function values = getnc_s(cell_args)% getnc_s is called by getnc in the script or non-interactive case. The% arguments passed to getnc have been bundled into the cell named cell_args% which is passed to getnc_s. For documentation do a help on getnc.  %% AUTHOR:   J. V. Mansbridge, CSIRO%---------------------------------------------------------------------%%     Copyright (C), J.V. Mansbridge, 1992%     Commonwealth Scientific and Industrial Research Organisation%     $Id: getnc_s.m Mon, 03 Jul 2006 17:16:40 $% %--------------------------------------------------------------------% The function getnc_s calls the following external functions:%      check_nc.m, check_st.m, fill_att.m, get_dods_dds.m, loaddap or%      loaddods, mexnc.m, pos_cds.m, uncmp_nc.m, y_rescal.m.% getnc_s also calls the internal functions :%      remove_quotes, error_handle, parse_args, substitute_new.%% This function is called by: getnc.m% Written by Jim Mansbridge december 10 1991% In November 1998 some code was added to deal better with byte type data. Note% that any values greater than 127 will have 256 subtracted from them. This is% because on some machines (an SGI running irix6.2 is an example) values are% returned in the range 0 to 255. Note that in the fix the values less than 128% are unaltered and so we do not have to know whether the particular problem has% occurred or not; for machines where there is no problem no values will be% altered. This is applied to byte type attributes (like _FillValue) as well as% the variable values.% Check that there are the correct number of arguments. If the 6th, 7th% or 8th arguments are missing then they are set here.  If the 3rd, 4th% or 5th arguments are missing then their defaults will be set later% when we find out the dimensions of the variable.  It produces an error% if the bl_corner is set but the tr_corner is not.[file, varid, bl_corner, tr_corner, stride, order, change_miss, new_miss, ... squeeze_it, rescale_opts, err_opt] = parse_args(cell_args);% Set whether values will be automatically rescaled or not.if isnumeric(rescale_opts)  if ndims(rescale_opts) ~= 2    error('rescale_opts must be [], -1 or a 2 element vector');  end  len_rescale_opts = length(rescale_opts);  if len_rescale_opts == 2    [rescale_var, rescale_att] = y_rescal(rescale_opts);  elseif len_rescale_opts < 2    [rescale_var, rescale_att] = y_rescal;  else    error('rescale_opts must be [], -1 or a 2 element vector')  endelse   error('rescale_opts must be numeric');end% Set some constants.blank = abs(' ');% Do some initialisation.CSIRO_add_jar_file_maybe;try  [mex_name, full_name, desc_das, file_status, exe_name] = ...      choose_mexnc_opendap(file);catch  cdfid = -1000;  mess_str = lasterr;  rcode = -1001;  values = error_handle(cdfid, mess_str, rcode, err_opt);  returnend  switch mex_name case 'mexnc'    % I make mexnc calls to find the integers that specify the attribute  % types  nc_byte = mexnc('parameter', 'nc_byte'); %1  nc_char = mexnc('parameter', 'nc_char'); %2  nc_short = mexnc('parameter', 'nc_short'); %3  nc_long = mexnc('parameter', 'nc_long'); %4  nc_float = mexnc('parameter', 'nc_float'); %5  nc_double = mexnc('parameter', 'nc_double'); %6  % Set the value of imap.  Note that this is used simply as a  % placeholder in calls to vargetg - its value is never used.  imap = 0;  % Open the netcdf file.  [cdfid, rcode] = mexnc('ncopen', full_name, 'NC_NOWRITE');  if rcode ~= 0    mess_str = ['ncopen ' full_name];    values = error_handle(cdfid, mess_str, rcode, err_opt);    return  end  % Suppress all error messages from netCDF   [rcode] = mexnc('setopts', 0);  % Collect information about the cdf file.  [ndimens, nvars, ngatts, recdim, rcode] =  mexnc('ncinquire', cdfid);  if rcode < 0    mess_str = ['ncinquire: ' full_name];    values = error_handle(cdfid, mess_str, rcode, err_opt);    return  end  % Determine the netcdf id number for the required variable.  If varid is a  % string then an appropriate call to mexnc is used to convert it to the  % relevant integer. If varid is a number then it is decremented.  This is done  % because inqnc & getnc count the variables from 1 to nvars whereas the calls  % to the mexnc routines use c-type counting, from 0 to nvars - 1.  varid_old = varid;  if ischar(varid)    [varid, rcode] = mexnc('ncvarid', cdfid, varid_old);    if rcode < 0      mess_str = ['ncvarid: ' full_name ': variable named ' varid_old];      values = error_handle(cdfid, mess_str, rcode, err_opt);      return    end  else    varid = varid - 1;  end  % Check the value of varid  if varid < 0 | varid >= nvars    error([ 'getnc_s was passed varid = ' int2str(varid) ])  end  % Find out info about the variable, in particular find nvdims, the number of  % dimensions that the variable has.  [varnam, vartypv, nvdims, vdims, nvatts, rcode] = ...      mexnc('ncvarinq', cdfid, varid);  if rcode < 0    mess_str = ['ncvarinq: ' full_name ': variable named ' varid_old];    values = error_handle(cdfid, mess_str, rcode, err_opt);    return  end  % Turn off the rescaling of the byte type data because mexnc does not do this  % for variables anyway. The rescaling of the VALUES array will be done  % explicitly.  if vartypv == nc_byte    rescale_var = 0;    rescale_att = 0;  end    % Do checks on bl_corner, tr_corner and stride. The cases where  % bl_corner, tr_corner and stride are -1 or -1*ones(nvdims, 1) are checked  % for and handled here.  Note that stride may also be a scalar 1 when a  % vector may seem to be required.  if nvdims == 0    bl_corner = 1;    tr_corner = 1;    stride = 1;  else    if length(bl_corner) == 1      if bl_corner < 0	bl_corner = ones(nvdims, 1);	tr_corner = -1*ones(nvdims, 1);      end    elseif length(bl_corner) ~= nvdims      error('The bl_corner vector is the wrong length')    end        if length(stride) == 1      if stride < 0 | stride == 1	stride = ones(nvdims, 1);      end    elseif length(stride) == nvdims      ff = find(stride < 0);      if ~isempty(ff)	stride(ff) = 1;      end    else      error('The stride vector is the wrong length')    end  end    bl_corner_min = min(size(bl_corner));  bl_corner_max = max(size(bl_corner));  tr_corner_min = min(size(tr_corner));  tr_corner_max = max(size(tr_corner));  stride_min = min(size(stride));  stride_max = max(size(stride));  if bl_corner_min ~= tr_corner_min | bl_corner_min ~= stride_min | ...	bl_corner_max ~= tr_corner_max | bl_corner_max ~= stride_max    error('The sizes of bl_corner, tr_corner and stride do not agree')  end  % Set take_stride which specifies whether strides need to be taken.  if max(stride) > 1    take_stride = 1;  else    take_stride = 0;  end  % Make bl_corner, tr_corner, stride and order into column vectors.  bl_corner = bl_corner(:);  tr_corner = tr_corner(:);  stride = stride(:);  order = order(:);  % Check order  if length(order) == 1    if order == 1 % Special case where the netcdf variable is a vector      order = -1;    elseif order ~= -1 & order ~= -2      error('ERROR: if order is a scalar it must be -1 or -2')    end  else    if length(order) ~= nvdims      error('The order vector is the wrong length')    elseif sum(abs(sort(order) - (1:nvdims)')) ~= 0      error(['The order vector must be a rearrangement of the numbers 1 to ' ...	     num2str(nvdims)])    end  end  % Find out whether to return a scalar, vector or matrix.  It is here  % that bl_corner is decremented and edge is calculated so that the c-style  % conventions in mexnc will be followed. We also check whether any of the  % dimensions have zero length (this is certainly possible for the record  % dimension).  if nvdims == 0    edge = 1;  else    edge = ones(nvdims, 1);    for i = 1:nvdims      dimid = vdims(i);      [name, sizem, rcode] = mexnc('ncdiminq', cdfid, dimid);      if rcode < 0	mess_str = ['ncdiminq: ' full_name ': dimid = ' dimid];	values = error_handle(cdfid, mess_str, rcode, err_opt);	return      end            % Check for a zero length dimension (this is certainly possible for the      % record dimension). If so then just return an empty array.            if sizem == 0	mess_str = [varnam ' has dimension ' name ' which has zero length'];	values = error_handle(cdfid, mess_str, rcode, err_opt);	return      end            % Apply the deaults if required.            if bl_corner(i) < 0	bl_corner(i) = 1;	tr_corner(i) = sizem;	stride(i) = 1;      end      if tr_corner(i) < 0	tr_corner(i) = sizem;      end            % Check that bl_corner & tr_corner are in the correct range.  If they      % are then calculate edge.  Note that because I am using the      % matlab & fortran conventions for counting indices I must      % subtract 1 from the bl_corner and end point values.	      bl_corner(i) = bl_corner(i) - 1;      tr_corner(i) = tr_corner(i) - 1;      if bl_corner(i) >= sizem | tr_corner(i) < 0 | tr_corner(i) >= sizem	s = [ 'getnc_s was passed bl_corner = ' int2str(bl_corner(i)+1) ...	      ' & tr_corner = ' int2str(tr_corner(i)+1) ...	      ' for dimension ' name ];	error(s)      end      if stride(i) > 1	edge(i) = fix( ( tr_corner(i) - bl_corner(i) )/stride(i) ) + 1;      else	edge(i) = tr_corner(i) - bl_corner(i) + 1;      end    end  end  num_edge = length( find(edge ~= 1) );  if num_edge == 0    % Get the scalar.    [values, rcode] = mexnc('ncvarget1', cdfid, varid, bl_corner, rescale_var);    if rcode < 0      mess_str = ['ncvarget1: ' full_name ': varid =  ' varid];      values = error_handle(cdfid, mess_str, rcode, err_opt);      return    end        % Do possible byte correction.        if vartypv == nc_byte      ff = find(values > 127);      if ~isempty(ff)	values(ff) = values(ff) - 256;      end    end  else    % Get the full hyperslab and return it as an array of the appropriate    % dimensions.  Note that we must allow for the C-type notation where    % the fastest changing index is the last mentioned.    if take_stride      [values, rcode] = mexnc('ncvargetg', cdfid, varid, bl_corner, edge, ...			      stride, imap, rescale_var);      if rcode < 0	mess_str = ['ncvargetg: ' full_name ': varid =  ' varid];	values = error_handle(cdfid, mess_str, rcode, err_opt);	return      end    else      [values, rcode] = mexnc('ncvarget', cdfid, varid, bl_corner, edge, ...			      rescale_var);      if rcode < 0	mess_str = ['ncvarget: ' full_name ': varid =  ' varid];	values = error_handle(cdfid, mess_str, rcode, err_opt);	return      end    end        % Do possible byte correction.        if vartypv == nc_byte      ff = find(values > 127);      if ~isempty(ff)	values(ff) = values(ff) - 256;      end    end    % Permute the array as required.  Note that the default behaviour is to    % reverse the order of the indices to map between the matlab and C    % conventions for ordering indices. If order is a vector then this    % reversing must be done before the permutation using the vector.        if length(order) == 1      if order == -1	values = permute(values, (ndims(values):-1:1));      end    else      values = permute(values, (ndims(values):-1:1));      values = permute(values, order);    end        % Squeeze the array if required.        if squeeze_it      values = squeeze(values);    end    % After squeezing a vector may be a row or column vector and so    % turn any row vector into a column vector for consistency.        if ndims(values) == 2      [m_temp, n_temp] = size(values);      if m_temp == 1	values = values(:);      end    end  end  % If the missing values are to be replaced then do it here.  scalef = [];  addoff = [];  if change_miss ~= 1    % Find any scale factors or offsets.    attstring = fill_att(cdfid, varid, nvatts);    if rescale_att == 1 | vartypv == nc_byte      pos = check_st('scale_factor', attstring, nvatts);      if pos > 0	[scalef, rcode] = mexnc('ncattget', cdfid, varid, 'scale_factor');	if rcode < 0	  mess_str = ['ncattget: ' full_name ': varid =  ' varid ...		      ': scale_factor'];	  values = error_handle(cdfid, mess_str, rcode, err_opt);	  return	end      end      pos = check_st('add_offset', attstring, nvatts);      if pos > 0	[addoff, rcode] = mexnc('ncattget', cdfid, varid, 'add_offset');	if rcode < 0	  mess_str = ['ncattget: ' full_name ': varid =  ' varid ...		      ': add_offset'];	  values = error_handle(cdfid, mess_str, rcode, err_opt);	  return	end      end    end    % check for missing values.  Note that a    % missing value is taken to be one less than valid_min, greater than    % valid_max or 'close to' _FillValue or missing_value.    % Note 1: valid_min and valid_max may be specified by the attribute    % valid_range and if valid_range exists than the existence of    % valid_min and valid_max is not checked.    % Note 2: a missing value must be OUTSIDE the valid range to be    % recognised.    % Note 3: a range does not make sense for character arrays.    % Note 4: By 'close to' _FillValue I mean that an integer or character    % must equal _FillValue and a real must be in the range    % 0.99999*_FillValue tp 1.00001*_FillValue.  This allows real*8     % rounding errors in moving the data from the netcdf file to matlab;    % these errors do occur although I don't know why given that matlab    % works in double precision.