clear all
clc
% This programme reads in Salinity data, interpolates on to the NEMO grid
% that you provide and outputs the points on the open boundaries, which you
% will also provide.
% Ingedients needed:
% 1) domain_cfg.nc % Your NEMO grid
% 2) bathy_meter.nc % Your bathymetry file
% 3) coordinates.bdy.nc % Your coordinates file, generated when tides
% you make tides
% 4) Daily parent data. This has struction ./U016_dir/JAN/Sal_16_0000.nc
% This code uses the parallel toolbox. This might have memory restrictions
% based on the computer you are using. If you want this to run quickly, use
% the following syntax: parpool(N) with N = 16 or N=31 if you have the
% resources.
% Note this is adapted only for Copernicus data but can easily adapted for
% other datasets. Email a.brereton@liverpool.ac.uk for help.
% we want to make the current directory visible so we can use subroutines
addpath(pwd)
% Control variables - make sure
prefix='INDIAN_bdy_'; % prefix to output filename
output_name='vomecrty'; % output variable name (3D)
mean_output_name='vobtcrty'; % output variable name (2D)
input_name='vo'; % variable from input file
filename_prefix='V'; % e.g. 'INDIAN_bdy_U...'
Input_directory='V017_dir'; % Input file directory
year = '2017'; % e.g. 'INDIAN_bdy_U_y2017...'
grid_data = 'domain_cfg.nc'; % NEMO grid information
% e.g. 'INDIAN_bdy_U_y2017m01.nc'
Input_month_suf{1}='01.nc';
Input_month_suf{2}='02.nc';
Input_month_suf{3}='03.nc';
Input_month_suf{4}='04.nc';
Input_month_suf{5}='05.nc';
Input_month_suf{6}='06.nc';
Input_month_suf{7}='07.nc';
Input_month_suf{8}='08.nc';
Input_month_suf{9}='09.nc';
Input_month_suf{10}='10.nc';
Input_month_suf{11}='11.nc';
Input_month_suf{12}='12.nc';
% Input directory month names e.g. ...../SAL16_dir/JAN/
Input_month{1}='JAN';
Input_month{2}='FEB';
Input_month{3}='MAR';
Input_month{4}='APR';
Input_month{5}='MAY';
Input_month{6}='JUN';
Input_month{7}='JUL';
Input_month{8}='AUG';
Input_month{9}='SEP';
Input_month{10}='OCT';
Input_month{11}='NOV';
Input_month{12}='DEC';
% x co-ordinate indice of boundary
nbidta = ncread('coordinates.bdy.nc','nbit'); % (yb, xb)
% y co-ordinate indice of boundary
nbjdta = ncread('coordinates.bdy.nc','nbjt'); % (yb,xb)
% rim level, this code is only set up for a rimwidth of 1.
nbrdta = nbidta*0+1; % (yb,xb)
% nav_lon - we have this in domain_cfg (y,x)
% nav_lat - we have this in domain_cfg (y,x)
nav_lon = ncread(grid_data,'nav_lon');
nav_lat = ncread(grid_data,'nav_lat');
% create a land-sea mask from bathymetry
B=ncread('bathy_meter.nc','Bathymetry');
B(B>0)=1; % 1 is Water
B(isnan(B))=0; % 0 is Land
bdy_msk=B;
for month=1:12
% e.g. 'INDIAN_bdy_SAL_y2017m01.nc'
output_filename = [prefix , filename_prefix , '_y',year,'m',Input_month_suf{month}];
% cd into the data directory
cd(Input_directory)
cd(Input_month{month})
filenames=dir('*.nc');
% This loops through daily files, interpolating onto NEMO grid and
% getting boundary points for the data.
parfor j=1:length(filenames)
if j==1
[Variable_obc,z_obc] = COPERNICUS_INTERP(filenames(j).name,grid_data,variable_name,nbidta,nbjdta);
deptht(:,:,:,j) = z_obc;
else
[Variable_obc,~] = COPERNICUS_INTERP(filenames(j).name,grid_data,variable_name,nbidta,nbjdta);
end
NEMO_variable_obc(:,:,:,j)=Variable_obc;
% Get time information. NEMO wants seconds since 1950. Copernicus data
% comes in hours since 1900.
time(j)=ncread( filenames(j).name , 'time');
time_counter(j) = (time(j) + 18262*24)*3600; % 18262 days between 1900 and 1950
end
cd ../..
for j=1:size(NEMO_variable_obc,4)
for i=1:size(NEMO_variable_obc,1)
zz=squeeze(deptht(i,1,:));
UU=squeeze( NEMO_variable_obc(i,1,:,j));
mean_NEMO_variable_obc(i,1,j) = trapz(zz,UU)/max(zz);
end
end
nccreate(output_filename,'nbrdta',...
'Dimensions',{'xb',length(nbidta),'yb',1},...
'Format','netcdf4_classic');
ncwrite(output_filename,'nbrdta',nbrdta);
nccreate(output_filename,'nbidta',...
'Dimensions',{'xb',length(nbidta),'yb',1},...
'Format','netcdf4_classic');
ncwrite(output_filename,'nbidta',nbidta);
nccreate(output_filename,'nbjdta',...
'Dimensions',{'xb',length(nbidta),'yb',1},...
'Format','netcdf4_classic');
ncwrite(output_filename,'nbjdta',nbjdta);
nccreate(output_filename,'nav_lon',...
'Dimensions',{'x',size(nav_lon,1),'y',size(nav_lon,2)},...
'Format','netcdf4_classic');
ncwrite(output_filename,'nav_lon',nav_lon);
nccreate(output_filename,'nav_lat',...
'Dimensions',{'x',size(nav_lat,1),'y',size(nav_lat,2)},...
'Format','netcdf4_classic');
ncwrite(output_filename,'nav_lat',nav_lat);
nccreate(output_filename,'bdy_msk',...
'Dimensions',{'x',size(bdy_msk,1),'y',size(bdy_msk,2)},...
'Format','netcdf4_classic');
ncwrite(output_filename,'bdy_msk',bdy_msk);
nccreate(output_filename,'time_counter',...
'Dimensions',{'time_counter',Inf},...
'Format','netcdf4_classic');
ncwrite(output_filename,'time_counter',time_counter);
nccreate(output_filename,'deptht',...
'Dimensions',{'xb',size(deptht,1),'yb',1,'z',size(deptht,3)},...
'Format','netcdf4_classic');
ncwrite(output_filename,'deptht',deptht);
nccreate(output_filename,output_name,...
'Dimensions',{'xb',size(NEMO_variable_obc,1),'yb',1,'z',size(NEMO_variable_obc,3),'time_counter',size(NEMO_variable_obc,4)},...
'Format','netcdf4_classic');
ncwrite(output_filename,output_name,NEMO_variable_obc);
nccreate(output_filename,mean_output_name,...
'Dimensions',{'xb',size(NEMO_variable_obc,1),'yb',1,'time_counter',size(NEMO_variable_obc,4)},...
'Format','netcdf4_classic');
ncwrite(output_filename,mean_output_name,mean_NEMO_variable_obc);
end