%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
%  Select the eddies in an eddy oct_netcdf file
%
%  Get the eddies only with coherent properties: 
%   minimum radius, maximum radius, minimum amplitude
%
%  Pierrick Penven, IRD, 2011.
%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
clear all
close all
%
% Minimum radius [m]
%
RadiusMin=0;
%
% Maximum radius [m]
%
RadiusMax=5000e3;
%
% Minimum amplitude [m]
%
AmpMin=0.02;
%
%fname_in='eddies_aviso_2014_2014.nc';
fname_in='eddies_croco_10_10.nc';
%
%fname_out='eddies_aviso_2014_2014_select.nc';
fname_out='eddies_croco_10_10_select.nc';
%
%%%%%%%%%%%%%%%%%%% END USERS DEFINED VARIABLES %%%%%%%%%%%%%%%%%%%%%%%
%
% Open the file
%
ncid = netcdf.open(fname_in, 'NC_NOWRITE');
%
% Read
%
time=netcdf.getVar(ncid, netcdf.inqVarID(ncid, 'time'));
ID=netcdf.getVar(ncid, netcdf.inqVarID(ncid, 'ID'));
lon=netcdf.getVar(ncid, netcdf.inqVarID(ncid, 'lon'));
lat=netcdf.getVar(ncid, netcdf.inqVarID(ncid, 'lat'));
Area=netcdf.getVar(ncid, netcdf.inqVarID(ncid, 'Area'));
Energy=netcdf.getVar(ncid, netcdf.inqVarID(ncid, 'Energy'));
Vorticity=netcdf.getVar(ncid, netcdf.inqVarID(ncid, 'Vorticity'));
Radius=netcdf.getVar(ncid, netcdf.inqVarID(ncid, 'Radius'));
MaxSSH=netcdf.getVar(ncid, netcdf.inqVarID(ncid, 'MaxSSH'));
MinSSH=netcdf.getVar(ncid, netcdf.inqVarID(ncid, 'MinSSH'));
MeanSSH=netcdf.getVar(ncid, netcdf.inqVarID(ncid, 'MeanSSH'));
Amplitude=netcdf.getVar(ncid, netcdf.inqVarID(ncid, 'Amplitude'));
Ueddy=netcdf.getVar(ncid, netcdf.inqVarID(ncid, 'Ueddy'));
Leddy=netcdf.getVar(ncid, netcdf.inqVarID(ncid, 'Leddy'));
U=netcdf.getVar(ncid, netcdf.inqVarID(ncid, 'U'));
V=netcdf.getVar(ncid, netcdf.inqVarID(ncid, 'V'));
netcdf.close(ncid);
%
% Select
%
igood=((Radius>RadiusMin) & ...
       (Radius<RadiusMax) & ...
       (Amplitude>AmpMin));
%
time=time(igood);
ID=ID(igood);
lon=lon(igood);
lat=lat(igood);
Area=Area(igood);
Energy=Energy(igood);
Vorticity=Vorticity(igood);
Radius=Radius(igood);
MaxSSH=MaxSSH(igood);
MinSSH=MinSSH(igood);
MeanSSH=MeanSSH(igood);
Amplitude=Amplitude(igood);
Ueddy=Ueddy(igood);
Leddy=Leddy(igood);
U=U(igood);
V=V(igood);
N=length(time)
%
% Create the file
%
ncid = netcdf.create(fname_out, 'NC_CLOBBER');
netcdf.reDef(ncid);
did_entries = netcdf.defDim(ncid, 'entries', N);
%
vid_time = netcdf.defVar(ncid, 'time', 'NC_DOUBLE', did_entries);
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'time'), 'long_name', 'Eddy time');
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'time'), 'units', 'Days since Yorig/1/1');

vid_ID = netcdf.defVar(ncid, 'ID', 'NC_DOUBLE', did_entries);
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'ID'), 'long_name', 'Eddy identification number');

vid_lon = netcdf.defVar(ncid, 'lon', 'NC_DOUBLE', did_entries);
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'lon'), 'long_name', 'Eddy longitude');
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'lon'), 'units', 'deg E');

vid_lat = netcdf.defVar(ncid, 'lat', 'NC_DOUBLE', did_entries);
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'lat'), 'long_name', 'Eddy latitude');
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'lat'), 'units', 'deg N');

vid_Area = netcdf.defVar(ncid, 'Area', 'NC_DOUBLE', did_entries);
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'Area'), 'long_name', 'Eddy area');
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'Area'), 'units', 'm2');

vid_Energy = netcdf.defVar(ncid, 'Energy', 'NC_DOUBLE', did_entries);
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'Energy'), 'long_name', 'Eddy surface energy');
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'Energy'), 'units', 'm4.s-2');

vid_Vorticity = netcdf.defVar(ncid, 'Vorticity', 'NC_DOUBLE', did_entries);
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'Vorticity'), 'long_name', 'Eddy mean surface oct_vorticity');
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'Vorticity'), 'units', 's-1');

vid_Radius = netcdf.defVar(ncid, 'Radius', 'NC_DOUBLE', did_entries);
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'Radius'), 'long_name', 'Eddy equivalent radius');
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'Radius'), 'units', 'm');

vid_MaxSSH = netcdf.defVar(ncid, 'MaxSSH', 'NC_DOUBLE', did_entries);
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'MaxSSH'), 'long_name', 'Eddy maximum SSH');
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'MaxSSH'), 'units', 'm');

vid_MinSSH = netcdf.defVar(ncid, 'MinSSH', 'NC_DOUBLE', did_entries);
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'MinSSH'), 'long_name', 'Eddy minimum SSH');
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'MinSSH'), 'units', 'm');

vid_MeanSSH = netcdf.defVar(ncid, 'MeanSSH', 'NC_DOUBLE', did_entries);
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'MeanSSH'), 'long_name', 'Eddy mean SSH');
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'MeanSSH'), 'units', 'm');

vid_Amplitude = netcdf.defVar(ncid, 'Amplitude', 'NC_DOUBLE', did_entries);
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'Amplitude'), 'long_name', 'Eddy amplitude');
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'Amplitude'), 'units', 'm');

vid_Ueddy = netcdf.defVar(ncid, 'Ueddy', 'NC_DOUBLE', did_entries);
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'Ueddy'), 'long_name', 'Eddy rotational speed (chelton et al., 2011)');
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'Ueddy'), 'units', '');

vid_Leddy = netcdf.defVar(ncid, 'Leddy', 'NC_DOUBLE', did_entries);
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'Leddy'), 'long_name', 'Eddy scale (chelton et al., 2011)');
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'Leddy'), 'units', 'm');

vid_U = netcdf.defVar(ncid, 'U', 'NC_DOUBLE', did_entries);
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'U'), 'long_name', 'Eddy zonal propagation speed');
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'U'), 'units', 'm.s-1');

vid_V = netcdf.defVar(ncid, 'V', 'NC_DOUBLE', did_entries);
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'V'), 'long_name', 'Eddy zonal propagation speed');
% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.inqVarID(ncid, 'V'), 'units', 'm.s-1');

% [conv] línea ncchar duplicada omitida
netcdf.putAtt(ncid, netcdf.getConstant('NC_GLOBAL'), 'date', date);
netcdf.endDef(ncid);
%
% Write
%
netcdf.putVar(ncid, netcdf.inqVarID(ncid, 'time'), time);
netcdf.putVar(ncid, netcdf.inqVarID(ncid, 'ID'), ID);
netcdf.putVar(ncid, netcdf.inqVarID(ncid, 'lon'), lon);
netcdf.putVar(ncid, netcdf.inqVarID(ncid, 'lat'), lat);
netcdf.putVar(ncid, netcdf.inqVarID(ncid, 'Area'), Area);
netcdf.putVar(ncid, netcdf.inqVarID(ncid, 'Energy'), Energy);
netcdf.putVar(ncid, netcdf.inqVarID(ncid, 'Vorticity'), Vorticity);
netcdf.putVar(ncid, netcdf.inqVarID(ncid, 'Radius'), Radius);
netcdf.putVar(ncid, netcdf.inqVarID(ncid, 'MaxSSH'), MaxSSH);
netcdf.putVar(ncid, netcdf.inqVarID(ncid, 'MinSSH'), MinSSH);
netcdf.putVar(ncid, netcdf.inqVarID(ncid, 'MeanSSH'), MeanSSH);
netcdf.putVar(ncid, netcdf.inqVarID(ncid, 'Amplitude'), Amplitude);
netcdf.putVar(ncid, netcdf.inqVarID(ncid, 'Ueddy'), Ueddy);
netcdf.putVar(ncid, netcdf.inqVarID(ncid, 'Leddy'), Leddy);
netcdf.putVar(ncid, netcdf.inqVarID(ncid, 'U'), U);
netcdf.putVar(ncid, netcdf.inqVarID(ncid, 'V'), V);
%
% Close the file
%
netcdf.close(ncid);