%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % template_get_adcp_data.m % ------------------------------- % Author : J�r�mie HABASQUE - IRD % ------------------------------- % INPUTS: % - binary raw file with .000 extension % OUTPUTS: % - U and V fields interpolated on a regulard grid, filtered and subsampled %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% % First part -------------------------------------------------------------------------------------------------------------------- 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='.\data_example\FR24_000.000'; % binary file with .000 extension % Directory for outputs fpath_output = '.\data_example\'; % Cruise/mooring info cruise.name = 'Cruise Name'; mooring.name='Lat Lon'; % 0N10W par exemple mooring.lat=00+00/60; %latitude en degr�s d�cimaux mooring.lon=-10+00/60; %longitude en degr�s d�cimaux % 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=280; % 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 = 9.29; magnetic_deviation_end = 9.05; rot=-(magnetic_deviation_ini+magnetic_deviation_end)/2; % Read rawfile fprintf('Read %s\n', rawfile); raw=read_os3(rawfile,'all'); figure;plot(raw.pressure);set(gca,'ydir','reverse'); title('pressure sensor');ylabel('Depth(m)');xlabel('Time index');grid on; saveas(gcf,[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(instr),'_','Pressure_sensor'],'fig') % Second part -------------------------------------------------------------------------------------------------------------------- % Determine first and last indiced when instrument was at depth (you can do this by plotting 'raw.pressure' for example first = 12; last = 17620; % amplitude of the bins / Correction ADCP's depth ea = squeeze(mean(raw.amp(:,:,first:last),2)); figure; imagesc(ea);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') % Third part -------------------------------------------------------------------------------------------------------------------- % If upward looking: range of surface bins used for instrument depth correction below! sbins= 31:38; % 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)); 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(adcp.direction,'dn') z = dpt1+(binmat-0.5)*blen+blnk; else error('Bin depth calculation: unknown direction!'); end saveas(figure(1),[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(instr),'_','Hist_diff_orig-depth_recon-depth'],'fig') saveas(figure(2),[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(instr),'_','Offset_depth'],'fig') saveas(figure(3),[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(instr),'_','Amplitude_bins_2'],'fig') %% 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)); % 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 saveas(figure(4),[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(instr),'_','Meridional_zonal_velocity'],'fig') %% 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); 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 interpolated data bin_start = 1; % bin indice where good interpolated data for the whole dataset start data.uintfilt=uintfilt(bin_start:length(Z),:); data.vintfilt=vintfilt(bin_start:length(Z),:); data.Z = Z(bin_start: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(bin_start:length(Z)),uintfilt(bin_start: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(bin_start:length(Z)),vintfilt(bin_start: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'); %% Write netcdf file [yr_start , ~, ~] = gregorian(inttim(1)); [yr_end, ~, ~] = gregorian(inttim(length(inttim))); ncid=netcdf.create([fpath_output,'ADCP_',mooring.name,'_',num2str(yr_start),'_',num2str(yr_end),'_1d.nc'],'NC_WRITE'); %create dimension dimidt = netcdf.defDim(ncid,'time',length(inttim)); dimidz = netcdf.defDim(ncid,'depth',length(Z)); %Define IDs for the dimension variables (pressure,time,latitude,...) time_ID=netcdf.defVar(ncid,'time','double',dimidt); depth_ID=netcdf.defVar(ncid,'depth','double',dimidz); %Define the main variable () u_ID = netcdf.defVar(ncid,'u','double',[dimidt dimidz]); v_ID = netcdf.defVar(ncid,'v','double',[dimidt dimidz]); %We are done defining the NetCdf netcdf.endDef(ncid); %Then store the dimension variables in netcdf.putVar(ncid,time_ID,inttim); netcdf.putVar(ncid,depth_ID,Z); %Then store my main variable netcdf.putVar(ncid,u_ID,uintfilt); netcdf.putVar(ncid,v_ID,vintfilt); %We're done, close the netcdf netcdf.close(ncid); % rmpath % rmpath('..\moored_adcp_proc'); clear all; close all; % -------------------------------------------------------------------------------------------