%function:      netcdf_ecco_create
%object:        create netcdf data files in the "MIT format"
%author:        Gael Forget (gforget@mit.edu)
%date:          Apr 17th, 2006
%
%main inputs: (structure arrays)
%	mystruct1D=struct('prof_YYYYMMDD',prof_YYYYMMDD,'prof_HHMMSS',...
%		prof_HHMMSS, 'prof_lon',prof_lon,'prof_lat',prof_lat);
%	mystruct=struct('prof_T',prof_T,'prof_Tweight',prof_Tweight,  etc );
%		OR mystruct=struct('prof_T',prof_T,'prof_Tmask',prof_Tmask,  etc );
%
%other inputs: file_name, file_characteristics, depth (1D vector), prof_descr (texte)
%	file_characteristics(1)=total number of profiles
%	file_characteristics(2)=last profile written
%       	if file_characteristics(2)==0 we create the file
%	file_characteristics(3)=length of the character description
%	file_characteristics(4)=missing_value
%
%asumptions about the inputs: 
%	T is potential temperature, we do not use the missing value 
%	but 0 for weight/mask (facilitate "cost" computation), 
%	units are the standard ones (see the netcdf attributes)
%
%usage:  see netcdf_postprocess_argoctd.m, netcdf_ecco_recompose.m
%
%Gael, June 7th 1007: I add the option to write interpolation information
%	assumption: varargin is mystructInterp (i,j,weights), while
%	XC11 etc. have been added to mystruct1D
%Left for later: genericity (read/compute dim4mygrid), additional info about interp stuff

function []=netcdf_ecco_create(file_name, file_characteristics, depth, prof_descr,  mystruct, mystruct1D,varargin);

%a couple of checks:
tmp1=length(mystruct1D.prof_lon);
if (file_characteristics(2)+tmp1>file_characteristics(1)); 
fprintf('problem: total number of profiles exceeded \n'); 
fprintf('writing aborted'); return; end;
if (file_characteristics(3)<size(prof_descr,2));
fprintf('problem: profiles description is too long \n');
fprintf('writing aborted'); return; end;

%incl interp coeffs for genericgrid option
if ~isempty(varargin)
	incl4mygrid=1; dim4mygridInterp=size(varargin{1}.prof_interp_i,2); %dim4mygridInterp=2;
else
	incl4mygrid=0;
end

%creation of the file:
if file_characteristics(2)==0

fcdf=netcdf(deblank(file_name), 'clobber');

%define netcdf dimensions : 
nb_lev=length(depth);
fcdf('iPROF') = file_characteristics(1);
fcdf('iDEPTH') = nb_lev;
fcdf('lTXT') = file_characteristics(3);
if incl4mygrid; fcdf('iINTERP') = dim4mygridInterp; end;
missing_value=file_characteristics(4);

%define netcdf variables :
fcdf{'depth'} = ncdouble('iDEPTH');
fcdf{'depth'}.units='meters';
fcdf{'prof_YYYYMMDD'} = ncdouble('iPROF');
        fcdf{'prof_YYYYMMDD'}.missing_value=missing_value;
        fcdf{'prof_YYYYMMDD'}.long_name='year (4 digits), month (2 digits), day (2 digits)';
fcdf{'prof_HHMMSS'} = ncdouble('iPROF');
        fcdf{'prof_HHMMSS'}.missing_value=missing_value;
        fcdf{'prof_HHMMSS'}.long_name='hour (2 digits), minute (2 digits), seconde (2 digits)';
fcdf{'prof_lon'} = ncdouble('iPROF');
        fcdf{'prof_lon'}.units='(degree E)';
        fcdf{'prof_lon'}.missing_value=missing_value;
fcdf{'prof_lat'} = ncdouble('iPROF');
        fcdf{'prof_lat'}.units='(degree N)';
        fcdf{'prof_lat'}.missing_value=missing_value;
fcdf{'prof_descr'} = ncchar('iPROF','lTXT');
        fcdf{'prof_descr'}.long_name='profile description';
fcdf{'depth'}(1:nb_lev)=depth;
if incl4mygrid; 
        fcdf{'prof_interp_XC11'} = ncdouble('iPROF'); fcdf{'prof_interp_YC11'} = ncdouble('iPROF');
        fcdf{'prof_interp_XCNINJ'} = ncdouble('iPROF'); fcdf{'prof_interp_YCNINJ'} = ncdouble('iPROF');
	fcdf{'prof_interp_i'} = ncdouble('iPROF','iINTERP');
        fcdf{'prof_interp_j'} = ncdouble('iPROF','iINTERP');
        fcdf{'prof_interp_lon'} = ncdouble('iPROF','iINTERP');
        fcdf{'prof_interp_lat'} = ncdouble('iPROF','iINTERP');
        fcdf{'prof_interp_weights'} = ncdouble('iPROF','iINTERP');
end

if isfield(mystruct,'prof_T')
fcdf{'prof_T'} = ncdouble('iPROF','iDEPTH');        
fcdf{'prof_T'}.long_name='potential temperature';        
fcdf{'prof_T'}.units='degree Celsius';        
fcdf{'prof_T'}.missing_value=missing_value;
end
if isfield(mystruct,'prof_Tweight')
fcdf{'prof_Tweight'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_Tweight'}.long_name='weights';
        fcdf{'prof_Tweight'}.units='(degree Celsius)^-2';
        fcdf{'prof_Tweight'}.missing_value=missing_value;
end
if isfield(mystruct,'prof_Tmask')
fcdf{'prof_Tmask'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_Tmask'}.long_name='model mask';
        fcdf{'prof_Tmask'}.units='no units';
        fcdf{'prof_Tmask'}.missing_value=missing_value;
end
if isfield(mystruct,'prof_S')
fcdf{'prof_S'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_S'}.long_name='salinity';
        fcdf{'prof_S'}.units='(no units)';
        fcdf{'prof_S'}.missing_value=missing_value;
end
if isfield(mystruct,'prof_Sweight')
fcdf{'prof_Sweight'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_Sweight'}.long_name='weights';
        fcdf{'prof_Sweight'}.units='(no units)^-2';
        fcdf{'prof_Sweight'}.missing_value=missing_value;
end
if isfield(mystruct,'prof_Smask')
fcdf{'prof_Smask'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_Smask'}.long_name='model mask';
        fcdf{'prof_Smask'}.units='no units';
        fcdf{'prof_Smask'}.missing_value=missing_value;
end
if isfield(mystruct,'prof_U')
fcdf{'prof_U'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_U'}.long_name='zonal velocity';
        fcdf{'prof_U'}.units='m/s';
        fcdf{'prof_U'}.missing_value=missing_value;
fcdf{'prof_V'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_V'}.long_name='meridional velocity';
        fcdf{'prof_V'}.units='m/s';
        fcdf{'prof_V'}.missing_value=missing_value;
end
if isfield(mystruct,'prof_Uweight')
fcdf{'prof_Uweight'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_Uweight'}.long_name='weights';
        fcdf{'prof_Uweight'}.units='(m/s)^-2';
        fcdf{'prof_Uweight'}.missing_value=missing_value;
fcdf{'prof_Vweight'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_Vweight'}.long_name='weights';
        fcdf{'prof_Vweight'}.units='(m/s)^-2';
        fcdf{'prof_Vweight'}.missing_value=missing_value;
end
if isfield(mystruct,'prof_Umask')
fcdf{'prof_Umask'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_Umask'}.long_name='model mask';
        fcdf{'prof_Umask'}.units='no units';
        fcdf{'prof_Umask'}.missing_value=missing_value;
fcdf{'prof_Vmask'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_Vmask'}.long_name='model mask';
        fcdf{'prof_Vmask'}.units='no units';
        fcdf{'prof_Vmask'}.missing_value=missing_value;
end
if isfield(mystruct,'prof_ptr')
fcdf{'prof_ptr'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_ptr'}.long_name='passive tracer';
        fcdf{'prof_ptr'}.units='XX';
        fcdf{'prof_ptr'}.missing_value=missing_value;
end
if isfield(mystruct,'prof_ptrweight')
fcdf{'prof_ptrweight'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_ptrweight'}.long_name='weights';
        fcdf{'prof_ptrweight'}.units='(XX)^-2';
        fcdf{'prof_ptrweight'}.missing_value=missing_value;
end
if isfield(mystruct,'prof_ptrmask')
fcdf{'prof_ptrmask'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_ptrmask'}.long_name='model mask';
        fcdf{'prof_ptrmask'}.units='no units';
        fcdf{'prof_ptrmask'}.missing_value=missing_value;
end
if isfield(mystruct,'prof_ssh')
fcdf{'prof_ssh'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_ssh'}.long_name='sea surface height';
        fcdf{'prof_ssh'}.units='m';
        fcdf{'prof_ssh'}.missing_value=missing_value;
end
if isfield(mystruct,'prof_sshweight')
fcdf{'prof_sshweight'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_sshweight'}.long_name='weights';
        fcdf{'prof_sshweight'}.units='(m)^-2';
        fcdf{'prof_sshweight'}.missing_value=missing_value;
end
if isfield(mystruct,'prof_sshmask')
fcdf{'prof_sshmask'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_sshmask'}.long_name='model mask';
        fcdf{'prof_sshmask'}.units='no units';
        fcdf{'prof_sshmask'}.missing_value=missing_value;
end

fcdf=close(fcdf);

end; %if file_characteristics(2)==0


fcdf=netcdf(deblank(file_name), 'write');

tmp1=length(mystruct1D.prof_lon);
tmp1=[1:tmp1]+file_characteristics(2);

%fill the date and position vectors :
    fcdf{'prof_YYYYMMDD'}(tmp1')=mystruct1D.prof_YYYYMMDD;
    fcdf{'prof_HHMMSS'}(tmp1')=mystruct1D.prof_HHMMSS;
    fcdf{'prof_lon'}(tmp1')=mystruct1D.prof_lon;
    fcdf{'prof_lat'}(tmp1')=mystruct1D.prof_lat;
tmp0=double(prof_descr); prof_descr(find(tmp0==0))=' ';
tmp2=file_characteristics(3)-size(prof_descr,2);
if (tmp2>0); prof_descr=[prof_descr char(double(' ')*ones(length(tmp1'),tmp2)) ]; end;
    fcdf{'prof_descr'}(tmp1',:)=prof_descr(:,:);

if incl4mygrid;
        fcdf{'prof_interp_XC11'}(tmp1')=mystruct1D.prof_interp_XC11; fcdf{'prof_interp_YC11'}(tmp1')=mystruct1D.prof_interp_YC11;
        fcdf{'prof_interp_XCNINJ'}(tmp1')=mystruct1D.prof_interp_XCNINJ; fcdf{'prof_interp_YCNINJ'}(tmp1')=mystruct1D.prof_interp_YCNINJ;
        fcdf{'prof_interp_i'}(tmp1',:)=varargin{1}.prof_interp_i;
        fcdf{'prof_interp_j'}(tmp1',:)=varargin{1}.prof_interp_j;
        fcdf{'prof_interp_lon'}(tmp1',:)=varargin{1}.prof_interp_lon;
        fcdf{'prof_interp_lat'}(tmp1',:)=varargin{1}.prof_interp_lat;
        fcdf{'prof_interp_weights'}(tmp1',:)=varargin{1}.prof_interp_weights;
end

%fill the data matrices :

if isfield(mystruct,'prof_T'); fcdf{'prof_T'}(tmp1',:)=mystruct.prof_T; end;
if isfield(mystruct,'prof_Tweight'); 
fcdf{'prof_Tweight'}(tmp1',:)=mystruct.prof_Tweight; end;
if isfield(mystruct,'prof_Tmask'); 
fcdf{'prof_Tmask'}(tmp1',:)=mystruct.prof_Tmask; end;

if isfield(mystruct,'prof_S'); fcdf{'prof_S'}(tmp1',:)=mystruct.prof_S; end;
if isfield(mystruct,'prof_Sweight'); 
fcdf{'prof_Sweight'}(tmp1',:)=mystruct.prof_Sweight; end;
if isfield(mystruct,'prof_Smask');  
fcdf{'prof_Smask'}(tmp1',:)=mystruct.prof_Smask; end;

if isfield(mystruct,'prof_U'); fcdf{'prof_U'}(tmp1',:)=mystruct.prof_U; end;
if isfield(mystruct,'prof_Uweight'); 
fcdf{'prof_Uweight'}(tmp1',:)=mystruct.prof_Uweight; end;
if isfield(mystruct,'prof_Umask');  
fcdf{'prof_Umask'}(tmp1',:)=mystruct.prof_Umask; end;

if isfield(mystruct,'prof_V'); fcdf{'prof_V'}(tmp1',:)=mystruct.prof_V; end;
if isfield(mystruct,'prof_Vweight'); 
fcdf{'prof_Vweight'}(tmp1',:)=mystruct.prof_Vweight; end;
if isfield(mystruct,'prof_Vmask');  
fcdf{'prof_Vmask'}(tmp1',:)=mystruct.prof_Vmask; end;

if isfield(mystruct,'prof_ptr');
fcdf{'prof_ptr'}(tmp1',:)=mystruct.prof_ptr; end;
if isfield(mystruct,'prof_ptrweight');
fcdf{'prof_ptrweight'}(tmp1',:)=mystruct.prof_ptrweight; end;
if isfield(mystruct,'prof_ptrmask');
fcdf{'prof_ptrmask'}(tmp1',:)=mystruct.prof_ptrmask; end;

if isfield(mystruct,'prof_ssh');
fcdf{'prof_ssh'}(tmp1',:)=mystruct.prof_ssh; end;
if isfield(mystruct,'prof_sshweight');
fcdf{'prof_sshweight'}(tmp1',:)=mystruct.prof_sshweight; end;
if isfield(mystruct,'prof_sshmask');
fcdf{'prof_sshmask'}(tmp1',:)=mystruct.prof_sshmask; end;

%close the file
fcdf=close(fcdf);