OPTIMA_convert_LOG_BIDS_4.m

function OPTIMA_convert_LOG_BIDS_4(BIDS, biomax_table)
%
% copies the logfiles into BIDS format
%
% Required fields of convert_LOG_BIDS:
%
% file history:
% created M. Czisch & F. Binder 8.11.2017
% last M. Czisch 13.11.2019 

fprintf('converting LOG files\n');

% create correct file name
%short_ID = data_set_short_ID(BIDS);
tmp_str = strsplit(BIDS.input.data_dir(1).PatientID{3},'PTP');

short_ID = ['P',tmp_str{2}];
%short_ID = ['P1808'];

cmd_str = sprintf('date >> %s/func/logfile_%s_%s_log_conversion.txt', ...
    BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{3}, BIDS.input.data_dir(1).GivenName{3});
system(cmd_str);

cd([BIDS.input.dir]);
cd('LOG');

filenames = dir([short_ID, '*.log']);
max = size(filenames,1);

% loop over all possible log files

logfile_name_general = ['*SIT1*.log'];
if size(dir(logfile_name_general),1) > 2; error('multiple log files found'); end

for i=1:max
    
    
    clear cmd_str;

    log_str = [short_ID,'-SIT1.log'];
    if strcmp(filenames(i).name,log_str) & biomax_table{{'SIT1'},{'Log'}}
        cmd_str = sprintf('cp %s %s/func/sub-%s_%s_task-sit1_bold.log',log_str, ...
            BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{3}, BIDS.input.data_dir(1).GivenName{3});
        system(cmd_str);
    end
    
    if exist('cmd_str')
        logfilename = sprintf('%s/func/logfile_%s_%s_log_conversion.txt', ...
            BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{3}, BIDS.input.data_dir(1).GivenName{3});
        fid = fopen(logfilename,'a');
        fprintf(fid,'%s\n',cmd_str);
        fclose(fid);
    end
end

filenames = dir([short_ID, '_S1.txt']);
if size(filenames,1) > 2; error('multiple log txt files found'); end
log_str = [short_ID,'_S1.txt'];
if size(filenames,1)
    if strcmp(filenames(1).name,log_str) & biomax_table{{'SIT1'},{'Log'}}
        cmd_str = sprintf('cp %s %s/func/sub-%s_%s_task-sit1_bold_extracted.txt',log_str, ...
            BIDS.output.dir, BIDS.input.data_dir(1).FamilyName{3}, BIDS.input.data_dir(1).GivenName{3});
        system(cmd_str);
    end
end


cd([BIDS.input.dir]);