Re: [netcdf-java] Reading HDF5 files with OPERA radar data by SMHI

• To: Hermann Schwarting <Hermann.Schwarting@xxxxxx>
• Subject: Re: [netcdf-java] Reading HDF5 files with OPERA radar data by SMHI
• From: John Caron <caron@xxxxxxxxxxxxxxxx>
• Date: Fri, 16 Jul 2010 06:25:39 -0600

Hi Hermann:

It looks like a bug in the HDF5 file format. Im working on a work-around, ill 
let you know when i have something. Thanks for reporting.

John

Hermann Schwarting wrote:

Hi,

I'm trying to use netcdf-java for reading HDF5 files with radar data.
As simple test program using NetcdfFile.open() was used.  I have tried
the sample files found on [ http://www.knmi.nl/opera/odc.html ]. The
files by SMHI fail with this stack trace:

java.lang.IllegalStateException: DataObject doesnt start with OHDR
    at ucar.nc2.iosp.hdf5.H5header$DataObject.<init>(H5header.java:1904)
    at ucar.nc2.iosp.hdf5.H5header$DataObject.<init>(H5header.java:1818)
    at ucar.nc2.iosp.hdf5.H5header.getDataObject(H5header.java:1668)
    at ucar.nc2.iosp.hdf5.H5header.access$800(H5header.java:64)

at ucar.nc2.iosp.hdf5.H5header$DataObjectFacade.<init>(H5header.java:1711)

    at ucar.nc2.iosp.hdf5.H5header.readGroupOld(H5header.java:3545)
    at ucar.nc2.iosp.hdf5.H5header.access$1000(H5header.java:64)
    at ucar.nc2.iosp.hdf5.H5header$H5Group.<init>(H5header.java:1787)
    at ucar.nc2.iosp.hdf5.H5header$H5Group.<init>(H5header.java:1756)
    at ucar.nc2.iosp.hdf5.H5header.readSuperBlock1(H5header.java:266)
    at ucar.nc2.iosp.hdf5.H5header.read(H5header.java:171)
    at ucar.nc2.iosp.hdf5.H5iosp.open(H5iosp.java:108)
    at ucar.nc2.NetcdfFile.<init>(NetcdfFile.java:1333)
    at ucar.nc2.NetcdfFile.open(NetcdfFile.java:769)
    at ucar.nc2.NetcdfFile.open(NetcdfFile.java:403)
    at ucar.nc2.NetcdfFile.open(NetcdfFile.java:373)
    at ucar.nc2.NetcdfFile.open(NetcdfFile.java:360)
    at ucar.nc2.NetcdfFile.open(NetcdfFile.java:348)
    at HDF5Test.main(HDF5Test.java:16)

Files by other institutions can be read without error messages. HDFView
and h5dump don’t seem to have problems with SMHI’s files. I have tried
netcdf-java 4.0, 4.1, and 4.2.

Do you have more insight into the HDF5 format an can comment on this
issue?

Please find attached the test program used and detailed debug output
for one of the files.

Thanks in advance,
Hermann


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• References:
  • [netcdf-java] Reading HDF5 files with OPERA radar data by SMHI
    • From: Hermann Schwarting