% load Grid
grd=rnt_gridload('Chile_10km_conf.txt');

% Check the bathymetry and resolution
figure; % create a figure
opt.shading='flat';
rnt_plcm(grd.h, grd, opt); % plot bathymetry using M_Map toolbox
clf; rnt_plcm(1./grd.pm/1000, grd); % Horizontal resolution
clf;rnt_plc2(grd.h, grd, 0, 7, 0,0); % alternative is not to use m_map

% create a ctl for output

files=rnt_getfilenames('.','ofes-extract-'); % This JUST makes a list
ctl=rnt_timectl(files, 'ocean_time', 'r',[1999 0 0]); % 'r' means a 360 days calendar

% Load variable: Temperature for June 2000

ind=find(ctl.year==2000 & ctl.month==5);
VAR=rnt_loadvar(ctl,ind,'salt');

% Plot the SST

figure;
rnt_plcm(VAR(:,:,end),grd)

% Make a plot of the 100 m temperature

zeta=rnt_loadvar(ctl, ind, 'zeta');
[zr,zw,hz]=rnt_setdepth(zeta, grd); % configuration of the sigma-coord
depths=[-50 -100 -200 -1000];
VARz=rnt_2z(VAR, zr, depths);
figure;
rnt_plcm(VARz(:,:,2), grd);


% Vertical sections

figure;
j=find (grd.latr(1,:) > -37); j=j(1);
rnt_sectx(VAR, j , grd); % in the zonal direction


% Cycle cycle of Surface Temperature

SST=rnt_loadvar_segp(ctl,1:length(ctl.datenum),'temp',1:grd.Lp,1:grd.Mp,grd.N); % Extract only the SURFACE (grd.N) temperature
[SST_anom SST_mean]=RemoveSeas(SST,ctl.month,3); % seperate anomaly from monthly mean
size(SST_mean)
SST_mean=SST_mean-repmat(mean(SST_mean,3),[1 1 12]); % Here I just remove the spatial mean to the seasonal cycle

mfig;  % plot each month
for k=1:12
subplot(4,3,k)
rnt_plcm(SST_mean(:,:,k),grd) % if you see white, you may use rnt_plc2 or make 12 figures separately
caxis([-4 4]);colorbar % put all figure with same color bar
title(datestr(ctl.datenum(k),'mmm')) % this is just fancy for your title :p
end



for in=1999:2000
ind=find(ctl.year==in & ctl.month==11);
VAR=rnt_loadvar(ctl,ind,'temp');

% Plot the SST

figure
rnt_plc2(VAR(:,:,end),grd,0,7,0,0)
hold on
caxis([8 26])
colorbar
hold on
V=[12 14 16 18]
[cs,h]=contour(grd.lonr,grd.latr,VAR(:,:,end),V,'-k');
hold on
clabel(cs,h,'fontsize',14,'color','k','rotation',0);
hold on
end