[netcdf-java] Using netcdf-java from Matlab

• To: netcdf-java@xxxxxxxxxxxxxxxx
• Subject: [netcdf-java] Using netcdf-java from Matlab
• From: Brian Schlining <bschlining@xxxxxxxxx>
• Date: Tue, 12 May 2009 09:34:18 -0700

Hi All,
I'm trying to use netcdf-java 4.0 from Matlab to access OpenDAP data and am
getting the following error:

>> import ucar.nc2.dataset.*
>> nc = NetcdfDataset.openDataset('
http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/deployments/m1/200810/m1_metsys_20081008_original.nc
')
Loading units database: com/mathworks/uk/units/Unit.xml
Fatal error: Could not open null
java.io.IOException: Could not open null
at
com.mathworks.toolbox.mbc.units.UnitXML.urlToInputSource(UnitXML.java:541)
at com.mathworks.toolbox.mbc.units.UnitXML.toXdoc(UnitXML.java:148)
at com.mathworks.toolbox.mbc.units.UnitXML.getFromXML(UnitXML.java:111)
at ucar.units.StandardUnitDB.addFromXML(StandardUnitDB.java:173)
at ucar.units.StandardUnitDB.<init>(StandardUnitDB.java:115)
at ucar.units.StandardUnitDB.instance(StandardUnitDB.java:137)
at ucar.units.UnitDBManager.instance(UnitDBManager.java:57)
at ucar.units.UnitFormatImpl.parse(UnitFormatImpl.java:57)
at ucar.nc2.units.SimpleUnit.<clinit>(SimpleUnit.java:62)
at
ucar.nc2.dataset.conv.COARDSConvention.getAxisType(COARDSConvention.java:78)
at ucar.nc2.dataset.conv.CSMConvention.getAxisType(CSMConvention.java:101)
at ucar.nc2.dataset.conv.CF1Convention.getAxisType(CF1Convention.java:226)
at
ucar.nc2.dataset.CoordSysBuilder.makeCoordinateAxes(CoordSysBuilder.java:622)
at
ucar.nc2.dataset.CoordSysBuilder.buildCoordinateSystems(CoordSysBuilder.java:482)
at
ucar.nc2.dataset.CoordSysBuilder.addCoordinateSystems(CoordSysBuilder.java:390)
at ucar.nc2.dataset.NetcdfDataset.enhance(NetcdfDataset.java:468)
at ucar.nc2.dataset.NetcdfDataset.<init>(NetcdfDataset.java:1125)
at ucar.nc2.dataset.NetcdfDataset.openDataset(NetcdfDataset.java:436)
at ucar.nc2.dataset.NetcdfDataset.openDataset(NetcdfDataset.java:413)
at ucar.nc2.dataset.NetcdfDataset.openDataset(NetcdfDataset.java:398)
at ucar.nc2.dataset.NetcdfDataset.openDataset(NetcdfDataset.java:385)
Unknown unit: "sec"
SimpleUnit initialization failed java.lang.ClassCastException:
java.lang.String
??? Java exception occurred:
java.lang.ExceptionInInitializerError
at
ucar.nc2.dataset.conv.COARDSConvention.getAxisType(COARDSConvention.java:78)
at ucar.nc2.dataset.conv.CSMConvention.getAxisType(CSMConvention.java:101)
at ucar.nc2.dataset.conv.CF1Convention.getAxisType(CF1Convention.java:226)
at
ucar.nc2.dataset.CoordSysBuilder.makeCoordinateAxes(CoordSysBuilder.java:622)
at
ucar.nc2.dataset.CoordSysBuilder.buildCoordinateSystems(CoordSysBuilder.java:482)
at
ucar.nc2.dataset.CoordSysBuilder.addCoordinateSystems(CoordSysBuilder.java:390)
at ucar.nc2.dataset.NetcdfDataset.enhance(NetcdfDataset.java:468)
at ucar.nc2.dataset.NetcdfDataset.<init>(NetcdfDataset.java:1125)
at ucar.nc2.dataset.NetcdfDataset.openDataset(NetcdfDataset.java:436)
at ucar.nc2.dataset.NetcdfDataset.openDataset(NetcdfDataset.java:413)
at ucar.nc2.dataset.NetcdfDataset.openDataset(NetcdfDataset.java:398)
at ucar.nc2.dataset.NetcdfDataset.openDataset(NetcdfDataset.java:385)
Caused by: java.lang.RuntimeException: SimpleUnit initialization failed
java.lang.ClassCastException:
java.lang.String
at ucar.nc2.units.SimpleUnit.<clinit>(SimpleUnit.java:77)
... 12 more


 I've added the following jars from the netcdf distribution onto the Matlab
classpath:

visadNoDods.jar
stax-api-1.0.1.jar
spring-2.5.jar
slf4j-log4j12-1.5.6.jar
slf4j-jdk14-1.5.6.jar
slf4j-api-1.5.6.jar
resourcesOptional.jar
opendap-2.1.jar
netcdfUI-4.0.jar
netcdf-4.0.jar
lucene.jar
log4j-1.2.15.jar
jpeg2000.jar
jdom.jar
grib-6.0.jar
forms-1.0.7.jar
ehcache-1.6.0-beta3.jar
commons-logging-1.1.jar
commons-httpclient-3.1.jar
commons-codec-1.3.jar
bufrTables-1.5.jar

And I noticed matlab has the following on its java classpath:

/Applications/MATLAB76/java/jarext/mwucarunits.jar

I'm pretty sure that the above jar is short for Mathworks ucar units. jar

Anyone familiar with the ucar units package and/or accessing opendap using
the netcdf libraries? Is there anyway to disable whatever units conversion
that NetcdfDataset.openDataset call seems to be trying? Other workaround
ideas?

Thanks

-- 
~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~
Brian Schlining
bschlining@xxxxxxxxx

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