Hi all,
for a project I have to import/read netcdf files with climatological and/or environmental data. These files are similar to some of those in the test-data folder of the geotools netcdf-plugin:
https://github.com/geotools/geotools/tree/71c3cca06462c8ce6678027c043d07aacff64fc2/modules/plugin/coverage-multidim/netcdf/src/test/resources/org/geotools/coverage/io/netcdf/test-data
For a start I tried to read the test-data files (e.g. "O3-NO2.nc") following the instructions on the NetCDF plugin user guide: http://docs.geotools.org/latest/userguide/library/coverage/multidim.html.
With this I'm able to retrieve the number of coverages in file and the coverage names. But I can't get the data values itself, e.g. the following line:
// Selection of the coverage associated to the name
GridCoverage2D grid = reader.read(first, null);
GridCoverage2D grid = reader.read(first, null);
throws the following error:
Okt 03, 2016 10:57:04 PM org.geotools.coverage.io.netcdf.NetCDFAccess access
SCHWERWIEGEND: Failed to access the NetCDF source
java.lang.AbstractMethodError: net.sourceforge.hatbox.jts.UpdateTrigger.close()V
at org.h2.schema.TriggerObject.close(TriggerObject.java:433)...
SCHWERWIEGEND: Failed to access the NetCDF source
java.lang.AbstractMethodError: net.sourceforge.hatbox.jts.UpdateTrigger.close()V
at org.h2.schema.TriggerObject.close(TriggerObject.java:433)...
Same when using other netcdf files or other gt-netcdf functions (e.g. reader.getCoordinateReferenceSystem(first)). I'm not very familiar with NetCDF and geotools either. Although I read lots of documentation (e.g. UNIDATA provides) in the last few weeks, apparently I missed some important steps?
Any help/assistance on this subject would be greatly appreciated.
Thank you in advance,
Christiane
Following the complete output messages:
23:28:37.073 [main] DEBUG Main - Summary information about GeoTools and the current environment:
23:28:37.169 [main] DEBUG Main - GeoTools version 16-SNAPSHOT (built from r99f8c073594af14aa03b144956d54835c1d768a3)
Java version: 1.8.0_101
Operating system: Windows 10 10.0
GeoTools jars on classpath:
Okt 03, 2016 11:28:38 PM org.geotools.imageio.netcdf.utilities.NetCDFUtilities <clinit>
INFORMATION: Value of Check Coordinate Plugins:null
Okt 03, 2016 11:28:38 PM org.geotools.imageio.netcdf.utilities.NetCDFUtilities <clinit>
INFORMATION: Should check for coordinate handler plugins:false
23:28:38.778 [main] INFO serverStartup - Nc4Iosp: NetCDF-4 C library loaded (jna_path='null', libname='netcdf').
23:28:38.787 [main] DEBUG ucar.nc2.jni.netcdf.Nc4Iosp - Netcdf nc_inq_libvers='4.4.1 of Jun 28 2016 14:35:06 $' isProtected=true
23:28:38.954 [main] DEBUG ucar.nc2.NetcdfFile - Using IOSP ucar.nc2.iosp.netcdf3.N3raf
23:28:39.244 [main] DEBUG ucar.nc2.NetcdfFile - Using IOSP ucar.nc2.iosp.netcdf3.N3raf
23:28:40.311 [main] INFO hsqldb.db.HSQLDB4AD417742A.ENGINE - dataFileCache open start
Okt 03, 2016 11:28:40 PM org.geotools.coverage.io.netcdf.NetCDFReader <init>
INFORMATION: ACCEPTED: O3-NO2.nc
23:28:40.858 [main] DEBUG Main - NetCDF store plugin
23:28:40.858 [main] DEBUG Main - Number of coverages in file: 2
23:28:40.858 [main] DEBUG Main - NO2
23:28:40.858 [main] DEBUG Main - O3
23:28:40.858 [main] DEBUG Main - start reading coverage: NO2
23:28:40.858 [main] DEBUG Main - org.geotools.coverage.io.netcdf.NetCDFReader@1df223b
Okt 03, 2016 11:28:50 PM org.geotools.coverage.io.netcdf.NetCDFAccess access
SCHWERWIEGEND: Failed to access the NetCDF source
java.lang.AbstractMethodError: net.sourceforge.hatbox.jts.UpdateTrigger.close()V
at org.h2.schema.TriggerObject.close(TriggerObject.java:433)
at org.h2.engine.Database.close(Database.java:1271)
at org.h2.engine.Database.removeSession(Database.java:1170)
at org.h2.engine.Session.close(Session.java:815)
at org.h2.jdbc.JdbcConnection.close(JdbcConnection.java:383)
at org.apache.commons.dbcp.DelegatingConnection.close(DelegatingConnection.java:247)
at org.apache.commons.dbcp.PoolableConnection.reallyClose(PoolableConnection.java:122)
at org.apache.commons.dbcp.PoolableConnectionFactory.destroyObject(PoolableConnectionFactory.java:628)
at org.apache.commons.dbcp.BasicDataSource.validateConnectionFactory(BasicDataSource.java:1562)
at org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1545)
at org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1388)
at org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
at org.geotools.data.jdbc.datasource.AbstractManageableDataSource.getConnection(AbstractManageableDataSource.java:48)
at org.geotools.jdbc.JDBCDataStore.createConnection(JDBCDataStore.java:2063)
at org.geotools.jdbc.JDBCDataStore.createTypeNames(JDBCDataStore.java:978)
at org.geotools.data.store.ContentDataStore.entry(ContentDataStore.java:581)
at org.geotools.data.store.ContentDataStore.ensureEntry(ContentDataStore.java:617)
at org.geotools.data.store.ContentDataStore.getFeatureSource(ContentDataStore.java:393)
at org.geotools.data.store.ContentDataStore.getFeatureSource(ContentDataStore.java:360)
at org.geotools.data.store.ContentDataStore.getSchema(ContentDataStore.java:344)
at org.geotools.coverage.io.catalog.CoverageSlicesCatalog.getSchema(CoverageSlicesCatalog.java:516)
at org.geotools.imageio.netcdf.VariableAdapter.updateDimensions(VariableAdapter.java:569)
at org.geotools.imageio.netcdf.VariableAdapter.initSpatialElements(VariableAdapter.java:532)
at org.geotools.imageio.netcdf.VariableAdapter.init(VariableAdapter.java:470)
at org.geotools.imageio.netcdf.VariableAdapter.<init>(VariableAdapter.java:1038)
at org.geotools.imageio.netcdf.NetCDFImageReader.getCoverageDescriptor(NetCDFImageReader.java:568)
at org.geotools.coverage.io.netcdf.NetCDFSource.<init>(NetCDFSource.java:52)
at org.geotools.coverage.io.netcdf.NetCDFAccess.access(NetCDFAccess.java:167)
at org.geotools.coverage.io.netcdf.NetCDFReader.getGridCoverageSource(NetCDFReader.java:649)
at org.geotools.coverage.io.netcdf.NetCDFReader.read(NetCDFReader.java:485)
at Main.main(Main.java:84)
23:28:37.169 [main] DEBUG Main - GeoTools version 16-SNAPSHOT (built from r99f8c073594af14aa03b144956d54835c1d768a3)
Java version: 1.8.0_101
Operating system: Windows 10 10.0
GeoTools jars on classpath:
Okt 03, 2016 11:28:38 PM org.geotools.imageio.netcdf.utilities.NetCDFUtilities <clinit>
INFORMATION: Value of Check Coordinate Plugins:null
Okt 03, 2016 11:28:38 PM org.geotools.imageio.netcdf.utilities.NetCDFUtilities <clinit>
INFORMATION: Should check for coordinate handler plugins:false
23:28:38.778 [main] INFO serverStartup - Nc4Iosp: NetCDF-4 C library loaded (jna_path='null', libname='netcdf').
23:28:38.787 [main] DEBUG ucar.nc2.jni.netcdf.Nc4Iosp - Netcdf nc_inq_libvers='4.4.1 of Jun 28 2016 14:35:06 $' isProtected=true
23:28:38.954 [main] DEBUG ucar.nc2.NetcdfFile - Using IOSP ucar.nc2.iosp.netcdf3.N3raf
23:28:39.244 [main] DEBUG ucar.nc2.NetcdfFile - Using IOSP ucar.nc2.iosp.netcdf3.N3raf
23:28:40.311 [main] INFO hsqldb.db.HSQLDB4AD417742A.ENGINE - dataFileCache open start
Okt 03, 2016 11:28:40 PM org.geotools.coverage.io.netcdf.NetCDFReader <init>
INFORMATION: ACCEPTED: O3-NO2.nc
23:28:40.858 [main] DEBUG Main - NetCDF store plugin
23:28:40.858 [main] DEBUG Main - Number of coverages in file: 2
23:28:40.858 [main] DEBUG Main - NO2
23:28:40.858 [main] DEBUG Main - O3
23:28:40.858 [main] DEBUG Main - start reading coverage: NO2
23:28:40.858 [main] DEBUG Main - org.geotools.coverage.io.netcdf.NetCDFReader@1df223b
Okt 03, 2016 11:28:50 PM org.geotools.coverage.io.netcdf.NetCDFAccess access
SCHWERWIEGEND: Failed to access the NetCDF source
java.lang.AbstractMethodError: net.sourceforge.hatbox.jts.UpdateTrigger.close()V
at org.h2.schema.TriggerObject.close(TriggerObject.java:433)
at org.h2.engine.Database.close(Database.java:1271)
at org.h2.engine.Database.removeSession(Database.java:1170)
at org.h2.engine.Session.close(Session.java:815)
at org.h2.jdbc.JdbcConnection.close(JdbcConnection.java:383)
at org.apache.commons.dbcp.DelegatingConnection.close(DelegatingConnection.java:247)
at org.apache.commons.dbcp.PoolableConnection.reallyClose(PoolableConnection.java:122)
at org.apache.commons.dbcp.PoolableConnectionFactory.destroyObject(PoolableConnectionFactory.java:628)
at org.apache.commons.dbcp.BasicDataSource.validateConnectionFactory(BasicDataSource.java:1562)
at org.apache.commons.dbcp.BasicDataSource.createPoolableConnectionFactory(BasicDataSource.java:1545)
at org.apache.commons.dbcp.BasicDataSource.createDataSource(BasicDataSource.java:1388)
at org.apache.commons.dbcp.BasicDataSource.getConnection(BasicDataSource.java:1044)
at org.geotools.data.jdbc.datasource.AbstractManageableDataSource.getConnection(AbstractManageableDataSource.java:48)
at org.geotools.jdbc.JDBCDataStore.createConnection(JDBCDataStore.java:2063)
at org.geotools.jdbc.JDBCDataStore.createTypeNames(JDBCDataStore.java:978)
at org.geotools.data.store.ContentDataStore.entry(ContentDataStore.java:581)
at org.geotools.data.store.ContentDataStore.ensureEntry(ContentDataStore.java:617)
at org.geotools.data.store.ContentDataStore.getFeatureSource(ContentDataStore.java:393)
at org.geotools.data.store.ContentDataStore.getFeatureSource(ContentDataStore.java:360)
at org.geotools.data.store.ContentDataStore.getSchema(ContentDataStore.java:344)
at org.geotools.coverage.io.catalog.CoverageSlicesCatalog.getSchema(CoverageSlicesCatalog.java:516)
at org.geotools.imageio.netcdf.VariableAdapter.updateDimensions(VariableAdapter.java:569)
at org.geotools.imageio.netcdf.VariableAdapter.initSpatialElements(VariableAdapter.java:532)
at org.geotools.imageio.netcdf.VariableAdapter.init(VariableAdapter.java:470)
at org.geotools.imageio.netcdf.VariableAdapter.<init>(VariableAdapter.java:1038)
at org.geotools.imageio.netcdf.NetCDFImageReader.getCoverageDescriptor(NetCDFImageReader.java:568)
at org.geotools.coverage.io.netcdf.NetCDFSource.<init>(NetCDFSource.java:52)
at org.geotools.coverage.io.netcdf.NetCDFAccess.access(NetCDFAccess.java:167)
at org.geotools.coverage.io.netcdf.NetCDFReader.getGridCoverageSource(NetCDFReader.java:649)
at org.geotools.coverage.io.netcdf.NetCDFReader.read(NetCDFReader.java:485)
at Main.main(Main.java:84)
23:28:50.115 [main] DEBUG Main - Reader closed.
Exception in thread "main" java.lang.IllegalArgumentException: Argument "value" should not be null.
at org.geotools.util.SoftValueHashMap.ensureNotNull(SoftValueHashMap.java:140)
at org.geotools.util.SoftValueHashMap.put(SoftValueHashMap.java:281)
at org.geotools.coverage.io.netcdf.NetCDFReader.getGridCoverageSource(NetCDFReader.java:651)
at org.geotools.coverage.io.netcdf.NetCDFReader.read(NetCDFReader.java:485)
at Main.main(Main.java:84)
Exception in thread "main" java.lang.IllegalArgumentException: Argument "value" should not be null.
at org.geotools.util.SoftValueHashMap.ensureNotNull(SoftValueHashMap.java:140)
at org.geotools.util.SoftValueHashMap.put(SoftValueHashMap.java:281)
at org.geotools.coverage.io.netcdf.NetCDFReader.getGridCoverageSource(NetCDFReader.java:651)
at org.geotools.coverage.io.netcdf.NetCDFReader.read(NetCDFReader.java:485)
at Main.main(Main.java:84)
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