[netcdf-java] compound attributes in NetCDF4 w/ NetCDF-java

• To: netcdf-java@xxxxxxxxxxxxxxxx
• Subject: [netcdf-java] compound attributes in NetCDF4 w/ NetCDF-java
• From: Tom Kunicki <tkunicki@xxxxxxxx>
• Date: Mon, 8 Feb 2010 12:33:08 -0600

Hi,

I'm having a problem parsing a NetCDF4 file in NetCDF-java.

I've using NetCDF 4.1 (C library with Java JNI bindings) in an attempt to 
produce a CDM compliant Station file in NetCDF4 format.  I want to put each 
stations observation in a compound field.  The file generates and parses using 
the ncgen and ncdump but I can't open it in NetCDF-Java 4.1.  I looks like 
there's trouble reading char[] or string fields in the compound attribute type. 
 The following stack trace is produced on read:

java.lang.NullPointerException
        at ucar.ma2.ArrayStructure.extractMemberArray(ArrayStructure.java:407)
        at ucar.nc2.iosp.hdf5.H5header.makeAttributes(H5header.java:587)
        at ucar.nc2.iosp.hdf5.H5header.makeVariable(H5header.java:1034)
        at ucar.nc2.iosp.hdf5.H5header.makeNetcdfGroup(H5header.java:388)
        at ucar.nc2.iosp.hdf5.H5header.read(H5header.java:182)
        at ucar.nc2.iosp.hdf5.H5iosp.open(H5iosp.java:108)
        at ucar.nc2.NetcdfFile.<init>(NetcdfFile.java:1325)
        at ucar.nc2.NetcdfFile.open(NetcdfFile.java:761)
        at ucar.nc2.NetcdfFile.open(NetcdfFile.java:395)
        at ucar.nc2.NetcdfFile.open(NetcdfFile.java:365)
        at ucar.nc2.NetcdfFile.open(NetcdfFile.java:352)
        at ucar.nc2.NetcdfFile.open(NetcdfFile.java:340)
        at edu.unidata.ucar.jni.NetCDFTest.main(NetCDFTest.java:147)

DIgging through the source it looks like 
ucar.nc2.iosp.hdf5.H5header.getNCtype(int hdfType, int size) is returning null 
for a char[] compound field type when trying to map the attributes to the 
compound fields.

With this be supported in the future?  Is there another way to assign 
attributes to compound type fields?

Here's the CDL I am trying to use (the observation dim will eventually be 
UNLIMITED):

netcdf gsod {
types:
  compound observation_type {
    int time ;
    float tempMean ;
    float tempMin ;
    float tempMax ;
  }; // observation_type
  compound observation_atts {
    char time(32) ;
    char tempMean(32) ;
    char tempMin(32) ;
    char tempMax(32) ;
  }; // observation_atts
dimensions:
        station = 2 ;
        observation = 3 ;
variables:
        int station_id(station) ;
        float station_description(station) ;
        float latitude(station) ;
                latitude:units = "degrees_north" ;
        float longitude(station) ;
                longitude:units = "degrees_east" ;
        float altitude(station) ;
                altitude:units = "feet" ;
                altitude:positive = "up" ;
        observation_type station_observations(station, observation) ;
                observation_atts station_observations:units = {{"days since 
1930-01-01 00 UTC"}, {"degF"}, {"degF"}, {"degF"}} ;

// global attributes:
                :cdm_datatype = "Stations" ;
                :stationDimension = "station" ;
                :observationDimension = "observation" ;
                :latitude_coordinate = "latitude" ;
                :longitude_coordinate = "longitude" ;
                :zaxis_coordinate = "altitude" ;
                :time_coordinate = "station_observations.time" ;
data:

 station_id = _, _ ;

 station_description = _, _ ;

 latitude = _, _ ;

 longitude = _, _ ;

 altitude = _, _ ;

 station_observations =
  {0, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 0, 0},
  {0, 0, 0, 0}, {0, 0, 0, 0}, {0, 0, 0, 0} ;
}


Thanks,

Tom Kunicki
Center for Integrated Data Analytics
U.S. Geological Survey
8505 Research Way
Middleton, WI  53562

• Follow-Ups:
  • Re: [netcdf-java] compound attributes in NetCDF4 w/ NetCDF-java
    • From: Ethan Davis