function []=profiles_prep_write_nc(InterOrFinal);

%InterOrFinal	1 -> intermediate stage, store in mat file
%		2 -> final stage, write nc

global rep_out filename_out;
global t_std s_std t_test s_test t_w s_w t_equi s_equi;
global ymd hms pnum pnum_txt lon lat direc dmod ilon ilat imonth;
global fill_value_output initChkFile;

%global vaiables used here only -> keep in memory
global num_cur_tmpfile data_value2D data_weights2D data_equi2D  data_i data_j data_t data_t2 data_test2D data_pnum_txt data_dir;

buffer_size=1000;
nb_lev=length(dmod); 
nb_char=30;

if fill_value_output~=-9999;
fprint('MITgcm assumes fill_value_output=-9999 \n');
return;
end

if InterOrFinal==1

%initialize arrays :
if isempty(data_pnum_txt)
num_cur_tmpfile=0;
data_value2D=NaN*zeros(2,buffer_size,length(dmod));
data_test2D=data_value2D; data_weights2D=data_value2D; data_equi2D=data_value2D;
data_i=NaN*zeros(buffer_size,1);
data_j=data_i;data_t=data_i; data_t2=data_i; data_dir=data_i;
data_pnum_txt=char(double(zeros(buffer_size,nb_char)));
end

%restriction of dates and positions :

%store information :
tmp_indice=min(find(isnan(data_i)));

data_value2D(1,tmp_indice,:)=t_std;
data_weights2D(1,tmp_indice,:)=t_w;
data_equi2D(1,tmp_indice,:)=t_equi;
data_test2D(1,tmp_indice,:)=t_test;

data_value2D(2,tmp_indice,:)=s_std;
data_weights2D(2,tmp_indice,:)=s_w;
data_equi2D(2,tmp_indice,:)=s_equi;
data_test2D(2,tmp_indice,:)=s_test;

data_t(tmp_indice)=ymd;
data_t2(tmp_indice)=hms;
data_pnum_txt(tmp_indice,1:length(pnum_txt))=pnum_txt;
data_i(tmp_indice)=lon;
data_j(tmp_indice)=lat;
data_dir(tmp_indice)=direc;

if tmp_indice>0.9*buffer_size; 
num_cur_tmpfile=num_cur_tmpfile+1;
eval(['save ' rep_out '/' filename_out 'tmp' num2str(num_cur_tmpfile) '.mat data_*;' ]);
data_value2D=NaN*zeros(2,buffer_size,length(dmod));
data_test2D=data_value2D; data_weights2D=data_value2D; data_equi2D=data_value2D;
data_i=NaN*zeros(buffer_size,1);
data_j=data_i;data_t=data_i; data_t2=data_i; data_dir=data_i;
data_pnum_txt=char(double(zeros(buffer_size,nb_char)));
end;


elseif InterOrFinal==2

num_cur_tmpfile=num_cur_tmpfile+1;
eval(['save ' rep_out '/' filename_out 'tmp' num2str(num_cur_tmpfile) '.mat data_*;' ]);

%remark :       moving to the rep_out directory seems needed because
%               the netcdf file creation can fail otherwise  
eval('rep_bak=pwd;'); eval(['cd ' rep_out]);


for file_content=1:2

%open the netcdf file : 
if file_content==1%the main file
fcdf=netcdf([filename_out '.nc'], 'clobber');
else
fcdf=netcdf([filename_out 'CHECK.nc'], 'clobber');
end

%nb of profiles to be assimilated :
nb_prof=0;
for cur_tmpfile=1:num_cur_tmpfile
eval(['load ' rep_out '/' filename_out 'tmp' num2str(cur_tmpfile) '.mat;' ]);
tmp_indice=min(find(isnan(data_i)));
if isempty(tmp_indice); tmp_indice=length(data_i)+1; end;
nb_prof=nb_prof+tmp_indice-1;
end


%define netcdf dimensions : 
fcdf('iPROF') = nb_prof;
fcdf('iDEPTH') = nb_lev;
fcdf('lTXT') = nb_char;

%define netcdf variables :
fcdf{'depth'} = ncdouble('iDEPTH');
fcdf{'depth'}.units='meters';
fcdf{'prof_YYYYMMDD'} = ncdouble('iPROF');
        fcdf{'prof_YYYYMMDD'}.missing_value=fill_value_output;
        fcdf{'prof_YYYYMMDD'}.long_name='year (4 digits), month (2 digits), day (2 digits)';
fcdf{'prof_HHMMSS'} = ncdouble('iPROF');
        fcdf{'prof_HHMMSS'}.missing_value=fill_value_output;
        fcdf{'prof_HHMMSS'}.long_name='hour (2 digits), minute (2 digits), seconde (2 digits)';
fcdf{'prof_dir'} = ncdouble('iPROF');
        fcdf{'prof_dir'}.missing_value=0;
	fcdf{'prof_dir'}.long_name='profile direction 1=asc  2=desc';
fcdf{'prof_lon'} = ncdouble('iPROF');
        fcdf{'prof_lon'}.units='(degree E)';
        fcdf{'prof_lon'}.missing_value=fill_value_output;
fcdf{'prof_lat'} = ncdouble('iPROF');
        fcdf{'prof_lat'}.units='(degree N)';
        fcdf{'prof_lat'}.missing_value=fill_value_output;
fcdf{'prof_T'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_T'}.long_name='potential temperature';
        fcdf{'prof_T'}.units='degree Celsius';
        fcdf{'prof_T'}.missing_value=fill_value_output;
fcdf{'prof_Tweight'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_Tweight'}.long_name='weights';
        fcdf{'prof_Tweight'}.units='(degree Celsius)^-2';
        fcdf{'prof_Tweight'}.missing_value=0;
fcdf{'prof_Ttest'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_Ttest'}.long_name='temperature flag';
	fcdf{'prof_Ttest'}.units='(no units)';
	fcdf{'prof_Ttest'}.missing_value=0;
fcdf{'prof_S'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_S'}.long_name='salinity';
        fcdf{'prof_S'}.units='(no units)';
        fcdf{'prof_S'}.missing_value=fill_value_output;
fcdf{'prof_Sweight'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_Sweight'}.long_name='weights';
        fcdf{'prof_Sweight'}.units='(no units)^-2';
        fcdf{'prof_Sweight'}.missing_value=0;
fcdf{'prof_Stest'} = ncdouble('iPROF','iDEPTH');
        fcdf{'prof_Stest'}.long_name='salinity flag';
	fcdf{'prof_Stest'}.units='(no units)';
	fcdf{'prof_Stest'}.missing_value=0;
fcdf{'prof_descr'} = ncchar('iPROF','lTXT');
        fcdf{'prof_descr'}.long_name='profile description';


%fill the vector of the standard depths :
fcdf{'depth'}(1:nb_lev)=dmod;

%fill the profiles arrays:
cur_prof_interv=[0 0];
for cur_tmpfile=1:num_cur_tmpfile
eval(['load ' rep_out '/' filename_out 'tmp' num2str(cur_tmpfile) '.mat;' ]);
tmp_indice=min(find(isnan(data_i)))-1;
if tmp_indice>0
cur_prof_interv=[cur_prof_interv(2)+1 cur_prof_interv(2)+tmp_indice];

%pre-treatment of the data :
if file_content==1%the main file
prof_T=squeeze(data_value2D(1,1:tmp_indice,:));
else
prof_T=squeeze(data_equi2D(1,1:tmp_indice,:));
end
prof_Tweight=squeeze(data_weights2D(1,1:tmp_indice,:));
prof_Ttest=squeeze(data_test2D(1,1:tmp_indice,:));
if file_content==1%the main file
prof_Tweight(prof_T==fill_value_output|prof_Ttest>0)=0;
else
prof_T(isnan(prof_T))=fill_value_output;
end


if file_content==1%the main file
prof_S=squeeze(data_value2D(2,1:tmp_indice,:));
else
prof_S=squeeze(data_equi2D(2,1:tmp_indice,:));
end
prof_Sweight=squeeze(data_weights2D(2,1:tmp_indice,:));
prof_Stest=squeeze(data_test2D(2,1:tmp_indice,:));
if file_content==1%the main file
prof_Sweight(prof_S==fill_value_output|prof_Stest>0)=0;
else
prof_S(isnan(prof_S))=fill_value_output;
end



tmp3=[1:tmp_indice];

%fill the date and position vectors :
    fcdf{'prof_YYYYMMDD'}(cur_prof_interv(1):cur_prof_interv(2))=data_t(tmp3);
    fcdf{'prof_HHMMSS'}(cur_prof_interv(1):cur_prof_interv(2))=data_t2(tmp3);
    fcdf{'prof_dir'}(cur_prof_interv(1):cur_prof_interv(2))=data_dir(tmp3);
    fcdf{'prof_lon'}(cur_prof_interv(1):cur_prof_interv(2))=data_i(tmp3);
    fcdf{'prof_lat'}(cur_prof_interv(1):cur_prof_interv(2))=data_j(tmp3);

%fill the data matrices :
    fcdf{'prof_T'}(cur_prof_interv(1):cur_prof_interv(2),1:nb_lev)=prof_T(tmp3,:);
    fcdf{'prof_Tweight'}(cur_prof_interv(1):cur_prof_interv(2),1:nb_lev)=prof_Tweight(tmp3,:);
    fcdf{'prof_Ttest'}(cur_prof_interv(1):cur_prof_interv(2),1:nb_lev)=prof_Ttest(tmp3,:);
    fcdf{'prof_S'}(cur_prof_interv(1):cur_prof_interv(2),1:nb_lev)=prof_S(tmp3,:);
    fcdf{'prof_Sweight'}(cur_prof_interv(1):cur_prof_interv(2),1:nb_lev)=prof_Sweight(tmp3,:);
    fcdf{'prof_Stest'}(cur_prof_interv(1):cur_prof_interv(2),1:nb_lev)=prof_Stest(tmp3,:);
%fill the field describing the instruments :
    fcdf{'prof_descr'}(cur_prof_interv(1):cur_prof_interv(2),1:nb_char)=data_pnum_txt(tmp3,:);
end; end;

%close the file :
fcdf=close(fcdf);

end %for file_content=1:2

eval(['cd ' rep_bak]);

for cur_tmpfile=1:num_cur_tmpfile
eval(['!rm -f ' rep_out '/' filename_out 'tmp' num2str(cur_tmpfile) '.mat;' ]);
end

%needed to reinitialize arrays in the next case :
data_pnum_txt=[];

end