clear all


load ADCP_Feb_2013_Site3_data

% load ADCP matlab structure file

time_adcp=data.time.val; %ADCP time in UTC
depth_adcp=data.Depth_adcp.val; % ADCP depth (above transducer or corrected from the bed/transducer distance?)


% load YSI files

files=dir('*.txt');

pmax=3; % arbitrary maximum water depth for profile interpolation
pint=(0:0.05:pmax); % interpolation every 5cm

for i=1:length(files)
input_file=[files(i).name];


fid=fopen(input_file);

ysidata=textscan(fid,'%f/%f/%f %f:%f:%f %f %f %f %f %f %f');
fclose(fid);


time_ysi=datenum(ysidata{3},ysidata{2},ysidata{1},ysidata{4},ysidata{5},ysidata{6})-1/24;
temp_ysi=ysidata{7};
sal_ysi=ysidata{8};
depth_ysi=ysidata{10};
turb_ysi=ysidata{11};
ssc_ysi=ysidata{12};

% save raw data in matlab structure
ysi(i).raw.time=time_ysi;
ysi(i).raw.temperature=temp_ysi;
ysi(i).raw.salinity=sal_ysi;
ysi(i).raw.depth=depth_ysi;
ysi(i).raw.turbidity=turb_ysi;
ysi(i).raw.ssc=ssc_ysi;

tmean_ysi=mean(time_ysi);

% find corresponding ADCP profile
iadcp=find(time_adcp>tmean_ysi,1,'first');
depth_profile=depth_adcp(iadcp);


tabletemp(:,1)=depth_ysi;
tabletemp(:,2)=temp_ysi;
tabletemp(:,3)=sal_ysi;
tabletemp(:,4)=turb_ysi;
tabletemp(:,5)=ssc_ysi;


tabletemp=sortrows(tabletemp,1); % sort if the YSI is not monotocally going down
% next average values if they do have the same pressure value
% requested prior to interpolation step


profile_array=zeros(length(pint),5);
profile_array(:,:)=-999;
profile_array(:,1)=pint;

    for j=1:5
        pp=1;
        tt=1;
        tmp=tabletemp(1,j);
        for l=2:length(tabletemp(:,1))
            
            if tabletemp(l,1)==tabletemp(l-1,1)
            tmp=tmp+tabletemp(l,j);
            tt=tt+1;
            else
                if tt>1
                    tabletemp2(pp,j)=tmp/tt;
                    tt=1;
                    tmp=tabletemp(l,j);
                else
                    tabletemp2(pp,j)=tmp;
                    tmp=tabletemp(l,j);
                    l=l-1;
                end
            pp=pp+1;
            
            end        
        end
               
        if j>1
        profile_array(:,j)=interp1(depth_profile-tabletemp2(:,1),tabletemp2(:,j),pint,'linear');
        end
        
        
    end
    profile_array(:,5)=profile_array(:,5)/1000; % in g/l
    profile_array(isnan(profile_array))=-999;
    
    ysi(i).profile.time=tmean_ysi;
    ysi(i).profile.depth=profile_array(:,1);
    ysi(i).profile.temperature=profile_array(:,2);
    ysi(i).profile.salinity=profile_array(:,3);
    ysi(i).profile.turbidity=profile_array(:,4);
    ysi(i).profile.ssc=profile_array(:,5);    
    
% 
% figure
% hold on
% plot(profile_array(:,5),profile_array(:,1))
% 
% plot(tabletemp2(:,5),depth_profile-tabletemp2(:,1),'+r')
% 
% pause

clear tabletemp tabletemp2

end

% 
% save('Aulne_experiment_20130214_site3_YSI_profiles.mat','ysi')

%% display

disp_p=ysi(1).profile.depth;
for i=1:length(ysi)
    disp_t(i)=ysi(i).profile.time;
    disp_sal(:,i)=ysi(i).profile.salinity;
    disp_temp(:,i)=ysi(i).profile.temperature;
    disp_turb(:,i)=ysi(i).profile.turbidity;
    disp_ssc(:,i)=ysi(i).profile.ssc;
end

salmax=10;
tempmax=12;
turbmax=500;
sscmax=2;
pmax=3;

fz=16;
tmin=min(disp_t);
tmax=max(disp_t);

cmap=jet(31);
cmap(1,:)=[1 1 1];

%salinity
figure
colormap(cmap)
imagesc(disp_t,disp_p,disp_sal)
caxis([0-salmax/30 salmax])
ylim([0 pmax])
set(gca,'YDir','normal','Xtick',(tmin:(tmax-tmin)/10:tmax),'XTickLabel',datestr((tmin:(tmax-tmin)/10:tmax),15),'Fontsize',12)
xlabel('Time UTC (HH:MM)','Fontsize',fz);ylabel('Depth (m)','Fontsize',fz);title('Aulne experiment - Site3 - Salinity - YSI profiles','Fontsize',fz)
colorbar

figure
for i=1:length(ysi)
    
    tmpx=disp_sal(:,i);
    tmpy=disp_p;
    tmpy(tmpx==-999)=[];
    tmpx(tmpx==-999)=[];
    
subplot(3,3,i)
plot(tmpx,tmpy)
xlabel('Salinity','Fontsize',fz);ylabel('Depth (m)','Fontsize',fz);title(datestr(disp_t(i),31),'Fontsize',fz)
axis([0 salmax,0 pmax])
end

%temperature
figure
colormap(cmap)
imagesc(disp_t,disp_p,disp_temp)
caxis([0-tempmax/30 tempmax])
ylim([0 pmax])
set(gca,'YDir','normal','Xtick',(tmin:(tmax-tmin)/10:tmax),'XTickLabel',datestr((tmin:(tmax-tmin)/10:tmax),15),'Fontsize',12)
xlabel('Time UTC  (HH:MM)','Fontsize',fz);ylabel('Depth (m)','Fontsize',fz);title('Aulne experiment - Site3 - Temperature - YSI profiles','Fontsize',fz)
colorbar


figure
for i=1:length(ysi)
    
    tmpx=disp_temp(:,i);
    tmpy=disp_p;
    tmpy(tmpx==-999)=[];
    tmpx(tmpx==-999)=[];
    
subplot(3,3,i)
plot(tmpx,tmpy)
xlabel('Temperature','Fontsize',fz);ylabel('Depth (m)','Fontsize',fz);title(datestr(disp_t(i),31),'Fontsize',fz)
axis([0 tempmax,0,pmax])
end

%ssc
figure
colormap(cmap)
imagesc(disp_t,disp_p,disp_ssc)
caxis([0-sscmax/30 sscmax])
ylim([0 pmax])
set(gca,'YDir','normal','Xtick',(tmin:(tmax-tmin)/10:tmax),'XTickLabel',datestr((tmin:(tmax-tmin)/10:tmax),15),'Fontsize',12)
xlabel('Time UTC  (HH:MM)','Fontsize',fz);ylabel('Depth (m)','Fontsize',fz);title('Aulne experiment - Site3 - SSC - YSI profiles','Fontsize',fz)
colorbar


figure
for i=1:length(ysi)
    
    tmpx=disp_ssc(:,i);
    tmpy=disp_p;
    tmpy(tmpx==-999)=[];
    tmpx(tmpx==-999)=[];
    
subplot(3,3,i)
plot(tmpx,tmpy)
xlabel('SSC','Fontsize',fz);ylabel('Depth (m)','Fontsize',fz);title(datestr(disp_t(i),31),'Fontsize',fz)
axis([0 sscmax,0,pmax])
end