OPTIMA_convert_EDF_BIDS_2.m

function OPTIMA_convert_EDF_BIDS_2(BIDS, biomax_table)
%
% copies the edf files into BIDS format
%
% Required fields of convert_EDF_BIDS:
%
% file history:
% created M. Czisch 31.1.2018
% last M. Czisch 10.9.2019

if logical(sum(biomax_table{:,{'EDF'}}))
    
    fprintf('converting EDF 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('mkdir %s/physio', BIDS.output.dir); system(cmd_str);
    
    cmd_str = sprintf('date >> %s/physio/logfile_%s_edf_conversion.txt', BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
    system(cmd_str);
    
    cd([BIDS.input.dir]);
    cd('EDF');
    
    filenames = dir(['*', short_ID, '*.edf']);
    max = size(filenames,1);
    
    % loop over all possible log files
    
    for i=1:max
        
        
        clear cmd_str cmd_str2;
        
        log_str = [short_ID,'S1.edf'];
        if strcmp(filenames(i).name,log_str) & biomax_table{{'SIT1'},{'EDF'}}
            cmd_str = sprintf('cp %s %s/physio/sub-%s_task-sit1_bold.edf',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
            system(cmd_str);
            log_str = [short_ID,'S1.asc'];
            if exist(log_str)
                cmd_str2 = sprintf('cp %s %s/physio/sub-%s_task-sit1_bold.asc',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
                system(cmd_str2);
            elseif exist(['/run/media/spectro/DATAPART1/FORSCHUNGSAMBULANZ/ASC/', short_ID,'S1.asc'])
                log_str = ['/run/media/spectro/DATAPART1/FORSCHUNGSAMBULANZ/ASC/', short_ID,'S1.asc'];
                cmd_str2 = sprintf('cp %s %s/physio/sub-%s_task-sit1_bold.asc',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
                system(cmd_str2);
            else
                cmd_str2 = sprintf('no asc file found');
            end
        end
        
        log_str = ['RS', short_ID,'.edf'];
        if strcmp(filenames(i).name,log_str) & biomax_table{{'rest1'},{'EDF'}}
            cmd_str = sprintf('cp %s %s/physio/sub-%s_task-rest_run-1_bold.edf',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
            system(cmd_str);
            log_str = ['RS', short_ID,'.asc'];
            if exist(log_str)
                cmd_str2 = sprintf('cp %s %s/physio/sub-%s_task-rest_run-1_bold.asc',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
                system(cmd_str2);
            elseif exist(['/run/media/spectro/DATAPART1/FORSCHUNGSAMBULANZ/ASC/RS', short_ID,'.asc'])
                log_str = ['/run/media/spectro/DATAPART1/FORSCHUNGSAMBULANZ/ASC/RS', short_ID,'.asc'];
                cmd_str2 = sprintf('cp %s %s/physio/sub-%s_task-rest_run-1_bold.asc',log_str, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
                system(cmd_str2);
            else
                cmd_str2 = sprintf('no asc file found');
            end
        end
                
        
        if exist('cmd_str')
            logfilename = sprintf('%s/physio/logfile_%s_edf_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
        if exist('cmd_str2')
            logfilename = sprintf('%s/physio/logfile_%s_edf_conversion.txt', BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
            fid = fopen(logfilename,'a');
            fprintf(fid,'%s\n',cmd_str2);
            fclose(fid);
        end
    end
    
end

cd([BIDS.input.dir]);