[netcdf-java] Fw: Syntax for opening and reading a BUFR file

Hi All, 

I'm stumped on how to get data out of the nested sequence data in the attached 
BUFR file using NetCDF-Java. I can read all variables in the top-level Sequence 
(obs), but I can't get them out of the nested Sequence (seq1). I've tried all 
the method calls I can think of. Any suggestions or help would be greatly 
appreciated? Here's some pseudo code I've used to get the variable and try to 
read it.:


netcdf = //  Open the BUFR file
seq1 = netcdf.findVariable("obs.seq1);

// --- METHOD 1L Try using the recommended structure iterator
i = seq1.getStructureIterator();
while (i.hasNext()) {
    v = i.next();
    d = v.getArray();
}

//  METHOD 1 OUTPUT
2013-05-14 14:55:24,154 [main] WARN  ucar.nc2.dataset.StructureDS  - 
StructureDataDS.convert Cant find member time
2013-05-14 14:55:24,154 [main] WARN  ucar.nc2.dataset.StructureDS  - 
StructureDataDS.convert Cant find member WMO block number
2013-05-14 14:55:24,154 [main] WARN  ucar.nc2.dataset.StructureDS  - 
StructureDataDS.convert Cant find member WMO station number
2013-05-14 14:55:24,155 [main] WARN  ucar.nc2.dataset.StructureDS  - 
StructureDataDS.convert Cant find member Type of station
2013-05-14 14:55:24,155 [main] WARN  ucar.nc2.dataset.StructureDS  - 
StructureDataDS.convert Cant find member Year
2013-05-14 14:55:24,155 [main] WARN  ucar.nc2.dataset.StructureDS  - 
StructureDataDS.convert Cant find member Month
2013-05-14 14:55:24,155 [main] WARN  ucar.nc2.dataset.StructureDS  - 
StructureDataDS.convert Cant find member Day
2013-05-14 14:55:24,155 [main] WARN  ucar.nc2.dataset.StructureDS  - 
StructureDataDS.convert Cant find member Hour
2013-05-14 14:55:24,155 [main] WARN  ucar.nc2.dataset.StructureDS  - 
StructureDataDS.convert Cant find member Minute
2013-05-14 14:55:24,155 [main] WARN  ucar.nc2.dataset.StructureDS  - 
StructureDataDS.convert Cant find member Latitude (coarse accuracy)
2013-05-14 14:55:24,155 [main] WARN  ucar.nc2.dataset.StructureDS  - 
StructureDataDS.convert Cant find member Longitude (coarse accuracy)
2013-05-14 14:55:24,155 [main] WARN  ucar.nc2.dataset.StructureDS  - 
StructureDataDS.convert Cant find member Height of station
2013-05-14 14:55:24,155 [main] WARN  ucar.nc2.dataset.StructureDS  - 
StructureDataDS.convert Cant find member Short station or site name
2013-05-14 14:55:24,155 [main] WARN  ucar.nc2.dataset.StructureDS  - 
StructureDataDS.convert Cant find member Type of measuring equipment used
2013-05-14 14:55:24,155 [main] WARN  ucar.nc2.dataset.StructureDS  - 
StructureDataDS.convert Cant find member Time significance
2013-05-14 14:55:24,155 [main] WARN  ucar.nc2.dataset.StructureDS  - 
StructureDataDS.convert Cant find member Time period or displacement
2013-05-14 14:55:24,156 [main] WARN  ucar.nc2.dataset.StructureDS  - 
StructureDataDS.convert Cant find member seq1
Java exception occurred:
java.lang.NullPointerException
at ucar.nc2.dataset.StructureDS.convert(StructureDS.java:445)
at ucar.nc2.dataset.SequenceDS$StructureDataConverter.next(SequenceDS.java:78)



// --- METHOD 2: Try calling read
vt = netcdf.findVariable('obs.seq1.Virtual temperature);
vt.read();

// METHOD 2 OUTPUT
java.lang.ClassCastException: ucar.ma2.ArrayObject$D1 cannot be cast to 
ucar.ma2.ArrayStructure
at ucar.nc2.Variable.reallyRead(Variable.java:854)
at ucar.nc2.Variable._read(Variable.java:831)
at ucar.nc2.Variable.read(Variable.java:709)
at ucar.nc2.dataset.VariableDS.reallyRead(VariableDS.java:518)
at ucar.nc2.dataset.VariableDS._read(VariableDS.java:502)
at ucar.nc2.Variable.read(Variable.java:709)




The CDL is:

netcdf 5900.20030601.rass {
 types:
  enum Type of station { 'Automatic' = 0, 'Manned' = 1, 'Hybrid: both manned 
and automatic' = 2, 'Missing value' = 3};
  enum Type of measuring equipment used { 'Pressure Instrument associated with 
wind measuring equipment' = 0, 'Optical theodolite' = 1, 'Radio theodolite' = 
2, 'Radar' = 3, 'VLF-Omega' = 4, 'Loran C' = 5, 'Wind profiler' = 6, 'Satellite 
navigation' = 7, 'Radio-acoustic Sounding System (RASS)' = 8, 'Sodar' = 9, 
'Pressure instrument associated with wind measuring equipment but pressure 
element failed during ascent' = 14, 'Missing value' = 15};
  enum Time significance { 'Time series' = 1, 'Time averaged (see Note 1)' = 2, 
'Accumulated' = 3, 'Forecast' = 4, 'Forecast time series' = 5, 'Forecast time 
averaged' = 6, 'Forecast accumulated' = 7, 'Ensemble mean (see Note 2)' = 8, 
'Ensemble mean time series' = 9, 'Ensemble mean time averaged' = 10, 'Ensemble 
mean accumulated' = 11, 'Ensemble mean forecast' = 12, 'Ensemble mean forecast 
time series' = 13, 'Ensemble mean forecast time averaged' = 14, 'Ensemble mean 
forecast accumulated' = 15, 'Start of phenomenon' = 17, 'Analysis' = 16, 'Start 
of orbit' = 19, 'Radiosonde launch time' = 18, 'Time of ascending node' = 21, 
'End of orbit' = 20, 'Monitoring period' = 23, 'Time of occurrence of wind 
shift' = 22, 'Nominal reporting time' = 25, 'Agreed time limit for report 
reception' = 24, 'First guess' = 27, 'Time of last known position' = 26, 'End 
of scan or time of ending' = 29, 'Start of scan' = 28, 'Missing value' = 31, 
'Time of occurrence' = 30};

 variables:

   Sequence {
     String time;
       :units = "minutes since 2003-06-01 00:00:00Z";
       :long_name = "time of observation";
       :_CoordinateAxisType = "Time";
     byte WMO block number;
       :missing_value = 127B; // byte
       :BUFR:TableB_descriptor = "0-1-1";
       :BUFR:bitWidth = 7; // int
     short WMO station number;
       :missing_value = 1023S; // short
       :standard_name = "station_WMO_id";
       :BUFR:TableB_descriptor = "0-1-2";
       :BUFR:bitWidth = 10; // int
     String Type of station;
       :units = "CodeTable 0-2-1";
       :BUFR:CodeTable = "Type of station (0-2-1)";
       :BUFR:TableB_descriptor = "0-2-1";
       :BUFR:bitWidth = 2; // int
     short Year;
       :units = "Year";
       :missing_value = 4095S; // short
       :BUFR:TableB_descriptor = "0-4-1";
       :BUFR:bitWidth = 12; // int
     byte Month;
       :units = "Month";
       :missing_value = 15B; // byte
       :BUFR:TableB_descriptor = "0-4-2";
       :BUFR:bitWidth = 4; // int
     byte Day;
       :units = "Day";
       :missing_value = 63B; // byte
       :BUFR:TableB_descriptor = "0-4-3";
       :BUFR:bitWidth = 6; // int
     byte Hour;
       :units = "Hour";
       :missing_value = 31B; // byte
       :BUFR:TableB_descriptor = "0-4-4";
       :BUFR:bitWidth = 5; // int
     byte Minute;
       :units = "Minute";
       :missing_value = 63B; // byte
       :BUFR:TableB_descriptor = "0-4-5";
       :BUFR:bitWidth = 6; // int
     float Latitude (coarse accuracy);
       :units = "degrees_north";
       :_CoordinateAxisType = "Lat";
       :BUFR:TableB_descriptor = "0-5-2";
       :BUFR:bitWidth = 15; // int
     float Longitude (coarse accuracy);
       :units = "degrees_east";
       :_CoordinateAxisType = "Lon";
       :BUFR:TableB_descriptor = "0-6-2";
       :BUFR:bitWidth = 16; // int
     float Height of station;
       :units = "m";
       :_CoordinateAxisType = "Height";
       :BUFR:TableB_descriptor = "0-7-1";
       :BUFR:bitWidth = 15; // int
     char Short station or site name(5);
       :standard_name = "station_id";
       :BUFR:TableB_descriptor = "0-1-18";
       :BUFR:bitWidth = 40; // int
     String Type of measuring equipment used;
       :units = "CodeTable 0-2-3";
       :BUFR:CodeTable = "Type of measuring equipment used (0-2-3)";
       :BUFR:TableB_descriptor = "0-2-3";
       :BUFR:bitWidth = 4; // int
     String Time significance;
       :units = "CodeTable 0-8-21";
       :BUFR:CodeTable = "Time significance (0-8-21)";
       :BUFR:TableB_descriptor = "0-8-21";
       :BUFR:bitWidth = 5; // int
     float Time period or displacement;
       :units = "Second";
       :BUFR:TableB_descriptor = "0-4-26";
       :BUFR:bitWidth = 13; // int

     Sequence {
       short Height above station;
         :units = "m";
         :missing_value = 32767S; // short
         :_CoordinateAxisType = "Height";
         :BUFR:TableB_descriptor = "0-7-6";
         :BUFR:bitWidth = 15; // int
       float Virtual temperature;
         :units = "K";
         :BUFR:TableB_descriptor = "0-12-7";
         :BUFR:bitWidth = 12; // int
       byte Wind profiler quality control test results;
         :units = "FlagTable 0-25-34";
         :missing_value = 15B; // byte
         :BUFR:TableB_descriptor = "0-25-34";
         :BUFR:bitWidth = 4; // int
     } seq1;

   } obs(*);


 :history = "Direct read of BUFR data by CDM";
 :location = "5900.20030601.rass";
 :BUFR:edition = 3; // int
 :BUFR:categoryName = "Vertical soundings (other than satellite)";
 :BUFR:category = 2; // int
 :BUFR:subCategory = 0; // int
 :BUFR:localSubCategory = -1; // int
 :BUFR:centerName = "59.0 (The NOAA Forecast Systems Laboratory, Boulder, CO, 
USA)";
 :BUFR:center = 59; // int
 :BUFR:subCenter = 0; // int
 :BUFR:table = 0; // int
 :BUFR:tableVersion = 3; // int
 :BUFR:localTableVersion = 3; // int
 :WMO Header = "";
 :Conventions = "BUFR/CDM";
 :_CoordSysBuilder = "ucar.nc2.dataset.conv.DefaultConvention";
}



-- 
Brian Schlining

Attachment: 5900.20030601.rass
Description: Binary data