%function:      netcdf_ecco_recompose
%object:        recompose a netcdf data files in the "ECCO format"
%		from binary and tiled model outputs (the default)
%author:        Gael Forget (gforget@mit.edu)
%date:          Apr 17th, 2006
%

warning off MATLAB:mir_warning_variable_used_as_function;

%choose files:
%[file_data,rep_data,tmp2]=uigetfile('*.nc','please pick a data file');
%tmp2=strfind(file_data,'.nc'); tmp1=file_data(1:tmp2-1);
%[file_model,rep_model,tmp2]=uigetfile([tmp1 '*'],...
%'please pick one of the \n associated model couterpart files');
%rep_out=uigetdir('please choose the output directory');

rep_model='./'; rep_data=rep_model; rep_out=rep_model;
file_data='prof_exemple.nc'; file_model='prof_exemple.001.001.equi.data';

%detect mode file type:
tmp2=strfind(file_model,'.'); model_file_type=file_model(tmp2(end)+1:end);

%process all the data files at once?
user_choice=input('Do you want to process all the other data files in this directory as well? y\n','s');
if ~isempty(findstr(user_choice,'y'))
%build up the list:
eval(['files_list=ls('' -1 ' rep_data '*.nc '');']);
tmp1=files_list;  tmp2=strfind(files_list,rep_data)+length(rep_data);  tmp3=strfind(files_list,'.nc')+2;
files_list='';
for tmp4=1:length(tmp2);
files_list=strvcat(files_list,  tmp1(tmp2(tmp4):tmp3(tmp4)) );
end
else
%one single file:
files_list=file_data;
end

%loop over files:
for f_cur=1:size(files_list,1)

%initialize the process:
clear prof_*; file_data2=files_list(f_cur,:);

%test whether this file is relevant:
eval(['ncload ' rep_data file_data2 ' prof_YYYYMMDD;' ]);
if ~isempty(prof_YYYYMMDD)&isempty(findstr(file_data2,'equi'))

%load the data:
eval(['ncload ' rep_data file_data2 ';' ]); list_var=zeros(6,1); nbvars=0;
if ~isempty(whos('prof_T')); nbvars=nbvars+1; list_var(1)=nbvars; prof_Tequi=0*prof_T; prof_Tmask=0*prof_T; end;
if ~isempty(whos('prof_S')); nbvars=nbvars+1; list_var(2)=nbvars; prof_Sequi=0*prof_S; prof_Smask=0*prof_S; end;
if ~isempty(whos('prof_U')); nbvars=nbvars+1; list_var(3)=nbvars; prof_Uequi=0*prof_U; prof_Umask=0*prof_U; end;
if ~isempty(whos('prof_V')); nbvars=nbvars+1; list_var(4)=nbvars; prof_Vequi=0*prof_V; prof_Vmask=0*prof_V; end;
if ~isempty(whos('prof_ptr')); nbvars=nbvars+1; list_var(5)=nbvars; prof_ptrequi=0*prof_ptr; prof_ptrmask=0*prof_ptr; end;
if ~isempty(whos('prof_ssh')); nbvars=nbvars+1; list_var(6)=nbvars; prof_sshequi=0*prof_ssh; prof_sshmask=0*prof_ssh; end;
nbdepths=length(depth);

%make the list associated with tiles/processors:
tmp1=strfind(file_data2,'.nc');
%I do the test with dir, because ls returns an error if no file is found
eval(['model_files_list=dir(''' rep_model file_data2(1:tmp1-1)  '*.' model_file_type   ''');']);
if size(model_files_list,1)~=0;
%RK: model_files_list(1).name; => name of the first struct element

eval(['model_files_list=ls('' -1 ' rep_model file_data2(1:tmp1-1)  '*.' model_file_type   ''');']);
list_beg=findstr(model_files_list,file_data2(1:tmp1-1));
list_end=findstr(model_files_list,['.' model_file_type])+length(model_file_type);

%OLD test: if ~isempty(list_beg) ... now ensured by the above test

%loop over model files:
for f_cur2=1:length(list_beg)
file_model2=model_files_list(list_beg(f_cur2):list_end(f_cur2));

%fill the global array:
%if ~isempty(findstr(file_model2(end-2:end),'bin')); 
if ~isempty(findstr(file_model2,'.equi.'));
fid0=fopen([rep_model file_model2],'r','b');
irec=1; recl=(nbdepths+1)*8;
while ~feof(fid0)
position0=recl*nbvars*2*(irec-1); status=fseek(fid0,position0,'bof');
if list_var(1)~=0; tmp1=fread(fid0,nbdepths+1,'float64'); if tmp1(end)~=0; prof_Tequi(tmp1(end),:)=tmp1(1:end-1)'; 
tmp1=fread(fid0,nbdepths+1,'float64'); prof_Tmask(tmp1(end),:)=tmp1(1:end-1)'; end; end;
if list_var(2)~=0; tmp1=fread(fid0,nbdepths+1,'float64'); if tmp1(end)~=0; prof_Sequi(tmp1(end),:)=tmp1(1:end-1)'; 
tmp1=fread(fid0,nbdepths+1,'float64'); prof_Smask(tmp1(end),:)=tmp1(1:end-1)'; end;  end;
if list_var(3)~=0; tmp1=fread(fid0,nbdepths+1,'float64'); if tmp1(end)~=0; 
prof_Uequi(tmp1(end),:)=tmp1(1:end-1)'; 
tmp1=fread(fid0,nbdepths+1,'float64'); prof_Umask(tmp1(end),:)=tmp1(1:end-1)'; end; end;
if list_var(4)~=0; tmp1=fread(fid0,nbdepths+1,'float64'); if tmp1(end)~=0; prof_Vequi(tmp1(end),:)=tmp1(1:end-1)'; 
tmp1=fread(fid0,nbdepths+1,'float64'); prof_Vmask(tmp1(end),:)=tmp1(1:end-1)'; end; end;
if list_var(5)~=0; tmp1=fread(fid0,nbdepths+1,'float64'); if tmp1(end)~=0; prof_ptrequi(tmp1(end),:)=tmp1(1:end-1)';
tmp1=fread(fid0,nbdepths+1,'float64'); prof_ptrmask(tmp1(end),:)=tmp1(1:end-1)'; end; end;
if list_var(6)~=0; tmp1=fread(fid0,nbdepths+1,'float64'); if tmp1(end)~=0; prof_sshequi(tmp1(end),:)=tmp1(1:end-1)';
tmp1=fread(fid0,nbdepths+1,'float64'); prof_sshmask(tmp1(end),:)=tmp1(1:end-1)'; end; end;

if ~isempty(find(tmp1>1e10));
1;
end;


irec=irec+1;
position0=recl*nbvars*2*(irec-1); status=fseek(fid0,position0,'bof'); tmp1=fread(fid0,1,'float64');
end;%while
fclose(fid0);

elseif ~isempty(findstr(file_model2(end-1:end),'nc'));
nc=netcdf([rep_model file_model2 '.nc'],'nowrite');
if list_var(1)~=0; tmp1=nc{'prof_Tmask'}(:); tmp2=find(sum(tmp1,1)>0); tmp3=nc{'prof_ind_glob'}(:);
tmp4=nc{'prof_T'}(:); prof_Tequi(tmp3(tmp2),:)=tmp4(tmp2,:); prof_Tmask(tmp3(tmp2),:)=tmp2(tmp3,:); end;
if list_var(2)~=0; tmp1=nc{'prof_Smask'}(:); tmp2=find(sum(tmp1,1)>0); tmp3=nc{'prof_ind_glob'}(:);
tmp4=nc{'prof_S'}(:); prof_Sequi(tmp3(tmp2),:)=tmp4(tmp2,:); prof_Smask(tmp3(tmp2),:)=tmp2(tmp3,:); end;
if list_var(3)~=0; tmp1=nc{'prof_Umask'}(:); tmp2=find(sum(tmp1,1)>0); tmp3=nc{'prof_ind_glob'}(:);
tmp4=nc{'prof_U'}(:); prof_Uequi(tmp3(tmp2),:)=tmp4(tmp2,:); prof_Umask(tmp3(tmp2),:)=tmp2(tmp3,:); end;
if list_var(4)~=0; tmp1=nc{'prof_Vmask'}(:); tmp2=find(sum(tmp1,1)>0); tmp3=nc{'prof_ind_glob'}(:);
tmp4=nc{'prof_V'}(:); prof_Vequi(tmp3(tmp2),:)=tmp4(tmp2,:); prof_Vmask(tmp3(tmp2),:)=tmp2(tmp3,:); end;
if list_var(5)~=0; tmp1=nc{'prof_ptrmask'}(:); tmp2=find(sum(tmp1,1)>0); tmp3=nc{'prof_ind_glob'}(:);
tmp4=nc{'prof_ptr'}(:); prof_ptrequi(tmp3(tmp2),:)=tmp4(tmp2,:); prof_ptrmask(tmp3(tmp2),:)=tmp2(tmp3,:); end;
if list_var(6)~=0; tmp1=nc{'prof_sshmask'}(:); tmp2=find(sum(tmp1,1)>0); tmp3=nc{'prof_ind_glob'}(:);
tmp4=nc{'prof_ssh'}(:); prof_sshequi(tmp3(tmp2),:)=tmp4(tmp2,:); prof_sshmask(tmp3(tmp2),:)=tmp2(tmp3,:); end;
nc = close(nc);
end;%if
end; %for f_cur2 

%save the global array to file:
tmp1=findstr(file_data2,'.nc'); file_model3=[file_data2(1:tmp1-1) '.equi.all.nc'];  
tmp1=dir([rep_out file_model3]);
	%tmp1=ls([rep_out file_model3]);
%complete an existing file:
if ~isempty(tmp1)
	%if isempty(strfind(tmp1,'No such file'));
fcdf=netcdf([rep_out file_model3],'write');
if ~isempty(whos('prof_T'));
prof_tmp=prof_Tmask; prof_T=fcdf{'prof_T'}(:,:); prof_Tmask=fcdf{'prof_Tmask'}(:,:);
tmp1=sum(prof_tmp,2); tmp1=find(tmp1>0);
if ~isempty(tmp1); prof_T(tmp1,:)=prof_Tequi(tmp1,:); prof_Tmask(tmp1,:)=prof_tmp(tmp1,:); end;
fcdf{'prof_T'}(:,:)=prof_T(:,:); fcdf{'prof_Tmask'}(:,:)=prof_Tmask(:,:); end;
if ~isempty(whos('prof_S'));
prof_tmp=prof_Smask; prof_S=fcdf{'prof_S'}(:,:); prof_Smask=fcdf{'prof_Smask'}(:,:);
tmp1=sum(prof_tmp,2); tmp1=find(tmp1>0); 
if ~isempty(tmp1); prof_S(tmp1,:)=prof_Sequi(tmp1,:); prof_Smask(tmp1,:)=prof_tmp(tmp1,:); end;
fcdf{'prof_S'}(:,:)=prof_S(:,:); fcdf{'prof_Smask'}(:,:)=prof_Smask(:,:); end;
if ~isempty(whos('prof_U'));
prof_tmp=prof_Umask; prof_U=fcdf{'prof_U'}(:,:); prof_Umask=fcdf{'prof_Umask'}(:,:);
tmp1=sum(prof_tmp,2); tmp1=find(tmp1>0); 
if ~isempty(tmp1); prof_U(tmp1,:)=prof_Uequi(tmp1,:); prof_Umask(tmp1,:)=prof_tmp(tmp1,:); end;
fcdf{'prof_U'}(:,:)=prof_U(:,:); fcdf{'prof_Umask'}(:,:)=prof_Umask(:,:); end;
if ~isempty(whos('prof_V'));
prof_tmp=prof_Vmask; prof_V=fcdf{'prof_V'}(:,:); prof_Vmask=fcdf{'prof_Vmask'}(:,:);
tmp1=sum(prof_tmp,2); tmp1=find(tmp1>0); 
if ~isempty(tmp1); prof_V(tmp1,:)=prof_Vequi(tmp1,:); prof_Vmask(tmp1,:)=prof_tmp(tmp1,:); end;
fcdf{'prof_V'}(:,:)=prof_V(:,:); fcdf{'prof_Vmask'}(:,:)=prof_Vmask(:,:); end;
if ~isempty(whos('prof_ptr'));
prof_tmp=prof_ptrmask; prof_ptr=fcdf{'prof_ptr'}(:,:); prof_ptrmask=fcdf{'prof_ptrmask'}(:,:);
tmp1=sum(prof_tmp,2); tmp1=find(tmp1>0);
if ~isempty(tmp1); prof_ptr(tmp1,:)=prof_ptrequi(tmp1,:); prof_ptrmask(tmp1,:)=prof_tmp(tmp1,:); end;
fcdf{'prof_ptr'}(:,:)=prof_ptr(:,:); fcdf{'prof_ptrmask'}(:,:)=prof_ptrmask(:,:); end;
if ~isempty(whos('prof_ssh'));
prof_tmp=prof_sshmask; prof_ssh=fcdf{'prof_ssh'}(:,:); prof_sshmask=fcdf{'prof_sshmask'}(:,:);
tmp1=sum(prof_tmp,2); tmp1=find(tmp1>0);
if ~isempty(tmp1); prof_ssh(tmp1,:)=prof_sshequi(tmp1,:); prof_sshmask(tmp1,:)=prof_tmp(tmp1,:); end;
fcdf{'prof_ssh'}(:,:)=prof_ssh(:,:); fcdf{'prof_sshmask'}(:,:)=prof_sshmask(:,:); end;
%close the file :
fcdf=close(fcdf);

%create a new file
else
mystruct_txt='mystruct=struct(';
if ~isempty(who('prof_T'));mystruct_txt=[mystruct_txt '''prof_T'',{prof_Tequi},'];
mystruct_txt=[mystruct_txt '''prof_Tmask'',{prof_Tmask},'];end;
if ~isempty(who('prof_S')); mystruct_txt=[mystruct_txt '''prof_S'',{prof_Sequi},'];
mystruct_txt=[mystruct_txt '''prof_Smask'',{prof_Smask},'];end;
if ~isempty(who('prof_U'));mystruct_txt=[mystruct_txt '''prof_U'',{prof_Uequi},'];
mystruct_txt=[mystruct_txt '''prof_Umask'',{prof_Umask},'];end;
if ~isempty(who('prof_V'));mystruct_txt=[mystruct_txt '''prof_V'',{prof_Vequi},'];
mystruct_txt=[mystruct_txt '''prof_Vmask'',{prof_Vmask},'];end;
if ~isempty(who('prof_ptr'));mystruct_txt=[mystruct_txt '''prof_ptr'',{prof_ptrequi},'];
mystruct_txt=[mystruct_txt '''prof_ptrmask'',{prof_ptrmask},'];end;
if ~isempty(who('prof_ssh'));mystruct_txt=[mystruct_txt '''prof_ssh'',{prof_sshequi},'];
mystruct_txt=[mystruct_txt '''prof_sshmask'',{prof_sshmask},'];end;
mystruct_txt=[mystruct_txt(1:end-1) ');']; eval(mystruct_txt);

mystruct1D=struct('prof_YYYYMMDD',prof_YYYYMMDD,'prof_HHMMSS',prof_HHMMSS,...
'prof_lon',prof_lon,'prof_lat',prof_lat);
file_characteristics=[length(prof_lon) 0 30 -9999]; 
prof_descr=ones(length(prof_lon),1)*double('model');
netcdf_ecco_create([rep_out file_model3], file_characteristics, depth, ...
prof_descr, mystruct, mystruct1D);
end;

fprintf(['file: ' file_data2 ' \n has been processed \n']);
else
fprintf(['file: ' file_data2 ' \n, no model files found\n']);
%OLD end; %if ~isempty(list_beg)...
end %if size(model_files_list,1)~=0;

else
fprintf(['file: ' file_data2 ' \n appeared irrelevant, and was skipped \n']);
end%if ~isempty(prof_YYYYMMDD)...
end%for f_cur=1:size(files_list,1)...