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

Dear John,

I found the problem. It was the old netcdf-4.0 in my class path 
additionally to the new one. Sorry for your troubles and thanks for the 
help.

Best regards
Eleonora


Am 20.12.2010 20:17, schrieb John Caron:
> Hi Eleonora :
>
> the latest version of 4.2 from here
>
> http://www.unidata.ucar.edu/software/netcdf-java/
>
> should read this file.
>
>
> On 12/20/2010 8:12 AM, Eleonora Lypovetska wrote:
> > Hi,
> >
> > I tried the release 4.1 release (4.1.20100721.1910)  you mentioned. 
> > Unfortunately I cannot open a HDF5 file any more at all:
> >
> > Caused by: java.io.IOException: Cant read 
> > ...\import\radar\hdf5\in\nordrad.scan-dbz-0_5.kkr.20100327T170000Z.data: 
> > not a valid NetCDF file.
> >     at ucar.nc2.NetcdfFile.open(NetcdfFile.java:759)
> >     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 
> > org.ninjoworkstation.data.hdf5.Hdf5Reader.readData(Hdf5Reader.java:34)
> >     ... 7 more
> >
> >
> > Could you please have a look at the problem. Did you try to open a 
> > HDF5 file Hermann had a problem with.
> >
> > Thanks in advance
> > Eleonora
> >
> >
> > Am 20:59, schrieb John Caron:
> > > Hi Hermann:
> > >
> > > Ive fixed this in the latest 4.1 release (4.1.20100721.1910)
> > >
> > > It will be in the 4.2 release in a day or two.
> > >
> > > please let me know if you see any more problems.
> > >
> > > John
> > >
> > > On 7/20/2010 12:49 PM, John Caron wrote:
> > > > Hi Hermann and HDF5/Netcdf4 users:
> > > >
> > > > Ok, I think I have a fix for this. It is a bug in all versions in 
> > > > reading the symbol table when sizeOffsets = 4. Im amazed we havent 
> > > > seen this before, but likely the default is sizeOffsets = 8. I dont 
> > > > see any way this could "silently fail" so if your hdf5 files are 
> > > > reading without an exception, you should be ok.
> > > >
> > > > Anyway, I will get a release out with this fix asap.
> > > >
> > > > Thanks for reporting!
> > > >
> > > >
> > > >
> > > > On 7/15/2010 10:39 AM, 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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