%function:      netcdf_ecco_GenericgridMat2Nc
%object:        complete an "ECCO format" data set with interpolation information 
%author:        Gael Forget (gforget@mit.edu)
%date:          June 12th, 2007
%
%inputs: an "ECCO format" data set and associated mat files generated by netcdf_ecco_GenericgridMatFirstStep
%output: an "ECCO format" data set specific to a chosen grid
function []=netcdf_ecco_GenericgridMat2Nc(file_data,rep_data,rep_mat,rep_out);


[depth,myvars,prof_descr,mystruct,mystruct1D]=netcdf_ecco_read(rep_data,file_data); 

tmp_name=findstr(file_data,'.nc'); tmp_name=file_data(1:tmp_name(end)-1);

eval(['files_list=ls('' -1 ' rep_mat tmp_name '_4mygrid.*.mat '');']);
tmp1=files_list;  tmp2=strfind(files_list,rep_mat)+length(rep_mat);
tmp3=strfind(files_list,'.mat')+3;
files_list='';
for tmp4=1:length(tmp2);
files_list=strvcat(files_list,  tmp1(tmp2(tmp4):tmp3(tmp4)) );
end

for icur=1:size(files_list,1)
eval(['load ' rep_mat deblank(files_list(icur,:)) ';']);
if icur==1; 
	prof_interp_XC11_all=prof_interp_XC11; prof_interp_YC11_all=prof_interp_YC11;
        prof_interp_XCNINJ_all=prof_interp_XCNINJ; prof_interp_YCNINJ_all=prof_interp_YCNINJ;
	prof_interp_i_all=prof_interp_i;
	prof_interp_j_all=prof_interp_j;
        prof_interp_lon_all=prof_interp_lon;
        prof_interp_lat_all=prof_interp_lat;
	prof_interp_weights_all=prof_interp_weights;
else
	tmp1=find(~isnan(prof_interp_XC11));
        prof_interp_XC11_all(tmp1)=prof_interp_XC11(tmp1); prof_interp_YC11_all(tmp1)=prof_interp_YC11(tmp1);
        prof_interp_XCNINJ_all(tmp1)=prof_interp_XCNINJ(tmp1); prof_interp_YCNINJ_all(tmp1)=prof_interp_YCNINJ(tmp1);
        prof_interp_i_all(tmp1,:)=prof_interp_i(tmp1,:);
        prof_interp_j_all(tmp1,:)=prof_interp_j(tmp1,:);
        prof_interp_lon_all(tmp1,:)=prof_interp_lon(tmp1,:);
        prof_interp_lat_all(tmp1,:)=prof_interp_lat(tmp1,:);
        prof_interp_weights_all(tmp1,:)=prof_interp_weights(tmp1,:);
end
end

tmp1=length(find(~isnan(prof_interp_XC11_all))); tmp2=length(prof_interp_XC11_all);
fprintf([' \n\n => coeffs defined for ' num2str(tmp1) ' profiles out of ' num2str(tmp2) ' \n']);

tmp3=find(isnan(prof_interp_XC11_all));
prof_interp_XC11_all(tmp3)=-9999; prof_interp_YC11_all(tmp3)=-9999;
prof_interp_XCNINJ_all(tmp3)=-9999; prof_interp_YCNINJ_all(tmp3)=-9999;
prof_interp_i_all(tmp3,:)=-9999; prof_interp_j_all(tmp3,:)=-9999;
prof_interp_lon_all(tmp3,:)=-9999; prof_interp_lat_all(tmp3,:)=-9999;
prof_interp_weights_all(tmp3,:)=-9999;


mystruct1D=struct('prof_YYYYMMDD',mystruct1D.prof_YYYYMMDD,'prof_HHMMSS',mystruct1D.prof_HHMMSS,...
'prof_lon',mystruct1D.prof_lon,'prof_lat',mystruct1D.prof_lat,...
'prof_interp_XC11',prof_interp_XC11_all,'prof_interp_YC11',prof_interp_YC11_all,...
'prof_interp_XCNINJ',prof_interp_XCNINJ_all,'prof_interp_YCNINJ',prof_interp_YCNINJ_all...
);


mystruct4mygrid=struct('prof_interp_i',prof_interp_i_all,...
'prof_interp_j',prof_interp_j_all,...
'prof_interp_lon',prof_interp_lon_all,...
'prof_interp_lat',prof_interp_lat_all,...
'prof_interp_weights',prof_interp_weights_all);

file_characteristics=[length(mystruct1D.prof_lon) 0 size(prof_descr,2) -9999];

netcdf_ecco_create([rep_out tmp_name '_4mygrid.nc'], file_characteristics, depth, ...
prof_descr, mystruct, mystruct1D,mystruct4mygrid);

fprintf([rep_out tmp_name '_4mygrid.nc written \n']);