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+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% template_get_adcp_data_down_only.m
+% -------------------------------
+% Author : Jérémie 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('C:\Workspace_Matlab\git\ADCP_mooring_data_processing\moored_adcp_proc');
+addpath('.\backscatter'); % Optionnel
+
+% Location rawfile
+fpath = '';
+rawfile='C:\Users\jhabasqu\Desktop\\PIRATA\ADCP_mooring_data\23W-0N\2004-2005 - kpo_0612\LR3173_2004.000';
+
+% Directory for outputs
+fpath_output = 'C:\Users\jhabasqu\Desktop\\PIRATA\ADCP_mooring_data\23W-0N\2004-2005 - kpo_0612\';
+
+% Cruise/mooring info
+cruise.name = '';
+mooring.name='23W0N';
+mooring.lat=00+00/60; %latitude en degrés décimaux
+mooring.lon=-23+00/60; %longitude en degrés décimaux
+
+% ADCP info
+adcp.sn='kpo_0612';
+adcp.type='150 khz Quartermaster'; % Type : ‘Quartermaster’, ‘longranger’
+adcp.direction='dn'; % upward-looking 'up', downward-looking 'dn'
+adcp.instr_depth=180; % 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 = 16.44;
+magnetic_deviation_end = 16.28;
+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');
+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 = 370;
+last = 11398;
+
+% 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');
+saveas(gcf,[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(instr),'_','Amplitude_bins'],'fig')
+
+% Third part --------------------------------------------------------------------------------------------------------------------
+
+% 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 = min(z(:)):blen:max(z(:))+blen;
+Zmin = min(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(abs(Zmin-z(1,i))/blen)+1;
+ % filling the grid
+ npts = min([length(Z)-ind+1 nbin]);
+ u_interp(i,ind:ind+npts-1) = u(1:npts,i);
+ v_interp(i,ind:ind+npts-1) = v(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 = 8; % bin indice where good interpolated data for the whole dataset start
+bin_end = length(Z)-4;
+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');
+
+%% 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: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,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: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,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;
+
+% -------------------------------------------------------------------------------------------
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