% extract 01-Mar-2012 to 31-Oct-2012
% lats 32N-36N, lons 197E-201E

% define desired region
nx=4320;
prec='real*4';
region_name='Box07';
minlat=32;
maxlat=36;
minlon=197;
maxlon=201;
mints=dte2ts('01-Mar-2012',25,2011,9,10);
maxts=dte2ts('01-Nov-2012',25,2011,9,10);

% extract indices for desired region
gdir='~dmenemen/llc_4320/grid/';
fnam=[gdir 'Depth.data'];
[fld fc ix jx] = ...
    quikread_llc(fnam,nx,1,prec,gdir,minlat,maxlat,minlon,maxlon);
quikpcolor(fld')
load ~dmenemen/llc_4320/grid/thk90.mat
bot90=dpt90+thk90/2;
kx=1:min(find(bot90>mmax(fld)));

% Get and save grid information
close all
pin='~dmenemen/llc_4320/grid/';
pout=['~dmenemen/llc_4320/regions/Boxes/' region_name '/grid/'];
eval(['mkdir ' pout])
eval(['cd ' pout])
for fnm={'Depth','RAC','XC','YC','hFacC'}
    fin=[pin fnm{1} '.data'];
    fout=[fnm{1} '_' int2str(length(ix)) 'x' int2str(length(jx))];
    switch fnm{1}
      case{'hFacC'}
        fld=read_llc_fkij(fin,nx,fc,kx,ix,jx);
        fout=[fout 'x' int2str(length(kx))];
      otherwise
        fld=read_llc_fkij(fin,nx,fc,1,ix,jx);
    end
    writebin(fout,fld);
end

% get and save regional Eta and PhiBot
pin='~dmenemen/llc_4320/MITgcm/run';
pout=['~dmenemen/llc_4320/regions/Boxes/' region_name '/'];
for fnm={'Eta','PhiBot'}
    eval(['mkdir ' pout fnm{1}])
    eval(['cd ' pout fnm{1}])
    for ts=mints:144:maxts, mydisp(ts)
        if ts<=485568
            fin=[pin '/' fnm{1} '.' myint2str(ts,10) '.data'];
        else
            fin=[pin '_485568/' fnm{1} '.' myint2str(ts,10) '.data'];
        end
        dy=ts2dte(ts,25,2011,9,10,30);
        fout=[fnm{1} '_' int2str(length(ix)) 'x' int2str(length(jx)) '.' dy];
        fld=read_llc_fkij(fin,nx,fc,1,ix,jx);
        writebin(fout,fld);
    end
end

% get and save regional S/T
for fnm={'Salt','Theta'}
    eval(['mkdir ' pout fnm{1}])
    eval(['cd ' pout fnm{1}])
    for ts=mints:144:maxts, mydisp(ts)
        if ts<=485568
            fin=[pin '/' fnm{1} '.' myint2str(ts,10) '.data'];
        else
            fin=[pin '_485568/' fnm{1} '.' myint2str(ts,10) '.data'];
        end
        dy=ts2dte(ts,25,2011,9,10,30);
        fout=[fnm{1} '_' int2str(length(ix)) 'x' int2str(length(jx)) 'x' int2str(length(kx)) '.' dy];
        for k=1:length(kx); mydisp(k)
            fld=read_llc_fkij(fin,nx,fc,kx(k),ix,jx);
            writebin(fout,fld,1,'real*4',k-1);
        end
    end
end

% get and save regional fields of U and V
% note that zonal velocity is U in faces 1/2 and V in faces 4/5
% and meridional velocity is V in faces 1/2 and -U in faces 4/5
eval(['mkdir ' pout 'U'])
eval(['mkdir ' pout 'V'])
eval(['cd ' pout])
for ts=mints:144:maxts, mydisp(ts)
    if ts<485568
        finu=[pin '/U.' myint2str(ts,10) '.data'];
        finv=[pin '/V.' myint2str(ts,10) '.data'];
    else
        finu=[pin '_485568/U.' myint2str(ts,10) '.data'];
        finv=[pin '_485568/V.' myint2str(ts,10) '.data'];
    end
    dy=ts2dte(ts,25,2011,9,10,30);
    foutu=['U/U_' int2str(length(ix)) 'x' int2str(length(jx)) 'x' int2str(length(kx)) '.' dy];
    foutv=['V/V_' int2str(length(ix)) 'x' int2str(length(jx)) 'x' int2str(length(kx)) '.' dy];
    for k=1:length(kx); mydisp(k)
        fld=read_llc_fkij(finv,nx,fc,kx(k),ix,jx);
        writebin(foutu,fld,1,'real*4',k-1);
        fld=-read_llc_fkij(finu,nx,fc,kx(k),ix,jx-1);
        writebin(foutv,fld,1,'real*4',k-1);
    end
end