template_get_adcp_data.m

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% template_get_adcp_data.m
% -------------------------------
% Author : Pierre ROUSSELOT - IRD (pierre.rousselot@ird.fr)
%          Jeremie HABASQUE - IRD (jeremie.habasque@ird.fr)
% -------------------------------
% INPUTS:
% - binary raw file with .000 extension
% OUTPUTS:
% - U and V fields interpolated on a regulard grid, filtered and subsampled
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

close all; clear
addpath(genpath('../ADCP_mooring_data_processing'));
addpath('/home/proussel/Documents/OUTILS/TOOLS/nansuite'); % NaNSuitePath

%% META information:
% Location rawfile
rawfile          = 'FR31/FR30_000.000';        % binary file with .000 extension
fpath_output     = './FR31/0-0/';                                                         % Output directory

% Cruise/mooring info
cruise.name      = 'PIRATA';                                                              % cruise name
mooring.name     = '0W0N';                                                                % '0N10W'
mooring.lat      = '0000.176';                                                           % latitude [°']
mooring.lon      = '-0003.920';                                                          % longitude [°']
clock_drift      = 146;                                                                   % [seconds]

% ADCP info
adcp.sn          = 22546;                                                                 % ADCP serial number
adcp.type        = '150 khz Quartermaster';                                               % Type : Quartermaster, longranger
adcp.direction   = 'up';                                                                  % upward-looking 'up', downward-looking 'dn'
adcp.instr_depth = 300;                                                                   % nominal instrument depth
instr            = 1;                                                                     % this is just for name convention and sorting of all mooring instruments
offset_pres_sens = 1;                                                                     % offset in m between pressure sensore and ADCP

% NCFILE info
d_fillvalue     = -9999; 

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

%% Convert variables
latDegInd               = strfind(mooring.lat,'');
lonDegInd               = strfind(mooring.lon,'');
if strfind(mooring.lon,'-')
    mooring.lat             = str2double(mooring.lat(1:latDegInd-1))-str2double(mooring.lat(latDegInd+1:end-1))/60;
else
    mooring.lat             = str2double(mooring.lat(1:latDegInd-1))+str2double(mooring.lat(latDegInd+1:end-1))/60;
end
if strfind(mooring.lon,'-')
    mooring.lon             = str2double(mooring.lon(1:lonDegInd-1))-str2double(mooring.lon(lonDegInd+1:end-1))/60;
else
    mooring.lon             = str2double(mooring.lon(1:lonDegInd-1))+str2double(mooring.lon(lonDegInd+1:end-1))/60;
end
clock_drift             = clock_drift/3600;  % convert into hrs

%% Read rawfile
disp('****')
raw_file                = [fpath_output, mooring.name '_' num2str(adcp.sn) '_instr_' sprintf('%02d',instr) '_raw.mat'];
if exist(raw_file)
    fprintf('Read %s\n', raw_file);
    load(raw_file)
else
    fprintf('Read %s\n', rawfile);
    raw                 = read_os3(rawfile,'all');
    save(raw_file,'raw','-v7.3');
end

%% Correct clock drift
time0                   = julian(raw.juliandate);
clockd                  = linspace(0, clock_drift, length(time0));
raw.juliandate          = raw.juliandate - clockd / 24;
disp('****')
disp('Correct clock drift')

%% Plot pressure and temperature sensor
figure;
subplot(2,1,1)
plot(raw.pressure);
detrend_sdata = detrend(raw.pressure);
trend         = raw.pressure - detrend_sdata;
hold on
plot(trend, 'r--')
hold off
title('Pressure sensor');
ylabel('Depth [m]');
xlabel('Time index');
grid on;

subplot(2,1,2)
plot(raw.temperature);
title('Temperature sensor');
ylabel('Temperature [cond1C]');
xlabel('Time index');
grid on;
saveas(gcf,[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(instr),'_','Pressure_Temp_sensor'],'fig')

%% Determine first and last indiced when instrument was at depth (you can do this by plotting 'raw.pressure' for example
disp('****')
first               = input('Determine first indice when instrument was at depth (with pres/temp plot): ');
disp('****')
last                = input('Determine last indice when instrument was at depth (with pres/temp plot): ');

%% Correct velocity data with external T/S sensor

%% Extract data
freq                = raw.config.sysconfig.frequency;
u2                  = squeeze(raw.vel(:,1,first:last));
v2                  = squeeze(raw.vel(:,2,first:last));
w                   = squeeze(raw.vel(:,3,first:last));
vel_err             = squeeze(raw.vel(:,4,first:last));
corr                = squeeze(mean(raw.cor(:,4,first:last),2));
ea                  = squeeze(mean(raw.amp(:,:,first:last),2));
pg                  = squeeze(raw.pg(:,4,first:last));
time                = raw.juliandate(first:last);
ang                 = [raw.pitch(first:last) raw.roll(first:last) raw.heading(first:last)];
soundspeed          = raw.soundspeed(first:last);
temp                = raw.temperature(first:last);
press               = raw.pressure(first:last);
if press < 0
    press = -press;
end
nbin                = raw.config.ncells;      % number of bins
bin                 = 1:nbin;                 % bin number
blen                = raw.config.cell;        % bin length
tlen                = raw.config.pulse;       % pulse length
lag                 = raw.config.lag;         % transmit lag distance
blnk                = raw.config.blank;       % blank distance after transmit
fbind               = raw.config.bin1distance;% middle of first bin distance
dt                  = (time(2)-time(1))*24;   % Sampling interval in hours
EA0                 = round(mean(ea(nbin,:)));

%% Calculate Magnetic deviation values
[a,~]                   = gregorian(raw.juliandate(1));
magnetic_deviation_ini  = magdev(mooring.lat,mooring.lon,0,a+(raw.juliandate(1)-julian(a,1,1,0,0,0))/365.25);
[a,~]                   = gregorian(raw.juliandate(end));
magnetic_deviation_end  = magdev(mooring.lat,mooring.lon,0,a+(raw.juliandate(end)-julian(a,1,1,0,0,0))/365.25);
rot                     = (magnetic_deviation_ini+magnetic_deviation_end)/2;
mag_dev                 = linspace(magnetic_deviation_ini, magnetic_deviation_end, length(time0));
mag_dev                 = mag_dev(first:last);

%% Correction of magnetic deviation
disp('****')
disp('Correct magnetic deviation')
mag_dev = -mag_dev * pi/180;
for ii = 1 : length(mag_dev)
    M(1,1) = cos(mag_dev(ii));
    M(1,2) = -sin(mag_dev(ii));
    M(2,1) = sin(mag_dev(ii));
    M(2,2) = cos(mag_dev(ii));
    vvel(1,:) = u2(:,ii);
    vvel(2,:) = v2(:,ii);
    vvvel = M * vvel;
    u(:,ii) = vvvel(1,:);
    v(:,ii) = vvvel(2,:);
end



%% Correct percent good: Exclude data with percent good below prct_good
figure;
colormap jet;
pcolor(pg);
shading flat;
title('Percent good of the bins'); colorbar;
ylabel('Bins');
xlabel('Time index');
saveas(gcf,[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(instr),'_','Perceent_good'],'fig')
disp('****')
prct_good           = input('Determine percent good threshold (generally 20): ');
igap                = find(pg<prct_good);           % Exclude data with percent good below prct_good
u(igap)             = NaN;
v(igap)             = NaN;
w(igap)             = NaN;
vel_err(igap)       = NaN;
ea(igap)            = NaN;
corr(igap)          = NaN;

%% Correction data with high attitude (pitch/roll)
figure;
subplot(2,1,1)
plot(abs(ang(:,1)));
hold on
plot(10*ones(1,length(ang(:,1))),'--r');
hold off
title('Attitude sensor');
ylabel('Pitch [cond1]');
xlabel('Time index');
axis([0 length(ang(:,1)) 0 20])
grid on;

subplot(2,1,2)
plot(abs(ang(:,2)));
hold on
plot(10*ones(1,length(ang(:,1))),'--r');
hold off
ylabel('Roll [cond1]');
xlabel('Time index');
axis([0 length(ang(:,1)) 0 20])
grid on;
saveas(gcf,[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(instr),'_','Attitude'],'fig')
disp('****')
disp('Delete high attitude ADCP data (>=10)');

high_pitch = find(abs(ang(:,1))>=10);
high_roll  = find(abs(ang(:,2))>=10);
if ~isempty(high_pitch) || ~isempty(high_roll)
    high_att           = input('Do you want to delete them? 1/0 [1]');
    if isempty(high_att)
        high_att = 1;
    end
    if high_att == 1
        high_att                = union(high_pitch,high_roll);
        offset(high_att)        = NaN;
        ang(high_att,1)         = NaN;
        ang(high_att,2)         = NaN;
        ang(high_att,3)         = NaN;
        mag_dev(high_att)       = NaN;
        u(high_att)             = NaN;
        v(high_att)             = NaN;
        w(high_att)             = NaN;
        vel_err(high_att)       = NaN;
        ea(high_att)            = NaN;
        corr(high_att)          = NaN;
        pg(high_att)            = NaN;
        time(high_att)          = NaN;
        z_bins(high_att)        = NaN;
        depth(high_att)         = NaN;
        temp(high_att)          = NaN;
        soundspeed(high_att)    = NaN;
    end
end

%% amplitude of the bins / Correction ADCP's depth
figure;
colormap jet;
pcolor(ea);
shading flat;
title('Amplitude of the bins'); colorbar;
ylabel('Bins');
xlabel('Time index');
saveas(gcf,[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(instr),'_','Amplitude_bins'],'fig')

%% Add external pressure sensor choice
disp('****')
pressure_data = input('Do you have external pressure data? 1/0 [0]');
if isempty(pressure_data)
    pressure_data = 0;
end
if pressure_data == 1
    [filename, path, ~] = uigetfile('*.cnv', 'Select external pressure file');
    press_file = fullfile(path, filename);
    press_file = read_sbe(press_file);
    real_depth = press_file.depSM(first:last);
    dpt        = sw_dpth(press,mooring.lat)';  % convert pressure to depth, press needs to have dimension (n x 1)
    plot(real_depth, 'b')
    grid on 
    hold on
    plot(dpt, 'r')
    legend('External sensor depth','ADCP sensor depth');   
    xlabel('Time Index')
    ylabel('Depth [m]')
    exsens_data = input('Do you want to use external sensor data? 1/0 [0]');
    if isempty(exsens_data)
        exsens_data = 1;
    end
    if exsens_data
        dpt    = real_depth-offset_pres_sens;
        dpt1   = repmat(dpt,nbin,1);
        binmat = repmat((1:nbin)',1,length(dpt1));
        z(1,:) = dpt1(1,:)-fbind;
        for ii = 2:length(binmat(:,1))
            z(ii,:) = z(1,:)-(binmat(ii,:)-1.5)*blen;
        end
    end
end

%% If upward looking: determine range of surface bins used for instrument depth correction below!
surface_bins = 0;
if pressure_data == 0
    disp('****')
    surface_bins = input('Do you want to apply an offset using surface reflection? 1/0 [1]');
    if isempty(surface_bins)
        surface_bins = 1;
    end
    if surface_bins == 1
        sbins               = input('Determine range of surface bins used for instrument depth correction (with aplitude plot, ie. 30:35): ');
        
        %% Calculate depth of each bin:
        dpt                 = sw_dpth(press,mooring.lat)';  % convert pressure to depth, press needs to have dimension (n x 1)
        dpt1                = repmat(dpt,nbin,1);
        binmat              = repmat((1:nbin)',1,length(dpt1));
        
        % If ADCP is upward-looking a depth correction can be inferred from the surface reflection, which is done in adcp_surface_fit
        disp('****')
        if strcmp(adcp.direction,'up')
            [z,dpt1,offset,xnull] = adcp_surface_fit(dpt,ea,sbins,blen,tlen,lag,blnk,nbin,fbind);
        elseif strcmp(adcp.direction,'dn')
            z(1,:) = dpt1(1,:)+(tlen+blen+lag)*0.5+blnk;
            for ii = 2:length(binmat(:,1))
                z(ii,:) = z(1,:)+(binmat(ii,:)-1.5)*blen;
            end
        else
            error('Bin depth calculation: unknown direction!');
        end
        
        saveas(figure(5),[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(instr),'_','Histdiff_depth'],'fig')
        saveas(figure(6),[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(instr),'_','Offset_depth'],'fig')
        saveas(figure(7),[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(instr),'_','Amplitude_bins_2'],'fig')
    else
        dpt                 = sw_dpth(press,mooring.lat)';  % convert pressure to depth, press needs to have dimension (n x 1)
        dpt1                = repmat(dpt,nbin,1);
        z                   = dpt;
        figure
        plot(dpt)
        hold on
        plot(adcp.instr_depth*ones(length(dpt),1),'--r')
        hold off
        grid on
        axis([0 length(dpt) min(min(dpt,adcp.instr_depth*ones(1,length(dpt))))-50 max(max(dpt,adcp.instr_depth*ones(1,length(dpt))))+50])
        xlabel('Ensembles')
        ylabel('Depth [m]')
        legend('Depth','Nominal Depth')
        offset = input('Do you want to apply a manual offset? 1/0 [0]');
        if isempty(offset)
            offset           = 0;
        elseif offset == 1
            offset          = input('->Enter new offset:');
            dpt             = dpt + offset;
            dpt1            = dpt1 + offset;
            z               = z + offset;
            hold on
            plot(dpt,'g')
            hold off
            legend('Depth', 'Nominal Depth', 'Corrected depth')
        elseif offset == 0
            offset           = 0;
        end
        
        binmat              = repmat((1:nbin)',1,length(dpt1));
        
        if strcmp(adcp.direction,'up')
            z(1,:) = dpt1(1,:)-(tlen+blen+lag)*0.5-blnk;
            for ii = 2:length(binmat(:,1))
                z(ii,:) = z(1,:)-(binmat(ii,:)-1.5)*blen;
            end
        elseif strcmp(adcp.direction,'dn')
            z(1,:) = dpt1(1,:)+(tlen+blen+lag)*0.5+blnk;
            for ii = 2:length(binmat(:,1))
                z(ii,:) = z(1,:)+(binmat(ii,:)-1.5)*blen;
            end
        else
            error('Bin depth calculation: unknown direction!');
        end
        
    end
end
%% Remove bad data if ADCP is looking upward
u1=u; v1=v; w1=w; vel_err1=vel_err; ea1=ea; corr1=corr; z1=z;
if surface_bins == 1
    disp('****')
    disp('Remove bad data near surface due to sidelobe');
    
    if strcmp(adcp.direction,'up')
        for i = 1:length(time)
            sz_dpt(i) = adcp_shadowzone(dpt1(i),raw.config.sysconfig.angle); % depending on the instrument depth and the beam angle the shadow zone, i.e. the depth below the surface which is contaminated by the surface reflection is determined
            iz(i)     = find(z(:,i)>sz_dpt(i),1,'last');
            sbin(i)   = bin(iz(i));
            %sbin(i)=30; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
            % here a manual criterion should be hard-coded if
            % adcp_check_surface (below) shows bad velocities close to the
            % surface
            u1(sbin(i)+1:end,i)       = NaN;
            v1(sbin(i)+1:end,i)       = NaN;
            w1(sbin(i)+1:end,i)       = NaN;
            vel_err1(sbin(i)+1:end,i) = NaN;
            ea1(sbin(i)+1:end,i)      = NaN;
            corr1(sbin(i)+1:end,i)    = NaN;
            z1(sbin(i)+1:end,i)       = NaN;
        end
        
        if 1
            bins           = nmedian(sbin)-4:nmedian(sbin)+4;
            adcp_check_surface(bins,u,u1,v,v1,corr,corr1,time,bin,z,z1,sz_dpt);
            % here the closest bins below the surface are plotted that are supposed to have good velocities, if there are still bad velocities a manual criterion needs to be found
            reply_sidelobe = input('Do you want to apply manual criterion? 1/0 [0]:');
            if isempty(reply_sidelobe)
                reply_sidelobe = 0;
            end
            if reply_sidelobe
                bin_cutoff = input('->Enter new bin cutoff value:');
                u1=u; v1=v; w1=w; vel_err1=vel_err; ea1=ea; corr1=corr; z1=z;
                u1(bin_cutoff+1:end,:)       = NaN;
                v1(bin_cutoff+1:end,:)       = NaN;
                w1(bin_cutoff+1:end,:)       = NaN;
                vel_err1(bin_cutoff+1:end,:) = NaN;
                ea1(bin_cutoff+1:end,:)      = NaN;
                corr1(bin_cutoff+1:end,:)    = NaN;
                z1(bin_cutoff+1:end,:)       = NaN;
                adcp_check_surface(bins,u,u1,v,v1,corr,corr1,time,bin,z,z1,sz_dpt);
            end
        end
    end
    saveas(figure(7),[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(instr),'_','Meridional_zonal_velocity'],'fig')
end

%% SAVE DATA
% More meta information
%adcp.comment='';
adcp.config         = raw.config;
if pressure_data == 0
    adcp.z_offset       = offset;
end
adcp.ang            = ang;
adcp.mag_dev        = rot;

% Data structure
data.u              = u1;
data.v              = v1;
data.w              = w1;
data.e              = vel_err1;
data.ea             = ea1;
data.pg             = pg;
data.time           = time;
data.z_bins         = z1;
data.depth          = dpt1;
data.temp           = temp;
data.sspd           = soundspeed;
data.lat            = mooring.lat;
data.lon            = mooring.lon;

disp('****')
reply_ts            = input('Do you want to calculate Target Strength? (CTD profile needed) 1/0 [0]:');
if isempty(reply_ts)
    reply_ts = 0;
end
if reply_ts == 1
    % EA0: noisefloor from ADCP electronic noise; a scalar
    disp('->Calculate Target Strength')
    disp(['->EA0=' num2str(EA0) '(noisefloor from ADCP electronic noise) ; pH=8.1; (seawater pH)'])
    file_ctd        = input('->Path to CTD .nc file [''*.nc'']:');
    if exist(file_ctd, 'file')
        ctd.depth = ncread(file_ctd, 'PRES');
        ctd.temp  = ncread(file_ctd, 'TEMP');
        ctd.sal   = ncread(file_ctd, 'PSAL');
        ctd.tempR = ones(size(z));
        ctd.salR  = ones(size(z));
        % for each ADCP bin, find salinity and temperature values
        for i_bin = 1:nbin
            [~,ind_depth]      = min(abs(z(i_bin,:)-ctd.depth(:)));
            ctd.salR(i_bin,:)  = ctd.sal(ind_depth);
            ctd.tempR(i_bin,:) = ctd.temp(ind_depth);
        end
        % Compute TS
        [sspd,~]  = meshgrid(soundspeed,1:nbin);
        data.ts   = target_strength(data.ea,EA0,ctd.salR,ctd.tempR,sspd,temp',soundspeed',z,adcp.config.cell,adcp.config.blank,adcp.config.sysconfig.angle,freq);
        figure;
        colormap jet;
        pcolor(data.ts.ts);
        shading flat;
        title('Target Strength'); colorbar;
        ylabel('Bins');
        xlabel('Time index');
        saveas(gcf,[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(instr),'_','target_strength'],'fig')
    else
        disp('CTD file doesn''t exist')
        reply_ts = 0;
    end
end

%% Save raw data
disp('****')
disp('Saving raw data')
save([fpath_output, mooring.name '_' num2str(adcp.sn) '_instr_' sprintf('%02d',instr) '.mat'],'adcp','mooring','data','-v7.3');

%% Interpolate data on a regular vertical grid
if strcmp(adcp.direction,'up')
    Z                   = fliplr(blen/2:blen:max(z(:))+blen);
    Zmax                = max(Z);
    u_interp            = NaN(length(time),length(Z));
    v_interp            = NaN(length(time),length(Z));
    if reply_ts == 1
        ts_interp       = NaN(length(time),length(Z));
    end
    
    for i=1:length(time)
        % indice correspondant sur la grille finale Z
        ind = round((Zmax-z(1,i))/blen)+1;
        % filling the grid
        npts = min([length(Z)+ind+1 length(bin)]);
        u_interp(i,ind:ind+npts-1) = u1(1:npts,i);
        v_interp(i,ind:ind+npts-1) = v1(1:npts,i);
        if reply_ts == 1
            ts_interp(i,ind:ind+npts-1) = data.ts.ts(1:npts,i);
        end
    end
else
    Z                   = (round(min(data.depth))+blen/2:blen:max(z(:))+blen);
    Zmax                = min(Z);
    u_interp            = NaN(length(time),length(Z));
    v_interp            = NaN(length(time),length(Z));
    if reply_ts == 1
        ts_interp       = NaN(length(time),length(Z));
    end
    
    for i=1:length(time)
        % indice correspondant sur la grille finale Z
        ind = -(round((Zmax-z(1,i))/blen)-1);
        % filling the grid
        npts = min([length(Z)-ind-1 length(bin)]);
        u_interp(i,ind:ind+npts-1) = u1(1:npts,i);
        v_interp(i,ind:ind+npts-1) = v1(1:npts,i);
        if reply_ts == 1
            ts_interp(i,ind:ind+npts-1) = data.ts.ts(1:npts,i);
        end
    end
end

if reply_ts == 0
    ts_interp       = NaN;
end
%% Horizontal interpolation, filtering and subsampling
disp('****')
horz_interp            = input('Do you want to do an horizontal interpolation? 1/0 [1]:');
if isempty(horz_interp)
    horz_interp        = 1;
end

if horz_interp
    filt            = input('Do you want to filter tide? 1/0 [1]:');
    if isempty(filt)
        filt        = 1;
    end
    
    sub            = input('Do you want to subsampling data daily? 1/0 [1]:');
    if isempty(filt)
        sub        = 1;
    end
    if filt
        if sub
            disp('Horizontal interpolation, Filtering & Subsampling')
        else
            disp('Horizontal interpolation & Filtering')
        end
        disp('Filtering using 40h Hamming filter (other disponible filter: FFT filter, tide model)')
    else
        if sub
            disp('Horizontal interpolation & Subsampling')
        else
            disp('Horizontal interpolation')
        end
    end
else
    filt = 0;
    sub  = 0;
end

[uintfilt,vintfilt,tsintfilt,inttim,utid_baro,vtid_baro] = adcp_filt_sub(data,u_interp',v_interp',ts_interp',1:length(Z),reply_ts, filt, sub);
saveas(figure(5),[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(instr),'_','data_raw_filt_subsampled_1'],'fig')
saveas(figure(6),[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(instr),'_','data_raw_filt_subsampled_2'],'fig')

if horz_interp == 0
    uintfilt      = u_interp';
    vintfilt      = v_interp';
    inttim        = data.time;
end

%% Save interpolated data
disp('****')
bin_start           = input('Determine first bin indice with good interpolated data: '); % bin indice where good interpolated data for the whole dataset start
disp('****')
bin_end             = input('Determine last bin indice with good interpolated data: '); % bin indice where good interpolated data for the whole dataset start
data.uintfilt       = uintfilt(bin_start:bin_end,:);
data.vintfilt       = vintfilt(bin_start:bin_end,:);
if reply_ts == 1
    data.tsintfilt  = tsintfilt(bin_start:bin_end,:);
end
data.Z              = Z(bin_start:bin_end);
data.inttim         = inttim;
save([fpath_output, mooring.name '_' num2str(adcp.sn) '_instr_' sprintf('%02d',instr) '_int_filt_sub.mat'],'adcp','mooring','data');

%% Figure
niv_u               = (-1:0.05:1);
niv_v               = (-1:0.05:1);
close all
hf=figure('position', [0, 0, 1400, 1000]);
%u
subplot(2,1,1);
colormap jet
[C,h] = contourf(inttim,Z(bin_start:bin_end),uintfilt(bin_start:bin_end,:),niv_u);
set(h,'LineColor','none');
caxis(niv_u([1 end]));
h=colorbar;
ylabel(h,'U [m s^-^1]');
set(gca,'ydir', 'reverse');
ylabel('Depth (m)');
ylim([0,round(max(max(z)))]);
%change figure label in HH:MM
gregtick;
if filt
    title({[mooring.name, ' - ZONAL VELOCITY - RDI ',num2str(freq),' kHz (filtered from tide)']});
else
    title({[mooring.name, ' - ZONAL VELOCITY - RDI ',num2str(freq),' kHz']});
end

%v
subplot(2,1,2);
[C,h] = contourf(inttim,Z(bin_start:bin_end),vintfilt(bin_start:bin_end,:),niv_v);
set(h,'LineColor','none');
caxis(niv_v([1 end]));
h     = colorbar;
ylabel(h,'V [m s^-^1]');
set(gca,'ydir', 'reverse');
ylabel('Depth (m)');
ylim([0,round(max(max(z)))]);
%change figure label in HH:MM
gregtick;
if filt
    title({[mooring.name, ' - MERIDIONAL VELOCITY - RDI ',num2str(freq),' kHz (filtered from tide)']});
else
    title({[mooring.name, ' - MERIDIONAL VELOCITY - RDI ',num2str(freq),' kHz']});
end

graph_name = [fpath_output, mooring.name '_', num2str(instr), '_U_V_int_filt_sub'];
set(hf,'Units','Inches');
pos        = get(hf,'Position');
set(hf,'PaperPositionMode','Auto','PaperUnits','Inches','PaperSize',[pos(3), pos(4)]);
print(hf,graph_name,'-dpdf','-r300');

if reply_ts == 1
    hf=figure('position', [0, 0, 1400, 500]);
    colormap jet
    pcolor(inttim,Z(bin_start:bin_end),tsintfilt(bin_start:bin_end,:)); shading interp;
    h     = colorbar;
    ylabel(h,'Target Strength [dB1]');
    set(gca,'ydir', 'reverse');
    ylabel('Depth (m)');
    ylim([0,round(max(max(z,adcp.instr_depth)))]);
    %change figure label in HH:MM
    gregtick;
    if filt
        title({[mooring.name, ' - TARGET STRENGTH - RDI ',num2str(freq),' kHz (filtered from tide)']});
    else
        title({[mooring.name, ' - TARGET STRENGTH - RDI ',num2str(freq),' kHz']});
    end
    
    graph_name = [fpath_output, mooring.name, '_', num2str(instr), '_TS_int_filt_sub'];
    set(hf,'Units','Inches');
    pos        = get(hf,'Position');
    set(hf,'PaperPositionMode','Auto','PaperUnits','Inches','PaperSize',[pos(3), pos(4)]);
    saveas(hf,graph_name,'jpeg');
end



% %% Plot tide
% hf=figure('position', [0, 0, 1400, 1000]);
% niv_tide = (-5:0.2:5);
% utid_baro = utid_baro * 100;
% vtid_baro = vtid_baro * 100;
% %u
% subplot(2,1,1);
% colormap jet
% [C,h] = contourf(inttim,Z(bin_start:bin_end),utid_baro(bin_start:bin_end,:),niv_tide);
% set(h,'LineColor','none');
% caxis(niv_tide([1 end]));
% h=colorbar;
% ylabel(h,'U [cm s^-^1]');
% set(gca,'ydir', 'reverse');
% ylabel('Depth (m)');
% ylim([0,adcp.instr_depth]);
% %change figure label in HH:MM
% gregtick;
% title({[mooring.name, ' - ZONAL TIDE VELOCITY - RDI ',num2str(freq),' kHz']});
%
% %v
% subplot(2,1,2);
% [C,h] = contourf(inttim,Z(bin_start:bin_end),vtid_baro(bin_start:bin_end,:),niv_tide);
% set(h,'LineColor','none');
% caxis(niv_tide([1 end]));
% h     = colorbar;
% ylabel(h,'V [cm s^-^1]');
% set(gca,'ydir', 'reverse');
% ylabel('Depth (m)');
% ylim([0,adcp.instr_depth]);
% %change figure label in HH:MM
% gregtick;
% title({[mooring.name, ' - MERIDIONAL TIDE VELOCITY - RDI ',num2str(freq),' kHz']});

%%  Write netcdf file
disp('****')
disp('Creating .nc file')

% Input parameters for NETCDF Global Attributes
tc_globAttFilename      = fullfile('tools/input_GlobalAttrParameters.xls'); % JLL 2020/12 Il serait judicieux de remonter cette valeur en début du script template_get_adcp_data.m

%% Prepare informations and variables required to create NETCDF file %% 
[yr_start , ~, ~]       = gregorian(data.inttim(1));
[yr_end,  ~, ~]         = gregorian(data.inttim(length(data.inttim)));

% Read inputs metadata required for NETCDF Global Attributes
[~,~,cell_ncAttributes] = xlsread(tc_globAttFilename);

% Complete output path and filename 
tc_ncFilenam_out        = fullfile(fpath_output,['ADCP_',mooring.name,'_',num2str(yr_start),'_',num2str(yr_end),'_1d.nc']);

% Assign a "4D-size" (TIME,DEPTH,LATITUDE,LONGITUDE) to the ADCP current variables : UINTFILT, VINTFILT
td_uADCP                = ones(numel(data.inttim),numel(data.Z),numel(data.lat),numel(data.lon)) * d_fillvalue;
td_uADCP(:,:,1,1)       = data.uintfilt';
td_vADCP                = ones(numel(data.inttim),numel(data.Z),numel(data.lat),numel(data.lon)) * d_fillvalue;
td_vADCP(:,:,1,1)       = data.vintfilt';

% Flip for convention
data.Z                  = fliplr(data.Z);
td_uADCP                = fliplr(td_uADCP);
td_vADCP                = fliplr(td_vADCP);

% Group general ADCP mooring informations and ADCP data to be written in NETCDF file format
struct_dataADCP         = struct('mooringName', mooring.name, 'mooringLat', mooring.lat,...
    'mooringLon', mooring.lon, 'time', data.inttim, 'depth', data.Z,...
    'u', td_uADCP, 'v', td_vADCP);

%%  Write netcdf file  %%        
f_w_ADCP_ncOS(tc_ncFilenam_out,cell_ncAttributes,struct_dataADCP,d_fillvalue);
disp('****')