%function: 	netcdf_ecco_read
%object:	read netcdf data files in the "MIT format"
%author:	Gael Forget (gforget@mit.edu)
%date:		june 21th, 2006
%
%usage:	   [depth,myvars,prof_descr,mystruct,mystruct1D]=...
%		netcdf_ecco_read(rep_data,file_data); 
%		---> loads a data set
%          [depth,myvars,prof_descr,mystruct,mystruct1D]=...
%               netcdf_ecco_read(rep_equi,file_equi); 
%               ---> loads model counterparts 
%	   [depth,myvars,prof_descr,mystruct,mystruct1D]=...
%		netcdf_ecco_read(rep_data,file_data,rep_equi,suff_equi); 
%		---> loads both the data set and model counterparts
%
%inputs:	rep_data	data file directory
%		file_data	data file name
%		rep_equi	model file directory
%		suff_equi	model file suffix
%
%asumption: 	file_data is 'blabla.nc', and the 
%		model file is named ['blabla' suff_equi]
%
%outputs:	depth		depth vector
%		myvars		list of the variables
%		prof_descr	instruments/cruises id
%		mystruct	struct array containing the 
%			data(+model counterparts) and weights(+model mask)
%		mystruct1D	struct array of dates and positions

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

list_vars=strvcat('T','S','U','V','ptr','ssh');

if isempty(varargin)
%either observations or model counterparts:
ncload(deblank([rep_data file_data]));
mystruct_txt='mystruct=struct('; myvars='';
for num_var=1:size(list_vars,1)
name_var=deblank(list_vars(num_var,:));
if ~isempty(who(['prof_' name_var])); 
	myvars=strvcat(myvars,name_var); 
	mystruct_txt=[mystruct_txt '''prof_' name_var ''',{prof_' name_var '}'];
	%for observations:
	if ~isempty(who(['prof_' name_var 'weight'])); 
		mystruct_txt=[mystruct_txt ',''prof_' name_var 'weight'',{prof_' name_var 'weight},'];
	%or for model counterparts case:
        else mystruct_txt=[mystruct_txt ',''prof_' name_var 'mask'',{prof_' name_var 'mask},']; end; 
end;
end;

else
%read both observations and model:
rep_equi=varargin{1}; suff_equi=varargin{2};
tmp1=strfind(file_data,'.nc');
%	read the model:
ncload(deblank([rep_equi file_data(1:tmp1-1) suff_equi]));
mystruct_txt='mystruct=struct('; myvars='';
for num_var=1:size(list_vars,1)
name_var=deblank(list_vars(num_var,:));
if ~isempty(who(['prof_' name_var]));
        myvars=strvcat(myvars,name_var);
        mystruct_txt=[mystruct_txt '''prof_' name_var ''',{prof_' name_var '},'];
        mystruct_txt=[mystruct_txt '''prof_' name_var 'weight'',{prof_' name_var 'weight},'];
        mystruct_txt=[mystruct_txt '''prof_' name_var 'equi'',{prof_' name_var 'equi},'];
        mystruct_txt=[mystruct_txt '''prof_' name_var 'mask'',{prof_' name_var 'mask},'];
        eval(['prof_' name_var 'equi=prof_' name_var ';']);
end
end
%	then read the observations:
tmp1=strfind(file_data,'.nc');
ncload(deblank([rep_data file_data(1:tmp1-1) '.nc']));
end

%structure the 2D arrays:
mystruct_txt=[mystruct_txt(1:end-1) ');']; 
eval(mystruct_txt);

%structure the 1D arrays:
mystruct1D=struct('prof_YYYYMMDD',prof_YYYYMMDD,'prof_HHMMSS',prof_HHMMSS,...
'prof_lon',prof_lon,'prof_lat',prof_lat);