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function []=profiles_prep_write_nc(InterOrFinal); |
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|
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%InterOrFinal 1 -> intermediate stage, store in mat file |
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% 2 -> final stage, write nc |
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|
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global rep_out filename_out; |
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global t_std s_std t_test s_test t_w s_w t_equi s_equi; |
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global ymd hms pnum pnum_txt lon lat direc dmod ilon ilat imonth; |
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global fill_value_output initChkFile; |
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|
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%global vaiables used here only -> keep in memory |
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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; |
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|
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buffer_size=1000; |
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nb_lev=length(dmod); |
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nb_char=30; |
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|
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if fill_value_output~=-9999; |
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fprint('MITgcm assumes fill_value_output=-9999 \n'); |
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return; |
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end |
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|
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if InterOrFinal==1 |
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|
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%initialize arrays : |
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if isempty(data_pnum_txt) |
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num_cur_tmpfile=0; |
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data_value2D=NaN*zeros(2,buffer_size,length(dmod)); |
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data_test2D=data_value2D; data_weights2D=data_value2D; data_equi2D=data_value2D; |
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data_i=NaN*zeros(buffer_size,1); |
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data_j=data_i;data_t=data_i; data_t2=data_i; data_dir=data_i; |
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data_pnum_txt=char(double(zeros(buffer_size,nb_char))); |
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end |
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|
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%restriction of dates and positions : |
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|
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%store information : |
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tmp_indice=min(find(isnan(data_i))); |
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|
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data_value2D(1,tmp_indice,:)=t_std; |
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data_weights2D(1,tmp_indice,:)=t_w; |
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data_equi2D(1,tmp_indice,:)=t_equi; |
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data_test2D(1,tmp_indice,:)=t_test; |
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|
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data_value2D(2,tmp_indice,:)=s_std; |
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data_weights2D(2,tmp_indice,:)=s_w; |
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data_equi2D(2,tmp_indice,:)=s_equi; |
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data_test2D(2,tmp_indice,:)=s_test; |
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|
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data_t(tmp_indice)=ymd; |
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data_t2(tmp_indice)=hms; |
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data_pnum_txt(tmp_indice,1:length(pnum_txt))=pnum_txt; |
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data_i(tmp_indice)=lon; |
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data_j(tmp_indice)=lat; |
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data_dir(tmp_indice)=direc; |
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|
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if tmp_indice>0.9*buffer_size; |
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num_cur_tmpfile=num_cur_tmpfile+1; |
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eval(['save ' rep_out '/' filename_out 'tmp' num2str(num_cur_tmpfile) '.mat data_*;' ]); |
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data_value2D=NaN*zeros(2,buffer_size,length(dmod)); |
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data_test2D=data_value2D; data_weights2D=data_value2D; data_equi2D=data_value2D; |
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data_i=NaN*zeros(buffer_size,1); |
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data_j=data_i;data_t=data_i; data_t2=data_i; data_dir=data_i; |
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data_pnum_txt=char(double(zeros(buffer_size,nb_char))); |
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end; |
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|
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|
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elseif InterOrFinal==2 |
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|
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num_cur_tmpfile=num_cur_tmpfile+1; |
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eval(['save ' rep_out '/' filename_out 'tmp' num2str(num_cur_tmpfile) '.mat data_*;' ]); |
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|
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%remark : moving to the rep_out directory seems needed because |
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% the netcdf file creation can fail otherwise |
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eval('rep_bak=pwd;'); eval(['cd ' rep_out]); |
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|
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|
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for file_content=1:2 |
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|
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%open the netcdf file : |
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if file_content==1%the main file |
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fcdf=netcdf([filename_out '.nc'], 'clobber'); |
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else |
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fcdf=netcdf([filename_out 'CHECK.nc'], 'clobber'); |
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end |
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|
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%nb of profiles to be assimilated : |
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nb_prof=0; |
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for cur_tmpfile=1:num_cur_tmpfile |
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eval(['load ' rep_out '/' filename_out 'tmp' num2str(cur_tmpfile) '.mat;' ]); |
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tmp_indice=min(find(isnan(data_i))); |
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if isempty(tmp_indice); tmp_indice=length(data_i)+1; end; |
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nb_prof=nb_prof+tmp_indice-1; |
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end |
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|
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|
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%define netcdf dimensions : |
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fcdf('iPROF') = nb_prof; |
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fcdf('iDEPTH') = nb_lev; |
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fcdf('lTXT') = nb_char; |
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|
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%define netcdf variables : |
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fcdf{'depth'} = ncdouble('iDEPTH'); |
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fcdf{'depth'}.units='meters'; |
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fcdf{'prof_YYYYMMDD'} = ncdouble('iPROF'); |
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fcdf{'prof_YYYYMMDD'}.missing_value=fill_value_output; |
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fcdf{'prof_YYYYMMDD'}.long_name='year (4 digits), month (2 digits), day (2 digits)'; |
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fcdf{'prof_HHMMSS'} = ncdouble('iPROF'); |
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fcdf{'prof_HHMMSS'}.missing_value=fill_value_output; |
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fcdf{'prof_HHMMSS'}.long_name='hour (2 digits), minute (2 digits), seconde (2 digits)'; |
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fcdf{'prof_dir'} = ncdouble('iPROF'); |
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fcdf{'prof_dir'}.missing_value=0; |
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fcdf{'prof_dir'}.long_name='profile direction 1=asc 2=desc'; |
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fcdf{'prof_lon'} = ncdouble('iPROF'); |
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fcdf{'prof_lon'}.units='(degree E)'; |
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fcdf{'prof_lon'}.missing_value=fill_value_output; |
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fcdf{'prof_lat'} = ncdouble('iPROF'); |
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fcdf{'prof_lat'}.units='(degree N)'; |
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fcdf{'prof_lat'}.missing_value=fill_value_output; |
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fcdf{'prof_T'} = ncdouble('iPROF','iDEPTH'); |
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fcdf{'prof_T'}.long_name='potential temperature'; |
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fcdf{'prof_T'}.units='degree Celsius'; |
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fcdf{'prof_T'}.missing_value=fill_value_output; |
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fcdf{'prof_Tweight'} = ncdouble('iPROF','iDEPTH'); |
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fcdf{'prof_Tweight'}.long_name='weights'; |
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fcdf{'prof_Tweight'}.units='(degree Celsius)^-2'; |
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fcdf{'prof_Tweight'}.missing_value=0; |
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fcdf{'prof_Ttest'} = ncdouble('iPROF','iDEPTH'); |
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fcdf{'prof_Ttest'}.long_name='temperature flag'; |
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fcdf{'prof_Ttest'}.units='(no units)'; |
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fcdf{'prof_Ttest'}.missing_value=0; |
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fcdf{'prof_S'} = ncdouble('iPROF','iDEPTH'); |
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fcdf{'prof_S'}.long_name='salinity'; |
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fcdf{'prof_S'}.units='(no units)'; |
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fcdf{'prof_S'}.missing_value=fill_value_output; |
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fcdf{'prof_Sweight'} = ncdouble('iPROF','iDEPTH'); |
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fcdf{'prof_Sweight'}.long_name='weights'; |
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fcdf{'prof_Sweight'}.units='(no units)^-2'; |
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fcdf{'prof_Sweight'}.missing_value=0; |
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fcdf{'prof_Stest'} = ncdouble('iPROF','iDEPTH'); |
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fcdf{'prof_Stest'}.long_name='salinity flag'; |
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fcdf{'prof_Stest'}.units='(no units)'; |
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fcdf{'prof_Stest'}.missing_value=0; |
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fcdf{'prof_descr'} = ncchar('iPROF','lTXT'); |
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fcdf{'prof_descr'}.long_name='profile description'; |
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|
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|
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%fill the vector of the standard depths : |
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fcdf{'depth'}(1:nb_lev)=dmod; |
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|
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%fill the profiles arrays: |
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cur_prof_interv=[0 0]; |
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for cur_tmpfile=1:num_cur_tmpfile |
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eval(['load ' rep_out '/' filename_out 'tmp' num2str(cur_tmpfile) '.mat;' ]); |
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tmp_indice=min(find(isnan(data_i)))-1; |
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if tmp_indice>0 |
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cur_prof_interv=[cur_prof_interv(2)+1 cur_prof_interv(2)+tmp_indice]; |
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|
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%pre-treatment of the data : |
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if file_content==1%the main file |
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prof_T=squeeze(data_value2D(1,1:tmp_indice,:)); |
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else |
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prof_T=squeeze(data_equi2D(1,1:tmp_indice,:)); |
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end |
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prof_Tweight=squeeze(data_weights2D(1,1:tmp_indice,:)); |
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prof_Ttest=squeeze(data_test2D(1,1:tmp_indice,:)); |
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if file_content==1%the main file |
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prof_Tweight(prof_T==fill_value_output|prof_Ttest>0)=0; |
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else |
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prof_T(isnan(prof_T))=fill_value_output; |
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end |
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|
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|
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if file_content==1%the main file |
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prof_S=squeeze(data_value2D(2,1:tmp_indice,:)); |
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else |
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prof_S=squeeze(data_equi2D(2,1:tmp_indice,:)); |
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end |
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prof_Sweight=squeeze(data_weights2D(2,1:tmp_indice,:)); |
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prof_Stest=squeeze(data_test2D(2,1:tmp_indice,:)); |
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if file_content==1%the main file |
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prof_Sweight(prof_S==fill_value_output|prof_Stest>0)=0; |
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else |
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prof_S(isnan(prof_S))=fill_value_output; |
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end |
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|
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|
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|
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tmp3=[1:tmp_indice]; |
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|
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%fill the date and position vectors : |
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fcdf{'prof_YYYYMMDD'}(cur_prof_interv(1):cur_prof_interv(2))=data_t(tmp3); |
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fcdf{'prof_HHMMSS'}(cur_prof_interv(1):cur_prof_interv(2))=data_t2(tmp3); |
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fcdf{'prof_dir'}(cur_prof_interv(1):cur_prof_interv(2))=data_dir(tmp3); |
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fcdf{'prof_lon'}(cur_prof_interv(1):cur_prof_interv(2))=data_i(tmp3); |
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fcdf{'prof_lat'}(cur_prof_interv(1):cur_prof_interv(2))=data_j(tmp3); |
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|
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%fill the data matrices : |
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fcdf{'prof_T'}(cur_prof_interv(1):cur_prof_interv(2),1:nb_lev)=prof_T(tmp3,:); |
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fcdf{'prof_Tweight'}(cur_prof_interv(1):cur_prof_interv(2),1:nb_lev)=prof_Tweight(tmp3,:); |
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fcdf{'prof_Ttest'}(cur_prof_interv(1):cur_prof_interv(2),1:nb_lev)=prof_Ttest(tmp3,:); |
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fcdf{'prof_S'}(cur_prof_interv(1):cur_prof_interv(2),1:nb_lev)=prof_S(tmp3,:); |
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fcdf{'prof_Sweight'}(cur_prof_interv(1):cur_prof_interv(2),1:nb_lev)=prof_Sweight(tmp3,:); |
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fcdf{'prof_Stest'}(cur_prof_interv(1):cur_prof_interv(2),1:nb_lev)=prof_Stest(tmp3,:); |
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%fill the field describing the instruments : |
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fcdf{'prof_descr'}(cur_prof_interv(1):cur_prof_interv(2),1:nb_char)=data_pnum_txt(tmp3,:); |
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end; end; |
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|
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%close the file : |
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fcdf=close(fcdf); |
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|
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end %for file_content=1:2 |
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|
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eval(['cd ' rep_bak]); |
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|
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for cur_tmpfile=1:num_cur_tmpfile |
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eval(['!rm -f ' rep_out '/' filename_out 'tmp' num2str(cur_tmpfile) '.mat;' ]); |
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end |
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|
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%needed to reinitialize arrays in the next case : |
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data_pnum_txt=[]; |
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|
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end |
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