pp2nc

 Child function to call the convsh program to convert the obscure pp
 format to a sensible NetCDF which we can more easily read.

 This requires the convsh and xconv functions available from:

   http://badc.nerc.ac.uk/help/software/xconv/index.html

 Follow the installation instructions for your platform (Linux, Windows,
 Mac etc.) prior to running this function.

 This requires the pp2nc.tcl script in the utilities subdirectory of the
 MATLAB fvcom-toolbox.

 INPUT:
   file - cell array of PP file(s) to convert to NetCDF. Include
       sub-directory in path, can include full path name or path relative
       to working directory.
   convsh - the path to the convsh binary (NB this can't contain spaces).
   pp2nc_tcl - the path to the TCL script (in the utilities fvcom-toolbox
       file).

 OUTPUT:
   NetCDF files in the same directory as the input PP files but with a .nc
   file extension.

 USAGE (PWC): Convert the PP files to NetCDF.
   files = {'/path/to/file1.pp', '/path/to/file2.pp', '/path/to/file3.pp'};
   convsh = '/users/modellers/pica/bin/convsh';
   tcl = '/users/modellers/pica/MATLAB/fvcom-toolbox/utilities/pp2nc.tcl';
   pp2nc(files, convsh, tcl);

 Author(s):
    Pierre Cazenave (Plymouth Marine Laboratory)
    Karen Amoudry (National Oceanography Centre, Liverpool)
    Judith Wolf (National Oceanography Centre, Liverpool)

 PWC Revision history:
   2013-06-24 Extracted version from the get_MetUM_forcing.m script and
   set as standalone version.

 KJA Revision history:
   2013-06-25 Added support for paths with spaces in. Also added support
   for creation of NetCDF files in Windows (convsh will only take a .nc
   filename, not a whole path).

 JW Revision history:
   2013-08-13 Problem for paths with spaces in, especially using Windows
   Add backslash after pwd to define directory
   Make sure convsh is pointing to right path (cannot use paths with
   spaces in command, use relative paths from starting directory,
   put output file in same working directory

0001 function pp2nc(file, convsh, pp2nc_tcl)
0002 % Child function to call the convsh program to convert the obscure pp
0003 % format to a sensible NetCDF which we can more easily read.
0004 %
0005 % This requires the convsh and xconv functions available from:
0006 %
0007 %   http://badc.nerc.ac.uk/help/software/xconv/index.html
0008 %
0009 % Follow the installation instructions for your platform (Linux, Windows,
0010 % Mac etc.) prior to running this function.
0011 %
0012 % This requires the pp2nc.tcl script in the utilities subdirectory of the
0013 % MATLAB fvcom-toolbox.
0014 %
0015 % INPUT:
0016 %   file - cell array of PP file(s) to convert to NetCDF. Include
0017 %       sub-directory in path, can include full path name or path relative
0018 %       to working directory.
0019 %   convsh - the path to the convsh binary (NB this can't contain spaces).
0020 %   pp2nc_tcl - the path to the TCL script (in the utilities fvcom-toolbox
0021 %       file).
0022 %
0023 % OUTPUT:
0024 %   NetCDF files in the same directory as the input PP files but with a .nc
0025 %   file extension.
0026 %
0027 % USAGE (PWC): Convert the PP files to NetCDF.
0028 %   files = {'/path/to/file1.pp', '/path/to/file2.pp', '/path/to/file3.pp'};
0029 %   convsh = '/users/modellers/pica/bin/convsh';
0030 %   tcl = '/users/modellers/pica/MATLAB/fvcom-toolbox/utilities/pp2nc.tcl';
0031 %   pp2nc(files, convsh, tcl);
0032 %
0033 % Author(s):
0034 %    Pierre Cazenave (Plymouth Marine Laboratory)
0035 %    Karen Amoudry (National Oceanography Centre, Liverpool)
0036 %    Judith Wolf (National Oceanography Centre, Liverpool)
0037 %
0038 % PWC Revision history:
0039 %   2013-06-24 Extracted version from the get_MetUM_forcing.m script and
0040 %   set as standalone version.
0041 %
0042 % KJA Revision history:
0043 %   2013-06-25 Added support for paths with spaces in. Also added support
0044 %   for creation of NetCDF files in Windows (convsh will only take a .nc
0045 %   filename, not a whole path).
0046 %
0047 % JW Revision history:
0048 %   2013-08-13 Problem for paths with spaces in, especially using Windows
0049 %   Add backslash after pwd to define directory
0050 %   Make sure convsh is pointing to right path (cannot use paths with
0051 %   spaces in command, use relative paths from starting directory,
0052 %   put output file in same working directory
0053 
0054 nf = length(file);
0055 
0056 for ff = 1:nf
0057     if ~isnan(file{ff})
0058         if exist(file{ff}, 'file') ~= 2
0059             error('File %s not found', file)
0060         end
0061 
0062         [pathname, filename, ext] = fileparts(file{ff});
0063         out = [filename, '.nc'];
0064 %        infile =  [filename, '.pp'];    % JW added clear definition of input file
0065 %        goback = pwd;
0066 %        goback = strcat(pwd,'\')       % JW - add backslash (for Windows),
0067 %        to define directory
0068 %        cd(pathname)
0069         % Warn if it failed for some reason
0070         [res, msg] = system([convsh, ' "', pp2nc_tcl, '" -i "', file{ff}, '" -o "', out, '"']);
0071 %        [res, msg] = system([convsh, ' "', pp2nc_tcl, '" -i "', infile, '" -o "', out, '"']);
0072 %        cd(goback)
0073         if res ~= 0
0074             warning('Conversion of %s to NetCDF failed. Conversion output:\n%s', file{ff}, msg)
0075         end
0076     end
0077 end