Documentation: Automation of Analysis over an Experimental Study

[subdir_list, session_name]= get_session_list('projekt_biomed2010');

results_file= [DATA_DIR 'results/' session_name '/grand_average_ERPs'];

opt_fig= strukt('folder', [TEX_DIR session_name '/pics_auto/'], ...
                'format', 'pdf');

% For each participant, experiments with the following conditions were performed:
taglist= {'Intensify','Rotate','Upsize'};
filelist= strcat('MatrixSpeller', taglist);

colOrder= [0.83 0.67 0; 0.4 0.4 0.4];
clear erp erp_r

for vp= 1:length(subdir_list),
 subdir= subdir_list{vp};
 sbj= subdir(1:find(subdir=='_',1,'first')-1);
 exp_id= strrep(subdir, '_', '');
 
  % default values
 disp_ival= [-200 1000];
 ref_ival= [-200 0];
 crit_maxmin= 70;
 crit_ival= [100 900];
 crit_clab= {'F9,z,10','AF3,4'};
 clab= {'Cz','PO7'};

 for ff = 1:length(filelist),
  fprintf('Processing %s - %s.\n', subdir, filelist{ff});
  opt_fig.prefix= [exp_id '_' taglist{ff} '_'];
    
  % subject-specific settings
  switch(sbj),
  end

  % load data
  clear cnt epo*
  file= [subdir '/' filelist{ff} sbj];
  [cnt, mrk, mnt]= eegfile_loadMatlab(file);

  b= procutil_firlsFilter(0.5, cnt.fs);
  cnt= proc_filtfilt(cnt, b);
  
  %% artifact rejection based on variance criterion
  mrk= reject_varEventsAndChannels(cnt, mrk, disp_ival, 'verbose', 1);
 
  % segmentation
  epo= cntToEpo(cnt, mrk, disp_ival);
  
  %% artifact rejection based on minmax difference criterion on frontal chans
  epo= proc_rejectArtifactsMaxMin(epo, crit_maxmin, ...
            'clab',crit_clab, 'ival',crit_ival, 'verbose',1);

  epo= proc_baseline(epo, ref_ival);
  epo_r= proc_r_square_signed(epo);
  epo_r.className= {'sgn r^2 ( T , NT )'};  %% just make it shorter
  
  fig_set(1);
  constraint= ...
      {{-1, [100 300], {'I#','O#','PO7,8','P9,10'}, [50 300]}, ...
       {1, [200 350], {'P3-4','CP3-4','C3-4'}, [200 400]}, ...
       {1, [400 500], {'P3-4','CP3-4','C3-4'}, [350 600]}};
  [ival_scalps, nfo]= ...
      select_time_intervals(epo_r, 'visualize', 1, 'visu_scalps', 1, ...
                            'title', [sbj ': ' taglist{ff}], ...
                            'clab',{'not','E*','Fp*','AF*'}, ...
                            'constraint', constraint);
  printFigure('r_matrix', [18 13], opt_fig);
  ival_scalps= visutil_correctIvalsForDisplay(ival_scalps, 'fs',epo.fs);

  fig_set(3)
  H= grid_plot(epo, mnt, defopt_erps, 'colorOrder',colOrder);
  grid_addBars(epo_r, 'h_scale',H.scale);
  printFigure(['erp'], [19 12], opt_fig);

  fig_set(2);
  H= scalpEvolutionPlusChannel(epo, mnt, clab, ival_scalps, ...
                               defopt_scalp_erp2, ...
                               'colorOrder',colOrder);
  grid_addBars(epo_r);
  printFigure(['erp_topo'], [20  4+5*size(epo.y,1)], opt_fig);

  fig_set(4, 'shrink',[1 2/3]);
  scalpEvolutionPlusChannel(epo_r, mnt, clab, ival_scalps, ...
                            defopt_scalp_r2);
  printFigure(['erp_topo_r'], [20 9], opt_fig);

% save averages for calculating grand averages later
  erp{vp,ff}= proc_average(epo);
  erp_r{vp,ff}= epo_r;
  
 end
end

save(results_file, 'erp','erp_r', 'clab', ...
     'session_name', 'subdir_list','filelist', 'taglist', 'mnt', 'opt_fig');

load(results_file);       % as defined in the example above

ival_scalps= [180 230; 250 350; 400 500];

% find unified scalings for all plots
range_grid= visutil_commonRangeForGA(erp, 'nice_range_erp',10);
range= visutil_commonRangeForGA(erp, 'clab_erp', clab, ...
                                'ival_scalp',ival_scalps);
range_r= visutil_commonRangeForGA(erp_r, 'clab_erp', clab, ...
                                'ival_scalp',ival_scalps);

for ff = 1:length(filelist),
  opt_fig.prefix= ['grand_average_ERPs_' taglist{ff} '_'];
  erp_ga= proc_grandAverage(erp{:,ff});
  erp_r_ga= proc_grandAverage(erp_r{:,ff});

  fig_set(1);
  grid_plot(erp_ga, mnt, defopt_erps, 'colorOrder',colOrder, ...
            'yLim', range_grid.erp);
  printFigure('erp', [19 12]*1.3, opt_fig);

  fig_set(2); clf;
  H= scalpEvolutionPlusChannel(erp_ga, ...
                               mnt, clab, ival_scalps, ...
                               defopt_scalp_erp2, ...
                               'colorOrder',colOrder, ...
                               'yLim', range.erp, ...
                               'colAx', range.scalp);
  printFigure('erp_topo', [25 16], opt_fig);

  fig_set(4, 'shrink',[1 2/3]);
  H= scalpEvolutionPlusChannel(erp_r_ga, mnt, clab, ival_scalps, ...
                               defopt_scalp_r2, ...
                               'channelAtBottom', 1, ...
                               'yLim', range_r.erp, ...
                               'colAx', range_r.scalp);
   printFigure('erp_r_topo', [25 10.5], opt_fig);
end

if isunix,
  latex_file= [TEX_DIR session_name filesep 'investigate_ERPs'];
  [filepath,filename]= fileparts(latex_file);
  cmd= sprintf('cd %s; LD_LIBRARY_PATH="" pdflatex %s %s', ...
               filepath, '-interaction nonstopmode', filename);
  unix(cmd);
end