diff --git a/moored_adcp_proc/.DS_Store b/moored_adcp_proc/.DS_Store
deleted file mode 100644
index 5008ddfcf53c02e82d7eee2e57c38e5672ef89f6..0000000000000000000000000000000000000000
Binary files a/moored_adcp_proc/.DS_Store and /dev/null differ
diff --git a/moored_adcp_proc/adcp_filt_sub.m b/moored_adcp_proc/adcp_filt_sub.m
index 9eb57d4dc4e546cdcb6fd342b7011b21117f0a34..cbc9459e586f8142463cb3121f9bf5d44af5b856 100644
--- a/moored_adcp_proc/adcp_filt_sub.m
+++ b/moored_adcp_proc/adcp_filt_sub.m
@@ -90,17 +90,14 @@ vtid_baro=0;
% uintfilt = uintfilt-utid_baro;
% vintfilt = vintfilt-vtid_baro;
-hf=figure('position', [0, 0, 1400, 1000]);
-subplot 121;
+hf=figure('position', [0, 0, 1400, 1000]);subplot 121;
imagesc(data.time,intdepvec,ui(intdepvec,:),[-1 1]);
%set(gca,'YLim',[min(intdepvec)-10 max(intdepvec)+10]);
gregtick;
ylabel('Bins');
-title('U field - data raw');
-subplot 122;
+title('U field - data raw');subplot 122;
imagesc(inttim,intdepvec,uintfilt,[-1 1]);
-%set(gca,'YLim',[min(intdepvec)-10 max(intdepvec)+10]);
-gregtick;
+%set(gca,'YLim',[min(intdepvec)-10 max(intdepvec)+10]);gregtick;
ylabel('Bins');
title('U field - data interpolated, filtered and subsampled');
@@ -116,4 +113,4 @@ imagesc(inttim,intdepvec,vintfilt,[-1 1]);
%set(gca,'YLim',[min(intdepvec)-10 max(intdepvec)+10]);
gregtick;
ylabel('Bins');
-title('V field - data interpolated, filtered and subsampled');
+title('V field - data interpolated, filtered and subsampled');
\ No newline at end of file
diff --git a/template_get_adcp_data.m b/template_get_adcp_data.m
index cd96120c53af50726d788df50f48d6f41feaba1d..3d5b28cf3fdd77a5c56981bfbc6aba5db27e883f 100644
--- a/template_get_adcp_data.m
+++ b/template_get_adcp_data.m
@@ -16,34 +16,26 @@ addpath(genpath('C:\Users\proussel\Documents\outils\ADCP\ADCP_mooring_data_proce
close all
clear all
-%% META information:
-
% Path
addpath('.\moored_adcp_proc'); % ou par exemple ('C:\Users\IRD_US_IMAGO\TRAITEMENTS\ADCP_MOUILLAGE\01_DATA_PROCESSING\moored_adcp_proc');
addpath('.\backscatter'); % (Optionnel) / ou par exemple ('C:\Users\IRD_US_IMAGO\TRAITEMENTS\ADCP_MOUILLAGE\01_DATA_PROCESSING\backscatter');
% Location rawfile
fpath = '';
-rawfile='.\FR27_000.000'; % binary file with .000 extension
-
+rawfile='.\FR27_000.000'; % binary file with .000 extension
% Directory for outputs
fpath_output = '.\FR29_bis\';
-
% Cruise/mooring info
cruise.name = 'PIRATA-FR29';
mooring.name = '0N10W'; % 0N10W par exemple
mooring.lat = 00+00.15/60; %latitude en degrés décimaux
mooring.lon = -09-53.15/60; %longitude en degrés décimaux
clock_drift = 208/3600; % convert into hrs
-
% ADCP info
adcp.sn = 15258;
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
-
-% If ADCP was not set up to correct for magnetic deviation internally
+adcp.instr_depth = 300; % nominal instrument depth% 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
@@ -51,11 +43,11 @@ instr = 1; % this is just for name convention and
magnetic_deviation_ini = -9;
magnetic_deviation_end = -8.77;
rot = (magnetic_deviation_ini+magnetic_deviation_end)/2;
-
% Read rawfile
fprintf('Read %s\n', rawfile);
raw = read_os3(rawfile,'all');
+
% Correct clock drift
time0 = julian(raw.juliandate);
clockd = linspace(0, clock_drift, length(time0));
@@ -91,13 +83,11 @@ saveas(gcf,[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(ins
% If upward looking: range of surface bins used for instrument depth correction below!
sbins = 32:39;%30:35; % here a range of bins is given which cover the surface reflection
-
% Exclude data with percent good below prct_good
prct_good = 20;
%% Read 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));
@@ -153,8 +143,7 @@ binmat = repmat((1:nbin)',1,length(dpt1));
if strcmp(adcp.direction,'up')
[z,dpt1,offset,xnull] = adcp_surface_fit(dpt,ea,sbins,blen,blnk,nbin);
elseif strcmp(adcp.direction,'dn')
- z = dpt1+(binmat-0.5)*blen+blnk;
-else
+ z = dpt1+(binmat-0.5)*blen+blnk;else
error('Bin depth calculation: unknown direction!');
end
@@ -241,6 +230,8 @@ end
[uintfilt,vintfilt,uifilt,vifilt,inttim,utid_baro,vtid_baro] = adcp_filt_sub(data,u_interp',v_interp',1:length(Z),40);
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(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')
save([fpath_output, mooring.name '_' num2str(adcp.sn) '_instr_' sprintf('%02d',instr) '_int_filt.mat'],'uifilt','vifilt','data');
@@ -250,8 +241,7 @@ bin_end = length(Z);
data.uintfilt = uintfilt(bin_start:bin_end,:);
data.vintfilt = vintfilt(bin_start:bin_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','raw');
+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 = (-1:0.05:1);
@@ -275,8 +265,7 @@ title({[mooring.name, ' - ZONAL VELOCITY - RDI ',num2str(freq),' kHz']});
%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');
+[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]');