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

%% Check Netcdf library version
% -----------------------------
switch ( version('-release') )
  case { '11', '12', '13', '14', '2006a', '2006b', '2007a', '2007b', '2008a' }
    read_netcdf_toolbox;
  otherwise
    read_netcdf_native;
end


%% Nested functions
% -----------------

% use Charles Dunham toolbox
% --------------------------
  function read_netcdf_toolbox
    % 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);
  end

% use native toolbox +netcdf since R2008b
% ---------------------------------------
  function read_netcdf_native
    
    % Open netCDF file
    % ----------------
    nc = netcdf_native(file);
    
    for key = keys(nc.VARIABLES)
      var = char(key);
      data = zeros( size( nc.VARIABLES.(var).data__ ) );
      data(:) = nc.VARIABLES.(var).data__;
      levitus.(var) = data;
    end
    
  end

% check if file exist
%--------------------
  function filesfound = checkforfiles( file )
    
    if exist(file,'file');
      filesfound = 1;
    else
      filesfound = 0;
    end
    
  end

end