template_get_adcp_data.m

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% template_get_adcp_data.m
% -------------------------------
% Author : Jrmie HABASQUE - IRD
% -------------------------------
% INPUTS:
% - binary raw file with .000 extension
% OUTPUTS:
% - U and V fields interpolated on a regulard grid, filtered and subsampled
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
close all
clear all
 
% path
addpath('.\moored_adcp_proc');

%% META information:

% Location rawfile
fpath = '';
rawfile='.\data_example\FR24_000.000'; % binary file with .000 extension
 
% Directory for outputs
fpath_output = '.\data_example\';

cruise.name = '';
mooring.name='';
mooring.lat=00+00/60; %latitude
mooring.lon=-10+00/60; %longitude

adcp.sn=15258;
adcp.type='150 khz Quartermaster';
adcp.direction='up';        % upward-looking 'up', downward-looking 'dn'
adcp.instr_depth=178;       % nominal instrument depth

instr=1;                    % this is just for name convention and sorting of all mooring instruments

% If ADCP was not set up to correct for magnetic deviation internally
% ("EA0" code in configuration file), use http://www.ngdc.noaa.gov/geomag-web/#declination
% Magnetic deviation: Mean of deviations at time of deployment and time of recovery 

% magnetic deviation values
magnetic_deviation_ini = 15.11;
magnetic_deviation_end = 15.01;
rot=-(magnetic_deviation_ini+magnetic_deviation_end)/2;  

% determine first and last indiced when instrument was at depth (you can do this by plotting 'raw.pressure' for example           
first = 8; 
last = 7963; 

% If upward looking: range of surface bins used for instrument depth correction below!
sbins= 17:28; % here a range of bins is given which cover the surface reflection

% Exclude data with percent good below prct_good
prct_good = 20;

% Read rawfile
fprintf('Read %s\n', rawfile);
raw=read_os3(rawfile,'all');
figure;plot(raw.pressure);set(gca,'ydir','reverse');
 
freq = raw.config.sysconfig.frequency;

%% Read data
ea = squeeze(mean(raw.amp(:,:,first:last),2));  % amplitude of the bins 
figure; imagesc(ea);title('Amplitude of the bins'); colorbar;

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));  % the difference in vertical velocity between the two pairs of transducers 
time = raw.juliandate(first:last);
ang = [raw.pitch(first:last) raw.roll(first:last) raw.heading(first:last)]; 
soundspeed = raw.soundspeed(first:last);
T = raw.temperature(first:last);
press = raw.pressure(first:last);

nbin = raw.config.ncells;  % number of bins
bin  = 1:nbin;
blen = raw.config.cell;    % bin length
blnk = raw.config.blank;   % blank distance after transmit

dt=(time(2)-time(1))*24;   % Sampling interval in hours

[u,v]=uvrot(u2,v2,-rot);   % Correction of magnetic deviation

pg = squeeze(raw.pg(:,4,first:last));  % percent good

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;

%% 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
if strcmp(adcp.direction,'up')  
    [z,dpt1,offset,xnull]=adcp_surface_fit(dpt,ea,sbins,blen,blnk,nbin);
elseif strcmp(direction,'dn')
    z = dpt1+(binmat-0.5)*blen+blnk;
else
    error('Bin depth calculation: unknown direction!');
end

%% Remove bad data if ADCP is looking upward
u1=u; v1=v; w1=w; vel_err1=vel_err; ea1=ea;

if strcmp(adcp.direction,'up')
    for i=1:length(time)
        sz_dpt(i)=adcp_shadowzone(dpt(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))-1;
        
        % here a manual criterion should be hard-coded if
        % adcp_check_surface (below) shows bad velocities close to the
        % surface

        fz(i)=z(iz(i),i);    
    end

    for i=1:length(time) 
        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;
    end

    if 1
        bins=nmedian(sbin)-4:nmedian(sbin)+2;
        adcp_check_surface(bins,u,u1,v,v1,time,bin,z); 
        % 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
    end
end

%% SAVE DATA
% More meta information
%adcp.comment='';
adcp.config=raw.config;
adcp.z_offset=offset;
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=z;
data.depth=dpt;
data.temp=T;
data.sspd = soundspeed;

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

%% Interpolate data on a regular vertical grid
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));
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);
end
  
%% Horizontal interpolation, filtering and subsampling
[uintfilt,vintfilt,inttim] = adcp_filt_sub(data,u_interp',v_interp',1:length(Z),40);

% Save interpolated data
data.uintfilt=uintfilt(1:length(Z),:);
data.vintfilt=vintfilt(1:length(Z),:);
data.Z = Z(1:length(Z));
data.inttim = inttim;
save([fpath_output, mooring.name '_' num2str(adcp.sn) '_instr_' sprintf('%02d',instr) '_int_filt_sub.mat'],'adcp','mooring','data','raw');

%% Figure
niv_u = (-1.5:0.1:1.5);
niv_v = (-0.5:0.1:0.5);

hf=figure('position', [0, 0, 1400, 1000]);
%u
subplot(2,1,1);
[C,h] = contourf(inttim,Z(1:length(Z)),uintfilt(1:length(Z),:),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,adcp.instr_depth]);
%change figure label in HH:MM
gregtick;
title({[mooring.name, ' - MERIDIONAL VELOCITY - RDI ',num2str(freq),' kHz']});

%v
subplot(2,1,2);
[C,h] = contourf(inttim,Z(1:length(Z)),vintfilt(1:length(Z),:),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,adcp.instr_depth]);
%change figure label in HH:MM
gregtick;
title({[mooring.name, ' - ZONAL VELOCITY - RDI ',num2str(freq),' kHz']});

graph_name = [fpath_output, mooring.name '_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');
 
% rmpath
rmpath('.\moored_adcp_proc');