function []=netcdf_ecco_mask(rep_data,file_data,x00,y00);
%
%object: reads a pkg/profiles netcdf file and masks all profiles that are out of a given region
%
%input: 
%	rep_data, file_data
%	x00 and y00 (vectors)	broken line that defines the region of interest.
%For example:	x00=[300 340 340 300 300]; y00=[60 60 70 70 60];
%
%result: [rep_data 'masked_' file_data]


%rep_data='./'; file_data='fileCur.nc';
%x00=[300 340 340 300 300]; y00=[60 60 70 70 60];


%flag valid profiles:
%--------------------

eval(['ncload ' rep_data file_data ' prof_lon prof_lat;']);
prof_lonALL=prof_lon;  prof_latALL= prof_lat;

 flag_profiles=zeros(size(prof_lonALL));
 length_div=1e3;
 num_div=ceil(length(prof_lonALL)/length_div);
 for cur_div=1:num_div
        list_profiles0=[(cur_div-1)*length_div+1:min(cur_div*length_div,length(prof_lonALL))];
        [tmp1]=netcdf_ecco_GenericgridLocateCell(x00,y00,prof_lonALL(list_profiles0),prof_latALL(list_profiles0));
        flag_profiles(list_profiles0(find(tmp1>0)))=1;
 end

flagged_profiles=find(flag_profiles==0);


%create final netcdf file:
%-------------------------

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

for vcur=1:size(myvars);
eval(['mystruct.prof_' deblank(myvars(vcur,:)) 'weight(flagged_profiles,:)=0;']);
end

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

eval(['ncload ' rep_data file_data ' prof_interp_XC11 prof_interp_YC11 prof_interp_i prof_interp_j prof_interp_lon prof_interp_lat prof_interp_weights;']);
if ~isempty(prof_interp_XC11)
prof_interp_XC11(flagged_profiles)=-9999; prof_interp_XCNINJ(flagged_profiles)=-9999;
prof_interp_YC11(flagged_profiles)=-9999; prof_interp_YCNINJ(flagged_profiles)=-9999;
prof_interp_i(flagged_profiles,:)=-9999; prof_interp_j(flagged_profiles,:)=-9999;
prof_interp_lon(flagged_profiles,:)=-9999; prof_interp_lat(flagged_profiles,:)=-9999;
prof_interp_weights(flagged_profiles,:)=-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,'prof_interp_YC11',prof_interp_YC11,...
'prof_interp_XCNINJ',prof_interp_XCNINJ,'prof_interp_YCNINJ',prof_interp_YCNINJ...
);

mystruct4mygrid=struct('prof_interp_i',prof_interp_i,...
'prof_interp_j',prof_interp_j,...
'prof_interp_lon',prof_interp_lon,...
'prof_interp_lat',prof_interp_lat,...
'prof_interp_weights',prof_interp_weights);

netcdf_ecco_create([rep_data 'masked_' file_data], file_characteristics, depth, ...
prof_descr, mystruct, mystruct1D,mystruct4mygrid);

else

netcdf_ecco_create([rep_data 'masked_' file_data], file_characteristics, depth, ...
prof_descr, mystruct, mystruct1D);

end

fprintf([rep_data 'masked_' file_data ' written \n']);