netCDF Import to Mathematica, perhaps via HDF or HDF5 file

[Mark Hadfield]

James D. Hanson wrote:
>
> Do anyone know of a netCDF to HDF or HDF5 file converter?
I am dealing with something like this at the moment (but for Tecplot, 
not Mathematica) and the best way I have found so far is a combination 
of the netCDF ncdump utility and the HDF4 ncgen utility.

To elaborate somewhat, the netCDF library from Unidata contains 
utilities ncdump and ncgen to convert between the netCDF binary format 
and a text format called CDL.  The HDF4 library from NCSA also contains 
utilities ncdump and ncgen that do the same thing, but this time the 
underlying binary file format is HDF. It is a little tricky to install 
both, because by default the HDF commands will overwrite the netCDF 
commands or vice versa. On my system I've modified the insttallation 
process and called the HDF versions hdf_ncdump and hdf_ncgen.

The procedure is

    ncdump -l 80 foo.nc > foo.cdl
    # Edit CDL file with a text editor to work around various
    # problems encountered by hdf_ncgen
    hdf_ncgen -b -o foo.hdf foo.cdl

The need to edit the CDL file arises because hdf_ncgen cannot read 
everything that ncdump can write. The "-l 80" option above is intended 
to work around one of hdf_ncgen's limitations: a maximum line length of 
80 characters. When hdf_ncgen encounters a problem, it halts and prints 
out the relevant line number in the CDL file. The error message will not 
necessarily make much sense, but when you go to that line you will 
usually find that problem is reasonably obvious and easily corrected. In 
the past I have had to strip out attributes containing zero-length 
strings, remove netCDF fill values (represented in CDL as an underscore) 
and replace NaNs with finite floating-point values. (NaNs are illegal in 
netCDF anyway, though some platforms allow them.)

This is all rather klunky and I would be keen to know of a better way.

There is a Windows executable called ncdf2hdf from Fortner Software 
(RIP) that does the conversion. However the HDF files that it generates 
seem to lack some of the structure that is available in the ones 
produced by the route above, and this affects the way they look to the 
Tecplot import filter.

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