diff --git a/.gitignore b/.gitignore
index a0130cfd4953dca0a06d9ece5cee3621001aac4d..d4562b664f03a07cc518cfbcf02d3051150dc820 100644
--- a/.gitignore
+++ b/.gitignore
@@ -4,6 +4,7 @@
*.docx
FR*/
IDMX*/
+AMAZOMIX/
old_data/
doc/*.pdf
*.jnl
diff --git a/moored_adcp_proc/adcp_surface_fit.m b/moored_adcp_proc/adcp_surface_fit.m
index 5b640fc179204ae89c336add365270d09adfc5c6..b045a238aabcfe237129c889c0ad8f43f7472c74 100644
--- a/moored_adcp_proc/adcp_surface_fit.m
+++ b/moored_adcp_proc/adcp_surface_fit.m
@@ -75,7 +75,7 @@ function [zbins,zadcp1,offset,x_null]=adcp_surface_fit(zadcp,ea,surface_bins,ble
plot(-((x_null-1)*blen+blen/2+fbind),'r');
legend('Original','Reconstructed from surface reflection');
- if abs(offset)>15
+ if any(abs(offset)>15)
reply = input('Do you want to overwrite offset? 1/0 [0]:');
if isempty(reply)
reply = 0;
@@ -83,6 +83,7 @@ function [zbins,zadcp1,offset,x_null]=adcp_surface_fit(zadcp,ea,surface_bins,ble
if reply==1
offset=input('->Enter new offset:');
+ offset=offset*ones(1,length(zadcp));
else
disp(['->Cleaned median filter offset is applied']);
end
diff --git a/multi_adcp_mooring/merge_data_finalfile.m b/multi_adcp_mooring/merge_data_finalfile.m
index 4646dabd28165611f43d4db585b6dfb74e48c1a3..716ed761bb058eb31576687de901dd34e80b9d0f 100644
--- a/multi_adcp_mooring/merge_data_finalfile.m
+++ b/multi_adcp_mooring/merge_data_finalfile.m
@@ -5,11 +5,11 @@
clear all; close all;
%% Variables
-FileToMerge1 = '/home/proussel/Documents/OUTILS/ADCP/ADCP_mooring_data_processing/ADCP_0W0N_2016_2020_1d.nc'; %.nc file to merge with
-FileToMerge2 = '/media/irdcampagnes/PIRATA/PIRATA-DATA/MOORING-PIRATA/0-0/ADCP_0W0N_2020_2021_1d.nc'; %.nc file to merge
+FileToMerge1 = '/media/irdcampagnes/PIRATA-DATA/MOORING-PIRATA/10W/merged_data/ADCP_10W0N_2001_2019.nc'; %.nc file to merge with
+FileToMerge2 = '/media/irdcampagnes/PIRATA-DATA/MOORING-PIRATA/10W/ADCP_10W0N_2021_2023_1d.nc'; %.nc file to merge
step_subsampling = 1; % 1=daily
plot_data = 1;
-mooring.name = '0W0N';
+mooring.name = '10W0N';
mooring.lat = 0;
mooring.lon = 0;
freq = '150 khz Quartermaster';
@@ -35,14 +35,14 @@ ncfile2.v = ncread(FileToMerge2,'VCUR');
%% Create depth matrix
%depth = max(vertcat(ncfile1.depth,ncfile2.depth)):ncfile1.depth(2)-ncfile1.depth(1):min(vertcat(ncfile1.depth,ncfile2.depth));
%depth = fliplr(depth);
-max(vertcat(ncfile1.depth,ncfile2.depth))
-min(vertcat(ncfile1.depth,ncfile2.depth))
+max(vertcat(ncfile1.depth,ncfile2.depth));
+min(vertcat(ncfile1.depth,ncfile2.depth));
depth = 0:5:320;
%% Create time matrix
time = vertcat(ncfile1.time,ncfile2.time);
[YY,MM,DD,hh,mm,ss] = datevec(time+datenum(1950,01,01));
-time = julian(YY,MM,DD,hh,mm,ss);
+%time = julian(YY,MM,DD,hh,mm,ss);
%% Create u/v matrix
for ii = 1:length(ncfile1.time)
@@ -57,10 +57,11 @@ end
u = vertcat(u1,u2);
v = vertcat(v1,v2);
+time = julian(YY,MM,DD,hh,mm,ss);
time = time*ones(1,length(depth));
% create a continuous series of daily data, ranging from min(d) to max(d)
-final_time = ceil(min(min(time))):0.25:floor(max(max(time)));
+final_time = ceil(min(min(time))):1:floor(max(max(time)));
ADCP_final.u = NaN(length(final_time),length(depth));
ADCP_final.v = NaN(length(final_time),length(depth));
diff --git a/template_get_adcp_data.m b/template_get_adcp_data.m
index 6e76b9e1e4f17714219fd3063df09d0b1e088b7c..225742c9e830d74423ba6081da3ae869eb4a11f0 100644
--- a/template_get_adcp_data.m
+++ b/template_get_adcp_data.m
@@ -16,26 +16,26 @@ addpath('/home/proussel/Documents/OUTILS/TOOLS/nansuite'); % NaNSuitePath
%% META information:
% Location rawfile
-rawfile = 'FR31/FR29_000.000'; % binary file with .000 extension
-fpath_output = './FR31/10Wtest/'; % Output directory
+rawfile = 'AMAZOMIX/AMAZ_002.000'; % binary file with .000 extension
+fpath_output = './AMAZOMIX/M2/'; % Output directory
% Cruise/mooring info
-cruise.name = 'PIRATA'; % cruise name
-mooring.name = '10W0N'; % '0N10W'
-mooring.lat = '00°00.017'; % latitude [°']
-mooring.lon = '-09°53.909'; % longitude [°']
-clock_drift = 418; % [seconds]
+cruise.name = 'AMAZOMIX'; % cruise name
+mooring.name = 'M2'; % '0N10W'
+mooring.lat = '03°56.971'; % latitude [°']
+mooring.lon = '-45°07.518'; % longitude [°']
+clock_drift = 0; % [seconds]
% ADCP info
-adcp.sn = 24629; % ADCP serial number
-adcp.type = '150 khz Quartermaster'; % Type : Quartermaster, longranger
+adcp.sn = 'ADCP709'; % ADCP serial number
+adcp.type = '75 khz Long Ranger'; % Type : Quartermaster, longranger
adcp.direction = 'up'; % upward-looking 'up', downward-looking 'dn'
-adcp.instr_depth = 300; % nominal instrument depth
+adcp.instr_depth = 400; % 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;
+d_fillvalue = -9999;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -60,419 +60,454 @@ 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);
+ prepross = 1;
load(raw_file)
else
fprintf('Read %s\n', rawfile);
+ prepross = 0;
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,:);
+if prepross == 1
+ cor_data = input('Do you want to apply a new correction to data? 1/0 [1]');
+ if isempty(cor_data)
+ cor_data = 0;
+ end
+else
+ cor_data = 1;
end
+if cor_data == 1
-
-%% 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;
+ %% 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
- 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;
+ 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
-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
+
+
+ %% 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(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;
+ 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]');
+ high_att = 0;
+ disp('WARNING you have high attitude ADCP data (>=10°) ---- check your data and be carefull');
+ disp('Press a key to continue');
+ pause
+ 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
-end
-%% If upward looking: determine range of surface bins used for instrument depth correction below!
-surface_bins = 0;
-if pressure_data == 0
+ %% 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('****')
- surface_bins = input('Do you want to apply an offset using surface reflection? 1/0 [1]');
- if isempty(surface_bins)
- surface_bins = 1;
+ pressure_data = input('Do you have external pressure data? 1/0 [0]');
+ if isempty(pressure_data)
+ pressure_data = 0;
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
+ 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
- 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')
+ hold on
+ plot(dpt, 'r')
+ legend('External sensor depth','ADCP sensor depth');
+ xlabel('Time Index')
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;
+ exsens_data = input('Do you want to use external sensor data? 1/0 [0]');
+ if isempty(exsens_data)
+ exsens_data = 1;
end
-
- binmat = repmat((1:nbin)',1,length(dpt1));
-
- if strcmp(adcp.direction,'up')
- z(1,:) = dpt1(1,:)-(tlen+blen+lag)*0.5-blnk;
+ 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
- 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;
+
+ %% 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]');
+ surface_bins = 1;
+ if isempty(surface_bins)
+ surface_bins = 1;
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;
+ 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
- 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);
+
+ 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
- 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;
+ %% 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');
-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);
+ 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;
+ if ~any(high_att ~= 0)
+ adcp_check_surface(bins,u,u1,v,v1,corr,corr1,time,bin,z,z1,sz_dpt);
+ end
+ % 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
- % 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')
+ 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
-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');
+ %% Save raw data
+ disp('****')
+ disp('Saving raw data')
+ save([fpath_output, mooring.name '_' num2str(adcp.sn) '_instr_' sprintf('%02d',instr) '.mat'],'adcp','mooring','data','z','time','-v7.3');
+
+else
+
+ load([fpath_output, mooring.name '_' num2str(adcp.sn) '_instr_' sprintf('%02d',instr) '_raw.mat']);
+ blen = raw.config.cell;
+ nbin = raw.config.ncells; % number of bins
+ bin = 1:nbin; % bin number
+ freq = raw.config.sysconfig.frequency;
+ reply_ts = 0;
+ clear raw
+ load([fpath_output, mooring.name '_' num2str(adcp.sn) '_instr_' sprintf('%02d',instr) '.mat'],'adcp','mooring','data','z','time');
+
+
+end
%% Interpolate data on a regular vertical grid
if strcmp(adcp.direction,'up')
@@ -483,14 +518,14 @@ if strcmp(adcp.direction,'up')
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);
+ u_interp(i,ind:ind+npts-1) = data.u(1:npts,i);
+ v_interp(i,ind:ind+npts-1) = data.v(1:npts,i);
if reply_ts == 1
ts_interp(i,ind:ind+npts-1) = data.ts.ts(1:npts,i);
end
@@ -503,14 +538,14 @@ else
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);
+ u_interp(i,ind:ind+npts-1) = data.u(1:npts,i);
+ v_interp(i,ind:ind+npts-1) = data.v(1:npts,i);
if reply_ts == 1
ts_interp(i,ind:ind+npts-1) = data.ts.ts(1:npts,i);
end
@@ -520,6 +555,7 @@ 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]:');
@@ -532,22 +568,26 @@ if horz_interp
if isempty(filt)
filt = 1;
end
-
+
sub = input('Do you want to subsampling data daily? 1/0 [1]:');
- if isempty(filt)
- sub = 1;
+ if isempty(filt)
+ sub = 1;
end
if filt
if sub
+ statut = 'tide_filtered_daily';
disp('Horizontal interpolation, Filtering & Subsampling')
else
+ statut = 'tide_filtered';
disp('Horizontal interpolation & Filtering')
end
disp('Filtering using 40h Hamming filter (other disponible filter: FFT filter, tide model)')
else
if sub
+ statut = 'daily';
disp('Horizontal interpolation & Subsampling')
else
+ statut = 'interp';
disp('Horizontal interpolation')
end
end
@@ -558,6 +598,7 @@ end
if horz_interp == 0
+ statut = 'gridded';
uintfilt = u_interp';
vintfilt = v_interp';
inttim = data.time;
@@ -565,14 +606,14 @@ else
[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);
end
-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')
+saveas(figure(1),[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(instr),'_','data_raw_U',statut],'fig')
+saveas(figure(2),[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(instr),'_','data_raw_V',statut],'fig')
%% 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
+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
@@ -580,7 +621,10 @@ if reply_ts == 1
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');
+save([fpath_output, mooring.name '_' num2str(adcp.sn) '_instr_' sprintf('%02d',instr) '_' statut '.mat'],'adcp','mooring','data');
+
+%% NetCDF with gridded data
+extract_to_netcdf(fpath_output, mooring, data, statut, d_fillvalue)
%% Figure
niv_u = (-1:0.05:1);
@@ -600,11 +644,8 @@ 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
+title({[mooring.name, ' - ZONAL VELOCITY - RDI ',num2str(freq),' kHz (' statut ')']}, 'Interpreter', 'none');
+
%v
subplot(2,1,2);
@@ -618,13 +659,10 @@ 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
+title({[mooring.name, ' - MERIDIONAL VELOCITY - RDI ',num2str(freq),' kHz (' statut ')']}, 'Interpreter', 'none');
+
-graph_name = [fpath_output, mooring.name '_', num2str(instr), '_U_V_int_filt_sub'];
+graph_name = [fpath_output, mooring.name '_', num2str(instr), '_U_V_', statut];
set(hf,'Units','Inches');
pos = get(hf,'Position');
set(hf,'PaperPositionMode','Auto','PaperUnits','Inches','PaperSize',[pos(3), pos(4)]);
@@ -641,12 +679,9 @@ if reply_ts == 1
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
-
+ title({[mooring.name, ' - TARGET STRENGTH - RDI ',num2str(freq),' kHz (' statut ')']}, 'Interpreter', 'none');
+
+
graph_name = [fpath_output, mooring.name, '_', num2str(instr), '_TS_int_filt_sub'];
set(hf,'Units','Inches');
pos = get(hf,'Position');
@@ -688,41 +723,4 @@ end
% 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('****')
\ No newline at end of file
+% title({[mooring.name, ' - MERIDIONAL TIDE VELOCITY - RDI ',num2str(freq),' kHz']});
\ No newline at end of file
diff --git a/tools/extract_to_netcdf.m b/tools/extract_to_netcdf.m
new file mode 100644
index 0000000000000000000000000000000000000000..99f15ab0e53a9b13f34105a40ab1444f7172fa7f
--- /dev/null
+++ b/tools/extract_to_netcdf.m
@@ -0,0 +1,40 @@
+function extract_to_netcdf(fpath_output, mooring, data, statut,d_fillvalue)
+
+%% 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),'_' statut '.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('****')
+
+end
\ No newline at end of file