alpha)   fprintf('Bootstrap confidence limits will be computed based on alpha = %g\n', g.alpha);else   fprintf('Bootstrap confidence limits will NOT be computed.\n'); endswitch g.plotphasecase 'on',     if strcmp(g.angleunit,'deg')       fprintf(['Coherence angles will be imaged in degrees.\n']);    elseif strcmp(g.angleunit,'rad')       fprintf(['Coherence angles will be imaged in radians.\n']);    elseif strcmp(g.angleunit,'ms')       fprintf(['Coherence angles will be imaged in ms.\n']);    endend;fprintf('\nProcessing trial (of %d): ',trials);% firstboot = 1;% Rn=zeros(trials,g.timesout);% X = X(:)'; % make X and Y column vectors% Y = Y(:)';% tfy = tfx;if strcmp(lower(g.compute), 'c')   % C PART   filename = [ 'tmpcrossf' num2str(round(rand(1)*1000)) ];   f = fopen([ filename '.in'], 'w');   fwrite(f, tmpsaveall, 'int32');   fwrite(f, g.detret, 'int32');   fwrite(f, g.srate, 'int32');   fwrite(f, g.maxfreq, 'int32');   fwrite(f, g.padratio, 'int32');   fwrite(f, g.cycles, 'int32');   fwrite(f, g.winsize, 'int32');   fwrite(f, g.timesout, 'int32');   fwrite(f, g.subitc, 'int32');   fwrite(f, g.type, 'int32');   fwrite(f, trials, 'int32');   fwrite(f, g.naccu, 'int32');   fwrite(f, length(X), 'int32');   fwrite(f, X, 'double');   fwrite(f, Y, 'double');   fclose(f);      command = [ '!cppcrosff ' filename '.in ' filename '.out' ];   eval(command);      f = fopen([ filename '.out'], 'r');   size1 = fread(f, 'int32', 1);   size2 = fread(f, 'int32', 1);   Rreal = fread(f, 'double', [size1 size2]);   Rimg  = fread(f, 'double', [size1 size2]);   Coher.R = Rreal + j*Rimg;   Boot.Coherboot.R = [];   Boot.Rsignif = [];else   % ------------------------   % MATLAB PART