[netcdf-java] Issue writing Netcdf4 unsigned int

• To: "netcdf-java@xxxxxxxxxxxxxxxx" <netcdf-java@xxxxxxxxxxxxxxxx>
• Subject: [netcdf-java] Issue writing Netcdf4 unsigned int
• From: "Gangl, Michael E (398H)" <Michael.E.Gangl@xxxxxxxxxxxx>
• Date: Thu, 2 Mar 2017 00:26:10 +0000

Hi all,

I’ve got a program that takes multiple files (HDF, NetCDF) and merges them into 
a single file. While this works for most files I’ve encountered, there is an 
issue I run into when I’m writing unsigned integer types (unsigned bytes are ok 
for now):

java.io.IOException: Unknown userType == 9
                at 
ucar.nc2.jni.netcdf.Nc4Iosp.readDataSection(Nc4Iosp.java:1578) 
~[netcdf4-4.6.8.jar:4.6.8]
                at ucar.nc2.jni.netcdf.Nc4Iosp.readData(Nc4Iosp.java:1488) 
~[netcdf4-4.6.8.jar:4.6.8]
                at ucar.nc2.NetcdfFile.readData(NetcdfFile.java:2020) 
~[cdm-4.6.8.jar:4.6.8]
                at ucar.nc2.Variable.reallyRead(Variable.java:913) 
~[cdm-4.6.8.jar:4.6.8]
                at ucar.nc2.Variable._read(Variable.java:898) 
~[cdm-4.6.8.jar:4.6.8]
                at ucar.nc2.Variable.read(Variable.java:709) 
~[cdm-4.6.8.jar:4.6.8]
                at ucar.nc2.Variable.read(Variable.java:655) 
~[cdm-4.6.8.jar:4.6.8]
                at 
gov.nasa.jpl.podaac.subsetter.netcdf.NetCDFSubsetter.mergeNetCDFFiles(NetCDFSubsetter.java:780)
 [l2ss.jar:?]
                at 
gov.nasa.jpl.podaac.queue.SubsettingJobIT.testMergeAquarius(SubsettingJobIT.java:226)
 [test-classes/:?]

Looking through some of the open source code, I don’t know why userType == 9 is 
giving a problem, as that should be the unsigned int type. I’m getting this 
issue when I’m reading out an array of the data:

Array copyTo = newVar.read(origin, arrayFrameSize);

The header of the variable I’m writing _to_ causing the error is as follows:

group: Aquarius_Flags {
  dimensions:
                phony_dim_13 = 178 ;
                phony_dim_14 = 3 ;
                phony_dim_15 = 2 ;
                phony_dim_16 = 12 ;
                phony_dim_17 = 4 ;
  variables:
…
                uint radiometer_flags(subset_index, phony_dim_13, phony_dim_14, 
phony_dim_17) ;
                                radiometer_flags:Cold_water = "COLDWATER" ;
                                
radiometer_flags:Direct_solar_flux_contamination = "FLUXD" ;
                                radiometer_flags:Galactic_contamination = 
"GALACTIC" ;
                                radiometer_flags:Land_contamination = "LAND" ;
                                radiometer_flags:Moon_contamination = "MOON" ;
                                radiometer_flags:Moon_Galaxy_contamination = 
"REFL_1STOKES" ;
                                radiometer_flags:Non-nominal_navigation = "NAV" 
;
                                radiometer_flags:Pointing_anomaly = "POINTING" ;
                                radiometer_flags:RFI_contamination = "RFI" ;
                                radiometer_flags:RFI_level = "TFTADIFF" ;
                                radiometer_flags:RFI_regional_contamination = 
"RFI_REGION" ;
                                radiometer_flags:Rain_in_main_beam = "RAIN" ;
                                
radiometer_flags:Reflected_solar_flux_contamination = "FLUXR" ;
                                radiometer_flags:Roughness_correction_failure = 
"ROUGH" ;
                                radiometer_flags:SA_overflow = "SAOVERFLOW" ;
                                radiometer_flags:Sea_ice_contamination = "ICE" ;
                                radiometer_flags:Solar_flare_contamination = 
"FLARE" ;
                                radiometer_flags:Sun_glint = "SUNGLINT" ;
                                radiometer_flags:Tb_consistency = "TBCONS" ;
                                radiometer_flags:Unusual_brighness_temperature 
= "TEMP" ;
                                radiometer_flags:Wind_foam_contamination = 
"WIND" ;
                                radiometer_flags:long_name = "Radiometer data 
quality flags" ;
                                radiometer_flags:valid_max = 0U ;
                                radiometer_flags:valid_min = 0U ;
                                radiometer_flags:_Unsigned = "true" ;

Any help or guidance would be great. I’m using netcdf4-4.6.8 and netcdf 4.3.3.1

Thanks,
Mike

• Follow-Ups:
  • Re: [netcdf-java] Issue writing Netcdf4 unsigned int
    • From: Christian Ward-Garrison