diff --git a/multi_adcp_mooring/merge_data.m b/multi_adcp_mooring/merge_data.m
new file mode 100644
index 0000000000000000000000000000000000000000..06d26e9f44be28da6457e6d30f256a4055753c74
--- /dev/null
+++ b/multi_adcp_mooring/merge_data.m
@@ -0,0 +1,182 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Merge subsurface ADCP mooring data %
+% Autor: P. Rousselot / Date: 03/2020 %
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+clear all; close all;
+
+%% Variables
+FileToMerge1 = 'F:\Encours\PIRATA_ADCP-MOORINGS\Convert_ADCP/ADCP_23W0N_2001_2015.nc'; %.nc file to merge with
+FileToMerge2 = 'F:\Encours\PIRATA_ADCP-MOORINGS\23W\0_Final_Files/ADCP_0N23W_2015_2016_1d_up_down.nc'; %.nc file to merge
+% FileToMerge3 = '/media/irdcampagnes/PIRATA/PIRATA_ADCP-MOORINGS/10W/0_Final_Files/ADCP_10W0N_2004_2005_1d.nc'; %.nc file to merge
+% FileToMerge1 = '/home/proussel/Documents/OUTILS/ADCP/ADCP_mooring_data_processing/IDMX/ADCP_0N130E_2013_2013_1d.nc'; %.nc file to merge with
+% FileToMerge2 = '/home/proussel/Documents/OUTILS/ADCP/ADCP_mooring_data_processing/IDMX/ADCP_0N130E_2013_2016_1d.nc'; %.nc file to merge
+step_subsampling = 1; % 1=daily
+plot_data = 1;
+mooring.name = '23W0N';
+freq = 'Variable';
+% mooring.name = '0N130E';
+% freq = '75';
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% Read first .nc file
+ncfile1.time = ncread(FileToMerge1,'TIME');
+ncfile1.depth = ncread(FileToMerge1,'DEPTH');
+ncfile1.u = ncread(FileToMerge1,'U')';
+ncfile1.v = ncread(FileToMerge1,'V')';
+
+%% Read second .nc file
+ncfile2.time = ncread(FileToMerge2,'TIME');
+ncfile2.depth = ncread(FileToMerge2,'DEPTH');
+ncfile2.u = ncread(FileToMerge2,'UCUR');
+ncfile2.v = ncread(FileToMerge2,'VCUR');
+
+% %% Read third .nc file
+% ncfile3.time = ncread(FileToMerge3,'TIME');
+% ncfile3.depth = ncread(FileToMerge3,'DEPTH');
+% ncfile3.u = ncread(FileToMerge3,'UCUR');
+% ncfile3.v = ncread(FileToMerge3,'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))
+depth = 0:5:1000;
+
+%% 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 = time + datenum(1950,1,1,0,0,0) + datenum(2020,01,01); % -0.5 is necessary to remove 12h00 introduced by datetime function starting at noon instead of midnight as performed by julian function previously used
+time = time*ones(1,length(depth));
+
+%% Create u/v matrix
+for ii = 1:length(ncfile1.time)
+ u1(ii,:) = interp1(ncfile1.depth,ncfile1.u(ii,:),depth);
+ v1(ii,:) = interp1(ncfile1.depth,ncfile1.v(ii,:),depth);
+end
+for ii = 1:length(ncfile2.time)
+ u2(ii,:) = interp1(ncfile2.depth,ncfile2.u(ii,:),depth);
+ v2(ii,:) = interp1(ncfile2.depth,ncfile2.v(ii,:),depth);
+end
+% for ii = 1:length(ncfile3.time)
+% u3(ii,:) = interp1(ncfile3.depth,ncfile3.u(ii,:),depth);
+% v3(ii,:) = interp1(ncfile3.depth,ncfile3.v(ii,:),depth);
+% end
+u = vertcat(u1,u2);
+v = vertcat(v1,v2);
+
+u = u';
+v = v';
+
+% create a continuous series of daily data, ranging from min(d) to max(d)
+final_time = ceil(min(min(time))):1:floor(max(max(time)));
+ADCP_final.u = NaN(length(depth),length(final_time));
+ADCP_final.v = NaN(length(depth),length(final_time));
+
+for i_time = 1:length(final_time)
+ for j_time = 1:length(time)
+ if final_time(i_time) == time(j_time,1)
+ ADCP_final.u(:,i_time)=u(:,j_time);
+ ADCP_final.v(:,i_time)=v(:,j_time);
+ end
+ end
+end
+
+time = final_time;
+time = time'*ones(1,length(depth));
+time = time';
+u = ADCP_final.u;
+v = ADCP_final.v;
+
+%% Plot data
+if plot_data
+ niv_u = (-1.5:0.05:1);
+ niv_v = (-1.8:0.05:1.5);
+ depth = depth.*ones(length(time),1);
+ depth = depth';
+ %date1 = julian(ncfile1.time(1));
+ %date2 = julian(ncfile2.time(end));
+ date1 = datestr(ncfile1.time(1)+datenum(1950,01,01),'yyyy');
+ date2 = datestr(ncfile2.time(end)+datenum(1950,01,01),'yyyy');
+
+ hf=figure('position', [0, 0, 1400, 1000]);
+ %u
+ subplot(2,1,1);
+ colormap jet
+ [C,h] = contourf(time,depth,u,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,max(max(depth))]);
+ %datetick('x','mm-yyyy');
+ gregtick;
+ title({[mooring.name, ' - ' num2str(date1) ' to ' num2str(date2) ' - ZONAL VELOCITY - RDI ',num2str(freq),' kHz (filtered from tide)']});
+
+ %v
+ subplot(2,1,2);
+ [C,h] = contourf(time,depth,v,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,max(max(depth))]);
+ gregtick;
+ title({[mooring.name, ' - ' num2str(date1) ' to ' num2str(date2) ' - MERIDIONAL VELOCITY - RDI ',num2str(freq),' kHz (filtered from tide)']});
+
+ graph_name = ['ADCP_' mooring.name '_' num2str(date1) '_' num2str(date2) '_U_V_daily'];
+ 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');
+end
+
+%% Write netcdf file
+time = time(1,:)';
+timed = gregorian(time);
+timed(:,5) = 0;
+timed(:,6) = 0;
+time = datenum(timed)-datenum(1950,01,01);
+
+disp('****')
+disp('Creating .nc file')
+yr_start = datestr(time(1)+datenum(1950,01,01), 'yyyy');
+yr_end = datestr(time(end)+datenum(1950,01,01), 'yyyy');
+
+ncid = netcdf.create(['ADCP_',mooring.name,'_',num2str(yr_start),'_',num2str(yr_end),'.nc'],'NC_CLOBBER');
+
+%create dimension
+dimidz = netcdf.defDim(ncid, 'DEPTH', size(depth,2));
+dimidt = netcdf.defDim(ncid, 'TIME', netcdf.getConstant('NC_UNLIMITED'));
+%Define IDs for the dimension variables (pressure,time,latitude,...)
+time_ID = netcdf.defVar(ncid,'TIME','double',dimidt);
+netcdf.putAtt(ncid, time_ID, 'long_name', 'Time');
+netcdf.putAtt(ncid, time_ID, 'axis', 'T');
+netcdf.putAtt(ncid, time_ID, 'units', 'days since 1950-01-01T00:00:00Z');
+netcdf.putAtt(ncid, time_ID, 'time_origin', '1-JAN-1950:00:00:00');
+depth_ID = netcdf.defVar(ncid,'DEPTH','double',dimidz);
+netcdf.putAtt(ncid, depth_ID, 'long_name', 'Depth');
+netcdf.putAtt(ncid, depth_ID, 'axis', 'Z');
+netcdf.putAtt(ncid, depth_ID, 'units', 'meters');
+netcdf.putAtt(ncid, depth_ID, 'positive', 'down');
+netcdf.putAtt(ncid, depth_ID, 'point_spacing', 'even');
+%Define the main variable ()
+u_ID = netcdf.defVar(ncid,'U','double',[dimidz dimidt]);
+netcdf.putAtt(ncid, u_ID, 'long_name', 'Zonal velocities');
+v_ID = netcdf.defVar(ncid,'V','double',[dimidz dimidt]);
+netcdf.putAtt(ncid, v_ID, 'long_name', 'Meridional velocities');
+%We are done defining the NetCdf
+netcdf.endDef(ncid);
+%Then store the dimension variables in
+netcdf.putVar(ncid, depth_ID, depth);
+netcdf.putVar(ncid, time_ID, 0, length(time), time);
+%Then store my main variable
+netcdf.putVar(ncid, u_ID, u);
+netcdf.putVar(ncid, v_ID, v);
+%We're done, close the netcdf
+netcdf.close(ncid);
+disp('****')
\ No newline at end of file
diff --git a/merge_data.m b/multi_adcp_mooring/merge_data_finalfile.m
similarity index 60%
rename from merge_data.m
rename to multi_adcp_mooring/merge_data_finalfile.m
index f4e2a4cb7e1eca1009c273db95eb215fccda0024..e1693a906fbe3273890f0b47f6a9bdc005dea26d 100644
--- a/merge_data.m
+++ b/multi_adcp_mooring/merge_data_finalfile.m
@@ -1,149 +1,162 @@
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-% Merge subsurface ADCP mooring data %
-% Autor: P. Rousselot / Date: 03/2020 %
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-clear all; close all;
-
-%% Variables
-FileToMerge1 = '/home/proussel/Documents/OUTILS/ADCP/ADCP_mooring_data_processing/IDMX2/ADCP_0N130E_2010_2010_1d.nc'; %.nc file to merge with
-FileToMerge2 = '/home/proussel/Documents/OUTILS/ADCP/ADCP_mooring_data_processing/IDMX/ADCP_0N130E_2013_2016_1d.nc'; %.nc file to merge
-FileToMerge3 = '/home/proussel/Documents/OUTILS/ADCP/ADCP_mooring_data_processing/IDMX2/ADCP_0N130E_2010_2012_1d.nc'; %.nc file to merge
-% FileToMerge1 = '/home/proussel/Documents/OUTILS/ADCP/ADCP_mooring_data_processing/IDMX/ADCP_0N130E_2013_2013_1d.nc'; %.nc file to merge with
-% FileToMerge2 = '/home/proussel/Documents/OUTILS/ADCP/ADCP_mooring_data_processing/IDMX/ADCP_0N130E_2013_2016_1d.nc'; %.nc file to merge
-step_subsampling = 1; % 1=daily
-plot_data = 1;
-mooring.name = '0N130E';
-freq = '75';
-% mooring.name = '0N130E';
-% freq = '75';
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% Read first .nc file
-ncfile1.time = ncread(FileToMerge1,'time');
-ncfile1.depth = ncread(FileToMerge1,'depth');
-ncfile1.u = ncread(FileToMerge1,'u');
-ncfile1.v = ncread(FileToMerge1,'v');
-
-%% Read second .nc file
-ncfile2.time = ncread(FileToMerge2,'time');
-ncfile2.depth = ncread(FileToMerge2,'depth');
-ncfile2.u = ncread(FileToMerge2,'u');
-ncfile2.v = ncread(FileToMerge2,'v');
-
-%% Read third .nc file
-ncfile3.time = ncread(FileToMerge3,'time');
-ncfile3.depth = ncread(FileToMerge3,'depth');
-ncfile3.u = ncread(FileToMerge3,'u');
-ncfile3.v = ncread(FileToMerge3,'v');
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% 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);
-
-%% Create time matrix
-time = vertcat(ncfile1.time,ncfile3.time,ncfile2.time);
-time = time*ones(1,length(depth));
-
-%% Create u/v matrix
-for ii = 1:length(ncfile1.time)
- u1(ii,:) = interp1(ncfile1.depth,ncfile1.u(ii,:),depth);
- v1(ii,:) = interp1(ncfile1.depth,ncfile1.v(ii,:),depth);
-end
-for ii = 1:length(ncfile2.time)
- u2(ii,:) = interp1(ncfile2.depth,ncfile2.u(ii,:),depth);
- v2(ii,:) = interp1(ncfile2.depth,ncfile2.v(ii,:),depth);
-end
-for ii = 1:length(ncfile3.time)
- u3(ii,:) = interp1(ncfile3.depth,ncfile3.u(ii,:),depth);
- v3(ii,:) = interp1(ncfile3.depth,ncfile3.v(ii,:),depth);
-end
-u = vertcat(u1,u3,u2);
-v = vertcat(v1,v3,v2);
-
-%% Plot data
-if plot_data
- niv_u = (-1.5:0.05:0.9);
- niv_v = (-1.8:0.05:1.5);
- depth = depth.*ones(length(time),1);
- date1 = julian(ncfile1.time(1));
- date2 = julian(ncfile2.time(end));
-
- hf=figure('position', [0, 0, 1400, 1000]);
- %u
- subplot(2,1,1);
- colormap jet
- [C,h] = contourf(time,depth,u,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,max(max(depth))]);
- gregtick;
- title({[mooring.name, ' - ' num2str(date1(1)) ' to ' num2str(date2(1)) ' - ZONAL VELOCITY - RDI ',num2str(freq),' kHz (filtered from tide)']});
-
- %v
- subplot(2,1,2);
- [C,h] = contourf(time,depth,v,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,max(max(depth))]);
- gregtick;
- title({[mooring.name, ' - ' num2str(date1(1)) ' to ' num2str(date2(1)) ' - MERIDIONAL VELOCITY - RDI ',num2str(freq),' kHz (filtered from tide)']});
-
- graph_name = ['ADCP_' mooring.name '_' num2str(date1(1)) '_' num2str(date2(1)) '_U_V_daily'];
- 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');
-end
-
-%% Write netcdf file
-time = time(:,1);
-timed = gregorian(time);
-timed(:,5) = 0;
-timed(:,6) = 0;
-time = datenum(timed)-datenum(1950,01,01);
-
-disp('****')
-disp('Creating .nc file')
-yr_start = datestr(time(1)+datenum(1950,01,01), 'yyyy');
-yr_end = datestr(time(end)+datenum(1950,01,01), 'yyyy');
-
-ncid = netcdf.create(['ADCP_',mooring.name,'_',num2str(yr_start),'_',num2str(yr_end),'.nc'],'NC_CLOBBER');
-
-%create dimension
-dimidz = netcdf.defDim(ncid, 'DEPTH', size(depth,2));
-dimidt = netcdf.defDim(ncid, 'TIME', netcdf.getConstant('NC_UNLIMITED'));
-%Define IDs for the dimension variables (pressure,time,latitude,...)
-time_ID = netcdf.defVar(ncid,'TIME','double',dimidt);
-netcdf.putAtt(ncid, time_ID, 'long_name', 'Time');
-netcdf.putAtt(ncid, time_ID, 'axis', 'T');
-netcdf.putAtt(ncid, time_ID, 'units', 'days since 1950-01-01T00:00:00Z');
-netcdf.putAtt(ncid, time_ID, 'time_origin', '1-JAN-1950:00:00:00');
-depth_ID = netcdf.defVar(ncid,'DEPTH','double',dimidz);
-netcdf.putAtt(ncid, depth_ID, 'long_name', 'Depth');
-netcdf.putAtt(ncid, depth_ID, 'axis', 'Z');
-netcdf.putAtt(ncid, depth_ID, 'units', 'meters');
-netcdf.putAtt(ncid, depth_ID, 'positive', 'down');
-netcdf.putAtt(ncid, depth_ID, 'point_spacing', 'even');
-%Define the main variable ()
-u_ID = netcdf.defVar(ncid,'U','double',[dimidz dimidt]);
-netcdf.putAtt(ncid, u_ID, 'long_name', 'Zonal velocities');
-v_ID = netcdf.defVar(ncid,'V','double',[dimidz dimidt]);
-netcdf.putAtt(ncid, v_ID, 'long_name', 'Meridional velocities');
-%We are done defining the NetCdf
-netcdf.endDef(ncid);
-%Then store the dimension variables in
-netcdf.putVar(ncid, depth_ID, depth(1,:));
-netcdf.putVar(ncid, time_ID, 0, length(time), time);
-%Then store my main variable
-netcdf.putVar(ncid, u_ID, u');
-netcdf.putVar(ncid, v_ID, v');
-%We're done, close the netcdf
-netcdf.close(ncid);
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% Merge subsurface ADCP mooring data %
+% Autor: P. Rousselot / Date: 03/2020 %
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%clear all; close all;
+
+%% Variables
+FileToMerge1 = 'F:\Encours\PIRATA_ADCP-MOORINGS\Convert_ADCP/ADCP_23W0N_2001_2015.nc'; %.nc file to merge with
+FileToMerge2 = 'F:\Encours\PIRATA_ADCP-MOORINGS\23W\0_Final_Files/ADCP_0N23W_2015_2016_1d_up_down.nc'; %.nc file to merge
+%FileToMerge2 = 'F:\Encours\PIRATA_ADCP-MOORINGS\23W\v2\2008-2009\ADCP_23W0N_2008_2009_1d.nc';
+% FileToMerge3 = '/media/irdcampagnes/PIRATA/PIRATA_ADCP-MOORINGS/10W/0_Final_Files/ADCP_10W0N_2004_2005_1d.nc'; %.nc file to merge
+% FileToMerge1 = '/home/proussel/Documents/OUTILS/ADCP/ADCP_mooring_data_processing/IDMX/ADCP_0N130E_2013_2013_1d.nc'; %.nc file to merge with
+% FileToMerge2 = '/home/proussel/Documents/OUTILS/ADCP/ADCP_mooring_data_processing/IDMX/ADCP_0N130E_2013_2016_1d.nc'; %.nc file to merge
+step_subsampling = 1; % 1=daily
+plot_data = 1;
+mooring.name = '23W0N';
+freq = 'Variable';
+% mooring.name = '0N130E';
+% freq = '75';
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% Read first .nc file
+ncfile1.time = ncread(FileToMerge1,'TIME');
+ncfile1.depth = ncread(FileToMerge1,'DEPTH');
+ncfile1.u = ncread(FileToMerge1,'U')';
+ncfile1.v = ncread(FileToMerge1,'V')';
+
+%% Read second .nc file
+ncfile2.time = ncread(FileToMerge2,'TIME');
+ncfile2.depth = ncread(FileToMerge2,'DEPTH');
+ncfile2.u = ncread(FileToMerge2,'UCUR');
+ncfile2.v = ncread(FileToMerge2,'VCUR');
+
+% %% Read third .nc file
+% ncfile3.time = ncread(FileToMerge3,'TIME');
+% ncfile3.depth = ncread(FileToMerge3,'DEPTH');
+% ncfile3.u = ncread(FileToMerge3,'UCUR');
+% ncfile3.v = ncread(FileToMerge3,'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))
+depth = 0:5:1000;
+
+%% 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 = time + datenum(1950,1,1,0,0,0) + datenum(2020,01,01); % -0.5 is necessary to remove 12h00 introduced by datetime function starting at noon instead of midnight as performed by julian function previously used
+%time = time*ones(1,length(depth));
+
+% time = time + datetime(1950,1,1,0,0,0); % -0.5 is necessary to remove 12h00 introduced by datetime function starting at noon instead of midnight as performed by julian function previously used
+% time = time*ones(1,length(depth));
+
+%% Create u/v matrix
+for ii = 1:length(ncfile1.time)
+ u1(ii,:) = interp1(ncfile1.depth,ncfile1.u(ii,:),depth);
+ v1(ii,:) = interp1(ncfile1.depth,ncfile1.v(ii,:),depth);
+end
+for ii = 1:length(ncfile2.time)
+ u2(ii,:) = interp1(ncfile2.depth,ncfile2.u(ii,:),depth);
+ v2(ii,:) = interp1(ncfile2.depth,ncfile2.v(ii,:),depth);
+end
+% for ii = 1:length(ncfile3.time)
+% u3(ii,:) = interp1(ncfile3.depth,ncfile3.u(ii,:),depth);
+% v3(ii,:) = interp1(ncfile3.depth,ncfile3.v(ii,:),depth);
+% end
+u = vertcat(u1,u2);
+v = vertcat(v1,v2);
+
+time = time*ones(1,length(depth));
+
+
+%% Plot data
+if plot_data
+ niv_u = (-1.5:0.05:0.9);
+ niv_v = (-1.8:0.05:1.5);
+ depth = depth.*ones(length(time),1);
+ date1 = datestr(ncfile1.time(1)+datenum(1950,01,01),'YYYY');
+ date2 = datestr(ncfile2.time(end)+datenum(1950,01,01),'YYYY');
+
+ hf=figure('position', [0, 0, 1400, 1000]);
+ %u
+ subplot(2,1,1);
+ colormap jet
+ [C,h] = contourf(time,depth,u,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,max(max(depth))]);
+ gregtick;
+ title({[mooring.name, ' - ' num2str(date1) ' to ' num2str(date2) ' - ZONAL VELOCITY - RDI ',num2str(freq),' kHz (filtered from tide)']});
+
+ %v
+ subplot(2,1,2);
+ [C,h] = contourf(time,depth,v,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,max(max(depth))]);
+ gregtick;
+ title({[mooring.name, ' - ' num2str(date1) ' to ' num2str(date2) ' - MERIDIONAL VELOCITY - RDI ',num2str(freq),' kHz (filtered from tide)']});
+
+ graph_name = ['ADCP_' mooring.name '_' num2str(date1) '_' num2str(date2) '_U_V_daily'];
+ 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');
+end
+
+%% Write netcdf file
+time = time(:,1);
+timed = gregorian(time);
+timed(:,5) = 0;
+timed(:,6) = 0;
+time = datenum(timed)-datenum(1950,01,01);
+
+disp('****')
+disp('Creating .nc file')
+yr_start = datestr(time(1)+datenum(1950,01,01), 'yyyy');
+yr_end = datestr(time(end)+datenum(1950,01,01), 'yyyy');
+
+ncid = netcdf.create(['ADCP_',mooring.name,'_',num2str(yr_start),'_',num2str(yr_end),'.nc'],'NC_CLOBBER');
+
+%create dimension
+dimidz = netcdf.defDim(ncid, 'DEPTH', size(depth,2));
+dimidt = netcdf.defDim(ncid, 'TIME', netcdf.getConstant('NC_UNLIMITED'));
+%Define IDs for the dimension variables (pressure,time,latitude,...)
+time_ID = netcdf.defVar(ncid,'TIME','double',dimidt);
+netcdf.putAtt(ncid, time_ID, 'long_name', 'Time');
+netcdf.putAtt(ncid, time_ID, 'axis', 'T');
+netcdf.putAtt(ncid, time_ID, 'units', 'days since 1950-01-01T00:00:00Z');
+netcdf.putAtt(ncid, time_ID, 'time_origin', '1-JAN-1950:00:00:00');
+depth_ID = netcdf.defVar(ncid,'DEPTH','double',dimidz);
+netcdf.putAtt(ncid, depth_ID, 'long_name', 'Depth');
+netcdf.putAtt(ncid, depth_ID, 'axis', 'Z');
+netcdf.putAtt(ncid, depth_ID, 'units', 'meters');
+netcdf.putAtt(ncid, depth_ID, 'positive', 'down');
+netcdf.putAtt(ncid, depth_ID, 'point_spacing', 'even');
+%Define the main variable ()
+u_ID = netcdf.defVar(ncid,'U','double',[dimidz dimidt]);
+netcdf.putAtt(ncid, u_ID, 'long_name', 'Zonal velocities');
+v_ID = netcdf.defVar(ncid,'V','double',[dimidz dimidt]);
+netcdf.putAtt(ncid, v_ID, 'long_name', 'Meridional velocities');
+%We are done defining the NetCdf
+netcdf.endDef(ncid);
+%Then store the dimension variables in
+netcdf.putVar(ncid, depth_ID, depth(1,:));
+netcdf.putVar(ncid, time_ID, 0, length(time), time);
+%Then store my main variable
+netcdf.putVar(ncid, u_ID, u');
+netcdf.putVar(ncid, v_ID, v');
+%We're done, close the netcdf
+netcdf.close(ncid);
disp('****')
\ No newline at end of file
diff --git a/multi_adcp_mooring/template_combine_adcp_up_and_down.m b/multi_adcp_mooring/template_combine_adcp_up_and_down.m
index a6e2009851db61043f5e8d6cd1feee6365a280a6..01247ea0ac5ac1aaeb0c722d2c818f020c560487 100644
--- a/multi_adcp_mooring/template_combine_adcp_up_and_down.m
+++ b/multi_adcp_mooring/template_combine_adcp_up_and_down.m
@@ -16,26 +16,26 @@ clear all;close all;
addpath('.\moored_adcp_proc');
% Location of ADCP up and down data
-fpath = '.\data_example\up_and_down\';
+fpath = 'F:\Encours\PIRATA_ADCP-MOORINGS\23W\v2\2015-2016\';
% Directory for outputs
-fpath_output = '.\data_example\up_and_down\';
+fpath_output = 'F:\Encours\PIRATA_ADCP-MOORINGS\23W\v2\2015-2016\';
% Contour levels for u anv v fields
niv_u = (-1.5:0.1:1.5);
niv_v = (-0.5:0.1:0.5);
%% combine up and down
-load([fpath, 'FR22-10W0N_508_instr_01_int_filt_sub']);
+load([fpath, 'up\23W0N_1140_instr_01_int_filt_sub']);
adcp_up=adcp;
up_u=data.uintfilt;
up_v=data.vintfilt;
up_z=data.Z;
up_time=data.inttim;
-npts_up= data.npts_up;
+%npts_up= data.npts_up;
freq_up=adcp_up.config.sysconfig.frequency;
-load([fpath, 'FR22-10W0N_509_instr_02_int_filt_sub_down']);
+load([fpath, 'dn\23W0N_2627_instr_01_int_filt_sub']);
adcp_down=adcp;
down_u=data.uintfilt;
down_v=data.vintfilt;
@@ -54,12 +54,15 @@ distance_between_instruments = 3;
distance_between_up_and_down = adcp_up.config.cell/2 + adcp_up.config.blank + distance_between_instruments + adcp_down.config.blank + adcp_down.config.cell/2;
%calculate real minimum down ADCP depth
up_z = fliplr(up_z);
-depth_down_ADCP = up_z(min(npts_up)+1) + ceil(distance_between_up_and_down);
+depth_down_ADCP = up_z(end) + ceil(distance_between_up_and_down);
%interval grid between up and down ADCP
interval_grid = max(up_z)+adcp_up.config.cell/2-1:adcp_up.config.cell/2:min(depth_down_ADCP)-adcp_up.config.cell/2+1;
%on applique l'offset sur les profondeurs de l'ADCP down
offset_ADCP_down = min(down_z) - min(depth_down_ADCP);
down_z = down_z - offset_ADCP_down;
+% down_z = flip(down_z);
+% down_u = flip(down_u);
+% down_v = flip(down_v);
% initialisation de la matrice combinée up + down
[B,a] = size(down_u); [B1,a1] = size(up_u);
@@ -79,72 +82,84 @@ for i = 1:length(down_u)
end
%% figure finale
-z_final = [up_z interval_grid down_z];
-
+Z = [up_z interval_grid down_z];
+inttim = down_time;
+bin_start = 1;
+bin_end = length(Z);
+uintfilt = u_final;
+vintfilt = v_final;
+
+%% Figure
+niv_u = (-1:0.05:1);
+niv_v = (-1:0.05:1);
+close all
hf=figure('position', [0, 0, 1400, 1000]);
%u
subplot(2,1,1);
-[~,h] = contourf(down_time,z_final,u_final,niv_u);
+colormap jet
+[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)');
-gregtick
-title({[mooring.name, ' - ZONAL VELOCITY - ADCP UP : RDI ',num2str(freq_up),' kHz - ADCP DOWN : RDI ',num2str(freq_down),' kHz']});
+ylim([0,round(max(Z))]);
+%change figure label in HH:MM
+gregtick;
+title({[mooring.name, ' - ZONAL VELOCITY - RDI 150 kHz and 75 kHz (filtered from tide)']});
+
%v
subplot(2,1,2);
-[C,h] = contourf(down_time,z_final,v_final,niv_v);
+[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;
+h = colorbar;
ylabel(h,'V [m s^-^1]');
set(gca,'ydir', 'reverse');
ylabel('Depth (m)');
-gregtick
-title({[mooring.name, ' - MERIDIONAL VELOCITY - ADCP UP : RDI ',num2str(freq_up),' kHz - ADCP DOWN : RDI ',num2str(freq_down),' kHz']});
-
-% Save combined data
-data.time = down_time;
-data.u_final = u_final;
-data.v_final = v_final;
-data.z_final = z_final;
-save([fpath, mooring.name '_UP_DOWN_int_filt_sub.mat'],'adcp','mooring','data','raw');
-
-graph_name = [fpath_output, mooring.name '_U_V_UP_DOWN_int_filt_sub'];
+ylim([0,round(max(Z))]);
+%change figure label in HH:MM
+gregtick;
+title({[mooring.name, ' - ZONAL VELOCITY - RDI 150 kHz and 75 kHz (filtered from tide)']});
+
+
+graph_name = [fpath_output, mooring.name '_up_down_U_V_int_filt_sub'];
set(hf,'Units','Inches');
-pos = get(hf,'Position');
-set(hf,'PaperPositionMode','Auto','PaperUnits','Inches','PaperSize',[pos(3), pos(4)])
+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');
+%% Write netcdf file
+disp('****')
+disp('Creating .nc file')
+[yr_start , ~, ~] = gregorian(inttim(1));
+[yr_end, ~, ~] = gregorian(inttim(length(inttim)));
-%% Write netcdf file
-[yr_start , ~, ~] = gregorian(down_time(1));
-[yr_end, ~, ~] = gregorian(down_time(length(down_time)));
+ncid = netcdf.create([fpath_output,'ADCP_',mooring.name,'_',num2str(yr_start),'_',num2str(yr_end),'_1d.nc'],'NC_WRITE');
-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(down_time));
-dimidz = netcdf.defDim(ncid,'depth',length(z_final));
+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);
+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]);
+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,down_time);
-netcdf.putVar(ncid,depth_ID,z_final);
+netcdf.putVar(ncid,time_ID,inttim);
+netcdf.putVar(ncid,depth_ID,Z);
%Then store my main variable
-netcdf.putVar(ncid,u_ID,u_final);
-netcdf.putVar(ncid,v_ID,v_final);
+netcdf.putVar(ncid,u_ID,uintfilt');
+netcdf.putVar(ncid,v_ID,vintfilt');
+
%We're done, close the netcdf
netcdf.close(ncid);
+disp('****')
+% -------------------------------------------------------------------------------------------
diff --git a/multi_adcp_mooring/template_combine_adcp_up_and_up.m b/multi_adcp_mooring/template_combine_adcp_up_and_up.m
new file mode 100644
index 0000000000000000000000000000000000000000..29990c9f4ba53fd9f0c2e58902491001ad86e888
--- /dev/null
+++ b/multi_adcp_mooring/template_combine_adcp_up_and_up.m
@@ -0,0 +1,164 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% template_combine_adcp_up_and_down.m
+% -------------------------------
+% Author : Jérémie HABASQUE - IRD
+% -------------------------------
+% INPUTS:
+% - ADCP up data processed (output of template_get_adcp_data.m)
+% - ADCP down data processed (output of template_get_adcp_data.m)
+% OUTPUTS:
+% - U and V fields interpolated on a regulard grid, filtered and subsampled
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+clear all;close all;
+
+% path
+addpath('.\moored_adcp_proc');
+
+% Location of ADCP up and down data
+fpath = '.\data_example\up_and_down\';
+
+% Directory for outputs
+fpath_output = './23W/';
+
+% Contour levels for u anv v fields
+niv_u = (-1.5:0.1:1.5);
+niv_v = (-0.5:0.1:0.5);
+
+%% combine up and down
+load('C:\Users\proussel\Documents\OUTILS\ADCP\ADCP_mooring_data_processing\23W\2008-2009\up\23W0N_1001_instr_01_int_filt_sub');
+adcp_up=adcp;
+up_u=data.uintfilt;
+up_v=data.vintfilt;
+up_z=data.Z;
+up_time=data.inttim;
+%npts_up= data.npts_up;
+freq_up=adcp_up.config.sysconfig.frequency;
+
+load('C:\Users\proussel\Documents\OUTILS\ADCP\ADCP_mooring_data_processing\23W\2008-2009\dn\23W0N_1023_instr_02_int_filt_sub');
+adcp_down=adcp;
+down_u=data.uintfilt;
+down_v=data.vintfilt;
+down_z=data.Z;
+down_time=data.inttim;
+freq_down = adcp_down.config.sysconfig.frequency;
+
+% distance between deepest measurement of the upward looking and
+% shallowest measurement of the downward looking ADCP
+% half distance of 1st bin in upward ADCP +
+% blank of upward ADCP +
+% distance between instruments +
+% blank of downward ADCP +
+% half distance of 1st bin in downward ADCP.
+distance_between_instruments = 3;
+distance_between_up_and_down = adcp_up.config.cell/2 + adcp_up.config.blank + distance_between_instruments + adcp_down.config.blank + adcp_down.config.cell/2;
+%calculate real minimum down ADCP depth
+up_z = fliplr(up_z);
+depth_down_ADCP = 148 + ceil(distance_between_up_and_down);
+%interval grid between up and down ADCP
+interval_grid = max(up_z)+adcp_up.config.cell/2-1:adcp_up.config.cell/2:min(depth_down_ADCP)-adcp_up.config.cell/2+1;
+%on applique l'offset sur les profondeurs de l'ADCP down
+offset_ADCP_down = min(down_z) - min(depth_down_ADCP);
+down_z = down_z - offset_ADCP_down;
+down_z = flip(down_z);
+down_u = flip(down_u);
+down_v = flip(down_v);
+
+% initialisation de la matrice combinée up + down
+[B,a] = size(down_u); [B1,a1] = size(up_u);
+BB = B+B1+1 ;
+DOWN = NaN(BB,a);
+V_DOWN = NaN(BB,a);
+u_final = NaN(BB,a);
+v_final = NaN(BB,a);
+
+% on alimente la matrice avec les données up
+u_final(1:B1,1:a1) = up_u(B1:-1:1,:);
+v_final(1:B1,1:a1) = up_v(B1:-1:1,:);
+
+for i = 1:length(down_u)
+ u_final(B1+length(interval_grid)+1:B1+length(interval_grid)+B,i) = down_u(:,i);
+ v_final(B1+length(interval_grid)+1:B1+length(interval_grid)+B,i) = down_v(:,i);
+end
+
+%% figure finale
+Z = [up_z interval_grid down_z];
+inttim = down_time;
+bin_start = 1;
+bin_end = 52;
+uintfilt = u_final;
+vintfilt = v_final;
+
+%% Figure
+niv_u = (-1:0.05:1);
+niv_v = (-1:0.05:1);
+close all
+hf=figure('position', [0, 0, 1400, 1000]);
+%u
+subplot(2,1,1);
+colormap jet
+[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,round(max(Z))]);
+%change figure label in HH:MM
+gregtick;
+title({[mooring.name, ' - ZONAL VELOCITY - RDI 150 kHz and 75 kHz (filtered from tide)']});
+
+
+%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,round(max(Z))]);
+%change figure label in HH:MM
+gregtick;
+title({[mooring.name, ' - ZONAL VELOCITY - RDI 150 kHz and 75 kHz (filtered from tide)']});
+
+
+graph_name = [fpath_output, mooring.name '_up_down_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
+disp('****')
+disp('Creating .nc 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(data.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,data.Z);
+%Then store my main variable
+netcdf.putVar(ncid,u_ID,data.uintfilt');
+netcdf.putVar(ncid,v_ID,data.vintfilt');
+
+%We're done, close the netcdf
+netcdf.close(ncid);
+disp('****')
+% -------------------------------------------------------------------------------------------
diff --git a/specific/template_get_adcp_data_10w.m b/specific/template_get_adcp_data_10w.m
new file mode 100644
index 0000000000000000000000000000000000000000..ae5109c73550d9cc3e25a7a8ef8d77adccd94db9
--- /dev/null
+++ b/specific/template_get_adcp_data_10w.m
@@ -0,0 +1,668 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% template_get_adcp_data.m
+% -------------------------------
+% Author : Pierre ROUSSELOT - IRD (pierre.rousselot@ird.fr)
+% Jeremie HABASQUE - IRD (jeremie.habasque@ird.fr)
+% -------------------------------
+% INPUTS:
+% - binary raw file with .000 extension
+% OUTPUTS:
+% - U and V fields interpolated on a regulard grid, filtered and subsampled
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+close all; clear
+addpath(genpath('../ADCP_mooring_data_processing'));
+addpath('/home/proussel/Documents/OUTILS/TOOLS/nansuite'); % NaNSuitePath
+
+%% META information:
+% Location rawfile
+rawfile = 'FR10W000.000'; % binary file with .000 extension
+fpath_output = './10W/'; % Output directory
+
+% Cruise/mooring info
+cruise.name = 'PIRATA'; % cruise name
+mooring.name = '10W0N'; % '0N10W'
+mooring.lat = '00°00.000'; % latitude [°']
+mooring.lon = '-10°00.000'; % longitude [°']
+clock_drift = 0; % [seconds]
+
+% ADCP info
+adcp.sn = 508; % ADCP serial number
+adcp.type = '300 khz Quartermaster'; % Type : Quartermaster, longranger
+adcp.direction = 'up'; % upward-looking 'up', downward-looking 'dn'
+adcp.instr_depth = 150; % nominal instrument depth
+instr = 1; % this is just for name convention and sorting of all mooring instruments
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%% Convert variables
+latDegInd = strfind(mooring.lat,'°');
+lonDegInd = strfind(mooring.lon,'°');
+mooring.lat = str2double(mooring.lat(1:latDegInd-1))+str2double(mooring.lat(latDegInd+1:end-1))/60;
+mooring.lon = str2double(mooring.lon(1:lonDegInd-1))+str2double(mooring.lon(lonDegInd+1:end-1))/60;
+clock_drift = clock_drift/3600; % convert into hrs
+
+%% Read rawfile
+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);
+% load(raw_file)
+% else
+% fprintf('Read %s\n', rawfile);
+% raw = read_os3(rawfile,'all');
+% save(raw_file,'raw','-v7.3');
+% end
+load('FR22-UP-508.mat')
+
+%% 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 = SerEmmpersec(first:last,:)'./1000; u2(u2<-30)=NaN;
+v2 = SerNmmpersec(first:last,:)'./1000; v2(v2<-30)=NaN;
+vel_err = SerErmmpersec(first:last,:)'./1000; vel_err(vel_err<-30)=NaN;
+pg=SerPG4(first:last,:)';
+
+% 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(SerC4cnt(first:last,:)');
+
+test(:,1,:) = SerEA1cnt'; test(:,2,:) = SerEA2cnt'; test(:,3,:) = SerEA3cnt'; test(:,4,:) = SerEA4cnt';
+
+ea = squeeze(mean(test(:,4,first:last),2));
+%pg = squeeze(raw.pg(:,4,first:last));
+%time = raw.juliandate(first:last);
+time = julian(SerYear(first:last)+2000,SerMon(first:last),SerDay(first:last),SerHour(first:last));
+time=time(1)+datenum(0,0,0,1,0,0).*[0:length(depth)-1]';
+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+(time(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+(time(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(time));
+%mag_dev = mag_dev(first:last);
+
+%% Correction of magnetic deviation
+disp('****')
+disp('Correct magnetic deviation')
+% for ii = 1 : length(mag_dev)
+% [u(:,ii),v(:,ii)] = uvrot(u2(:,ii), v2(:,ii), -mag_dev(ii));
+% end
+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
+
+
+
+%% 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;
+ 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
+
+%% 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')
+
+%% If upward looking: determine range of surface bins used for instrument depth correction below!
+disp('****')
+surface_bins = input('Do you want to apply an offset using surface reflection? 1/0 [1]');
+if isempty(surface_bins)
+ surface_bins = 1;
+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
+ 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
+
+ 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
+
+%% 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;
+ 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;
+ 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
+ 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;
+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 = 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
+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');
+
+%% 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));
+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);
+ if reply_ts == 1
+ ts_interp(i,ind:ind+npts-1) = data.ts.ts(1:npts,i);
+ end
+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]:');
+if isempty(horz_interp)
+ horz_interp = 1;
+end
+
+if horz_interp
+ filt = input('Do you want to filter tide? 1/0 [1]:');
+ if isempty(filt)
+ filt = 1;
+ end
+
+ sub = input('Do you want to subsampling data daily? 1/0 [1]:');
+ if isempty(filt)
+ sub = 1;
+ end
+ if filt
+ if sub
+ disp('Horizontal interpolation, Filtering & Subsampling')
+ else
+ disp('Horizontal interpolation & Filtering')
+ end
+ disp('Filtering using 40h Hamming filter (other disponible filter: FFT filter, tide model)')
+ else
+ if sub
+ disp('Horizontal interpolation & Subsampling')
+ else
+ disp('Horizontal interpolation')
+ end
+ end
+else
+ filt = 0;
+ sub = 0;
+end
+
+[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);
+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')
+
+if horz_interp == 0
+ uintfilt = u_interp';
+ vintfilt = v_interp';
+ inttim = data.time;
+end
+
+%% 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
+data.uintfilt = uintfilt(bin_start:bin_end,:);
+data.vintfilt = vintfilt(bin_start:bin_end,:);
+if reply_ts == 1
+ data.tsintfilt = tsintfilt(bin_start:bin_end,:);
+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');
+
+%% Figure
+niv_u = (-1:0.05:1);
+niv_v = (-1:0.05:1);
+close all
+hf=figure('position', [0, 0, 1400, 1000]);
+%u
+subplot(2,1,1);
+colormap jet
+[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,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
+
+%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,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
+
+graph_name = [fpath_output, mooring.name '_', num2str(instr), '_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');
+
+if reply_ts == 1
+ hf=figure('position', [0, 0, 1400, 500]);
+ colormap jet
+ pcolor(inttim,Z(bin_start:bin_end),tsintfilt(bin_start:bin_end,:)); shading interp;
+ h = colorbar;
+ ylabel(h,'Target Strength [dB1]');
+ set(gca,'ydir', 'reverse');
+ ylabel('Depth (m)');
+ 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
+
+ graph_name = [fpath_output, mooring.name, '_', num2str(instr), '_TS_int_filt_sub'];
+ set(hf,'Units','Inches');
+ pos = get(hf,'Position');
+ set(hf,'PaperPositionMode','Auto','PaperUnits','Inches','PaperSize',[pos(3), pos(4)]);
+ saveas(hf,graph_name,'jpeg');
+end
+
+
+
+% %% Plot tide
+% hf=figure('position', [0, 0, 1400, 1000]);
+% niv_tide = (-5:0.2:5);
+% utid_baro = utid_baro * 100;
+% vtid_baro = vtid_baro * 100;
+% %u
+% subplot(2,1,1);
+% colormap jet
+% [C,h] = contourf(inttim,Z(bin_start:bin_end),utid_baro(bin_start:bin_end,:),niv_tide);
+% set(h,'LineColor','none');
+% caxis(niv_tide([1 end]));
+% h=colorbar;
+% ylabel(h,'U [cm 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 TIDE VELOCITY - RDI ',num2str(freq),' kHz']});
+%
+% %v
+% subplot(2,1,2);
+% [C,h] = contourf(inttim,Z(bin_start:bin_end),vtid_baro(bin_start:bin_end,:),niv_tide);
+% set(h,'LineColor','none');
+% caxis(niv_tide([1 end]));
+% h = colorbar;
+% ylabel(h,'V [cm 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 TIDE VELOCITY - RDI ',num2str(freq),' kHz']});
+
+%% Write netcdf file
+disp('****')
+disp('Creating .nc 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(data.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]);
+if reply_ts == 1
+ ts_ID = netcdf.defVar(ncid,'ts','double',[dimidt dimidz]);
+end
+%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,data.Z);
+%Then store my main variable
+netcdf.putVar(ncid,u_ID,data.uintfilt');
+netcdf.putVar(ncid,v_ID,data.vintfilt');
+if reply_ts == 1
+ netcdf.putVar(ncid,ts_ID,data.tsintfilt');
+end
+%We're done, close the netcdf
+netcdf.close(ncid);
+disp('****')
+% -------------------------------------------------------------------------------------------
diff --git a/specific/template_get_adcp_data_10w_down.m b/specific/template_get_adcp_data_10w_down.m
new file mode 100644
index 0000000000000000000000000000000000000000..ef18be4fb2a3d2f15fed5ea872f0c202789ab4c8
--- /dev/null
+++ b/specific/template_get_adcp_data_10w_down.m
@@ -0,0 +1,682 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% template_get_adcp_data.m
+% -------------------------------
+% Author : Pierre ROUSSELOT - IRD (pierre.rousselot@ird.fr)
+% Jeremie HABASQUE - IRD (jeremie.habasque@ird.fr)
+% -------------------------------
+% INPUTS:
+% - binary raw file with .000 extension
+% OUTPUTS:
+% - U and V fields interpolated on a regulard grid, filtered and subsampled
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+close all; clear
+addpath(genpath('../ADCP_mooring_data_processing'));
+addpath('/home/proussel/Documents/OUTILS/TOOLS/nansuite'); % NaNSuitePath
+
+%% META information:
+% Location rawfile
+rawfile = 'FR10W000.000'; % binary file with .000 extension
+fpath_output = './10W/'; % Output directory
+
+% Cruise/mooring info
+cruise.name = 'PIRATA'; % cruise name
+mooring.name = '10W0N'; % '0N10W'
+mooring.lat = '00°00.000'; % latitude [°']
+mooring.lon = '-10°00.000'; % longitude [°']
+clock_drift = 0; % [seconds]
+
+% ADCP info
+adcp.sn = 509; % ADCP serial number
+adcp.type = '300 khz Quartermaster'; % Type : Quartermaster, longranger
+adcp.direction = 'down'; % 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
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%% Convert variables
+latDegInd = strfind(mooring.lat,'°');
+lonDegInd = strfind(mooring.lon,'°');
+mooring.lat = str2double(mooring.lat(1:latDegInd-1))+str2double(mooring.lat(latDegInd+1:end-1))/60;
+mooring.lon = str2double(mooring.lon(1:lonDegInd-1))+str2double(mooring.lon(lonDegInd+1:end-1))/60;
+clock_drift = clock_drift/3600; % convert into hrs
+
+%% Read rawfile
+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);
+% load(raw_file)
+% else
+% fprintf('Read %s\n', rawfile);
+% raw = read_os3(rawfile,'all');
+% save(raw_file,'raw','-v7.3');
+% end
+load('10W0N_509_instr_02.mat')
+load('FR22-DOWN-509.mat')
+
+%% 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): ');
+first = 17; % time point of ADCP into and out of water
+last = 12856; % determined by pressure time series
+%% Correct velocity data with external T/S sensor
+
+%% Extract data
+freq = raw.config.sysconfig.frequency;
+
+u2 = SerEmmpersec(first:last,:)'./1000; u2(u2<-30)=NaN;
+v2 = SerNmmpersec(first:last,:)'./1000; v2(v2<-30)=NaN;
+vel_err = SerErmmpersec(first:last,:)'./1000; vel_err(vel_err<-30)=NaN;
+pg=SerPG4(first:last,:)';
+
+% 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(SerC4cnt(first:last,:)');
+
+test(:,1,:) = SerEA1cnt'; test(:,2,:) = SerEA2cnt'; test(:,3,:) = SerEA3cnt'; test(:,4,:) = SerEA4cnt';
+
+ea = squeeze(mean(test(:,4,first:last),2));
+%pg = squeeze(raw.pg(:,4,first:last));
+% %time = raw.juliandate(first:last);
+% d0=datenum(2006,06,26,01,0,0);
+% d1=datenum(2008,09,28,21,0,0);
+% time=d0:1/24:d1;
+% [YY,MM,DD,hh,mm,ss] = datevec(time);
+% time=julian(YY,MM,DD,hh,mm,ss);
+
+depth = AnDepthmm(first:last)./1000;
+time = julian(SerYear(first:last)+2000,SerMon(first:last),SerDay(first:last),SerHour(first:last));
+time=time(1)+datenum(0,0,0,1,0,0).*[0:length(depth)-1]';
+
+% 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+(time(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+(time(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(time));
+%mag_dev = mag_dev(first:last);
+
+%% Correction of magnetic deviation
+disp('****')
+disp('Correct magnetic deviation')
+% for ii = 1 : length(mag_dev)
+% [u(:,ii),v(:,ii)] = uvrot(u2(:,ii), v2(:,ii), -mag_dev(ii));
+% end
+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
+
+
+
+%% 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<20); % 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;
+% 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
+
+%% 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')
+
+%% If upward looking: determine range of surface bins used for instrument depth correction below!
+disp('****')
+surface_bins = 0;%input('Do you want to apply an offset using surface reflection? 1/0 [1]');
+if isempty(surface_bins)
+ surface_bins = 1;
+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
+% 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
+%
+% 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
+
+%% 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;
+ 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;
+ 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
+ saveas(figure(7),[fpath_output,mooring.name,'_',num2str(adcp.sn),'_instr_',num2str(instr),'_','Meridional_zonal_velocity'],'fig')
+end
+
+%% SAVE DATA
+z1 = data.z_bins;
+dpt1 = data.depth;
+z = data.z_bins;
+
+% 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 = z1;
+data.depth = dpt1;
+%data.temp = temp;
+%data.sspd = soundspeed;
+data.lat = mooring.lat;
+data.lon = mooring.lon;
+
+disp('****')
+reply_ts = 0;%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);
+ 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');
+
+%% Interpolate data on a regular vertical grid
+Z = (round(min(data.depth))+blen/2:blen:max(z(:))+blen);
+Zmax = min(Z);
+u_interp = NaN(length(time),length(Z));
+v_interp = NaN(length(time),length(Z));
+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);
+ if reply_ts == 1
+ ts_interp(i,ind:ind+npts-1) = data.ts.ts(1:npts,i);
+ end
+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]:');
+if isempty(horz_interp)
+ horz_interp = 1;
+end
+
+if horz_interp
+ filt = input('Do you want to filter tide? 1/0 [1]:');
+ if isempty(filt)
+ filt = 1;
+ end
+
+ sub = input('Do you want to subsampling data daily? 1/0 [1]:');
+ if isempty(filt)
+ sub = 1;
+ end
+ if filt
+ if sub
+ disp('Horizontal interpolation, Filtering & Subsampling')
+ else
+ disp('Horizontal interpolation & Filtering')
+ end
+ disp('Filtering using 40h Hamming filter (other disponible filter: FFT filter, tide model)')
+ else
+ if sub
+ disp('Horizontal interpolation & Subsampling')
+ else
+ disp('Horizontal interpolation')
+ end
+ end
+else
+ filt = 0;
+ sub = 0;
+end
+
+[uintfilt,vintfilt,tsintfilt,inttim,utid_baro,vtid_baro] = adcp_filt_sub_down(data,u_interp',v_interp',ts_interp',1:length(Z),reply_ts, filt, sub);
+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')
+
+if horz_interp == 0
+ uintfilt = u_interp';
+ vintfilt = v_interp';
+ inttim = data.time;
+end
+
+%% 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
+data.uintfilt = uintfilt(bin_start:bin_end,:);
+data.vintfilt = vintfilt(bin_start:bin_end,:);
+if reply_ts == 1
+ data.tsintfilt = tsintfilt(bin_start:bin_end,:);
+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');
+
+%% Figure
+niv_u = (-1:0.05:1);
+niv_v = (-1:0.05:1);
+close all
+hf=figure('position', [0, 0, 1400, 1000]);
+%u
+subplot(2,1,1);
+colormap jet
+[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,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
+
+%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,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
+
+graph_name = [fpath_output, mooring.name '_', num2str(instr), '_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');
+
+if reply_ts == 1
+ hf=figure('position', [0, 0, 1400, 500]);
+ colormap jet
+ pcolor(inttim,Z(bin_start:bin_end),tsintfilt(bin_start:bin_end,:)); shading interp;
+ h = colorbar;
+ ylabel(h,'Target Strength [dB1]');
+ set(gca,'ydir', 'reverse');
+ ylabel('Depth (m)');
+ 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
+
+ graph_name = [fpath_output, mooring.name, '_', num2str(instr), '_TS_int_filt_sub'];
+ set(hf,'Units','Inches');
+ pos = get(hf,'Position');
+ set(hf,'PaperPositionMode','Auto','PaperUnits','Inches','PaperSize',[pos(3), pos(4)]);
+ saveas(hf,graph_name,'jpeg');
+end
+
+
+
+% %% Plot tide
+% hf=figure('position', [0, 0, 1400, 1000]);
+% niv_tide = (-5:0.2:5);
+% utid_baro = utid_baro * 100;
+% vtid_baro = vtid_baro * 100;
+% %u
+% subplot(2,1,1);
+% colormap jet
+% [C,h] = contourf(inttim,Z(bin_start:bin_end),utid_baro(bin_start:bin_end,:),niv_tide);
+% set(h,'LineColor','none');
+% caxis(niv_tide([1 end]));
+% h=colorbar;
+% ylabel(h,'U [cm 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 TIDE VELOCITY - RDI ',num2str(freq),' kHz']});
+%
+% %v
+% subplot(2,1,2);
+% [C,h] = contourf(inttim,Z(bin_start:bin_end),vtid_baro(bin_start:bin_end,:),niv_tide);
+% set(h,'LineColor','none');
+% caxis(niv_tide([1 end]));
+% h = colorbar;
+% ylabel(h,'V [cm 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 TIDE VELOCITY - RDI ',num2str(freq),' kHz']});
+
+%% Write netcdf file
+disp('****')
+disp('Creating .nc 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(data.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]);
+if reply_ts == 1
+ ts_ID = netcdf.defVar(ncid,'ts','double',[dimidt dimidz]);
+end
+%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,data.Z);
+%Then store my main variable
+netcdf.putVar(ncid,u_ID,data.uintfilt');
+netcdf.putVar(ncid,v_ID,data.vintfilt');
+if reply_ts == 1
+ netcdf.putVar(ncid,ts_ID,data.tsintfilt');
+end
+%We're done, close the netcdf
+netcdf.close(ncid);
+disp('****')
+% -------------------------------------------------------------------------------------------
diff --git a/specific/template_get_adcp_data_10w_olddata.m b/specific/template_get_adcp_data_10w_olddata.m
new file mode 100644
index 0000000000000000000000000000000000000000..5c4137c6904bec4ee26dfb5e974a29031e3b371d
--- /dev/null
+++ b/specific/template_get_adcp_data_10w_olddata.m
@@ -0,0 +1,253 @@
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+% template_get_adcp_data.m
+% -------------------------------
+% Author : Pierre ROUSSELOT - IRD (pierre.rousselot@ird.fr)
+% Jeremie HABASQUE - IRD (jeremie.habasque@ird.fr)
+% -------------------------------
+% INPUTS:
+% - binary raw file with .000 extension
+% OUTPUTS:
+% - U and V fields interpolated on a regulard grid, filtered and subsampled
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+close all; clear
+addpath(genpath('../ADCP_mooring_data_processing'));
+addpath('/home/proussel/Documents/OUTILS/TOOLS/nansuite'); % NaNSuitePath
+
+%% META information:
+% Location rawfile
+rawfile = 'FR10W000.000'; % binary file with .000 extension
+fpath_output = './10W/'; % Output directory
+
+% Cruise/mooring info
+cruise.name = 'PIRATA'; % cruise name
+mooring.name = '10W0N'; % '0N10W'
+mooring.lat = '00°00.000'; % latitude [°']
+mooring.lon = '-10°00.000'; % longitude [°']
+clock_drift = 0; % [seconds]
+
+% ADCP info
+adcp.sn = 500; % ADCP serial number
+adcp.type = '300 khz'; % Type : Quartermaster, longranger
+adcp.direction = 'up'; % upward-looking 'up', downward-looking 'dn'
+adcp.instr_depth = 100; % nominal instrument depth
+instr = 1; % this is just for name convention and sorting of all mooring instruments
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+
+%% Convert variables
+latDegInd = strfind(mooring.lat,'°');
+lonDegInd = strfind(mooring.lon,'°');
+mooring.lat = str2double(mooring.lat(1:latDegInd-1))+str2double(mooring.lat(latDegInd+1:end-1))/60;
+mooring.lon = str2double(mooring.lon(1:lonDegInd-1))+str2double(mooring.lon(lonDegInd+1:end-1))/60;
+clock_drift = clock_drift/3600; % convert into hrs
+
+%% Read rawfile
+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);
+% load(raw_file)
+% else
+% fprintf('Read %s\n', rawfile);
+% raw = read_os3(rawfile,'all');
+% save(raw_file,'raw','-v7.3');
+% end
+load('UV_hour_10w_int10.mat')
+d0=datenum(2004,2,6,0,0,0);
+d1=datenum(2005,6,17,22,0,0);
+adcp_2003_time=d0:1/12:d1;
+adcp_2003_time = adcp_2003_time';
+u2 = uvmat(:,1:5976)/100;
+v2 = uvmat(:,5977:5976*2)/100;
+adcp_2003_bin_length = 4;
+dpt1 = 4:adcp_2003_bin_length:104;
+[YY,MM,DD,hh,mm,ss] = datevec(adcp_2003_time);
+time=julian(YY,MM,DD,hh,mm,ss);
+
+
+
+
+% Data structure
+u_interp = u2';
+v_interp = v2';
+ts_interp = NaN;
+data.time = time;
+Z = dpt1;
+reply_ts = 0;
+
+%% Horizontal interpolation, filtering and subsampling
+disp('****')
+horz_interp = 1;
+filt = 1;
+sub = 1;
+
+
+[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);
+% 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')
+
+if horz_interp == 0
+ uintfilt = u_interp';
+ vintfilt = v_interp';
+ inttim = data.time;
+end
+
+%% 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
+data.uintfilt = uintfilt(bin_start:bin_end,:);
+data.vintfilt = vintfilt(bin_start:bin_end,:);
+if reply_ts == 1
+ data.tsintfilt = tsintfilt(bin_start:bin_end,:);
+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');
+
+%% Figure
+niv_u = (-1:0.05:1);
+niv_v = (-1:0.05:1);
+close all
+hf=figure('position', [0, 0, 1400, 1000]);
+%u
+subplot(2,1,1);
+colormap jet
+[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,round(max(Z))]);
+%change figure label in HH:MM
+gregtick;
+if filt
+ title({['10W0N - ZONAL VELOCITY - RDI 150 kHz (filtered from tide)']});
+else
+ title({[mooring.name, ' - ZONAL VELOCITY - RDI ',num2str(freq),' kHz']});
+end
+
+%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,round(max(Z))]);
+%change figure label in HH:MM
+gregtick;
+if filt
+ title({['10W0N - MERIDIONAL VELOCITY - RDI 150 kHz (filtered from tide)']});
+else
+ title({[mooring.name, ' - MERIDIONAL VELOCITY - RDI ',num2str(freq),' kHz']});
+end
+
+graph_name = ['10W0N_nb150khz_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');
+
+if reply_ts == 1
+ hf=figure('position', [0, 0, 1400, 500]);
+ colormap jet
+ pcolor(inttim,Z(bin_start:bin_end),tsintfilt(bin_start:bin_end,:)); shading interp;
+ h = colorbar;
+ ylabel(h,'Target Strength [dB1]');
+ set(gca,'ydir', 'reverse');
+ ylabel('Depth (m)');
+ ylim([0,round(max(Z))]);
+ %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
+
+ graph_name = [fpath_output, mooring.name, '_nb150khz_TS_int_filt_sub'];
+ set(hf,'Units','Inches');
+ pos = get(hf,'Position');
+ set(hf,'PaperPositionMode','Auto','PaperUnits','Inches','PaperSize',[pos(3), pos(4)]);
+ saveas(hf,graph_name,'jpeg');
+end
+
+
+
+% %% Plot tide
+% hf=figure('position', [0, 0, 1400, 1000]);
+% niv_tide = (-5:0.2:5);
+% utid_baro = utid_baro * 100;
+% vtid_baro = vtid_baro * 100;
+% %u
+% subplot(2,1,1);
+% colormap jet
+% [C,h] = contourf(inttim,Z(bin_start:bin_end),utid_baro(bin_start:bin_end,:),niv_tide);
+% set(h,'LineColor','none');
+% caxis(niv_tide([1 end]));
+% h=colorbar;
+% ylabel(h,'U [cm 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 TIDE VELOCITY - RDI ',num2str(freq),' kHz']});
+%
+% %v
+% subplot(2,1,2);
+% [C,h] = contourf(inttim,Z(bin_start:bin_end),vtid_baro(bin_start:bin_end,:),niv_tide);
+% set(h,'LineColor','none');
+% caxis(niv_tide([1 end]));
+% h = colorbar;
+% ylabel(h,'V [cm 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 TIDE VELOCITY - RDI ',num2str(freq),' kHz']});
+
+%% Write netcdf file
+disp('****')
+disp('Creating .nc file')
+[yr_start , ~, ~] = gregorian(inttim(1));
+[yr_end, ~, ~] = gregorian(inttim(length(inttim)));
+
+ncid = netcdf.create(['ADCP_10W0N_',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(data.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]);
+if reply_ts == 1
+ ts_ID = netcdf.defVar(ncid,'ts','double',[dimidt dimidz]);
+end
+%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,data.Z);
+%Then store my main variable
+netcdf.putVar(ncid,u_ID,data.uintfilt');
+netcdf.putVar(ncid,v_ID,data.vintfilt');
+if reply_ts == 1
+ netcdf.putVar(ncid,ts_ID,data.tsintfilt');
+end
+%We're done, close the netcdf
+netcdf.close(ncid);
+disp('****')
+% -------------------------------------------------------------------------------------------
diff --git a/template_get_adcp_data.m b/template_get_adcp_data.m
index 3bc09df2d91921c623b462f31df4884c69d5cd9a..23ddeadffd33e8ab89d64aa78cd959155190ea80 100644
--- a/template_get_adcp_data.m
+++ b/template_get_adcp_data.m
@@ -16,21 +16,21 @@ addpath('/home/proussel/Documents/OUTILS/TOOLS/nansuite'); % NaNSuitePath
%% META information:
% Location rawfile
-rawfile = 'IDMX2/_RDI_000.000'; % binary file with .000 extension
-fpath_output = './IDMX2/'; % Output directory
+rawfile = '_RDI_000.000'; % binary file with .000 extension
+fpath_output = './10W/'; % Output directory
% Cruise/mooring info
-cruise.name = 'INDOMIX'; % cruise name
-mooring.name = '0N130E'; % '0N10W'
-mooring.lat = '00°04.066'; % latitude [°']
-mooring.lon = '129°12.41'; % longitude [°']
+cruise.name = 'PIRATA'; % cruise name
+mooring.name = '10W0N'; % '0N10W'
+mooring.lat = '00°00.000'; % latitude [°']
+mooring.lon = '-10°00.000'; % longitude [°']
clock_drift = 0; % [seconds]
% ADCP info
-adcp.sn = 13952; % ADCP serial number
-adcp.type = '75 khz Quartermaster'; % Type : Quartermaster, longranger
+adcp.sn = 509; % ADCP serial number
+adcp.type = '150 khz Quartermaster'; % Type : Quartermaster, longranger
adcp.direction = 'up'; % upward-looking 'up', downward-looking 'dn'
-adcp.instr_depth = 632; % nominal instrument depth
+adcp.instr_depth = 300; % nominal instrument depth
instr = 1; % this is just for name convention and sorting of all mooring instruments
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -428,23 +428,45 @@ disp('Saving raw data')
save([fpath_output, mooring.name '_' num2str(adcp.sn) '_instr_' sprintf('%02d',instr) '.mat'],'adcp','mooring','data','-v7.3');
%% 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));
-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);
+if strcmp(adcp.direction,'up')
+ 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));
+ 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);
+ if reply_ts == 1
+ ts_interp(i,ind:ind+npts-1) = data.ts.ts(1:npts,i);
+ end
+ end
+else
+ Z = (round(min(data.depth))+blen/2:blen:max(z(:))+blen);
+ Zmax = min(Z);
+ u_interp = NaN(length(time),length(Z));
+ v_interp = NaN(length(time),length(Z));
if reply_ts == 1
- ts_interp(i,ind:ind+npts-1) = data.ts.ts(1:npts,i);
+ 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);
+ if reply_ts == 1
+ ts_interp(i,ind:ind+npts-1) = data.ts.ts(1:npts,i);
+ end
end
end