% rdWETLabs.m
clear; close all; clc; tic
folder='/Volumes/dav/CE01ISSP/R00001/extract';
save_dir = '/Users/michaesm/Documents/CE01ISSP/R00002/data';

cd(folder);
% ACS = ac-s instrument
% DBG = BAT battery, PDBG profiler debug
% PPB = ADCP VELPT, CTD, OCR SPKIR, OPT DOSTA, PARS, TRIP FLORT.
% SNA = SUNA nitrate insturment
% WC = winch controller. HMR depth heading pitch roll, SBE pressure & velocity
%      WDBG winch debug, WM winch motor data
len=1e3;
nodepth=1; % depth didn't transfer to file
disp('ac-s files are raw files, which need WL software for interpreting');

ctd=[]; vel=[]; opt=[]; par=[]; eco=[]; ocr=[]; suna=[];
files=ls;
for i=1:size(files,1)
    if ~isempty(strfind(files(i,:),'CTD')) % CTD profile
        fid=fopen(files(i,1:26));
        for j=1:7; 
            f=fgetl(fid);
        end
        cnt=0;
        data=ones(len,5)*NaN;
        while f~=-1
            cnt=cnt+1;
            if length(f)>15
                data(cnt,1)=eval(['[',f(1:15),']']);
                tmp=eval(['[',f(17:end),']']);
                data(cnt,2:5)=tmp;
            end
            f=fgetl(fid);
        end
        if cnt<len
            data=data(1:cnt,:);
        end
        CTD.dnum=datenum(1970,1,1)+data(:,1)'/24/3600;
        CTD.cels=data(:,2)';
        CTD.cond=data(:,3)';
        CTD.pres=data(:,4)';
        CTD.salt=data(:,5)';
        fclose(fid);
        ctd{length(ctd)+1}=CTD;
        clear data CTD
    elseif ~isempty(strfind(files(i,:),'ADCP')) % VELPT Aquadopp
        fid=fopen(files(i,1:27));
        for j=1:7; f=fgetl(fid); end
        cnt=0;
        data=ones(len,14)*NaN;
        while f~=-1
            tmp=strfind(f,'	');
            if length(tmp)==14
                cnt=cnt+1;
                tmp=strfind(f,'n');
                if isempty(tmp)
                    tmp=strfind(f,'y');
                end
                f=f([1:(tmp-1),(tmp+2):end]);
                tmp=eval(['[',f,']']);
                data(cnt,:)=tmp;
            end
            f=fgetl(fid);
        end
        if cnt<len
            data=data(1:cnt,:);
        end
        VEL.dnum=datenum(1970,1,1)+data(:,1)'/24/3600;
        VEL.depth=data(:,2)';
        VEL.soundspeed=data(:,3)';
        VEL.heading=data(:,4)';
        VEL.pitch=data(:,5)';
        VEL.roll=data(:,6)';
        VEL.dbar=data(:,7)';
        VEL.cels=data(:,8)';
        VEL.V1=data(:,9)';
        VEL.V2=data(:,10)';
        VEL.V3=data(:,11)';
        VEL.amp1=data(:,12)';
        VEL.amp2=data(:,13)';
        VEL.amp3=data(:,14)';
        %disp(files(i,:));
        fclose(fid);
        vel{length(vel)+1}=VEL;
        clear data VEL
    elseif ~isempty(strfind(files(i,:),'OPT')) % DOSTA
        fid=fopen(files(i,1:26));
        for j=1:7; f=fgetl(fid); end
        cnt=0;
        data=ones(len,13)*NaN;
        while f~=-1
            if length(f)>15
                if not(isempty(strfind(f,'?%'))) % ?% shows up mostly in the first line
                    tmp=strfind(f,'?%');
                    f=[f(1:(tmp-1)),f((tmp+2):end)];
                end
                if not(isempty(strfind(f,'%')))
                    tmp=strfind(f,'%');
                    f=[f(1:(tmp-1)),f((tmp+1):end)];
                end
                if not(isempty(strfind(f,'n')))
                    tmp=strfind(f,'n');
                    f=[f(1:(tmp-1)),f((tmp+2):end)];
                end
                if not(isempty(strfind(f,'y')))
                    tmp=strfind(f,'y');
                    f=[f(1:(tmp-1)),f((tmp+2):end)];
                end
                tmp=strfind(f,'	');
                if length(tmp)==12
                    cnt=cnt+1;
                    try
                        tmp=eval(['[',f,']']);
                        data(cnt,:)=tmp;
                    catch
                        disp(f);
                    end
                elseif length(tmp)==13
                    cnt=cnt+1;
                    try
                        tmp=eval(['[',f,']']);
                        data(cnt,:)=tmp([1:5,7:end]);
                    catch
                        disp(f);
                    end                    
                end
            end
            f=fgetl(fid);
        end
        if cnt<len
            data=data(1:cnt,:);
        end
        OPT.dnum=datenum(1970,1,1)+data(:,1)'/24/3600;
        OPT.depth=data(:,2)';
        OPT.modelNum=data(:,3)';
        OPT.serialNum=data(:,4)';
        OPT.mmol=data(:,5)';
        OPT.cels=data(:,6)';
        OPT.a=data(:,7)';
        OPT.b=data(:,8)';
        OPT.c=data(:,9)';
        OPT.d=data(:,10)';
        OPT.e=data(:,11)';
        OPT.f=data(:,12)';
        OPT.g=data(:,13)';
        %disp(files(i,:));
        fclose(fid);
        opt{length(opt)+1}=OPT;
        clear data OPT
    elseif ~isempty(strfind(files(i,:),'PARS')) % PARAD WET Labs PARS
        fid=fopen(files(i,1:27));
        for j=1:7; f=fgetl(fid); end
        cnt=0;
        data=ones(len,4)*NaN;
        while f~=-1
            if not(isempty(strfind(f,'n')))
                tmp=strfind(f,'n');
                f=[f(1:(tmp-1)),f((tmp+2):end)];
            end
            if not(isempty(strfind(f,'y')))
                tmp=strfind(f,'y');
                f=[f(1:(tmp-1)),f((tmp+2):end)];
            end
            tmp=strfind(f,'	');
            if length(strfind(f,'/'))==2 &&  length(strfind(f,':'))==2 && length(tmp)==4
                cnt=cnt+1;
                data(cnt,1:2)=eval(['[',f(1:tmp(2)),']']);
                tmp=eval(['[',f(tmp(4):end),']']);
                if ~isempty(tmp)
                    data(cnt,3)=tmp;
                end
            end
            f=fgetl(fid);
        end
        if cnt<len
            data=data(1:cnt,:);
        end
        PAR.dnum=datenum(1970,1,1)+data(:,1)'/24/3600;
        PAR.depth=data(:,2)';
        PAR.par=data(:,3)';
        %disp(files(i,:));
        fclose(fid);
        par{length(par)+1}=PAR;
        clear data
    elseif ~isempty(strfind(files(i,:),'TRIP')) % FLORT WET Labs ECO Triplet
        fid=fopen(files(i,1:27));
        for j=1:7; f=fgetl(fid); end
        cnt=0;
        data=ones(len,10)*NaN; dates=[];
        while f~=-1
            tmp=strfind(f,'	');
            tpm=f(1:tmp(2));
            f=f((tmp(3)+1):end);
            tmp=strfind(f,'	');
            if length(strfind(f,'/'))==2 &&  length(strfind(f,':'))==2  && length(tmp)==8
                cnt=cnt+1;
                data(cnt,10)=datenum(['[',f(1:tmp(2)),']']);
                tmp=eval(['[',f(tmp(2):end),']']);
                if length(tmp)==7
                    data(cnt,3:9)=tmp;
                    data(cnt,1:2)=eval(['[',tpm,']']);
                end
            else
                % get offset and scale
                tmp=strfind(f,'M1d'); if ~isempty(tmp); M1d=eval(['[',f(4:end),']']); end
                tmp=strfind(f,'M2d'); if ~isempty(tmp); M2d=eval(['[',f(4:end),']']); end
                tmp=strfind(f,'M3d'); if ~isempty(tmp); M3d=eval(['[',f(4:end),']']); end
                tmp=strfind(f,'M1s'); if ~isempty(tmp); M1s=eval(['[',f(4:end),']']); end
                tmp=strfind(f,'M2s'); if ~isempty(tmp); M2s=eval(['[',f(4:end),']']); end
                tmp=strfind(f,'M3s'); if ~isempty(tmp); M3s=eval(['[',f(4:end),']']); end
            end
            f=fgetl(fid);
        end
        if cnt<len
            data=data(1:cnt,:);
        end
        if ~exist('M1d');M1d=46;end
        if ~exist('M2d');M2d=50;end
        if ~exist('M3d');M3d=41;end
        if ~exist('M1s');M1s=3.016E-06;end
        if ~exist('M2s');M2s=1.210E-02;end
        if ~exist('M3s');M3s=9.040E-02;end
        ECO.dnum=datenum(1970,1,1)+data(:,1)'/24/3600;
        ECO.depth=data(:,2)';
        ECO.ddnum=data(:,10)';
        ECO.freq1=data(:,3)'; %700 OBS
        ECO.OBS=(data(:,4)'-M1d)*M1s;
        ECO.freq2=data(:,5)'; %695 Chlorophyll
        ECO.CHLa=(data(:,6)'-M2d)*M2s;
        ECO.freq3=data(:,7)'; % 460 CDOM
        ECO.CDOM=(data(:,8)'-M3d)*M3s;
        ECO.cnt=data(:,9)';
        %disp(files(i,:));
        fclose(fid);
        eco{length(eco)+1}=ECO;
        clear data
    elseif ~isempty(strfind(files(i,:),'OCR')) % SPKIR Satlantic OCR507
        fid=fopen(files(i,1:27));
        for j=1:7; f=fgetl(fid); end
        cnt=0;
        data=ones(len,16)*NaN; dates=[];
        while f~=-1
            tmp=strfind(f,'	');
            tpm=f(1:tmp(2));
            f=f((tmp(3)+1):end);
            tmp=strfind(f,'	');
            if not(isempty(strfind(f,'SATDI'))) && length(tmp)==15
                cnt=cnt+1;
                data(cnt,1:2)=eval(['[',tpm,']']);
                data(cnt,3:16)=eval(['[',f(tmp(1):tmp(15)),']']);
            end
            f=fgetl(fid);
        end
        if cnt<len
            data=data(1:cnt,:);
        end
        OCR.dnum=datenum(1970,1,1)+data(:,1)'/24/3600;
        OCR.depth=data(:,2)';
        OCR.SN=data(:,3)';
        OCR.one=data(:,4)';
        OCR.two=data(:,5)';
        OCR.freq=data(:,6:12)';
        OCR.cnts=data(:,13:15)';
        OCR.num=data(:,16)';
        %disp(files(i,:));
        fclose(fid);
        ocr{length(par)+1}=OCR;
        clear data
    elseif ~isempty(strfind(files(i,:),'SNA')) % SUNA Nitrate
        fid=fopen(files(i,1:26));
        for j=1:8; f=fgetl(fid); end
        cnt=0;
        data=ones(len,4)*NaN;
        while f~=-1
            if strfind(f,'SLB') % light only.  Dark is SDB
                tmp=strfind(f,'	');
                if length(tmp)>10
                    cnt=cnt+1;
                    data(cnt,1:2)=eval(['[',f(1:tmp(2)),']']);
                    dex=strfind(f,'SLB'); f=f(dex:end); tmp=strfind(f,'	');
                    data(cnt,3:4)=eval(['[',f(tmp(4):tmp(6)),']']);
                end
            end
            f=fgetl(fid);
        end
        if cnt>0
            if cnt<len
                data=data(1:cnt,:);
            end
            SNA.dnum=datenum(1970,1,1)+data(:,1)'/24/3600;
            SNA.depth=data(:,2)';
            SNA.NO3umol=data(:,3)';
            SNA.NmgL=data(:,4)'; %full spectra are in the files. It's metadata, so I'm not going to read them here.
            %disp(files(i,:));
            fclose(fid);
            suna{length(suna)+1}=SNA;
            clear data SNA
        end
    else
        if isempty(strfind(files(i,:),'WC'))
            disp([files(i,:),' XXXXXXXXX']);
        end
    end
end
toc
disp('done data files'); tic
%%
% WC = winch controller. HMR depth heading pitch roll, SBE pressure & velocity
%      WDBG winch debug, WM winch motor data
hmr=[]; sbe=[]; wdbg=[]; wm=[]; wb=[]; wsum=[];
files=ls;
for i=1:size(files,1)
    if ~isempty(strfind(files(i,:),'HMR')) % heading, pitch, roll
        fid=fopen(files(i,1:26));
        for j=1:7; f=fgetl(fid); end
        cnt=0;
        data=ones(len,5);
        while f~=-1
            cnt=cnt+1;
            if not(isempty(strfind(f,'n')))
                tmp=strfind(f,'n');
                f=[f(1:(tmp-1)),f((tmp+2):end)];
            end
            if not(isempty(strfind(f,'y')))
                tmp=strfind(f,'y');
                f=[f(1:(tmp-1)),f((tmp+2):end)];
            end
            data(cnt,:)=eval(['[',f,']']);
            f=fgetl(fid);
        end
        fclose(fid);
        if cnt<len
            data=data(1:cnt,:);
        end
        HMR.dnum=datenum(1970,1,1)+data(:,1)'/24/3600;
        HMR.depth=data(:,2)';
        HMR.pitch=data(:,3)';
        HMR.roll =data(:,4)';
        HMR.heading=data(:,5)';
        hmr{length(hmr)+1}=HMR;
        clear HMR;
%         disp(files(i,:));
    elseif ~isempty(strfind(files(i,:),'SBE')) % fast pressure
        fid=fopen(files(i,1:26));
        for j=1:7; f=fgetl(fid);end% disp(f); end
        cnt=0;
        data=ones(len,3);
        while f~=-1
            cnt=cnt+1;
            if not(isempty(strfind(f,'n')))
                tmp=strfind(f,'n');
                f=[f(1:(tmp-1)),f((tmp+2):end)];
            end
            if not(isempty(strfind(f,'y')))
                tmp=strfind(f,'y');
                f=[f(1:(tmp-1)),f((tmp+2):end)];
            end
            tmp=eval(['[',f,']']);
            if length(tmp)==3
                data(cnt,:)=tmp';
            else
                cnt = cnt-1; 
            end
            f=fgetl(fid);
        end
        fclose(fid);
        if cnt<len
            data=data(1:cnt,:);
        end
        SBE.dnum=datenum(1970,1,1)+data(:,1)'/3600/24;
        SBE.depth=data(:,2)';
        SBE.velocity=data(:,3)';
        sbe{length(sbe)+1}=SBE;
        clear SBE;
%         disp(files(i,:));
    elseif ~isempty(strfind(files(i,:),'WDBG')) % notes
        wdbg{length(wdbg)+1}='place holder';
    elseif ~isempty(strfind(files(i,:),'WM')) % winch status
        fid=fopen(files(i,1:25));
        for j=1:7; f=fgetl(fid); end
        cnt=0; data=ones(len,11);
        while f~=-1
            cnt=cnt+1;
            f(f=='F')='0';
            if not(isempty(strfind(f,'n')))
                tmp=strfind(f,'n');
                f=[f(1:(tmp-1)),f((tmp+2):end)];
            end
            if not(isempty(strfind(f,'y')))
                tmp=strfind(f,'y');
                f=[f(1:(tmp-1)),f((tmp+2):end)];
            end
            if not(isempty(strfind(f,'A')))
                tmp=strfind(f,'A');
                f=[f(1:(tmp-1)),f((tmp+2):end)];
            end
            data(cnt,:)=eval(['[',f,']']);
            f=fgetl(fid);
        end
        fclose(fid);
        WM.dnum=datenum(1970,1,1)+data(:,1)'/24/3600;
        WM.depth=data(:,2)';
        WM.encoderCounts=data(:,3)';
        WM.amps=data(:,4)';
        WM.status=data(:,5)';
        WM.vel=data(:,6)';% cm/s
        WM.cels=data(:,7)';
        WM.volt=data(:,8)';
        WM.timeCounts=data(:,9)';
        WM.dischargeCounts=data(:,10)';
        WM.ropeOnDrum=data(:,11)'; % m
        wm{length(wm)+1}=WM;
        clear WM;
%         disp(files(i,:));
    elseif ~isempty(strfind(files(i,:),'SUM')) % wave summary
        fid=fopen(files(i,1:12)); %disp(['SUM ',files(i,:)]);
        for jj=1:22
            f=fgetl(fid); 
        end
        fclose(fid);
        WSUM.Hs=eval(['[',f(9:17),']']); % calculated wave height
        % open WC_SBE file to get the date
        fid=fopen(['ucspp_',files(i,1:8),'_PPB_CTD.txt']); 
        for j=1:7
            f=fgetl(fid);
        end
        tmp=eval(f(1:14));
        WSUM.dnum=datenum(1970,1,1)+tmp'/3600/24;
        fclose(fid);
        wsum{length(wsum)+1}=WSUM;
    elseif ~isempty(strfind(files(i,:),'WB')) % wave burst
        fid=fopen(files(i,1:11));
        f=fgetl(fid); f=fgetl(fid);
        cnt=0; data=ones(len,4);
        while f~=-1
            cnt=cnt+1;
            data(cnt,:)=eval(['[',f,']']);
            f=fgetl(fid);
        end
        fclose(fid);
        if cnt<len
            data=data(1:cnt,:);
        end
        psi=mean(data,2); dbar=psi/.689;
        % dt=0.0625*4; plot((1:cnt)*dt,d); % ASSUME 12 sec wave
        % linearWaveVsDepth.m
        % h=25; z=0:h; plot(1./cosh((h-z)*2*pi/165),h-z); set(gca,'ydir','rev');
        % h=87; z=0:h; plot(1./cosh((h-z)*2*pi/220),h-z); set(gca,'ydir','rev');
        % pressure attenuation.  Divide by 0.75 for 25m site, 0.25 for 87m site.
        % sig wave height = 4 * std
        WB.Hs=4*std(dbar); % m.  Needs pressure attenuation correction
        WB.dbar=dbar;
        % open WC_SBE file to get the date
        fid=fopen(['ucspp_',files(i,1:8),'_PPB_CTD.txt']);
        for j=1:7
            f=fgetl(fid);
        end
        tmp=eval(f(1:14));
        WB.dnum=datenum(1970,1,1)+tmp'/3600/24;
        tmp=eval(['[',f(17:end),']']);
        WB.start=tmp(3);
        fclose(fid);
        wb{length(wb)+1}=WB;
    else
        % disp([files(i,:),' XXXXXXXXX']);
    end
end
%%
toc
disp('done winch files');
% no acs yet
save([save_dir '/wetcspp'], 'suna', 'wb', 'wsum', 'ctd', 'par', 'vel',...
    'ocr', 'opt', 'eco', 'sbe', 'hmr', 'wm', 'files', 'wdbg');

toc