OPTIMA_convert_ANALYZER_BIDS_2.m

function convert_ANALYZER_BIDS_2(BIDS, biomax_table)
%
% copies the ANALYZER files into BIDS format
%
%
% file history:
% created M. Czisch 26.2.2018
% last M. Czisch 27.3.2018

number_of_days = size(BIDS.input.data_dir,2);

%if number_of_days > 1   % to consider possible missing day 2
    
    fprintf('converting Analyzer files\n');
    
    cmd_str = sprintf('mkdir %s/physio', BIDS.output.dir); system(cmd_str);
    
    logfilename = sprintf('%s/physio/logfile_%s_analyzer_conversion.txt', BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
    cmd_str = sprintf('date >> %s', logfilename);
    system(cmd_str);
    fid = fopen(logfilename,'a');
    
    cd([BIDS.input.dir]);
    cd('ANALYZER');
    
    
    fprintf(fid,'%s\n',cmd_str);
    
    % work on faces
    if biomax_table{{'rest1'},{'Analyzer'}}
        filename = [BIDS.input.data_dir(1).PatientID{3},'_faces'];
        
        cmd_str = sprintf('cp %s.eeg %s/physio/sub-%s_task-rest1_eeg.eeg',...
            filename, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        system(cmd_str); fprintf(fid,'%s\n',cmd_str);
        cmd_str = sprintf('cp %s.vhdr %s/physio/sub-%s_task-rest1_eeg.vhdr',...
            filename, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        system(cmd_str); fprintf(fid,'%s\n',cmd_str);
        cmd_str = sprintf('cp %s.vmrk %s/physio/sub-%s_task-rest1_eeg.vmrk',...
            filename, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        system(cmd_str); fprintf(fid,'%s\n',cmd_str);
    end
    % work on IST
    if biomax_table{{'SIT1'},{'Analyzer'}}
        filename = [BIDS.input.data_dir(1).PatientID{3},'_ist'];
        
        cmd_str = sprintf('cp %s.eeg %s/physio/sub-%s_task-sit1_eeg.eeg',...
            filename, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        system(cmd_str); fprintf(fid,'%s\n',cmd_str);
        cmd_str = sprintf('cp %s.vhdr %s/physio/sub-%s_task-sit1_eeg.vhdr',...
            filename, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        system(cmd_str); fprintf(fid,'%s\n',cmd_str);
        cmd_str = sprintf('cp %s.vmrk %s/physio/sub-%s_task-sit1_eeg.vmrk',...
            filename, BIDS.output.dir, BIDS.input.data_dir(1).PatientID{3});
        system(cmd_str); fprintf(fid,'%s\n',cmd_str);
    end
    
    fclose(fid);
    
%end

cd([BIDS.input.dir]);