Plot salinity contour

clc;clear all;close all;

%% save google map as background
figure(1);clf;hold on;box on;
set(gca,'tickdir','out');
% axis([-88.155 -88.145 47.227 47.2325]);
axis([-88.16 -88.14 47.22 47.24]);
plot_google_map('maptype','satellite','scale',2,...
                'FigureResizeUpdate',0,'AutoAxis',1,'Refresh',1);

gmapfile=['fig_google_map_png_superior_tobacco.fig']
saveas(gcf,[gmapfile],'fig');

%%
boundary_tobacco=load('../superior_boundary_noaa_refined_tobacco.dat');

% ncload('superior_0001.nc','nv','lon','lat','h');
% lat_grid=lat;
% lon_grid=lon-360;
% [x_grid,y_grid]=ll2utm(lon_grid,lat_grid,16);
% [m,n]=size(nv);
% 
% for i=1:n
%     i
%     a1(i)=nv(1,i);%nv means nodes surrounding element
%     a2(i)=nv(2,i);
%     a3(i)=nv(3,i);
% 
%     b1(:,i)=[a1(i) a2(i) a3(i) a1(i)];   
% end

for i=5:5

    i
ncfile=['cur_sal_',num2str(i,'%.4i'),'.nc'];
ncload([ncfile]);

xlon1=lon-360;
xlat1=lat;
xlonc1=lonc-360;
xlatc1=latc;
Times1=Times;
u1=u;
v1=v;
salinity1=squeeze(salinity(:,:,:));

clear ind1 ind12 ind2 ind3
% ind1=inpolygon(xlon1,xlat1,box(:,1),box(:,2));
ind1=find(xlon1>-88.157 & xlon1<-88.134 & xlat1>47.225 & xlat1<47.237);
xlon0=xlon1(ind1);
xlat0=xlat1(ind1);
%salinity1(:,~ind1)=nan;
salinity0=salinity1(:,ind1);

ind12=find(xlonc1>-88.2 & xlonc1<-88.0 & xlatc1>47.2 & xlatc1<47.4);
xlonc0=xlonc1(ind12);
xlatc0=xlatc1(ind12);
uu1=squeeze(u1(:,:,ind12));
vv1=squeeze(v1(:,:,ind12));


ind3=readselect(xlonc0,xlatc0,xlonc0,0.0005);

cmin=0;cinc=10;cmax=100;
ncc=round([cmax-cmin]/cinc);
ccmap=flipud(spectral(ncc));
fts=12;
sf1=1e-2*2;

for t=21:21
t
    close all;
     openfig([gmapfile]);hold on;
    figure(1);hold on;
    scattercontourf_ch(xlon0,xlat0,salinity0(t,:)',[cmin:cinc:cmax]);
    quiver(xlonc0(ind3),xlatc0(ind3),uu1(t,ind3)'.*sf1,vv1(t,ind3)'.*sf1,0,'m');
    plot_fvcom_obc(boundary_tobacco,[210 180 140]/255);
    % plot(boundary_tobacco(:,1),boundary_tobacco(:,2),'LineWidth',2)
    % plot (lon_grid(b1(:,ind12)), lat_grid(b1(:,ind12)),'color','r','LineWidth',0.005)
    caxis([cmin cmax]);
    colormap(ccmap);
    lcb=colorbar('location','northoutside');
    axis([-88.156 -88.135 47.226 47.236]);
    % axis([-88.16 -88.14 47.22 47.24]);
 
    text(-88.1557,47.2355,['arrowsizesizesize'],...
        'color','w','background','w','edgecolor','k','fontsize',fts,'fontweight','bold');
    quiver(-88.1557,47.2355,0.1.*sf1,0.*sf1,0,'color','m','linewidth',1.5,'maxheadsize',2);
    text(-88.153,47.2355,['0.1 m/s '],'color','k','fontsize',fts,'fontweight','bold');
    %text(-88.141,47.2355,[Times1(t,1:19)],...
     %     'color','k','background','w','edgecolor','k','fontsize',fts,'fontweight','bold')  
      %text(-88.1415,47.2355,[Times1(t,1:10),' Afternoon'],...
       %   'color','k','background','w','edgecolor','k','fontsize',fts,'fontweight','bold')  
      text(-88.141,47.2355,[Times1(t,1:10),' Morning'],...
          'color','k','background','w','edgecolor','k','fontsize',fts,'fontweight','bold')  
  
    saveas(gcf,['figure_sal_cur/surface_sal_day',num2str(i,'%.3i'),'_hour',num2str(t,'%.2i'),'.png'],'png');  
end

end