% rawm_all_scr;
run_dir = '/Volumes/DATADRIVE/argo/AtlanticIndex/';
tmp = dir(run_dir);
numfiles=length(tmp);
name2=tmp(1).name;
for ndo=1:numfiles
    name1=tmp(ndo).name;
    % Want to know if there's already a mat file.
    doneflag=0;
    if name2(1)=='a'
        if name2(end-1)=='a'
        if strcmp(name1(1:end-3),name2(1:end-3))
            doneflag=1;
        end
        end
    end
    if doneflag==0
        if name1(1)=='a'
            if name1(end-1)=='x'
                % Then it's a txt file starting with at
                [colname,data]=read_argotxt_write_mat(run_dir,name1(1:end-4),run_dir);
%                plot_argo(data);

            end
        end
    end
    name2=name1;
end
%%
fid = fopen('plot_argo3.xyz','w+'); % updated to 3 in Sept 2011
sdo=0;
for tdo=1:numfiles
    name1=tmp(tdo).name;
    if name1(1)=='a'&name1(end-1)=='a' % then is a mat-file
        eval(['load ',run_dir,name1]);
    
        for ndo=1:length(data)
            callsign1 = data(ndo).callSign;
            lat1 = num2str(data(ndo).latitude);
            lon1 = num2str(data(ndo).longitude);
            mydatestr=data(ndo).date;
            date = datenum(data(ndo).date,'yyyy-mm-dd');
            yr = year(date);
            yday=myyearday(date);
            printstr = [lat1,' ',lon1,' ',mydatestr,' ',callsign1,'\n'];
            fprintf(fid,printstr);
            
            
            sdo=sdo+1;
            alldata(sdo).callsign=callsign1;
            alldata(sdo).lat=lat1;
            alldata(sdo).lon=lon1;
            alldata(sdo).date=date;
        end
        
    end
end
fclose(fid);
%% Plot argo floats by month in a daterange
dstart=datenum(2003,01,01);
dend=datenum(2005,12,31);
latlim=[54 70];
lonlim=[-65 -42];
qdo=0;
SS=length(alldata);
clear allcallsign alllat alllon alldate
for sdo=1:SS
    date1=alldata(sdo).date;
    if date1>=dstart&date1<=dend
        lat1=str2num(alldata(sdo).lat);
        lon1=str2num(alldata(sdo).lon);
        isbetw=findbetw(lat1,latlim)*findbetw(lon1,lonlim);
        if length(isbetw)
            qdo=qdo+1;
            allcallsign(qdo)=str2num(alldata(sdo).callsign);
            alllat(qdo)=lat1;
            alllon(qdo)=lon1;
            alldate(qdo)=date1;
        end
    end
end

disp(['In the geographic region ',num2str(latlim),'N and ',num2str(lonlim),'E, '])
disp(['There are ',num2str(qdo),' profiles between ',datestr(dstart),' and ',datestr(dend),'.'])
uniqCS=unique(allcallsign);
disp(['There are ',num2str(length(uniqCS)),' unique floats ']);

if ~exist('bathy')
    load /Users/eleanor/matlab/_bathy/etopo2/widesubp_bathy_struct.mat
end
figure(3)
clf
contour(bathy.lon,bathy.lat,bathy.depth,[-4000:1000:0],'k')
hold on
plot(alllon,alllat,'*')
%% Plot profiles by month
lonlim1=[minmin(alllon) maxmax(alllon)];
latlim1=[minmin(alllat) maxmax(alllat)];
for yr=2003:2005
    figure(yr)
    clf
    for month=1:12
        dstart1=datenum(yr,month,01);
        dend1=datenum(yr,month+1,0);
        ifind=findbetw(alldate,[dstart1 dend1]);
        nummo(month)=length(ifind);
        if 0
        subplot(3,4,month)
        contour(bathy.lon,bathy.lat,bathy.depth,[-4000:1000:0],'k')
        hold on
        plot(alllon(ifind),alllat(ifind),'*')
        set(gca,'xlim',lonlim1,'ylim',latlim1);
        text(-48.5,latlim1(2)-1,datestr(datenum(0,month,1),'mmm'))
        if month==2
            title([num2str(yr),': Argo profiles by month'])
        end
        end
    end
    disp(['For ',num2str(yr),' total: ',num2str(sum(nummo))])
    num2str(nummo)
    if 0
    packboth(3,4)
    fontsize('default')
    papersize('landscape')
    end
end
%% Load glider profiles
if 0
load /Users/eleanor/matlab/glider/sg004b/labseaeven_sg004_200807.mat
sg004.date=meanNaN(TI3/86400,2);
sg004.lon=meanNaN(LON3,2);
sg004.lat=meanNaN(LAT3,2);
sg004.s = S3;
sg004.t = T3;
sg004.p = peven;

load /Users/eleanor/matlab/glider/sg008b/labseaeven_sg008_200807.mat
sg008.date=meanNaN(TI3/86400,2);
sg008.lon=meanNaN(LON3,2);
sg008.lat=meanNaN(LAT3,2);
sg008.s = S3;
sg008.t = T3;
sg008.p = peven;

load /Users/eleanor/matlab/glider/sg015b/labseaeven_sg015_200807.mat
sg015.date=meanNaN(TI3/86400,2);
sg015.lon=meanNaN(LON3,2);
sg015.lat=meanNaN(LAT3,2);
sg015.s = S3;
sg015.t = T3;
sg015.p = peven;

load /Users/eleanor/matlab/glider/sg014b/process/labseagrid_sg014_200711.mat
sg014.date=meanNaN(TI2/86400,2);
sg014.lon=meanNaN(LON2,2);
sg014.lat=meanNaN(LAT2,2);
sg014.s = S2;
sg014.t = T2;
sg014.p = pgrid;

load /Users/eleanor/matlab/glider/sg016b/labseaeven_sg016_200901ox.mat
sg016.date=meanNaN(TI3/86400,2);
sg016.lon=meanNaN(LON3,2);
sg016.lat=meanNaN(LAT3,2);
sg016.s = S3;
sg016.t = T3;
sg016.p = peven;
%% Create a big list
clear gliderdate gliderlon gliderlat
MM=length(sg004.date);
r1=1:MM;
gliderdate(r1)=sg004.date;
gliderlon(r1)=sg004.lon;
gliderlat(r1)=sg004.lat;
for rdo=1:MM
    glider(r1(rdo)).date=sg004.date(rdo);
    glider(r1(rdo)).s = sg004.s(rdo,:);
    glider(r1(rdo)).t = sg004.t(rdo,:); 
    glider(r1(rdo)).p = sg004.p;
end

MM=length(sg008.date);
r1=r1(end)+[1:MM];
gliderdate(r1)=sg008.date;
gliderlon(r1)=sg008.lon;
gliderlat(r1)=sg008.lat;
for rdo=1:MM
    glider(r1(rdo)).date=sg008.date(rdo);
    glider(r1(rdo)).s = sg008.s(rdo,:);
    glider(r1(rdo)).t = sg008.t(rdo,:); 
    glider(r1(rdo)).p = sg008.p;
end

MM=length(sg014.date);
r1=r1(end)+[1:MM];
gliderdate(r1)=sg014.date;
gliderlon(r1)=sg014.lon;
gliderlat(r1)=sg014.lat;
for rdo=1:MM
    glider(r1(rdo)).date=sg014.date(rdo);
    glider(r1(rdo)).s = sg014.s(rdo,:);
    glider(r1(rdo)).t = sg014.t(rdo,:); 
    glider(r1(rdo)).p = sg014.p;
end



MM=length(sg015.date);
r1=r1(end)+[1:MM];
gliderdate(r1)=sg015.date;
gliderlon(r1)=sg015.lon;
gliderlat(r1)=sg015.lat;
for rdo=1:MM
    glider(r1(rdo)).date=sg015.date(rdo);
    glider(r1(rdo)).s = sg015.s(rdo,:);
    glider(r1(rdo)).t = sg015.t(rdo,:); 
    glider(r1(rdo)).p = sg015.p;
end

MM=length(sg016.date);
r1=r1(end)+[1:MM];
gliderdate(r1)=sg016.date;
gliderlon(r1)=sg016.lon;
gliderlat(r1)=sg016.lat;
for rdo=1:MM
    glider(r1(rdo)).date=sg016.date(rdo);
    glider(r1(rdo)).s = sg016.s(rdo,:);
    glider(r1(rdo)).t = sg016.t(rdo,:); 
    glider(r1(rdo)).p = sg016.p;
end

dt=30;
[glidermld] = do_glider_mld(glider,dt);


%% Plot glider and argo profiles by month
plotflag=1;
lonlim1=[minmin([alllon gliderlon]) maxmax([alllon gliderlon])];
latlim1=[minmin([alllat gliderlat]) maxmax([alllat gliderlat])];
for yr=2003:2005
    if plotflag
    figure(yr)
    clf
    papersize('landscape')
    end
    for month=1:12
        dstart1=datenum(yr,month,01);
        dend1=datenum(yr,month+1,0);
        ifind=findbetw(alldate,[dstart1 dend1]);
        ifind2=findbetw(gliderdate,[dstart1 dend1]);
        nummo(month)=length(ifind);
        nummo2(month)=length(ifind2);
        if plotflag
            subplot(3,4,month)
            contour(bathy.lon,bathy.lat,bathy.depth,[-4000:1000:0],'k')
            hold on
            plot(gliderlon(ifind2),gliderlat(ifind2),'r.')
            plot(alllon(ifind),alllat(ifind),'*')
            set(gca,'xlim',lonlim1,'ylim',latlim1);
            text(-48.5,latlim1(2)-1,datestr(datenum(0,month,1),'mmm'))
            if month==2
                title([num2str(yr),': Glider+Argo profiles by month'])
            end
        end
    end
    disp(['For ',num2str(yr),' #Argo: ',num2str(sum(nummo)),', #glider: ',num2str(sum(nummo2))])
    num2str(nummo)
    num2str(nummo2)
    if plotflag
        packboth(3,4)
        fontsize('default')
    end
end
end
%% Gunzip and untar them
% DO YOU REALLY DO THIS, OR READ OTHER DATA FILES?  RNWM_ALL_SCR3.m??
% After downloading the float .tgz files
cd /Volumes/DATADRIVE/argo/AtlanticData/tgz
eval(['!gunzip *gz'])
for sdo=1:length(uniqCS)
    
    eval(['!tar -xvf ',num2str(uniqCS(sdo)),'.tar'])
end
%% Find a particular argo float
latrange = [50 68]; lonrange = [-70 -40];
latrange = [63 64]; lonrange = [-55 -65];
for ddo=1:length(dvec)
   ystr = num2str(dvec(ddo,1));
    if dvec(ddo,2)<10
        mstr = ['0' num2str(dvec(ddo,2))];
    else
        mstr = num2str(dvec(ddo,2));
    end
    filename = ['at',ystr,mstr,'_argoinv'];
    eval(['load ',output_dir,filename,'.mat']);

    for ndo=1:length(data)
        lat1 = data(ndo).latitude;
        if (lat1 > min(latrange))&(lat1<=max(latrange))
            lon1 = data(ndo).longitude;
            if (lon1>min(lonrange))&(lon1<=max(lonrange))
                disp(['Float ',data(ndo).callSign,' is at datacenter ',data(ndo).data_center,' at ',num2str(lat1),'N and ',num2str(lon1),' E'])
    data(ndo)
            end
        end
    end
end
%%
allsign=[];
labsealat = [52 67];
labsealon = [-70 -45];
fid = fopen('plot_argo6900274.xyz','w+');
for ddo=1
    ystr = num2str(dvec(ddo,1));
    if dvec(ddo,2)<10
        mstr = ['0' num2str(dvec(ddo,2))];
    else
        mstr = num2str(dvec(ddo,2));
    end
    filename = ['at',ystr,mstr,'_argoinv'];
    eval(['load ',output_dir,filename,'.mat']);
    [days]=  plot_argo(data);

    for ndo=1:length(data)
        callsign1 = data(ndo).callSign;
        lat1 = str2num(data(ndo).latitude);
        lon1 = str2num(data(ndo).longitude);
        if (lat1>min(labsealat))&(lat1<=max(labsealat))
            if (lon1>min(labsealon))&(lon1<=max(labsealon))
                allsign = union(allsign,str2num(callsign1));
                if str2num(callsign1) ==6900274
                    file1 = data(ndo).file;
                    profnum =str2num(file1(end-5:end-3));
                    if sum(profnum==[11:22])
                        daynum = num2str(days(ndo));
                        yday = data(ndo).date;
                        printstr = [num2str(lat1),' ',num2str(lon1),' ',yday,' ',daynum,' ',callsign1,'\n'];
                        fprintf(fid,printstr);
                    end
                end
            end
        end
    end
end
fclose(fid);