input_dir = '/home/eleanor/data/WOD/wod05/';
filename1 = 'ocldb1169076334.845.'; % FAROES SMALL
rep = [4 1 4 1 3];
filename1 = 'ocldb1170103337.8037.'; % FAROES BIG
rep = [25 1 19 2 12];
inst = ['CTD';'DRB';'OSD';'PFL';'XBT'];

filename1 = 'ocldb1170866160.12282.'; % LABRADOR SEA
input_dir = '/home/eleanor/data/WOD/wod05/labsea/';
output_dir = '/home/eleanor/matlab/bin/glider/WOD/wod05/mat/';

% CTD, CTD2, CTD3, CTD4, DRB, OSD, OSD2, OSD3, OSD4,PFL, XBT, XBT2, XBT3
inst = ['DRB';'OSD';'PFL';'XBT';'MBT';'CTD'];
inst = ['DRB';'PFL';'OSD';'XBT';'MBT';'CTD']
rep = [1 11 12 16 34 56]; % DRB, PFL, OSD, XBT,MBT, CTD for Lab sea
rep = [1 11 12 16 34 56]; % CRASHED ON OSD7, data(:,11) L 99, depth=
%rep = [4 1 4 1 3];
ext4 = '.csv';

%% Make sure all the data files exist first
for ff = 1:length(inst)
    for rr = 1:rep(ff)
        if rr==1
            filename2 = inst(ff,:);
        else
            filename2 = [inst(ff,:),num2str(rr)];
        end
        filename = [filename1,filename2];
        longfile = [input_dir,filename,ext4];
        fid=fopen(longfile);
        if fid==-1
            disp(['Missing file ',longfile]);
        end
        fclose(fid);
    end
end
disp('All data files exist.');
disp('Type any key to continue...');
pause
%% Clean files
disp('Cleaning...')
qdo=0;
for ff = 1:length(inst)
    for rr = 1:rep(ff)
        if rr==1
            filename2 = inst(ff,:);
        else
            filename2 = [inst(ff,:),num2str(rr)];
        end
        filename = [filename1,filename2];
        ext4 = '.csv';
        replace_str ='       ';
        find_str = '---.---';
        tic
        file_clean = clean_files(input_dir,filename,ext4,find_str,replace_str,input_dir);
        qdo=qdo+1;
        time1(qdo)=toc;
        avetime = mean(time1);
        disp(['Cleaned ',filename,' in ',num2str(time1(qdo)),'.  Ave time = ',num2str(avetime)]);
    end
end
disp('All data files are cleaned of ---.---');
disp('Type any key to continue...');
pause
%% Read cleaned .csv files and write to .mat
for ff = 1:length(inst)
    for rr = 1:rep(ff)
        if rr==1
            filename2 = inst(ff,:);
        else
            filename2 = [inst(ff,:),num2str(rr)];
        end
        file_clean = [filename1,filename2,'C'];
%        if ~exist([output_dir,file_clean,'.mat'])
            disp(['Parsing ',file_clean]);
            read_ocldb_write_mat(input_dir,file_clean,output_dir,inst(ff,:));
%        end
    end
end
disp('All data files have been parsed to .mat');
disp('Type any key to continue...');
pause
%% Create huge array structure, all_cast
zdo=0;
for ff = 1:length(inst)
    for rr = 1:rep(ff)
        if rr==1
            filename2 = inst(ff,:);
        else
            filename2 = [inst(ff,:),num2str(rr)];
        end
        file_clean = [filename1,filename2,'C'];
        eval(['load ',output_dir,file_clean,'.mat']);
%        cast1=cast;
 %       eval(['save ',output_dir,file_clean,'.mat cast1']);
        CC = length(cast1);
        
        all_cast(zdo+1:zdo+CC) = cast1(1:CC);
        
        zdo=zdo+CC
    end
end

disp('All casts have been loaded into variable all_cast')
disp('Type "save allcast_long.mat all_cast to save the variable');