IST_logfile_flipped_bids.m

% logfile extraction script for FOR/FOK cases of I.S.T.
% - only for cases without the flip/logfile extraction issue
% - also saves .tsv file
% - split time bug fixed IE 08/2017
% adapted from A. Kuehnel
% M. Czisch 25.1.2018

function IST_logfile_flipped_bids(BIDS)

    subject_path = BIDS.input.dir;
    log = dir([subject_path,'/LOG/*IST_final*.log']);

    %clearvars -except m root subs tracksep1 tracksep2

    logfile=readtext([subject_path,'/LOG/',log.name],'\t');

    string_logfile = cellfun(@num2str, logfile(:,4), 'UniformOutput', 0);
    ende = find(strcmp(string_logfile, 'startpause'));


    %Check if logfile is complete
    ende_ind = find(strcmp(string_logfile, 'last_frame'));
    if isempty(ende_ind); error('Logfile incomplete!');end


    f = cell2table(logfile(6:ende(end)+2,1:8));
    Var_Names = strrep(logfile(4,1:8),' ','');
    f.Properties.VariableNames = Var_Names;

    f.Code = string(f.Code);

    % reduce table to relevant columns and remove "pulse" code
    t1 = f(:,{'Code','Time'});
    t1.Time = t1.Time/10000;

    % Start of first pulse is zerotime -> substracted from all further events
    %tmp = t1{t1.Code == "miniblock",2}(1); 
    tmp1 = t1{t1.Code == "10",2};
    tmp = tmp1(1);
    t1{:,2} = t1{:,2} - tmp;

    pulses = t1{t1.Code == "10",2}; % for major separator action
    t1 = t1(f.Code ~= "10",:); % now remove 'pulse' codes

    % extract onsets: onst1 = calculus; onst2 = motor; onst3 = fb_correct; onst4 =
    % fb_false; onst5 = fb_timeout



    t11 = t1(t1.Code ~= "1" & t1.Code ~= "2" & t1.Code ~= "3",:);

    tmp1  = find(t11.Code == "startpause") -1;
    tmp2  = find(t11.Code == "verbf_long") -1;
    tmp3  = [tmp1;tmp2];
    tmp3  = sort(tmp3);

    tmp   = t11.Code == "fb_correct";
    tmp(tmp3) = 0;
    onst11 = t11{tmp,2} + 6000 ;

    tmp   = t11.Code == "fb_false";
    tmp(tmp3) = 0;
    onst12 = t11{tmp,2} + 6000;

    tmp   = t11.Code == "fb_timeout";
    tmp(tmp3) = 0;
    onst13 = t11{tmp,2} + 6000;


    tmp   = t11.Code == "miniblock";
    tmp   = t11{tmp,2} + 1666;
    onst1 = [onst11; onst12; onst13; tmp];
    onst1 = sort(onst1);
    nr_calc = repmat({'calc'},length(onst1),1);
    % Calculate drt1

    for i = 1:numel(onst1)
        drt1(i) =  min(t1.Time(t1.Time > onst1(i))) - onst1(i);
    end

    % motor onsets are a bit tricky: because multiple buttons and variable
    % ammount of hits and sometimes motoractivity soutside of calculus answer
    % subission

    onst2 = zeros(size(t1.Code,1),1);
    tmp = find(strncmp(t1.Code, "fb_", 3)) + 1;
    onst2(tmp) = 1;

    rm1 = strncmp(t1.Code, "antic_", 6);
    rm2 = t1.Code == "startpause";
    rm3 = strncmp(f.Code, "verbf", 5);
    rm4 =  find(t1.Code == "startpause") - 1;
    onst2(rm1) = 0;
    onst2(rm2) = 0;
    onst2(rm3) = 0;
    onst2(rm4) = 0;
    onst2 = t1{onst2,2};

    tmp = t1{strncmp(t1.Code, "antic_", 6),2};
    for i = 1:numel(onst2)
        drt2(i) =  min(tmp(tmp > onst2(i))) - onst2(i);
    end

    nr_motor = repmat({'Motor'},length(onst2),1);

%         % motor onsets are a bit tricky: because multiple buttons and variable
%         % amount of hits and sometimes motor activity outside the calculus answer
%         % submission
%         
%         tmp = find(tmp == 1)+1; % what ever follows calculus presentation is a first motor event
%         tmp1 = find(strncmp(t1.Code, "antic", 5)); % unless no motor response was given, then it is a "antic_" event
%         
%         ind = tmp ~= tmp1; % determine which events following a calculus event are not antic events
%         tmp = tmp(ind); % and exclude all others
%         
%         onst2 = t1{tmp,2};


    % antic and feedback events will be concatinated and treated as one
    % for designfiles 
    onst3 = t1{t1.Code == 'antic_correct', 2};
    onst4 = t1{t1.Code == 'antic_false', 2};
    onst5 = t1{t1.Code == 'antic_timeout', 2};
    a_correct = ones(length(onst3),1);
    nr_antic_corr = repmat({'antic_correct'},length(onst3),1);
    a_false = repmat(2,length(onst4),1);
    nr_antic_false = repmat({'antic_false'},length(onst4),1);
    a_timeout = repmat(3,length(onst5),1);
    nr_antic_timeout = repmat({'antic_timeout'},length(onst5),1);
    tmp   = find(strncmp(t1.Code, "verbf", 5));
    onst9 = t1.Time(tmp);
    nr_vfb = repmat({'vb_feedback'},3,1);
    %separate feedback events for .tsv

    onst6 = t1{t1.Code == 'fb_correct', 2};
    onst7 = t1{t1.Code == 'fb_false', 2};
    onst8 = t1{t1.Code == 'fb_timeout', 2};
    nr_fb_corr = repmat({'fb_correct'},length(onst6),1);
    nr_fb_false = repmat({'fb_false'},length(onst7),1);
    nr_fb_timeout = repmat({'fb_timeout'},length(onst8),1);



    % extract durations
    % calculus durations are defined as begin calculus until first motor response

    tmp  = strncmp(t1.Code, "calculus", 8);
    drt1 = t1{find(tmp==1) +1,2} - t1{find(tmp==1),2};

    % define drt2 as any 'antic_*' event - whatever followed the preceding calculus event
    tmp1 = strncmp(t1.Code, "antic", 5);
    drt2 = t1{find(tmp1==1),2} - t1{find(tmp==1) +1,2};
    drt2 = drt2(ind); % use indicator of missing motorevents to remove 0 durations

    % define drt3/4/5 as respective 'fb' event - preceeding 'antic' event
    tmp2 = t1.Code == "antic_correct";
    tmp3 = t1.Code == "fb_correct";
    drt3 = t1{find(tmp3==1),2} - t1{find(tmp2==1),2};
    drt6 = t1{find(tmp3==1)+1,2} - t1{find(tmp3==1),2};
    drt3_des = t1{find(tmp3==1)+1,2} - t1{find(tmp2==1),2}; %concetaned antic+feedback for design
    % drt3tst = t1{find(tmp3==1) +1,2} - t1{find(tmp3==1),2};

    tmp2 = t1.Code == "antic_false";
    tmp3 = t1.Code == "fb_false";
    drt4 = t1{find(tmp3==1),2} - t1{find(tmp2==1),2};
    drt7 = t1{find(tmp3==1)+1,2} - t1{find(tmp3==1),2};
    drt4_des = t1{find(tmp3==1)+1,2} - t1{find(tmp2==1),2};
    % drt4tst = t1{find(tmp3==1) +1,2} - t1{find(tmp3==1),2};

    tmp2 = t1.Code == "antic_timeout";
    tmp3 = t1.Code == "fb_timeout";
    drt5 = t1{find(tmp3==1),2} - t1{find(tmp2==1),2};
    drt8 = t1{find(tmp3==1)+1,2} - t1{find(tmp3==1),2};
    drt5_des = t1{find(tmp3==1)+1,2} - t1{find(tmp2==1),2};


    % duration of verbal feedback is 10 or 15 seconds
    tmp4 = strncmp(t1.Code, "verbf", 5);
    drt9(1) = 100000; drt9(2) = 150000; drt9(3) = 150000;


    % build tsv file inclusive feedback vector (1=correct 2=false 3=timeout)
    [event_onsets,idx] = sort([onst1;onst2;onst3;onst4;onst5;onst6;onst7;onst8;onst9]);
    event_durations = [drt1;drt2;drt3;drt4;drt5;drt6;drt7;drt8;drt9'];
    events = [nr_calc;nr_motor;nr_antic_corr;nr_antic_false;nr_antic_timeout;nr_fb_corr;nr_fb_false;nr_fb_timeout;nr_vfb];
    event_durations = event_durations(idx);
    events = events(idx);
    log_table=table(events,event_onsets,event_durations);
    log_table.events=string(log_table.events);

    [~,idx1]=sort([onst3;onst4;onst5]);
    fb = [a_correct;a_false;a_timeout];
    fb = fb(idx1);
    feedback = nan(size(log_table,1),1);
    feedback(log_table.events=="calc")=fb;
    RT = nan(size(log_table,1),1);
    RT(feedback==1|feedback==2,1)=event_durations(feedback==1|feedback==2);
    log_table = [log_table,table(RT,feedback)];



    log_cell=[log_table.Properties.VariableNames;table2cell(log_table)];
    fid = fopen([subject_path,'/func/sub-',subject_path(end-6:end),'_task-ist_events.tsv'],'wt');
    if fid>0
        fprintf(fid, '%s\t%s\t%s\t%s\t%s\n',log_cell{1,:});
        for k=2:size(log_cell,1)
            fprintf(fid,'%s\t%f\t%f\t%f\t%f\n',log_cell{k,:});
        end
        fclose(fid);
    end





end