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function FASTER_grandaverage(startDir,option_wrapper,all_errors,top_log,plist,nlist)
if ~option_wrapper.options.averaging_options.make_GA
return;
end
using_ALLEEG=option_wrapper.options.file_options.using_ALLEEG;
save_ALLEEG=option_wrapper.options.file_options.save_ALLEEG;
outDir=option_wrapper.options.file_options.output_folder_name;
if using_ALLEEG
length_ALLEEG=evalin('base','length(ALLEEG);');
if ~(length(plist)==length_ALLEEG)
plist=cell(1,length_ALLEEG);
end
end
try
if (option_wrapper.options.averaging_options.make_GA && (~isempty(plist) || using_ALLEEG))
GA_markers=option_wrapper.options.averaging_options.GA_markers;
if ~isempty(GA_markers)
GAs=cell(size(GA_markers));
p=ones(size(GA_markers));
else
p=1;
end
GA_epoch_length=option_wrapper.options.averaging_options.GA_epoch_length;
%% Do per-file or per-ALLEEG-dataset averaging
for i=1:length(plist)
% If the output folder option is set, get the proper subdirectory
% under that, otherwise use the original directory
if ~using_ALLEEG && ~isempty(outDir)
dir_structure=get_dir_structure(plist{i},option_wrapper.options.file_options.folder_name);
filepath=outDir;
for v=1:length(dir_structure)
filepath=[filepath filesep dir_structure{v}];
end
else
filepath=plist{i};
end
if (~isempty(option_wrapper.options.file_options.searchstring))
searchstring2=option_wrapper.options.file_options.searchstring;
else
searchstring2=nlist{i};
end
if using_ALLEEG || (~isempty(strfind(nlist{i},searchstring2)) || ~isempty(strfind(filepath,searchstring2))) && exist([filepath filesep option_wrapper.options.file_options.file_prefix nlist{i}(1:end-4) '.set'],'file')
if ~using_ALLEEG
EEGt=pop_loadset('filepath',filepath,'filename',[option_wrapper.options.file_options.file_prefix nlist{i}(1:end-4) '.set']);
elseif ~evalin('base',sprintf('isempty(ALLEEG(%d).data);',i))
EEGt=evalin('base',sprintf('ALLEEG(%d);',i));
end
if ~isempty(option_wrapper.options.averaging_options.GA_markers) && ~isempty(EEGt) && ~isempty(EEGt.data)
if iscell(GA_markers)
for v=1:length(GA_markers)
[EEGt1 did_epoch]=h_epoch(EEGt,GA_markers{v},GA_epoch_length + [2/EEGt.srate -2/EEGt.srate]);
if ~isempty(EEGt1.data) && size(EEGt1.data,3)>1 && did_epoch
if exist('trimmean','file')==2
trim_mean_on=option_wrapper.options.averaging_options.GA_trimmed_mean;
trim_mean_perc=option_wrapper.options.averaging_options.GA_trimmed_mean_perc;
GAs{v}(:,:,p(v))=trimmean(EEGt1.data,trim_mean_on*trim_mean_perc,3);
else
GAs{v}(:,:,p(v))=mean(EEGt1.data,3);
end
p(v)=p(v)+1;
end
end
%p=p+1;
else
for v=1:length(GA_markers)
[EEGt1 did_epoch]=h_epoch(EEGt,GA_markers(v),GA_epoch_length + [2/EEGt.srate -2/EEGt.srate]);
if ~isempty(EEGt1.data) && size(EEGt1.data,3)>1 && did_epoch
if exist('trimmean','file')==2
trim_mean_on=option_wrapper.options.averaging_options.GA_trimmed_mean;
trim_mean_perc=option_wrapper.options.averaging_options.GA_trimmed_mean_perc;
GAs{v}(:,:,p(v))=trimmean(EEGt1.data,trim_mean_on*trim_mean_perc,3);
else
GAs{v}(:,:,p(v))=mean(EEGt1.data,3);
end
p(v)=p(v)+1;
else
end
end
%p=p+1;
end
elseif ~isempty(EEGt.data) && size(EEGt.data,3)>1
if exist('trimmean','file')==2
trim_mean_on=option_wrapper.options.averaging_options.GA_trimmed_mean;
trim_mean_perc=option_wrapper.options.averaging_options.GA_trimmed_mean_perc;
GAs(:,:,p)=trimmean(EEGt.data,trim_mean_on*trim_mean_perc,3);
else
GAs(:,:,p)=mean(EEGt.data,3);
end
p=p+1;
elseif size(EEGt.data,3)==1
warning('Continuous dataset not included in grand average. A blank epoch may be present.');
else
warning('Empty dataset not included in grand average. A blank epoch may be present.');
end
end
end
%% Do rejection
if ~isempty(option_wrapper.options.averaging_options.GA_markers) && exist('GAs','var') && ~isempty(GAs)
if iscell(GA_markers)
for v=1:length(GA_markers)
if ~isempty(GAs{v})
cl=EEGt.chanlocs; ci=EEGt.chaninfo;
EEGt=make_EEG(GAs{v},GA_markers{v},EEGt.srate,GA_epoch_length + [2/EEGt.srate -2/EEGt.srate]);
EEGt.chanlocs=cl; EEGt.chaninfo=ci;
if (option_wrapper.options.averaging_options.subject_removal_on) && size(EEGt.data,3)>1
list_properties=GA_properties(EEGt,option_wrapper.options.channel_options.eeg_chans,option_wrapper.options.ica_options.EOG_channels);
lengths=min_z(list_properties,option_wrapper.options.averaging_options.rejection_options);
if ~isempty(find(lengths, 1))
bad_subjs=find(lengths);
EEGt=pop_rejepoch(EEGt,bad_subjs,0);
fprintf(top_log,'In the grand average for marker %s, the following files were removed:',GA_markers{v});
fprintf(top_log,'%s%s%s\n',plist{bad_subjs},filesep,nlist{bad_subjs});
fprintf(top_log,'\n');
end
end
EEGt=eeg_checkset(EEGt);
if ~isempty(outDir)
pop_saveset(EEGt,'filename',[option_wrapper.options.file_options.file_prefix EEGt.setname '.set'],'filepath',outDir);
elseif ~using_ALLEEG || save_ALLEEG
pop_saveset(EEGt,'filename',[option_wrapper.options.file_options.file_prefix EEGt.setname '.set'],'filepath',startDir);
end
if using_ALLEEG
assignin('base','FASTER_Temp_EEG',EEGt);
evalin('base','[ALLEEG EEG CURRENTSET] = eeg_store(ALLEEG, FASTER_Temp_EEG);clear FASTER_Temp_EEG;eeglab redraw;');
end
else
fprintf(top_log,'No markers %s detected in any files.\n',GA_markers{v})
end
end
else
for v=1:length(GA_markers)
if ~isempty(GAs{v})
cl=EEGt.chanlocs; ci=EEGt.chaninfo;
EEGt=make_EEG(GAs{v},GA_markers(v),EEGt.srate,GA_epoch_length + [2/EEGt.srate -2/EEGt.srate]);
EEGt.chanlocs=cl; EEGt.chaninfo=ci;
if (option_wrapper.options.averaging_options.subject_removal_on) && size(EEGt.data,3)>1
list_properties=GA_properties(EEGt,option_wrapper.options.channel_options.eeg_chans,option_wrapper.options.ica_options.EOG_channels);
lengths=min_z(list_properties,option_wrapper.options.averaging_options.rejection_options);
if ~isempty(find(lengths, 1))
bad_subjs=find(lengths);
EEGt=pop_rejepoch(EEGt,bad_subjs,0);
fprintf(top_log,'In the grand average for marker %d, the following files were removed:',GA_markers(v));
fprintf(top_log,'%s%s%s\n',plist{bad_subjs},filesep,nlist{bad_subjs});
fprintf(top_log,'\n');
end
end
EEGt=eeg_checkset(EEGt);
if ~isempty(outDir)
pop_saveset(EEGt,'filename',[option_wrapper.options.file_options.file_prefix EEGt.setname '.set'],'filepath',outDir);
elseif ~using_ALLEEG || save_ALLEEG
pop_saveset(EEGt,'filename',[option_wrapper.options.file_options.file_prefix EEGt.setname '.set'],'filepath',startDir);
end
if using_ALLEEG
assignin('base','FASTER_Temp_EEG',EEGt);
evalin('base','[ALLEEG EEG CURRENTSET] = eeg_store(ALLEEG, FASTER_Temp_EEG);clear FASTER_Temp_EEG;eeglab redraw;');
end
else
fprintf(top_log,'No markers %d detected in any files.\n',GA_markers(v))
end
end
end
elseif exist('GAs','var') && ~isempty(GAs)
cl=EEGt.chanlocs; ci=EEGt.chaninfo;
EEGt=make_EEG(GAs,1,EEGt.srate,GA_epoch_length + [2/EEGt.srate -2/EEGt.srate]);
EEGt.chanlocs=cl; EEGt.chaninfo=ci;
if (option_wrapper.options.averaging_options.subject_removal_on) && size(EEGt.data,3)>1
list_properties=GA_properties(EEGt,option_wrapper.options.channel_options.eeg_chans,option_wrapper.options.ica_options.EOG_channels);
lengths=min_z(list_properties,option_wrapper.options.averaging_options.rejection_options);
if ~isempty(find(lengths, 1))
bad_subjs=find(lengths);
EEGt=pop_rejepoch(EEGt,bad_subjs,0);
fprintf(top_log,'In the grand average, the following files were removed:');
fprintf(top_log,'%s%s%s\n',plist{bad_subjs},filesep,nlist{bad_subjs});
fprintf(top_log,'\n');
end
end
EEGt=eeg_checkset(EEGt);
if ~isempty(outDir)
pop_saveset(EEGt,'filename',[option_wrapper.options.file_options.file_prefix 'GA.set'],'filepath',outDir);
elseif ~using_ALLEEG || save_ALLEEG
pop_saveset(EEGt,'filename',[option_wrapper.options.file_options.file_prefix 'GA.set'],'filepath',startDir);
end
if using_ALLEEG
assignin('base','FASTER_TMP_EEG',EEGt);
evalin('base','[ALLEEG EEG CURRENTSET] = eeg_store(ALLEEG, FASTER_TMP_EEG);clear FASTER_TMP_EEG;eeglab redraw;');
end
else
fprintf(top_log,'No epoched files were found.\n')
end
end
catch
m=lasterror;
fprintf('Error - %s.\n',m.message);
fprintf(top_log,'Error in grand averaging - %s.\n',m.message);
if option_wrapper.debug
if exist('EEGt','var')
EEG_state{1}=evalc('disp(EEGt)');
end
EEG_state{2}=option_wrapper;
EEG_state{3}=builtin('version');
if exist('eeg_getversion','file')
EEG_state{4}=eeg_getversion;
else
EEG_state{4}=which('eeglab');
end
all_errors{end+1,1}=m;
all_errors{end,2}=EEG_state;
save([startDir filesep option_wrapper.options.file_options.file_prefix 'FASTER_errors.mat'],'all_errors','-mat');
end
end
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