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gforget |
1.1 |
%function: netcdf_ecco_recompose |
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%object: recompose a netcdf data files in the "ECCO format" |
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% from binary and tiled model outputs (the default) |
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%author: Gael Forget (gforget@mit.edu) |
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%date: Apr 17th, 2006 |
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% |
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warning off MATLAB:mir_warning_variable_used_as_function; |
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%choose files: |
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%[file_data,rep_data,tmp2]=uigetfile('*.nc','please pick a data file'); |
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%tmp2=strfind(file_data,'.nc'); tmp1=file_data(1:tmp2-1); |
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%[file_model,rep_model,tmp2]=uigetfile([tmp1 '*'],... |
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%'please pick one of the \n associated model couterpart files'); |
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%rep_out=uigetdir('please choose the output directory'); |
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%rep_model='/net/ross/raid2/gforget/MITgcm/jobs/job_fwd/weddell-raid/'; |
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%file_data='ARGOifremer_r9_post_4mygrid.nc'; file_model='ARGOifremer_r9_post_4mygrid.001.001.equi.data'; |
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%file_data='TestCS2nonoise_4mygrid.nc'; file_model='TestCS2nonoise_4mygrid.001.001.equi.data'; |
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rep_model='/net/weddell/raid3/gforget/MITgcmrundir/'; file_data='ARGOifremer_r9_post_4mygrid.nc'; file_model='ARGOifremer_r9_post_4mygrid.001.001.equi.data'; |
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rep_data=rep_model; |
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rep_out=rep_model; |
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%detect mode file type: |
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tmp2=strfind(file_model,'.'); model_file_type=file_model(tmp2(end)+1:end); |
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%process all the data files at once? |
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user_choice=input('Do you want to process all the other data files in this directory as well? y\n','s'); |
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if ~isempty(findstr(user_choice,'y')) |
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%build up the list: |
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eval(['files_list=ls('' -1 ' rep_data '*.nc '');']); |
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tmp1=files_list; tmp2=strfind(files_list,rep_data)+length(rep_data); tmp3=strfind(files_list,'.nc')+2; |
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files_list=''; |
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for tmp4=1:length(tmp2); |
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files_list=strvcat(files_list, tmp1(tmp2(tmp4):tmp3(tmp4)) ); |
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end |
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else |
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%one single file: |
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files_list=file_data; |
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end |
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%loop over files: |
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for f_cur=1:size(files_list,1) |
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%initialize the process: |
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clear prof_*; file_data2=files_list(f_cur,:); |
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%test whether this file is relevant: |
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eval(['ncload ' rep_data file_data2 ' prof_YYYYMMDD;' ]); |
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if ~isempty(prof_YYYYMMDD)&isempty(findstr(file_data2,'equi')) |
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%load the data: |
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eval(['ncload ' rep_data file_data2 ';' ]); list_var=zeros(6,1); nbvars=0; |
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if ~isempty(whos('prof_T')); nbvars=nbvars+1; list_var(1)=nbvars; prof_Tequi=0*prof_T; prof_Tmask=0*prof_T; end; |
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if ~isempty(whos('prof_S')); nbvars=nbvars+1; list_var(2)=nbvars; prof_Sequi=0*prof_S; prof_Smask=0*prof_S; end; |
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if ~isempty(whos('prof_U')); nbvars=nbvars+1; list_var(3)=nbvars; prof_Uequi=0*prof_U; prof_Umask=0*prof_U; end; |
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if ~isempty(whos('prof_V')); nbvars=nbvars+1; list_var(4)=nbvars; prof_Vequi=0*prof_V; prof_Vmask=0*prof_V; end; |
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if ~isempty(whos('prof_ptr')); nbvars=nbvars+1; list_var(5)=nbvars; prof_ptrequi=0*prof_ptr; prof_ptrmask=0*prof_ptr; end; |
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if ~isempty(whos('prof_ssh')); nbvars=nbvars+1; list_var(6)=nbvars; prof_sshequi=0*prof_ssh; prof_sshmask=0*prof_ssh; end; |
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nbdepths=length(depth); |
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%make the list associated with tiles/processors: |
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tmp1=strfind(file_data2,'.nc'); |
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%I do the test with dir, because ls returns an error if no file is found |
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eval(['model_files_list=dir(''' rep_model file_data2(1:tmp1-1) '*.' model_file_type ''');']); |
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if size(model_files_list,1)~=0; |
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%RK: model_files_list(1).name; => name of the first struct element |
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eval(['model_files_list=ls('' -1 ' rep_model file_data2(1:tmp1-1) '*.' model_file_type ''');']); |
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list_beg=findstr(model_files_list,file_data2(1:tmp1-1)); |
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list_end=findstr(model_files_list,['.' model_file_type])+length(model_file_type); |
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%OLD test: if ~isempty(list_beg) ... now ensured by the above test |
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%loop over model files: |
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for f_cur2=1:length(list_beg) |
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file_model2=model_files_list(list_beg(f_cur2):list_end(f_cur2)); |
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%fill the global array: |
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%if ~isempty(findstr(file_model2(end-2:end),'bin')); |
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if ~isempty(findstr(file_model2,'.equi.')); |
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fid0=fopen([rep_model file_model2],'r','b'); |
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irec=1; recl=(nbdepths+1)*8; |
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while ~feof(fid0) |
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position0=recl*nbvars*2*(irec-1); status=fseek(fid0,position0,'bof'); |
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if list_var(1)~=0; tmp1=fread(fid0,nbdepths+1,'float64'); if tmp1(end)~=0; prof_Tequi(tmp1(end),:)=tmp1(1:end-1)'; |
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tmp1=fread(fid0,nbdepths+1,'float64'); prof_Tmask(tmp1(end),:)=tmp1(1:end-1)'; end; end; |
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if list_var(2)~=0; tmp1=fread(fid0,nbdepths+1,'float64'); if tmp1(end)~=0; prof_Sequi(tmp1(end),:)=tmp1(1:end-1)'; |
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tmp1=fread(fid0,nbdepths+1,'float64'); prof_Smask(tmp1(end),:)=tmp1(1:end-1)'; end; end; |
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if list_var(3)~=0; tmp1=fread(fid0,nbdepths+1,'float64'); if tmp1(end)~=0; |
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prof_Uequi(tmp1(end),:)=tmp1(1:end-1)'; |
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tmp1=fread(fid0,nbdepths+1,'float64'); prof_Umask(tmp1(end),:)=tmp1(1:end-1)'; end; end; |
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if list_var(4)~=0; tmp1=fread(fid0,nbdepths+1,'float64'); if tmp1(end)~=0; prof_Vequi(tmp1(end),:)=tmp1(1:end-1)'; |
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tmp1=fread(fid0,nbdepths+1,'float64'); prof_Vmask(tmp1(end),:)=tmp1(1:end-1)'; end; end; |
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if list_var(5)~=0; tmp1=fread(fid0,nbdepths+1,'float64'); if tmp1(end)~=0; prof_ptrequi(tmp1(end),:)=tmp1(1:end-1)'; |
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tmp1=fread(fid0,nbdepths+1,'float64'); prof_ptrmask(tmp1(end),:)=tmp1(1:end-1)'; end; end; |
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if list_var(6)~=0; tmp1=fread(fid0,nbdepths+1,'float64'); if tmp1(end)~=0; prof_sshequi(tmp1(end),:)=tmp1(1:end-1)'; |
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tmp1=fread(fid0,nbdepths+1,'float64'); prof_sshmask(tmp1(end),:)=tmp1(1:end-1)'; end; end; |
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if ~isempty(find(tmp1>1e10)); |
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1; |
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end; |
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irec=irec+1; |
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position0=recl*nbvars*2*(irec-1); status=fseek(fid0,position0,'bof'); tmp1=fread(fid0,1,'float64'); |
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end;%while |
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fclose(fid0); |
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elseif ~isempty(findstr(file_model2(end-1:end),'nc')); |
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nc=netcdf([rep_model file_model2 '.nc'],'nowrite'); |
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if list_var(1)~=0; tmp1=nc{'prof_Tmask'}(:); tmp2=find(sum(tmp1,1)>0); tmp3=nc{'prof_ind_glob'}(:); |
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tmp4=nc{'prof_T'}(:); prof_Tequi(tmp3(tmp2),:)=tmp4(tmp2,:); prof_Tmask(tmp3(tmp2),:)=tmp2(tmp3,:); end; |
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if list_var(2)~=0; tmp1=nc{'prof_Smask'}(:); tmp2=find(sum(tmp1,1)>0); tmp3=nc{'prof_ind_glob'}(:); |
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tmp4=nc{'prof_S'}(:); prof_Sequi(tmp3(tmp2),:)=tmp4(tmp2,:); prof_Smask(tmp3(tmp2),:)=tmp2(tmp3,:); end; |
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if list_var(3)~=0; tmp1=nc{'prof_Umask'}(:); tmp2=find(sum(tmp1,1)>0); tmp3=nc{'prof_ind_glob'}(:); |
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tmp4=nc{'prof_U'}(:); prof_Uequi(tmp3(tmp2),:)=tmp4(tmp2,:); prof_Umask(tmp3(tmp2),:)=tmp2(tmp3,:); end; |
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if list_var(4)~=0; tmp1=nc{'prof_Vmask'}(:); tmp2=find(sum(tmp1,1)>0); tmp3=nc{'prof_ind_glob'}(:); |
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tmp4=nc{'prof_V'}(:); prof_Vequi(tmp3(tmp2),:)=tmp4(tmp2,:); prof_Vmask(tmp3(tmp2),:)=tmp2(tmp3,:); end; |
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if list_var(5)~=0; tmp1=nc{'prof_ptrmask'}(:); tmp2=find(sum(tmp1,1)>0); tmp3=nc{'prof_ind_glob'}(:); |
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tmp4=nc{'prof_ptr'}(:); prof_ptrequi(tmp3(tmp2),:)=tmp4(tmp2,:); prof_ptrmask(tmp3(tmp2),:)=tmp2(tmp3,:); end; |
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if list_var(6)~=0; tmp1=nc{'prof_sshmask'}(:); tmp2=find(sum(tmp1,1)>0); tmp3=nc{'prof_ind_glob'}(:); |
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tmp4=nc{'prof_ssh'}(:); prof_sshequi(tmp3(tmp2),:)=tmp4(tmp2,:); prof_sshmask(tmp3(tmp2),:)=tmp2(tmp3,:); end; |
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nc = close(nc); |
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end;%if |
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end; %for f_cur2 |
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%save the global array to file: |
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tmp1=findstr(file_data2,'.nc'); file_model3=[file_data2(1:tmp1-1) '.equi.all.nc']; |
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tmp1=dir([rep_out file_model3]); |
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%tmp1=ls([rep_out file_model3]); |
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%complete an existing file: |
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if ~isempty(tmp1) |
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%if isempty(strfind(tmp1,'No such file')); |
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fcdf=netcdf([rep_out file_model3],'write'); |
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if ~isempty(whos('prof_T')); |
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prof_tmp=prof_Tmask; prof_T=fcdf{'prof_T'}(:,:); prof_Tmask=fcdf{'prof_Tmask'}(:,:); |
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tmp1=sum(prof_tmp,2); tmp1=find(tmp1>0); |
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if ~isempty(tmp1); prof_T(tmp1,:)=prof_Tequi(tmp1,:); prof_Tmask(tmp1,:)=prof_tmp(tmp1,:); end; |
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fcdf{'prof_T'}(:,:)=prof_T(:,:); fcdf{'prof_Tmask'}(:,:)=prof_Tmask(:,:); end; |
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if ~isempty(whos('prof_S')); |
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prof_tmp=prof_Smask; prof_S=fcdf{'prof_S'}(:,:); prof_Smask=fcdf{'prof_Smask'}(:,:); |
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tmp1=sum(prof_tmp,2); tmp1=find(tmp1>0); |
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if ~isempty(tmp1); prof_S(tmp1,:)=prof_Sequi(tmp1,:); prof_Smask(tmp1,:)=prof_tmp(tmp1,:); end; |
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fcdf{'prof_S'}(:,:)=prof_S(:,:); fcdf{'prof_Smask'}(:,:)=prof_Smask(:,:); end; |
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if ~isempty(whos('prof_U')); |
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prof_tmp=prof_Umask; prof_U=fcdf{'prof_U'}(:,:); prof_Umask=fcdf{'prof_Umask'}(:,:); |
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tmp1=sum(prof_tmp,2); tmp1=find(tmp1>0); |
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if ~isempty(tmp1); prof_U(tmp1,:)=prof_Uequi(tmp1,:); prof_Umask(tmp1,:)=prof_tmp(tmp1,:); end; |
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fcdf{'prof_U'}(:,:)=prof_U(:,:); fcdf{'prof_Umask'}(:,:)=prof_Umask(:,:); end; |
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if ~isempty(whos('prof_V')); |
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prof_tmp=prof_Vmask; prof_V=fcdf{'prof_V'}(:,:); prof_Vmask=fcdf{'prof_Vmask'}(:,:); |
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tmp1=sum(prof_tmp,2); tmp1=find(tmp1>0); |
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if ~isempty(tmp1); prof_V(tmp1,:)=prof_Vequi(tmp1,:); prof_Vmask(tmp1,:)=prof_tmp(tmp1,:); end; |
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fcdf{'prof_V'}(:,:)=prof_V(:,:); fcdf{'prof_Vmask'}(:,:)=prof_Vmask(:,:); end; |
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if ~isempty(whos('prof_ptr')); |
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prof_tmp=prof_ptrmask; prof_ptr=fcdf{'prof_ptr'}(:,:); prof_ptrmask=fcdf{'prof_ptrmask'}(:,:); |
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tmp1=sum(prof_tmp,2); tmp1=find(tmp1>0); |
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if ~isempty(tmp1); prof_ptr(tmp1,:)=prof_ptrequi(tmp1,:); prof_ptrmask(tmp1,:)=prof_tmp(tmp1,:); end; |
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fcdf{'prof_ptr'}(:,:)=prof_ptr(:,:); fcdf{'prof_ptrmask'}(:,:)=prof_ptrmask(:,:); end; |
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if ~isempty(whos('prof_ssh')); |
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prof_tmp=prof_sshmask; prof_ssh=fcdf{'prof_ssh'}(:,:); prof_sshmask=fcdf{'prof_sshmask'}(:,:); |
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tmp1=sum(prof_tmp,2); tmp1=find(tmp1>0); |
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if ~isempty(tmp1); prof_ssh(tmp1,:)=prof_sshequi(tmp1,:); prof_sshmask(tmp1,:)=prof_tmp(tmp1,:); end; |
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fcdf{'prof_ssh'}(:,:)=prof_ssh(:,:); fcdf{'prof_sshmask'}(:,:)=prof_sshmask(:,:); end; |
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%close the file : |
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fcdf=close(fcdf); |
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%create a new file |
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else |
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mystruct_txt='mystruct=struct('; |
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if ~isempty(who('prof_T'));mystruct_txt=[mystruct_txt '''prof_T'',{prof_Tequi},']; |
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mystruct_txt=[mystruct_txt '''prof_Tmask'',{prof_Tmask},'];end; |
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if ~isempty(who('prof_S')); mystruct_txt=[mystruct_txt '''prof_S'',{prof_Sequi},']; |
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mystruct_txt=[mystruct_txt '''prof_Smask'',{prof_Smask},'];end; |
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if ~isempty(who('prof_U'));mystruct_txt=[mystruct_txt '''prof_U'',{prof_Uequi},']; |
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mystruct_txt=[mystruct_txt '''prof_Umask'',{prof_Umask},'];end; |
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if ~isempty(who('prof_V'));mystruct_txt=[mystruct_txt '''prof_V'',{prof_Vequi},']; |
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mystruct_txt=[mystruct_txt '''prof_Vmask'',{prof_Vmask},'];end; |
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if ~isempty(who('prof_ptr'));mystruct_txt=[mystruct_txt '''prof_ptr'',{prof_ptrequi},']; |
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mystruct_txt=[mystruct_txt '''prof_ptrmask'',{prof_ptrmask},'];end; |
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if ~isempty(who('prof_ssh'));mystruct_txt=[mystruct_txt '''prof_ssh'',{prof_sshequi},']; |
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mystruct_txt=[mystruct_txt '''prof_sshmask'',{prof_sshmask},'];end; |
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mystruct_txt=[mystruct_txt(1:end-1) ');']; eval(mystruct_txt); |
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mystruct1D=struct('prof_YYYYMMDD',prof_YYYYMMDD,'prof_HHMMSS',prof_HHMMSS,... |
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'prof_lon',prof_lon,'prof_lat',prof_lat); |
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file_characteristics=[length(prof_lon) 0 30 -9999]; |
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prof_descr=ones(length(prof_lon),1)*double('model'); |
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netcdf_ecco_create([rep_out file_model3], file_characteristics, depth, ... |
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prof_descr, mystruct, mystruct1D); |
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end; |
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fprintf(['file: ' file_data2 ' \n has been processed \n']); |
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else |
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fprintf(['file: ' file_data2 ' \n, no model files found\n']); |
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%OLD end; %if ~isempty(list_beg)... |
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end %if size(model_files_list,1)~=0; |
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else |
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fprintf(['file: ' file_data2 ' \n appeared irrelevant, and was skipped \n']); |
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end%if ~isempty(prof_YYYYMMDD)... |
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end%for f_cur=1:size(files_list,1)... |
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