%contourEnCTD.m
%
%Program to take the cast data from the Endeavor Cruise and create contour
%plots of temperature and salinity vs. distance from station 10 and depth
%
%Soupy Alexander
%3/27/02
%
%Modified 4/5/02 to add fluorecsence and beam attenuation

load C:\NewYork\NewYorkCD\Data_Files\CTD_Data\Mat_Files\en_ctd_mat.mat

Tlimits = [5 10];
Tdelim = [5:0.5:10];
temp_conts = [6.0:0.25:8.25];
Slimits = [29 34];
Sdelim = [25.5:0.5:34];
sal_conts = [25.5:0.25:34.0];
Flimits = [0 10];
Fdelim = [0:2:10];
F_conts = [0:1:10];
attnlimits = [0 5];
attndelim = [0:0.5:5];
attn_conts = [0:0.25:5];
sigmatlimits = [22 27];
sigmatdelim = [22:1:27];
sigmat_conts = [22:0.5:27];

%Set up empty matrices of the data
temp = repmat(NaN,165,10);
sal = repmat(NaN,165,10);
F = repmat(NaN,165,10);
attn = repmat(NaN,165,10);
lat = repmat(NaN,1,10);
lon = repmat(NaN,1,10);
depth = repmat(NaN,165,10);

%Fill in the data
for index = 1:10;
    
    cast = evalin('base',['ctd' num2str(index,'%02d') 'b']);
    [m,n] = size(cast);
    temp(1:m,index) = cast(:,6);
    sal(1:m,index) = cast(:,10);
    F(1:m,index) = cast(:,23);
    attn(1:m,index) = -4*log((cast(:,24)./100));
    sigmat(1:m,index) = cast(:,22);
    lat(1,index) = nanmean(cast(:,4));
    lon(1,index) = nanmean(cast(:,5));
    depth(1:m,index) = cast(:,25);
    
end

%Set up the distance matrix
dist1 = repmat(NaN,1,10);
dist1(10) = 0;

dist = repmat(NaN,1,10);
dist(10) = 0;

for index = 1:9;
    dist1(index) = latlon2dist(lat(index),lon(index),lat(index+1),lon(index+1));
end

for index = 1:9;
    dist(index) = sum(dist1(index:10));
end

%Convert distances to kilometers
distkm = dist./1000;

%Grid the temperature and salinity data (i.e., line up depth bins
depth_mat = 1:0.5:83;
temp_grid = repmat(NaN,length(depth_mat),10);
sal_grid = repmat(NaN,length(depth_mat),10);
F_grid = repmat(NaN,length(depth_mat),10);
attn_grid = repmat(NaN,length(depth_mat),10);
sigmat_grid = repmat(NaN,length(depth_mat),10);

for index = 1:10;
    for index2 = 1:length(depth_mat);
        clear in
        in = value2Index(depth(:,index),depth_mat(index2),0.4);
        if isnan(in) == 0;
        temp_grid(index2,index) = temp(in,index);
        sal_grid(index2,index) = sal(in,index);
        F_grid(index2,index) = F(in,index);
        attn_grid(index2,index) = attn(in,index);
        sigmat_grid(index2,index) = sigmat(in,index);
        end    
    end
end

depth_grid = repmat(depth_mat',1,10);
distkm_grid = repmat(distkm,165,1);

[c,h] = contourf(distkm_grid,depth_grid,temp_grid,temp_conts);
shading flat
set(gca,'fontsize',12)
xlabel('Distance to Station 10 (km)')
ylabel('Depth (m)')
title('Temperature Contours of CTD Data from Endeavor','fontsize',16)
axis ij
hold on
[c2,h2] = contour(distkm_grid,depth_grid,temp_grid,Tdelim,'k');
clabel(c2,h2,'rotation',0)
for index = 1:10;
    l = line([distkm(index) distkm(index)],[0 85]);
    set(l,'color',[0.25 0.25 0.25],'linestyle','-.');
    t = text(distkm(index)+0.5,80,[num2str(index)]);
    set(t,'color',[0.25 0.25 0.25]);
end
axis([-1 62 0 85])
fig = gca;

cb = colorbar;
axes(cb)
ylabel('Temperature (^o C)')
axes(cb)
set(gca,'ytick',temp_conts)
set(gca,'dataaspectratio',[17 2 2])
axes(fig)
set(gca,'plotboxaspectratio',[1 0.5 1])
orient landscape

figure
[c,h] = contourf(distkm_grid,depth_grid,sal_grid,sal_conts);
shading flat
set(gca,'fontsize',12)
xlabel('Distance to Station 10 (km)')
ylabel('Depth (m)')
title('Salinity Contours of CTD Data from Endeavor','fontsize',16)
axis ij
hold on
[c2,h2] = contour(distkm_grid,depth_grid,sal_grid,Sdelim,'k');
clabel(c2,h2,'rotation',0)
for index = 1:10;
    l = line([distkm(index) distkm(index)],[0 85]);
    set(l,'color',[0.25 0.25 0.25],'linestyle','-.');
    t = text(distkm(index)+0.5,80,[num2str(index)]);
    set(t,'color',[0.25 0.25 0.25]);
end
axis([-1 62 0 85])
fig = gca;
cb = colorbar;
axes(cb)
ylabel('Salinity (o/oo)')
set(gca,'ytick',min(Sdelim):1:max(Sdelim))
set(gca,'dataaspectratio',[4.5 2 1])
axes(fig)
set(gca,'plotboxaspectratio',[1 0.5 1])
orient landscape

figure
[c,h] = contourf(distkm_grid,depth_grid,F_grid,F_conts);
shading flat
set(gca,'fontsize',12)
xlabel('Distance to Station 10 (km)')
ylabel('Depth (m)')
title('Fluorescence Contours of CTD Data from Endeavor','fontsize',16)
axis ij
hold on
[c2,h2] = contour(distkm_grid,depth_grid,F_grid,Fdelim,'k');
clabel(c2,h2,'rotation',0)
for index = 1:10;
    l = line([distkm(index) distkm(index)],[0 85]);
    set(l,'color',[0.25 0.25 0.25],'linestyle','-.');
    t = text(distkm(index)+0.5,80,[num2str(index)]);
    set(t,'color',[0.25 0.25 0.25]);
end
axis([-1 62 0 85])
fig = gca;
cb = colorbar;
axes(cb)
ylabel('Fluorescence')
set(gca,'ytick',min(Fdelim):1:max(Fdelim))
set(gca,'dataaspectratio',[4 2 1])
axes(fig)
set(gca,'plotboxaspectratio',[1 0.5 1])
orient landscape

figure
[c,h] = contourf(distkm_grid,depth_grid,attn_grid,attn_conts);
shading flat
set(gca,'fontsize',12)
xlabel('Distance to Station 10 (km)')
ylabel('Depth (m)')
title('Beam Attenuation Contours of CTD Data from Endeavor','fontsize',16)
axis ij
hold on
[c2,h2] = contour(distkm_grid,depth_grid,attn_grid,attndelim,'k');
clabel(c2,h2,'rotation',0)
for index = 1:10;
    l = line([distkm(index) distkm(index)],[0 85]);
    set(l,'color',[0.25 0.25 0.25],'linestyle','-.');
    t = text(distkm(index)+0.5,80,[num2str(index)]);
    set(t,'color',[0.25 0.25 0.25]);
end
axis([-1 62 0 85])
fig = gca;
cb = colorbar;
axes(cb)
ylabel('Beam Attenuation (m-1)')
set(gca,'ytick',min(attndelim):1:max(attndelim))
set(gca,'dataaspectratio',[10 2 1])
axes(fig)
set(gca,'plotboxaspectratio',[1 0.5 1])
orient landscape

figure
[c,h] = contourf(distkm_grid,depth_grid,sigmat_grid,sigmat_conts);
shading flat
set(gca,'fontsize',12)
xlabel('Distance to Station 10 (km)')
ylabel('Depth (m)')
title('Sigma T Contours of CTD Data from Endeavor','fontsize',16)
axis ij
hold on
[c2,h2] = contour(distkm_grid,depth_grid,sigmat_grid,sigmatdelim,'k');
clabel(c2,h2,'rotation',0)
for index = 1:10;
    l = line([distkm(index) distkm(index)],[0 85]);
    set(l,'color',[0.25 0.25 0.25],'linestyle','-.');
    t = text(distkm(index)+0.5,80,[num2str(index)]);
    set(t,'color',[0.25 0.25 0.25]);
end
axis([-1 62 0 85])
fig = gca;
cb = colorbar;
axes(cb)
ylabel('Sigma T (mg/cm^3)')
set(gca,'ytick',min(sigmatdelim):1:max(sigmatdelim))
set(gca,'dataaspectratio',[10 2 1])
axes(fig)
set(gca,'plotboxaspectratio',[1 0.5 1])
orient landscape