Thank you,
A temporary hack
path = path.replaceAll(" ", "_");
now works for me.
there are also troubles reading some NetCDF4 files (I posted the question
in November 2014):
http://www.unidata.ucar.edu/support/help/MailArchives/netcdf-java/msg02075.html
Initially I thought that was NCO issue since I get this error (see below)
after applying ncks for chunking NetCDF3 file and get NetCDF4 as output.
NetCDF-Java output:
[ucar.nc2.NetcdfFile] DEBUG Using IOSP ucar.nc2.iosp.hdf5.H5iosp
[ucar.nc2.iosp.hdf5.H5header] ERROR bad version 72 at filePos 22386
But it could be the NetCDF-Java library issue: Charlie worked hard on the
discovering the problem with NCO but seems like we were digging at the
wrong direction.
Any ideas?
2015-01-13 23:59 GMT+03:00 Ryan May <rmay@xxxxxxxx>:
> Hi,
>
> So in discussions with John Caron, the change of spaces to underscores is
> intentional. From our perspective, supporting spaces for identifiers for
> the CDM was just too much trouble for too little gain, so in mapping the
> HDF5 data model to the CDM, spaces get converted.
>
> One solution (as I suggested earlier) is to convert all spaces in the hard
> coded paths you're using to underscores. The other is to walk the groups in
> the file to find the actual group name from the HDF5 file.
>
> Ryan
>
> On Tue, Jan 13, 2015 at 9:03 AM, Joe Lee <hyoklee@xxxxxxxxxxxx> wrote:
>
>> Yes, I had the same issue when I was writing Minecraft World map
>> generation code from HDF-EOS [1]:
>>
>>
>>
>> nc = NetcdfDataset.openFile(filename, null);
>>
>> // Variable v = nc.findVariable("l3m_data"); // for Aquarius
>> product
>>
>> // Please note that "Data Fields" have underscore. HDF5 does
>> not have it.
>>
>> // Variable v =
>> nc.findVariable("/HDFEOS/GRIDS/ColumnAmountO3/Data_Fields/TerrainHeight");
>>
>> Variable v = nc.findVariable(
>> "/Northern_Hemisphere/Data_Fields/Extent");
>>
>> Variable v2 = nc.findVariable(
>> "/Southern_Hemisphere/Data_Fields/Extent");
>>
>>
>>
>>
>>
>> [1]
>> https://github.com/hyoklee/Glowstone/blob/master/src/main/java/net/glowstone/GlowWorld.java
>>
>>
>>
>>
>>
>> *From:* netcdf-java-bounces@xxxxxxxxxxxxxxxx [mailto:
>> netcdf-java-bounces@xxxxxxxxxxxxxxxx] *On Behalf Of *Ryan May
>> *Sent:* Tuesday, January 13, 2015 9:44 AM
>> *To:* Antonio Rodriges
>> *Cc:* netcdf-java@xxxxxxxxxxxxxxxx
>> *Subject:* Re: [netcdf-java] Problem reading HDF files
>>
>>
>>
>> (Sending again to make sure the list gets it).
>>
>>
>>
>> Antonio,
>>
>>
>>
>> Thanks for the information, and sorry it's taken so long to get back--I
>> blame the holidays and the AMS meeting.
>>
>>
>>
>> I've found the cause of the problem: the "Data Fields" group in the hdf5
>> file is getting converted in netcdf-java to "Data_Fields". So as a
>> workaround, you could get it working by making sure any spaces in the path
>> variable (or at least the groups) are replaced with "_". I still need to
>> find out if this is deliberate behavior in netcdf-java for some reason, or
>> just a bug.
>>
>>
>>
>> On Tue, Dec 30, 2014 at 1:13 PM, Antonio Rodriges <antonio.rrz@xxxxxxxxx>
>> wrote:
>>
>> Ryan,
>>
>> The path is
>>
>> /HDFEOS/GRIDS/ColumnAmountNO2/Data
>> Fields//ColumnAmountNO2TropCloudScreened
>>
>> and the HDF5 file is attached. There are also HDF4 files with the same
>> problem
>>
>> This worked fine under netcdf-4.2 but now I need new features
>> introduced in later versions so I consider switching to 4.3 at least
>> or higher
>>
>>
>> 2014-12-30 20:57 GMT+03:00 Ryan May <rmay@xxxxxxxx>:
>> > Antonio,
>> >
>> > It would be helpful to see a sample file as well as the value of the
>> path
>> > variable in order to understand the problem.
>> >
>> > Ryan
>> >
>> > On Sun, Dec 28, 2014 at 9:25 AM, Antonio Rodriges <
>> antonio.rrz@xxxxxxxxx>
>> > wrote:
>> >>
>> >> Hello,
>> >>
>> >> the code
>> >>
>> >> String path = groupInFile + SUBDATASETS_GROUP_DELIMITER +
>> >> nameInGroup;
>> >> Variable findVariable = file.findVariable(path);
>> >>
>> >> Worked with netcdf-4.2 Java lib but does not with netcdf-4.3 and 4.5
>> >> (returns findVariable = null)
>> >> What is the problem?
>> >>
>> >> _______________________________________________
>> >> netcdf-java mailing list
>> >> netcdf-java@xxxxxxxxxxxxxxxx
>> >> For list information or to unsubscribe, visit:
>> >> http://www.unidata.ucar.edu/mailing_lists/
>> >>
>> >
>> >
>> >
>> > --
>> > Ryan May
>> > Software Engineer
>> > UCAR/Unidata
>> > Boulder, CO
>>
>>
>>
>>
>>
>> --
>>
>> Ryan May
>>
>> Software Engineer
>>
>> UCAR/Unidata
>>
>> Boulder, CO
>>
>
>
>
> --
> Ryan May
> Software Engineer
> UCAR/Unidata
> Boulder, CO
>
