use native NetCDF for Matlab >= R2008b

rename @netcdf directory to @netcdf_native (conflict with C Dunham NetCDF toolbox)

Remove FillValue_ attribute for <PARAM>_CALCOEFF_CONV, <PARAM>_LINCOEFF_CONV and SSPS_EXT_BOTTLE

@dynaload/display.m

@@ -13,7 +13,7 @@ result = elements(self);
 %       % -----------------------
 %       wks = whos('global');
 %       for i=1:length(wks)
-%         if strcmp(wks(i).class, 'us191.dynaload')
+%         if strcmp(wks(i).class, 'dynaload')
 %           var = wks(i).name;
 %         end
 %       end

@dynaload/dynaload.m

@@ -104,23 +104,23 @@ function self = dynaload(varargin)
 % test constructor argument
 % -------------------------
 switch nargin
-  
+
   case 0  % can't create default object
     [file, path, filterIndex] = uigetfile(...
       {'*.csv','Ascii-file (*.csv)';...
       '*.xls','Excel-file (*.xls)'}, 'Select file');
     if ~any(file)
       self.file = 'memory';
-      return
+      filterIndex = -1;
+    else
+      self.file = fullfile(path, file);
     end
-    self.file = fullfile(path, file);
-    
+
   case 1
     if strcmp(varargin{1}, 'memory')
       self.file = 'memory';
-      return
-    end
-    if( isa(varargin{1}, 'char'))
+      filterIndex = -1;
+    elseif( isa(varargin{1}, 'char'))
       file = which(varargin{1});
       if isempty( file)
         file = varargin{1};
@@ -138,10 +138,10 @@ switch nargin
     else
       error('Wrong input argument');
     end
-    
+
   otherwise
     error('Wrong number of input arguments');
-    
+
 end
 
 % init class properties

@dynaload/save.m

 function save(self, varargin)
-% us191.dynaload.save
-% it's a wrapper on us191.dynaload.write method
+% dynaload save
+% it's a wrapper on dynaload.write method
 %
 % $Id$
 

@dynaload/write.m

    function write(self, varargin)
    % write dynaload memory structure to ASCII CSV file (Comma Separated Value)
 % nc is a dynaload objet in memory load from xls file. for example:
-% >> nc = us191.dynaload('test.xls');
+% >> nc = dynaload('test.xls');
 % >> nc
-% us191.dynaload
+% dynaload
 % 
 % 	file:	test.xls
 % 
-% 	DIMENSIONS               	us191.hashtable
-% 	VARIABLES                	us191.hashtable
-% 	ATTRIBUTES               	us191.hashtable
+% 	DIMENSIONS               	hashtable
+% 	VARIABLES                	hashtable
+% 	ATTRIBUTES               	hashtable
 % 
 % >> s = nc.VARIABLES.SSTP
 % 

@hashtable/elements.m

@@ -8,6 +8,10 @@ function data = elements(hash)
 
 % Copyright (c) 2004 Matthew Krauski (mkrauski@uci.edu), CNLM, UC Irvine
 
-data(:,1) = hash.keys;
-data(:,2) = hash.data;
+if isempty( hash )
+  data = {};
+else
+  data(:,1) = hash.keys;
+  data(:,2) = hash.data;
+end
 

@hashtable/size.m

+function out = size(self)
+% get hashtable size
+
+% Return the number of keys in hashtable
+% --------------------------------------
+out = numel(self.keys);

@netcdf_native/display.m

+function display(self)
+% display netcdf object
+
+
+% diplay help in hypertext link
+% -----------------------------
+fprintf('<a href="matlab:help netcdf">netcdf</a>\n\n');
+if self.mode ~= -1
+  fprintf('\tfile:      ''%s''\n', self.file);
+end
+%fprintf('\tdynaload:  ''%s''\n', self.dynaload);
+fprintf('\tmode:      ''%s''\n', self.mode);
+if self.autonan
+  theAutonan = 'true';
+else
+  theAutonan = 'false';
+end
+fprintf('\tautonan:    %s\n', theAutonan);
+if self.autoscale
+  theAutoscale = 'true';
+else
+  theAutoscale = 'false';
+end
+fprintf('\tautoscale:  %s\n\n', theAutoscale);
+
+% call protected function hashtable.elements that return
+% <nx2> cell array of key/value
+% ------------------------------------------------------
+result = elements(self);
+
+%       % get workspace variables
+%       % -----------------------
+%       wks = whos('global');
+%       for i=1:length(wks)
+%         if strcmp(wks(i).class, '.netcdf')
+%           var = wks(i).name;
+%         end
+%       end
+
+% loop over key
+% -------------
+%nb = size(result);
+
+for key = result'
+  fprintf('\t%-25s\t%2d [%-10s]\n', ...
+    key{1}, size(key{2}), class(key{2}));
+end
+fprintf('\n');
+
+% diplay methods list in hypertext link
+% -------------------------------------
+disp('list of <a href="matlab:methods(''.netcdf'')">methods</a>');
+end
\ No newline at end of file

@netcdf_native/file.m

+function file = file(self)
+
+file = self.file;
+
+end
\ No newline at end of file

@netcdf_native/get.m

+function value = get( self, prop )
+% GET: Get profil properties from specified object
+
+% $Id: get.m 121 2007-02-05 17:16:33Z jgrelet $
+
+if nargin==1  % list properties if only object is given
+  disp('profil properties:')
+  fprintf(' file, mode, nc_id, autonan, autoscale');
+  return
+end
+
+if ~ischar(prop), error('GET: prop must be string.'), end
+
+switch prop
+  
+  case 'file'
+    value = self.file;
+  case 'mode'
+    value = self.mode;
+  case 'nc_id'
+    value = self.nc_id;
+  case 'autonan'
+    value = self.autonan;
+  case 'autoscale'
+    value = self.autoscale;
+  otherwise
+   error(['GET: ', prop,' is not a valid netcdf property.']);
+end
\ No newline at end of file

@netcdf_native/getConstantNames.m

+function name = getConstantNames(self, xtype)
+switch xtype
+  case  1   % NC_BYTE 1
+    name = 'byte';
+  case  2   % NC_CHAR 2
+    name = 'char';
+  case  3   % NC_SHORT 3
+    name = 'short';
+  case  4   % NC_INT, NC_LONG 4
+    name = 'int';
+  case  5   %NC_FLOAT 5
+    name = 'float';
+  case  6   % NC_DOUBLE 6
+    name = 'double';
+  otherwise
+    error( 'unhandled data type %d\n', xtype );
+end

@netcdf_native/mode.m

+function mode = mode(self)
+
+mode = self.mode;
+
+end
\ No newline at end of file

@netcdf_native/netcdf_native.m

+function self = netcdf_native(varargin)
+%
+% file @netcdf_native/netcdf_native
+
+arg = nargin;
+
+if arg == 1 && isempty(varargin{1})
+  arg = 0;
+end
+
+theFile = ''; theDynaload = 'memory'; theMode = 'MEMORY';
+
+switch arg
+  
+  % with not arg, read netcdf file with uigetfile
+  % ---------------------------------------------
+  case 0
+    [theFileName, thePathName] = uigetfile(...
+      {'*.nc;*.cdf','NetCDF (*.nc,*.cdf)'}, 'Select file');
+    if any(theFileName)
+      theFile = fullfile(thePathName, theFileName);
+      theMode = 'NC_NOWRITE';
+      theDynaload = 'memory';
+    else
+      theFile = '';
+    end
+    
+    % with one arg, read given netcdf filename
+    % ----------------------------------------
+  case 1
+    if( strcmp(varargin{1}, 'memory'))
+      theDynaload = 'memory';
+      theFile = 'memory';
+      theMode = 'MEMORY';
+      
+    elseif( isa(varargin{1}, 'char'))
+      theFile = varargin{1};
+      if isempty(exist(theFile, 'file'))
+        error('netcdf: %s file don''t exist.\n', theFile );
+      end
+      [thePathName, theFileName, theFileExt] = fileparts(varargin{1});
+      
+      switch theFileExt
+        case {'.nc', 'cdf'}
+          theMode = 'NC_NOWRITE';
+          % a revoir ...
+          theDynaload = 'memory';
+        case {'.csv', '.xls'}
+          theDynaload = varargin{1};
+          theMode = 'DYNALOAD';
+        otherwise
+          error('Wrong file type');
+      end
+      
+    else
+      error('Wrong input argument');
+    end
+    
+    % work on given netcdf filename with mode and dynaload dexcriptor
+    % file
+    % ---------------------------------------------------------------
+  case 2
+    
+    % is the mode numeric.
+    if ischar(varargin{2})
+      %  convert it in numeric value
+      switch (varargin{2})
+        case { 'NC_WRITE', 'NC_CLOBBER', 'NC_NOCLOBBER', 'NC_SHARE' };
+          theMode = varargin{2};
+        otherwise
+          error('Wrong mode to create netcdf file: %s', varargin{2});
+      end
+    else
+      % a modifier sur mode est numeric
+      theMode = varargin{2};
+    end
+    
+  otherwise
+    error('Wrong number of input arguments');
+end
+
+d = dynaload( theDynaload );
+
+self.file      = theFile;
+%self.dynaload = theDynaload;
+self.mode      = theMode;
+self.nc_id     = 0;
+self.autonan   = logical(1);
+self.autoscale = logical(0);
+
+% constants for netcdf data types
+% -------------------------------
+self.NC_BYTE             = netcdf.getConstant('NC_BYTE');    % 1
+self.NC_CHAR             = netcdf.getConstant('NC_CHAR');    % 2
+self.NC_SHORT            = netcdf.getConstant('NC_SHORT');   % 3
+self.NC_INT              = netcdf.getConstant('NC_INT');     % 4
+self.NC_LONG             = netcdf.getConstant('NC_LONG');    % 4
+self.NC_FLOAT            = netcdf.getConstant('NC_FLOAT');   % 5
+self.NC_DOUBLE           = netcdf.getConstant('NC_DOUBLE');  % 6
+
+self.NC_MEMORY           = -1;
+
+% constants for netcdf.open()
+% ---------------------------
+%self.NC_NOWRITE:	Read-only access
+self.NC_NOWRITE          = netcdf.getConstant('NC_NOWRITE');   % 0
+
+%self.NC_WRITE:      	Read-write access
+self.NC_WRITE            = netcdf.getConstant('NC_WRITE');     % 1
+
+% constants for netcdf.create()
+% -----------------------------
+self.NC_CLOBBER          = netcdf.getConstant('NC_CLOBBER');   % 0
+
+%self.NC_NOCLOBBER:    Prevent overwriting of existing file with the same name.
+self.NC_NOCLOBBER        = netcdf.getConstant('NC_NOCLOBBER'); % 4
+
+%self.NC_SHARE:	       Allow synchronous file updates.
+self.NC_SHARE            = netcdf.getConstant('NC_SHARE');     % 2048
+
+%self.NC_64BIT_OFFSET: Allow easier creation of files and variables which
+%                  are larger than two gigabytes.
+self.NC_64BIT_OFFSET     = netcdf.getConstant('NC_64BIT_OFFSET');  % 512
+
+self.NC_ERR             = netcdf.getConstant('NC2_ERR');      % -1
+self.NC_EBADDIM          = netcdf.getConstant('NC_EBADDIM');
+self.NC_EBADID           = netcdf.getConstant('NC_EBADID');
+self.NC_EBADNAME         = netcdf.getConstant('NC_EBADNAME');
+self.NC_EBADTYPE         = netcdf.getConstant('NC_EBADTYPE');
+self.NC_ECHAR            = netcdf.getConstant('NC_ECHAR');
+self.NC_EDIMSIZE         = netcdf.getConstant('NC_EDIMSIZE');
+self.NC_EEDGE            = netcdf.getConstant('NC_EEDGE');
+self.NC_EEXIST           = netcdf.getConstant('NC_EEXIST');
+self.NC_EGLOBAL          = netcdf.getConstant('NC_EGLOBAL');
+self.NC_EINDEFINE        = netcdf.getConstant('NC_EINDEFINE');
+self.NC_EINVAL           = netcdf.getConstant('NC_EINVAL');
+self.NC_EINVALCOORDS     = netcdf.getConstant('NC_EINVALCOORDS');
+self.NC_EMAXATTS         = netcdf.getConstant('NC_EMAXATTS');
+self.NC_EMAXDIMS         = netcdf.getConstant('NC_EMAXDIMS');
+self.NC_EMAXNAME         = netcdf.getConstant('NC_EMAXNAME');
+self.NC_EMAXVARS         = netcdf.getConstant('NC_EMAXVARS');
+self.NC_ENAMEINUSE       = netcdf.getConstant('NC_ENAMEINUSE');
+self.NC_ENFILE           = netcdf.getConstant('NC_ENFILE');
+self.NC_ENOMEM           = netcdf.getConstant('NC_ENOMEM');
+self.NC_ENORECVARS       = netcdf.getConstant('NC_ENORECVARS');
+self.NC_ENOTATT          = netcdf.getConstant('NC_ENOTATT');
+self.NC_ENOTINDEFINE     = netcdf.getConstant('NC_ENOTINDEFINE');
+self.NC_ENOTNC           = netcdf.getConstant('NC_ENOTNC');
+self.NC_ENOTVAR          = netcdf.getConstant('NC_ENOTVAR');
+self.NC_EPERM            = netcdf.getConstant('NC_EPERM');
+self.NC_ERANGE           = netcdf.getConstant('NC_ERANGE');
+self.NC_ESTRIDE          = netcdf.getConstant('NC_ESTRIDE');
+self.NC_ESTS             = netcdf.getConstant('NC_ESTS');
+self.NC_ETRUNC           = netcdf.getConstant('NC_ETRUNC');
+self.NC_EUNLIMIT         = netcdf.getConstant('NC_EUNLIMIT');
+self.NC_EUNLIMPOS        = netcdf.getConstant('NC_EUNLIMPOS');
+self.NC_EVARSIZE         = netcdf.getConstant('NC_EVARSIZE');
+self.NC_FATAL            = netcdf.getConstant('NC_FATAL');       % 1
+self.NC_FILL             = netcdf.getConstant('NC_FILL');        % 0
+self.NC_FILL_BYTE        = netcdf.getConstant('NC_FILL_BYTE');   % -127
+self.NC_FILL_CHAR        = netcdf.getConstant('NC_FILL_CHAR');   % 0
+self.NC_FILL_DOUBLE      = netcdf.getConstant('NC_FILL_DOUBLE'); % 9.9692e+036
+self.NC_FILL_FLOAT       = netcdf.getConstant('NC_FILL_FLOAT');  % 9.9692e+036
+self.NC_FILL_INT         = netcdf.getConstant('NC_FILL_INT');    % -2.1475e+009
+self.NC_FILL_SHORT       = netcdf.getConstant('NC_FILL_SHORT');  % -32767
+self.NC_FORMAT_64BIT     = netcdf.getConstant('NC_FORMAT_64BIT');   % 2
+self.NC_FORMAT_CLASSIC   = netcdf.getConstant('NC_FORMAT_CLASSIC'); % 1
+self.NC_GLOBAL           = netcdf.getConstant('NC_GLOBAL');       % -1
+self.NC_LOCK             = netcdf.getConstant('NC_LOCK');         % 1024
+self.NC_MAX_ATTRS        = netcdf.getConstant('NC_MAX_ATTRS');    % 8192
+self.NC_MAX_DIMS         = netcdf.getConstant('NC_MAX_DIMS');     % 1024
+self.NC_MAX_NAME         = netcdf.getConstant('NC_MAX_NAME');     % 256
+self.NC_MAX_VARS         = netcdf.getConstant('NC_MAX_VARS');     % 8192
+self.NC_MAX_VAR_DIMS     = netcdf.getConstant('NC_MAX_VAR_DIMS'); % 1024
+self.NC_NAT              = netcdf.getConstant('NC_NAT');          % 0
+self.NC_NOERR            = netcdf.getConstant('NC_NOERR');        % 0
+self.NC_NOFILL           = netcdf.getConstant('NC_NOFILL');       % 256
+self.NC_SIZEHINT_DEFAULT = netcdf.getConstant('NC_SIZEHINT_DEFAULT');  % 0
+self.NC_UNLIMITED        = netcdf.getConstant('NC_UNLIMITED');    % 0
+self.NC_VERBOSE          = netcdf.getConstant('NC_VERBOSE');      % 2
+
+% bless class
+% -----------
+self = class(self, 'netcdf_native', d);
+
+% call private function following mode state
+% a revoir !!!!!!!!!!!!!!!
+% ------------------------------------------
+switch self.mode
+  case 'NC_NOWRITE'     % NOWRITE mode
+    [self] = read(self, true);
+  case 'NC_WRITE'     % READ/WRITE mode
+    self = put(self,'DIMENSIONS', hashtable);
+    self = put(self,'VARIABLES',  hashtable);
+    self = put(self,'ATTRIBUTES', hashtable);
+  case 'NC_NOCLOBBER'     % NOCLOBBER mode
+  case 'NC_CLOBBER'     % NOCLOBBER mode
+    self = put(self,'DIMENSIONS', hashtable);
+    self = put(self,'VARIABLES',  hashtable);
+    self = put(self,'ATTRIBUTES', hashtable);
+    %         case self.NC_SHARE  % SHARE mode
+    %           % not implemeted
+  case 'NC_64BIT_OFFSET'
+    %           %
+  case 'DYNALOAD'
+    %           %
+  case 'MEMORY'
+    self = put(self,'DIMENSIONS', hashtable);
+    self = put(self,'VARIABLES',  hashtable);
+    self = put(self,'ATTRIBUTES', hashtable);
+  otherwise
+    error('Wrong mode argument');
+end
+
+
+
+

@netcdf_native/private/read.m

+function self = read(self, varargin)
+%
+%varargin{1} ........... waitbar (boolean)
+%
+% $Id$
+
+% no waitbar per default
+% ----------------------
+wbool = false;
+
+% check varargin
+% --------------
+if nargin > 1
+  if varargin{1}
+    wbool = true;
+  end
+end
+
+% check file validity
+% -------------------
+self.nc_id = netcdf.open(self.file, self.mode);
+if self.nc_id == -1
+  error(['netcdf:netcdf', ...
+    'The specified data file ''%s'' does not exist\n' ...
+    'or is not in the directory which is on the MATLAB path'],...
+    self.file);
+end
+
+% update waitbar title with Tex mode disable
+% ------------------------------------------
+if wbool
+  %set(0,'DefaulttextInterpreter','none')
+  wb = waitbar(0, ['Loading file.  Please  wait...']);
+  hchild = get(wb,'children');
+  htitle = get(hchild,'title');
+  set(htitle,'Interpreter','None');
+end
+
+% create a temporary hashtable use to store data read in file
+% -----------------------------------------------------------
+hash = hashtable;
+
+% returns the number of dimensions, variables, global attributes and
+% eventually unlimited dimension in a netCDF file.
+% ------------------------------------------------------------------
+[n_dims, nvars, ngatts, unlimdimid] = netcdf.inq(self.nc_id);
+
+% get dimensions and store to netcdf hashtable
+% --------------------------------------------
+for dimid = 0:n_dims-1
+  
+  % initialize empty structure
+  % --------------------------
+  s = [];
+  
+  % Get name and length of id dimension
+  % -------------------------------------
+  [dimname, dimlen] = netcdf.inqDim(self.nc_id, dimid);
+  
+  % Get dimid (dimension id) from name
+  % normalement pas besoin, a verifier....
+  % ----------------------------------
+  %dimid = netcdf.inqDimId(self.nc_id, dimname);
+  
+  % fill dimension structure with name and boolean for unlimdimid
+  % -------------------------------------------------------------
+  s.dimlen = dimlen;
+  if(dimid == unlimdimid)
+    s.unlimited = true;
+  else
+    s.unlimited = false;
+  end
+  
+  % put dimension name and length to temporary hashtable
+  % ----------------------------------------------------
+  hash = put(hash, dimname, s);
+end
+
+% put dimensions hashtable to netcdf hashtable
+% --------------------------------------------
+self = put(self, 'DIMENSIONS', hash);
+
+% clear temporary hashtable for next use
+% --------------------------------------
+hash = clear(hash);
+% bug (TODO), on ne peut pas utiliser hash = hash.clear !!!!
+% 09/03/2009: ce n'est pas un bug, voir subsref de hashtable
+
+% get variables and store to netcdf hashtable
+% -------------------------------------------
+for id = 0:nvars-1
+  
+  % moves the waitbar cursor
+  % ------------------------
+  if wbool
+    waitbar( id/nvars, wb);
+  end
+  
+  % initialize empty structure
+  % --------------------------
+  s = [];
+  
+  % return information about variable
+  % ---------------------------------
+  [varName, xtype, dimids, natts] = netcdf.inqVar(self.nc_id, id);
+  
+  % fill structure s with variable attribute names and values
+  % ---------------------------------------------------------
+  for attid = 0:natts-1
+    
+    % get attribute name
+    % ------------------
+    attName = netcdf.inqAttName(self.nc_id, id, attid);
+    
+    % if attribute name is '_FillValue', transforme to 'FillValue,
+    % because Matlab dosn't handle member name begining with '_'
+    % ------------------------------------------------------------
+    if strcmp(attName, '_FillValue')
+      s.('FillValue_') = netcdf.getAtt(self.nc_id, id, attName);
+      
+    else
+      
+      % otherwise, dynamically fill attribute member of structure s
+      % with it's value
+      % -----------------------------------------------------------
+      s.(attName) = netcdf.getAtt(self.nc_id, id, attName);
+    end
+    
+  end  % end for loop over variable attributes
+  
+  % add internal type__ member from xtype 2->char, 6->double
+  % --------------------------------------------------------
+  s.type__ = getConstantNames(self, xtype);
+  
+  % fill temporary structure s with value
+  % -------------------------------------
+  s.data__ = netcdf.getVar(self.nc_id, id);
+  
+  % If a NetCDF variable has valid scale_factor and add_offset
+  % attributes, then the data is scaled accordingly.
+  % ----------------------------------------------------------
+  if self.autoscale
+    if isfield(s, 'scale_factor') && isfield(s, 'add_offset')
+      s.data__ = s.data__ * s.scale_factor + s.add_offset;
+    end
+  end
+  
+  % replace FillValue_ by NaN only for numeric variable
+  % autonan mode is set to true by default
+  % ---------------------------------------------------
+  if self.autonan && isfield(s, 'FillValue_')
+    switch(xtype)
+      case self.NC_CHAR
+        % For now, do nothing.
+        
+      case { self.NC_DOUBLE, self.NC_FLOAT, self.NC_LONG,...
+          self.NC_SHORT, self.NC_BYTE }
+        
+        % sometimes, FillValue could be a char a badformed netcdf
+        % files
+        % --------------------------------------------------------
+        if isnumeric(s.('FillValue_'))
+          s.data__(s.data__ == s.('FillValue_')) = NaN;
+        else
+          s.data__(s.data__ == str2double(s.('FillValue_'))) = NaN;
+          
+          % verrue, pour les fichiers Roscop netcdf mal forms
+          % --------------------------------------------------
+          if str2double(s.('FillValue_')) > 1e35
+            s.data__(s.data__ >= 1e35) = NaN;
+          end
+        end
+        
+      otherwise
+        error( 'unhandled datatype %d\n', xtype );
+    end
+  end
+  
+  % if var is char and as vertical alignment, transpose it
+  % ------------------------------------------------------
+  %         if xtype == self.NC_CHAR && (size(s.data__, 1) ~= 1)
+  %           s.data__ = s.data__';
+  %         end
+  
+  % add internal dimension__ member
+  % Because MATLAB uses FORTRAN-style ordering, however, the order of
+  % the dimension IDs is reversed relative to what would be obtained
+  % from the C API
+  % ----------------------------
+  if length(dimids) > 1
+    s.data__ = permute(s.data__, fliplr(1:length(dimids)));
+    dimids = fliplr(dimids);
+  end
+  
+  
+  for dimid = 1:numel(dimids)
+    dimname = netcdf.inqDim(self.nc_id, dimids(dimid));
+    
+    % we need to reverse dimid
+    % a verifier imperativement avec plusieurs dimensions
+    % ---------------------------------------
+    s.dimension__{dimid} = dimname;
+  end
+  
+  % put variable name and value to temporary hashtable
+  % --------------------------------------------------
+  hash = put(hash, varName, s);
+  
+end
+
+
+% put variable temporary hash to netcdf hashtable
+% -----------------------------------------------
+self = put(self, 'VARIABLES', hash);
+
+% clear temporary hashtable for next use
+% --------------------------------------
+hash = clear(hash);
+
+% get gloabal attributes and store to netcdf hashtable
+% -----------------------------------------------------
+for id = 0:ngatts-1
+  
+  % initialize empty structure
+  % --------------------------
+  s = [];
+  
+  % Get the name of the global attribute associated with the
+  % variable.
+  % --------------------------------------------------------
+  gattName = netcdf.inqAttName(self.nc_id, ...
+    self.NC_GLOBAL, id);
+  
+  % Get value of global attribute.
+  % ------------------------------
+  attVal = netcdf.getAtt(self.nc_id, ...
+    self.NC_GLOBAL, gattName);
+  
+  % fill global attribute structure
+  % -------------------------------
+  s.key__  = gattName;
+  s.data__ = attVal;
+  
+  % put attribute name and value to temporary hashtable
+  % ---------------------------------------------------
+  hash = put(hash, gattName, s);
+end
+
+% put attribute temporary hash to netcdf hashtable
+% ------------------------------------------------
+self = put(self, 'ATTRIBUTES', hash);
+
+% Close waitbar
+% -------------
+if wbool
+  close(wb)
+end
+
+% close netcdf file
+% -----------------
+netcdf.close(self.nc_id)
+
+end % end of read function
\ No newline at end of file

@netcdf_native/save.m

+function save(self, varargin)
+% netcdf.save
+% it's a wrapper on netcdf write method
+%
+% $Id$
+
+write(self, varargin);

@netcdf_native/set.m

+function self = set( self, varargin )
+
+% modifier set pour modifier plusieurs propriete
+% (voir doc Programing Matlab, page 8-41)
+
+if nargin == 3
+  prop  = varargin{1};
+  value = varargin{2};
+  
+  switch prop
+    
+    case 'file'
+      self.file = value;
+    case 'mode'
+      self.mode = value;
+    case 'nc_id'
+      self.nc_id = value;
+    case 'autonan'
+      self.autonan = value;
+    case 'autoscale'
+      self.autoscale = value;
+   otherwise
+      error('Unrecognized property name ''%s''.', prop); 
+  end
+  
+end
\ No newline at end of file

@netcdf_native/subsasgn.m

+function self = subsasgn(self, s, val)
+% Subscripted assignment for object Hashtable
+% -------------------------------------------
+
+% see help for subsasgn
+% ---------------------
+switch (length(s))
+  case 3
+    switch s(3).type
+      case '.'
+        h = get(self.dynaload, s(1).subs);
+        t = get(h, s(2).subs);
+        t.(s(3).subs) = val;
+        h = put(h, s(2).subs, t);
+        self = put(self, s(1).subs, h);
+      otherwise
+        error('Invalid type.')
+    end
+  case 2
+    switch s(1).type
+      case '.'
+        if isstruct(val)
+          h = get(self.dynaload, s(1).subs);
+          h = put(h, s(2).subs, val);
+          self = put(self, s(1).subs, h);
+        else
+          error('value must be a structure');
+        end
+      otherwise
+        error('Invalid type.')
+    end
+  case 1
+    switch s.type
+      case '()'
+        if (length(s.subs) ~= 1)
+          error('Only single indexing is supported.');
+        end
+        self = put(self, s.subs{1}, val);
+      case '.'
+        switch s.subs
+          case {'autonan', 'autoscale'  }       
+            builtin('subsasgn', self, s, val);
+          otherwise
+            self = put(self, s.subs, val);
+        end
+      otherwise
+        error('Invalid type.')
+    end
+end

@netcdf_native/subsref.m

+function val = subsref(self, s)
+% overloading subscripted reference for objects
+% Dot Notation vs. Function Notation
+%
+% MATLAB classes support both function and dot notation syntax for calling methods. 
+% For example, if write is a method of the class of object nc, then calling 
+% write with function notation would be:
+%
+% nc = write(nc, 'mode');
+%
+% The equivalent method call using dot notation is:
+%
+% nc = nc.write('mode')
+%
+% However, in certain cases, the results for dot notation can differ with respect 
+% to how MATLAB dispatching works:
+%
+%   If there is an overloaded subsref, it is invoked whenever using dot-notation. 
+%   That is, the statement is first tested to see if it is subscripted assignment.
+%
+%   If there is no overloaded subsref, then setColor must be a method of X.
+%   An ordinary function or a class constructor is never called using this notation.
+%
+% $Id: subsref.m 411 2009-07-23 16:26:40Z jgrelet $
+
+% see help from substruct and subsref
+% -----------------------------------
+switch s(1).type
+  case '.'
+    switch s(1).subs
+      case {'write', 'save'}
+        builtin('subsref', self, s);
+      case {'autonan','autoscale'}
+        val = builtin('subsref', self, s);   
+      otherwise
+        
+        % call dynaload subsref
+        % ---------------------
+        val = subsref(self.dynaload, s);
+    end
+end

@netcdf/tsgqc_netcdf.csv → @netcdf_native/tsgqc_netcdf.csv

@@ -3,7 +3,7 @@
 %
 %
 $DIMENSIONS$
-#;key__;value;unlimited;#
+#;key__;dimlen;unlimited;#
 #;char;integer;logical;#
 #;DAYD;;0;#
 #;DAYD_EXT;;0;#
@@ -36,18 +36,18 @@ $VARIABLES$
 #;CNDC_CAL;'DAYD';float;CONDUCTIVITY CALIBRATED;sea_water_electrical_conductivity;S/meter;;0;7;%6.3f;99999;;;0.001;Conductivity calibrated using linearization coefficient;;DAYD;#
 #;CNDC_FREQ;'DAYD';float;SENSOR CONDUCTIVITY FREQUENCY;;hz;;0;20000;%9.3f;99999;;;0.001;Sensor conductivity frequency measured by TSG;;DAYD;#
 #;CNDC_CALCOEF;'NCOEF_CAL';double;CONDUCTIVITY CALIBRATION COEFFICIENTS;;;;;;;99999;;;;Calibration coefficients are real value, date is in julian day from REFERENCE_DATE_TIME;;;#
-#;CNDC_CALCOEF_CONV;'NCOEF_CAL','STRING8';char;CONDUCTIVITY CALIBRATION COEFFICIENTS CONVENTION;;;;;;;NaN;;;;Calibration coefficient convention is an enumeration of coefficients name, ex: 'date','a','b','c','d','f0';;;#
+#;CNDC_CALCOEF_CONV;'NCOEF_CAL','STRING8';char;CONDUCTIVITY CALIBRATION COEFFICIENTS CONVENTION;;;;;;;;;;;Calibration coefficient convention is an enumeration of coefficients name, ex: 'date','a','b','c','d','f0';;;#
 #;CNDC_LINCOEF;'NCOEF_LIN';double;CONDUCTIVITY LINEAR DRIFT CORRECTION COEFFICIENTS;;;;;;;99999;;;;Calibration coefficients are real value, date is in julian day from REFERENCE_DATE_TIME;;;#
-#;CNDC_LINCOEF_CONV;'NCOEF_LIN','STRING8';char;CONDUCTIVITY LINEAR DRIFT CORRECTION COEFFICIENTS CONVENTION;;;;;;;NaN;;;;Calibration coefficient convention is an enumeration of coefficients name, ex: 'date','offset','slope';;;#
+#;CNDC_LINCOEF_CONV;'NCOEF_LIN','STRING8';char;CONDUCTIVITY LINEAR DRIFT CORRECTION COEFFICIENTS CONVENTION;;;;;;;;;;;Calibration coefficient convention is an enumeration of coefficients name, ex: 'date','offset','slope';;;#
 #;SSJT;'DAYD';float;WATER JACKET TEMPERATURE;;degree_Celsius;;-1.5;38;%6.3f;99999;;;0.001;Temperature within TSG or (Water Jacket Temperature). Warning, this is not ocean SST temperature. Is is used for salinity computation. The reduction applied is the same as for conductivity. Temperature is ITS-90;;DAYD;#
 #;SSJT_QC;'DAYD';byte;WATER JACKET TEMPERATURE QUALITY FLAG;;;;0;9;%1d;;;;;Quality flag applied on water jacket temperature values;0;DAYD;#
 #;SSJT_STD;'DAYD';float;WATER JACKET TEMPERATURE STANDARD DEVIATION;;degree_Celsius;;-1.5;38;%6.3f;99999;;;0.001;Water jacket temperature standard deviation for data wich have been reduced (with a mean or median);;DAYD;#
 #;SSJT_CAL;'DAYD';float;WATER JACKET TEMPERATURE CALIBRATED;;degree_Celsius;;-1.5;38;%6.3f;99999;;;0.001;Water jacket temperature calibrated using linearization coefficients;;DAYD;#
 #;SSJT_FREQ;'DAYD';float;WATER JACKET SENSOR TEMPERATURE FREQUENCY;;hz;;0;20000;%9.3f;99999;;;0.001;Frequency of water jacket temperature sensor ;;DAYD;#
 #;SSJT_CALCOEF;'NCOEF_CAL';double;TEMPERATURE CALIBRATION COEFFICIENTS;;;;;;;99999;;;;Calibration coefficients are real value, date is in julian day from REFERENCE_DATE_TIME;;;#
-#;SSJT_CALCOEF_CONV;'NCOEF_CAL','STRING8';char;TEMPERATURE CALIBRATION COEFFICIENTS CONVENTION;;;;;;;NaN;;;;Calibration coefficient convention is an enumeration of coefficients name, ex: 'date','a','b','c','d','f0';;;#
+#;SSJT_CALCOEF_CONV;'NCOEF_CAL','STRING8';char;TEMPERATURE CALIBRATION COEFFICIENTS CONVENTION;;;;;;;;;;;Calibration coefficient convention is an enumeration of coefficients name, ex: 'date','a','b','c','d','f0';;;#
 #;SSJT_LINCOEF;'NCOEF_LIN';double;TEMPERATURE LINEAR DRIFT CORRECTION COEFFICIENTS;;;;;;;99999;;;;Calibration coefficients are real value, date is in julian day from REFERENCE_DATE_TIME;;;#
-#;SSJT_LINCOEF_CONV;'NCOEF_LIN','STRING8';char;TEMPERATURE LINEAR DRIFT CORRECTION COEFFICIENTS CONVENTION;;;;;;;NaN;;;;Calibration coefficient convention is an enumeration of coefficients name, ex: 'date','offset','slope';;;#
+#;SSJT_LINCOEF_CONV;'NCOEF_LIN','STRING8';char;TEMPERATURE LINEAR DRIFT CORRECTION COEFFICIENTS CONVENTION;;;;;;;;;;;Calibration coefficient convention is an enumeration of coefficients name, ex: 'date','offset','slope';;;#
 #;SSJT_ADJUSTED;'DAYD';float;WATER JACKET TEMPERATURE ADJUSTED;;degree_Celsius;;-1.5;38;%6.3f;99999;;;0.001;Adjusted water jacket temperature with external data (ARGO,CTD,XBT,...);;DAYD;#
 #;SSJT_ADJUSTED_ERROR;'DAYD';float;ERROR ON ADJUSTED WATER JACKET TEMPERATURE;;degree_Celsius;;-1.5;38;%6.3f;99999;;;0.001;Error on adjusted water jacket temperature with external data (ARGO,CTD, XBT,);;DAYD;#
 #;SSJT_ADJUSTED_QC;'DAYD';byte;WATER JACKET TEMPERATURE QUALITY FLAG;;;;0;9;%1d;;;;;Quality flag applied on adjusted water jacket temperature values;0;DAYD;#
@@ -74,9 +74,9 @@ $VARIABLES$
 #;SSTP_DEPH_MIN;'N1';float;MINIMUM DEPTH OF WATER INTAKE FOR TEMPERATURE MEASUREMENT;;meter;;0;100;%6.3f;99999;;;;;;;#
 #;SSTP_DEPH_MAX;'N1';float;MAXIMUM DEPTH OF WATER INTAKE FOR TEMPERATURE MEASUREMENT;;meter;;0;100;%6.3f;99999;;;;;;;#
 #;SSTP_CALCOEF;'NCOEF_CAL';double;TEMPERATURE CALIBRATION COEFFICIENTS;;;;;;;99999;;;;Calibration coefficients are real value, date is in julian day from REFERENCE_DATE_TIME;;;#
-#;SSTP_CALCOEF_CONV;'NCOEF_CAL','STRING8';char;TEMPERATURE CALIBRATION COEFFICIENTS CONVENTION;;;;;;;NaN;;;;Calibration coefficient convention is an enumeration of coefficients name, ex: 'date','a','b','c','d','f0';;;#
+#;SSTP_CALCOEF_CONV;'NCOEF_CAL','STRING8';char;TEMPERATURE CALIBRATION COEFFICIENTS CONVENTION;;;;;;;;;;;Calibration coefficient convention is an enumeration of coefficients name, ex: 'date','a','b','c','d','f0';;;#
 #;SSTP_LINCOEF;'NCOEF_LIN';double;TEMPERATURE LINEAR DRIFT CORRECTION COEFFICIENTS;;;;;;;99999;;;;Calibration coefficients are real value, date is in julian day from REFERENCE_DATE_TIME;;;#
-#;SSTP_LINCOEF_CONV;'NCOEF_LIN','STRING8';char;TEMPERATURE LINEAR DRIFT CORRECTION COEFFICIENTS CONVENTION;;;;;;;NaN;;;;Calibration coefficient convention is an enumeration of coefficients name, ex: 'date','offset','slope';;;#
+#;SSTP_LINCOEF_CONV;'NCOEF_LIN','STRING8';char;TEMPERATURE LINEAR DRIFT CORRECTION COEFFICIENTS CONVENTION;;;;;;;;;;;Calibration coefficient convention is an enumeration of coefficients name, ex: 'date','offset','slope';;;#
 #;SSTP_EXT;'DAYD_EXT';float;SEA SURFACE TEMPERATURE FROM EXTERNAL DATA;sea_surface_temperature;degree_Celsius;;-1.5;38;%6.3f;99999;;;0.001;Sea Surface Temperature (SST) from external data instrument (ARGO,CTD, XBT);;DAYD_EXT;#
 #;SSTP_EXT_QC;'DAYD_EXT';byte;SEA SURFACE TEMPERATURE FROM EXTERNAL DATA QUALITY FLAG;;;;0;9;%1d;;;;;Quality flag applied on external sea surface temperature data values;0;DAYD_EXT;#
 #;SSTP_EXT_TYPE;'DAYD_EXT','STRING4';char;TYPE OF EXTERNAL SEA SURFACE TEMPERATURE  DATA ORIGIN;;;;;;;;;;;ARGO,CTD,XBT,...;;DAYD_EXT;#
@@ -84,7 +84,7 @@ $VARIABLES$
 #;SSPS_EXT_QC;'DAYD_EXT';byte;SEA SURFACE SALINITY FROM EXTERNAL DATA QUALITY FLAG;;;;0;9;%1d;;;;;Quality flag applied on external sea surface salinity data values;0;DAYD_EXT;#
 #;SSPS_EXT_TYPE;'DAYD_EXT','STRING4';char;TYPE OF EXTERNAL SEA SURFACE SALINITY DATA ORIGIN;;;;;;;;;;;WS (Water Sample),ARGO,CTD,XBT,...;;DAYD_EXT;#
 #;SSPS_EXT_ANALDATE;'DAYD_EXT','STRING14';char;DATE OF WATER SAMPLE SURFACE SALINITY ANALYSIS;;;yyyymmddhhmmss;;;;;;;;Date of sea surface salinity water sample analysis;;DAYD_EXT;#
-#;SSPS_EXT_BOTTLE;'DAYD_EXT','STRING4';char;SEA SURFACE SALINITY BOTTLE NUMBER;;;;;;;NaN;;;;Number of sea surface salinity water sample;;DAYD_EXT;#
+#;SSPS_EXT_BOTTLE;'DAYD_EXT','STRING4';char;SEA SURFACE SALINITY BOTTLE NUMBER;;;;;;;;;;;Number of sea surface salinity water sample;;DAYD_EXT;#
 %
 $ATTRIBUTES$
 #;key__;name;conventions;uicontrolType;string;value;length;height;horizontalAlignment;comment;#

@netcdf_native/tsgqc_netcdf.m

+% tsgqc_netcdf.m
+% convert Excel file to csv
+
+d = dynaload('tsgqc_netcdf.xls')
+write( d, 'tsgqc_netcdf.csv')
\ No newline at end of file