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



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 donât seem to have problems with SMHIâs 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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