read_file_woa.m

function levitus = read_file_woa(file)
% levitus = read_file_woa(file)
% Read WOA01 Levitus T-S-O2, Stddev & nb_obs Netcdf file in memory
%
% $Id$

% check for file existence
% ------------------------
filesfound = checkforfiles( file );
if filesfound == 0; 
   warning(['Couldn''t find ', file]);
   levitus = -1;
   return;
end

% il existe un "bug" dans netcdf ligne 409, ncitem retourne une
% erreur dans la variable result

% open file in read mode
% ----------------------
nc = netcdf(which(file), 'nowrite');

% Initialise la waitbar de chargement du fichier netCDF
% -----------------------------------------------------
%wb = waitbar(0,'');

% We cannot change title property to 'none' (default set as 'tex') inside
% waitbar function (line 81), see
% http://www.mathworks.co.uk/matlabcentral/newsreader/view_thread/115725
% -----------------------------------------------------------------------
% hchild = get(wb,'children');
% htitle = get(hchild,'title');
% set(htitle,'Interpreter','None');
% ('none' as opposed to 'latex') to leave underscores as underscores
set(0,'DefaulttextInterpreter','none')


% update waitbar title with Tex mode disable
% ------------------------------------------
wb = waitbar(0, ['Loading file: ' file ' Please  wait...']);

% loop for every variable
% -----------------------
for i = 1:length(var(nc))
  
  % first initialize the dimensions of the data array, this is due to a bug
  % (?) in netcdf toolbox, with an array [1,1,n,m], netcdf operator (:)
  % return only [n,m]. This is true for surface climatology file !!!!!
  % -------------------------------------------------------------------
  data = zeros(size(nc{i}));
  
  % return current variable (object)
  % --------------------------------
  nv = nc{i};
  
  % use autonan mode on this variable (object), remplace fillValue with NaN
  % -----------------------------------------------------------------------
  nv = autonan(nv, true);
  
  % then fill with values, we use a temporary object data, because nv
  % is an netcdf object, see line 75
  % -----------------------------------------------------------------
  data(:) = nv(:);
  
  % other Matlab way to replace fillValue by NaN
  % --------------------------------------------
  %   if ~isempty(fillval(nc{i}))
  %     data(data == fillval(nc{i})) = NaN;
  %   end
  
  % assign dynamically variable in structure levitus
  % ------------------------------------------------
  % be carreful !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
  % don't use data(:) ... 
  % whem data dimensions are [1,1,m,n]
  % [m,n]     = data(:) 
  % [1,1,m,n] = data
  % ------------------------------------------------
  levitus.(name(nv)) = data;
  
  % moves the waitbar cursor 
  % ------------------------
  waitbar( i/length(nv), wb);
  
end

% close waitbar
% -------------
close(wb);

% close netcdf file
% -----------------
close(nc);


%----------------------------------------------------------------------
%----------------------------------------------------------------------
function filesfound = checkforfiles( file )

if exist(file,'file');
   filesfound = 1;
else 
   filesfound = 0;
end