repair_PPG_BIDS.m

function repair_PPG_BIDS(BIDS, biomax_table)
%
% copies the ppg files into BIDS format
% for datasets before 29.5.2018 (old Become Version 1.0.1)
%
% file history:
% created M. Czisch 29.5.2018

sum_table = sum(biomax_table{:,{'PPG'}});

if sum_table > 0
    
    fprintf('converting PPG and RESP files\n');
    
    % create correct file name
    
    short_ID = data_set_short_ID(BIDS);
    
    %cmd_str = sprintf('mkdir %s/physio', BIDS.output.dir); system(cmd_str);
    
    cmd_str = sprintf('date >> %s/physio/logfile_%s_ppg_resp_conversion.txt', BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
    system(cmd_str);
    
    cd([BIDS.input.dir]);
    cd('PPG_Tag1');
    
    filenames_ppg = dir(['PPGData_epiRT_*']);
    max = size(filenames_ppg,1);
    filenames_resp = dir(['RESPData_epiRT_*']);
    
%     if max ~= sum_table
%         error('Error. \nnumber of ppg files does not match biomax_out\n');
%     end
    
    j = 1;
    clear cmd_str;
    
    if biomax_table{4,{'PPG'}}  % rest1
        cmd_str = sprintf('cp %s %s/physio/sub-%s_task-rest_run-1_ppg.txt',filenames_ppg(j).name, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        system(cmd_str); print2log(cmd_str);
        cmd_str = sprintf('cp %s %s/physio/sub-%s_task-rest_run-1_resp.txt',filenames_resp(j).name, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        system(cmd_str); print2log(cmd_str);
        j = j+1;
    end
    if biomax_table{6,{'PPG'}}  % TET
        cmd_str = sprintf('cp %s %s/physio/sub-%s_task-tet_ppg.txt',filenames_ppg(j).name, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        system(cmd_str); print2log(cmd_str);
        cmd_str = sprintf('cp %s %s/physio/sub-%s_task-tet_resp.txt',filenames_resp(j).name, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        system(cmd_str); print2log(cmd_str);
        j = j+1;
    end
    if biomax_table{8,{'PPG'}}  % Reward
        cmd_str = sprintf('cp %s %s/physio/sub-%s_task-reward_ppg.txt',filenames_ppg(j).name, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        system(cmd_str); print2log(cmd_str);
        cmd_str = sprintf('cp %s %s/physio/sub-%s_task-reward_resp.txt',filenames_resp(j).name, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        system(cmd_str); print2log(cmd_str);
        j = j+1;
    end
    if biomax_table{11,{'PPG'}}  % nack
        cmd_str = sprintf('cp %s %s/physio/sub-%s_task-nback_ppg.txt',filenames_ppg(j).name, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        system(cmd_str); print2log(cmd_str);
        cmd_str = sprintf('cp %s %s/physio/sub-%s_task-nback_resp.txt',filenames_resp(j).name, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        system(cmd_str); print2log(cmd_str);
    end
    
end

cd([BIDS.input.dir]);


    function print2log(cmd_str)
        logfilename = sprintf('%s/physio/logfile_%s_ppg_resp_conversion.txt', BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        fid = fopen(logfilename,'a');
        fprintf(fid,'%s\n',cmd_str);
        fclose(fid);
    end

end