% Tasmania region for Kyla Drushka and Luc Rainville
% extract Eta, Phibot, Salt, and Theta
% for 13-Sep-2011 to 15-Nov-2012
% lats 48S to 40S, 141E to 154E
% (example extraction on face 2-4)

% define desired region
nx=4320;
prec='real*4';
region_name='Tasmania';
minlat=-48;
maxlat=-40;
minlon=141;
maxlon=154;
mints=dte2ts('13-Sep-2011',25,2011,9,10);
maxts=dte2ts('15-Nov-2012',25,2011,9,10);

% extract indices for desired region
gdir='~dmenemen/llc_4320/grid/';
fnam=[gdir 'Depth.data'];
[tmp fc ix jx] = ...
    quikread_llc(fnam,nx,1,prec,gdir,minlat,maxlat,minlon,maxlon);
m(1)=0;
for f=1:length(fc)
    m(f+1)=length(ix{fc(f)});
end
n=length(jx{fc(1)});
fld=zeros(sum(m),n);
for f=1:length(fc)
    fld((sum(m(1:f))+1):sum(m(1:(f+1))),:)=tmp{fc(f)};
end
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/' region_name '/grid/'];
eval(['mkdir ' pout])
eval(['cd ' pout])
for fnm={'DXC','DXG','DYC','DYG','Depth', ...
         'RAC','RAS','RAW','RAZ', ...
         'XC','XG','YC','YG','hFacC','hFacS','hFacW'}
    fin=[pin fnm{1} '.data'];
    fout=[fnm{1} '_' int2str(sum(m)) 'x' int2str(n)];
    switch fnm{1}
      case{'hFacC','hFacS','hFacW'}
        fld=zeros(sum(m),n,length(kx));
        for f=1:length(fc)
            fld((sum(m(1:f))+1):sum(m(1:(f+1))),:,:) = ...
                read_llc_fkij(fin,nx,fc(f),kx,ix{fc(f)},jx{fc(f)});
        end
        fout=[fout 'x' int2str(length(kx))];
      otherwise
        fld=zeros(sum(m),n);
        for f=1:length(fc)
            fld((sum(m(1:f))+1):sum(m(1:(f+1))),:) = ...
                read_llc_fkij(fin,nx,fc(f),1,ix{fc(f)},jx{fc(f)});
        end
    end
    writebin(fout,fld);
end

% create commands for extracting model output fields
pout=['~dmenemen/llc_4320/regions/' region_name '/'];
extract='/home4/bcnelson/MITgcm/extract/v1.10/extract4320 -g ';
timesteps=[int2str(mints) '-' int2str(maxts) ' '];
startPoint=[int2str((fc(1)-1)*nx+min(ix{fc(1)})) ',' int2str(min(jx{fc(1)})) ',1 '];

% get and save regional 2D fields
extent=[int2str(sum(m)) ',' int2str(n) ',1'];
for fnm={'Eta','PhiBot','KPPhbl','oceFWflx','oceQnet','oceQsw'}
    eval(['mkdir ' pout fnm{1}])
    eval(['cd ' pout fnm{1}])
    fieldNames=[fnm{1} ' '];
    system([extract timesteps  fieldNames  startPoint  extent '  > joblist']);
    disp(['cd ' pout fnm{1}])
    disp('parallel --slf $PBS_NODEFILE -j2 -a joblist')
end

% Get and save regional 3D fields
extent=[int2str(sum(m)) ',' int2str(n) ',' int2str(length(kx))];
for fnm={'Salt','Theta','W'}
    eval(['mkdir ' pout fnm{1}])
    eval(['cd ' pout fnm{1}])
    fieldNames=[fnm{1} ' '];
    system([extract timesteps  fieldNames  startPoint  extent '  > joblist']);
    disp(['cd ' pout fnm{1}])
    disp('parallel --slf $PBS_NODEFILE -j2 -a joblist')
end