Possibility to play with filtering without all the processing + change offset algo

.gitignore

@@ -4,6 +4,7 @@
 *.docx
 FR*/
 IDMX*/
+AMAZOMIX/
 old_data/
 doc/*.pdf
 *.jnl

moored_adcp_proc/adcp_surface_fit.m

@@ -75,7 +75,7 @@ function [zbins,zadcp1,offset,x_null]=adcp_surface_fit(zadcp,ea,surface_bins,ble
     plot(-((x_null-1)*blen+blen/2+fbind),'r');
     legend('Original','Reconstructed from surface reflection');
     
-    if abs(offset)>15
+    if any(abs(offset)>15)
        reply = input('Do you want to overwrite offset? 1/0 [0]:');
        if isempty(reply)
           reply = 0;
@@ -83,6 +83,7 @@ function [zbins,zadcp1,offset,x_null]=adcp_surface_fit(zadcp,ea,surface_bins,ble
        
        if reply==1
            offset=input('->Enter new offset:');
+           offset=offset*ones(1,length(zadcp));
        else
             disp(['->Cleaned median filter offset is applied']);          
        end

multi_adcp_mooring/merge_data_finalfile.m

@@ -5,11 +5,11 @@
 clear all; close all;
 
 %% Variables
-FileToMerge1     = '/home/proussel/Documents/OUTILS/ADCP/ADCP_mooring_data_processing/ADCP_0W0N_2016_2020_1d.nc'; %.nc file to merge with
-FileToMerge2     = '/media/irdcampagnes/PIRATA/PIRATA-DATA/MOORING-PIRATA/0-0/ADCP_0W0N_2020_2021_1d.nc'; %.nc file to merge
+FileToMerge1     = '/media/irdcampagnes/PIRATA-DATA/MOORING-PIRATA/10W/merged_data/ADCP_10W0N_2001_2019.nc'; %.nc file to merge with
+FileToMerge2     = '/media/irdcampagnes/PIRATA-DATA/MOORING-PIRATA/10W/ADCP_10W0N_2021_2023_1d.nc'; %.nc file to merge
 step_subsampling = 1; % 1=daily
 plot_data        = 1;
-mooring.name     = '0W0N';
+mooring.name     = '10W0N';
 mooring.lat      = 0;
 mooring.lon      = 0;
 freq             = '150 khz Quartermaster';
@@ -35,14 +35,14 @@ ncfile2.v     = ncread(FileToMerge2,'VCUR');
 %% Create depth matrix
 %depth = max(vertcat(ncfile1.depth,ncfile2.depth)):ncfile1.depth(2)-ncfile1.depth(1):min(vertcat(ncfile1.depth,ncfile2.depth));
 %depth = fliplr(depth);
-max(vertcat(ncfile1.depth,ncfile2.depth))
-min(vertcat(ncfile1.depth,ncfile2.depth))
+max(vertcat(ncfile1.depth,ncfile2.depth));
+min(vertcat(ncfile1.depth,ncfile2.depth));
 depth = 0:5:320;
 
 %% Create time matrix
 time  = vertcat(ncfile1.time,ncfile2.time);
 [YY,MM,DD,hh,mm,ss] = datevec(time+datenum(1950,01,01));
-time = julian(YY,MM,DD,hh,mm,ss);
+%time = julian(YY,MM,DD,hh,mm,ss);
 
 %% Create u/v matrix
 for ii = 1:length(ncfile1.time)
@@ -57,10 +57,11 @@ end
 u     = vertcat(u1,u2);
 v     = vertcat(v1,v2);
 
+time  = julian(YY,MM,DD,hh,mm,ss);
 time  = time*ones(1,length(depth));
 
 % create a continuous series of daily data, ranging from min(d) to max(d)
-final_time = ceil(min(min(time))):0.25:floor(max(max(time)));
+final_time = ceil(min(min(time))):1:floor(max(max(time)));
 ADCP_final.u = NaN(length(final_time),length(depth));
 ADCP_final.v = NaN(length(final_time),length(depth));
 

tools/extract_to_netcdf.m

+function extract_to_netcdf(fpath_output, mooring, data, statut,d_fillvalue)
+
+%%  Write netcdf file
+disp('****')
+disp('Creating .nc file')
+
+% Input parameters for NETCDF Global Attributes
+tc_globAttFilename      = fullfile('tools/input_GlobalAttrParameters.xls'); % JLL 2020/12 Il serait judicieux de remonter cette valeur en début du script template_get_adcp_data.m
+
+%% Prepare informations and variables required to create NETCDF file %%
+[yr_start , ~, ~]       = gregorian(data.inttim(1));
+[yr_end,  ~, ~]         = gregorian(data.inttim(length(data.inttim)));
+
+% Read inputs metadata required for NETCDF Global Attributes
+[~,~,cell_ncAttributes] = xlsread(tc_globAttFilename);
+
+% Complete output path and filename
+tc_ncFilenam_out        = fullfile(fpath_output,['ADCP_',mooring.name,'_',num2str(yr_start),'_',num2str(yr_end),'_' statut '.nc']);
+
+% Assign a "4D-size" (TIME,DEPTH,LATITUDE,LONGITUDE) to the ADCP current variables : UINTFILT, VINTFILT
+td_uADCP                = ones(numel(data.inttim),numel(data.Z),numel(data.lat),numel(data.lon)) * d_fillvalue;
+td_uADCP(:,:,1,1)       = data.uintfilt';
+td_vADCP                = ones(numel(data.inttim),numel(data.Z),numel(data.lat),numel(data.lon)) * d_fillvalue;
+td_vADCP(:,:,1,1)       = data.vintfilt';
+
+% Flip for convention
+data.Z                  = fliplr(data.Z);
+td_uADCP                = fliplr(td_uADCP);
+td_vADCP                = fliplr(td_vADCP);
+
+% Group general ADCP mooring informations and ADCP data to be written in NETCDF file format
+struct_dataADCP         = struct('mooringName', mooring.name, 'mooringLat', mooring.lat,...
+    'mooringLon', mooring.lon, 'time', data.inttim, 'depth', data.Z,...
+    'u', td_uADCP, 'v', td_vADCP);
+
+%%  Write netcdf file  %%
+f_w_ADCP_ncOS(tc_ncFilenam_out,cell_ncAttributes,struct_dataADCP,d_fillvalue);
+disp('****')
+
+end
\ No newline at end of file