Hello,
I am trying to use gpt command in Ubuntu to export a BEAN-DIMAP file to NetCDF but I am not getting it.
My intention is using gpt command to get a DEM band, and then to transform to netcdf file.
I use
./gpt AddElevation /home/user/Documents/S1A_IW_GRDH_1SDV_20150907T061013_20150907T061038_007605_00A887_68C1.zip
and obtain
S1A_IW_GRDH_1SDV_20150907T061013_20150907T061038_007605_00A887_68C1.data
and
S1A_IW_GRDH_1SDV_20150907T061013_20150907T061038_007605_00A887_68C1.dim
However, I am trying to use ./gpt Write -f NetCDF-CF /home/user/Documents/S1A_IW_GRDH_1SDV_20150907T061013_20150907T061038_007605_00A887_68C1.dim
but errors occur. Can you help me, please? How must I use this command?
SLF4J: Failed to load class “org.slf4j.impl.StaticLoggerBinder”.
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
org.esa.beam.framework.gpf.OperatorException: [output] is null
at org.esa.beam.framework.gpf.internal.OperatorExecutor$GPFImagingListener.errorOccurred(OperatorExecutor.java:385)
at com.sun.media.jai.util.SunTileScheduler.sendExceptionToListener(SunTileScheduler.java:1646)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:921)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at com.sun.media.jai.util.RequestJob.compute(SunTileScheduler.java:247)
at com.sun.media.jai.util.WorkerThread.run(SunTileScheduler.java:468)
Caused by: java.lang.IllegalArgumentException: [output] is null
at org.esa.beam.util.Guardian.assertNotNull(Guardian.java:70)
at org.esa.beam.framework.dataio.AbstractProductWriter.writeProductNodes(AbstractProductWriter.java:104)
at org.esa.beam.gpf.operators.standard.WriteOp.writeProductNodes(WriteOp.java:265)
at org.esa.beam.gpf.operators.standard.WriteOp.computeTile(WriteOp.java:276)
at org.esa.beam.framework.gpf.internal.OperatorImage.computeRect(OperatorImage.java:78)
at javax.media.jai.SourcelessOpImage.computeTile(SourcelessOpImage.java:137)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
… 3 more
I have already tried but I get a java.lang.OutOfMemoryError: Java heap space error. Is there any way to extract only the variables that I need and then export to netcdf?
Yes, but you don’t need to specify -Ssource. Just provide the source file as last parameter.
Following the command line with format and target file parameter.
Exception in thread “SunTileScheduler0Standard2” java.lang.OutOfMemoryError: Java heap space
Exception in thread “SunTileScheduler0Standard3” java.lang.OutOfMemoryError: Java heap space
Exception in thread “SunTileScheduler0Standard1” java.lang.OutOfMemoryError: Java heap space
Exception in thread “SunTileScheduler0Standard0” java.lang.OutOfMemoryError: Java heap space
edu.ucar.ral.nujan.hdf.HdfException: must call endDefine first
at edu.ucar.ral.nujan.hdf.BaseBlk.throwerr(BaseBlk.java:155)
at edu.ucar.ral.nujan.hdf.HdfGroup.writeDataSub(HdfGroup.java:1026)
at edu.ucar.ral.nujan.hdf.HdfGroup.writeData(HdfGroup.java:987)
at edu.ucar.ral.nujan.netcdf.NhFileWriter.writeTreeDimData(NhFileWriter.java:481)
at edu.ucar.ral.nujan.netcdf.NhFileWriter.endDefine(NhFileWriter.java:446)
at org.esa.snap.dataio.netcdf.nc.N4FileWriteable.create(N4FileWriteable.java:174)
at org.esa.snap.dataio.netcdf.NetCdfWriteProfile.writeProduct(NetCdfWriteProfile.java:50)
at org.esa.snap.dataio.netcdf.DefaultNetCdfWriter.writeProductNodesImpl(DefaultNetCdfWriter.java:62)
at org.esa.snap.core.dataio.AbstractProductWriter.writeProductNodes(AbstractProductWriter.java:109)
at org.esa.snap.core.gpf.common.WriteOp.doExecute(WriteOp.java:287)
at org.esa.snap.core.gpf.internal.OperatorContext.executeOperator(OperatorContext.java:1272)
at org.esa.snap.core.gpf.internal.OperatorImage.computeRect(OperatorImage.java:65)
at javax.media.jai.SourcelessOpImage.computeTile(SourcelessOpImage.java:137)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at com.sun.media.jai.util.RequestJob.compute(SunTileScheduler.java:247)
at com.sun.media.jai.util.WorkerThread.run(SunTileScheduler.java:468)
edu.ucar.ral.nujan.hdf.HdfException: close: the following dataset chunks still need to written:
/elevation chunk indices: [0 0]
/elevation chunk indices: [0 620]
/elevation chunk indices: [0 1240]
/elevation chunk indices: [0 1860]
/elevation chunk indices: [0 2480]
/elevation chunk indices: [0 3100]
/elevation chunk indices: [0 3720]
/elevation chunk indices: [0 4340]
/elevation chunk indices: [0 4960]
at edu.ucar.ral.nujan.hdf.BaseBlk.throwerr(BaseBlk.java:155)
at edu.ucar.ral.nujan.hdf.HdfFileWriter.close(HdfFileWriter.java:531)
at edu.ucar.ral.nujan.netcdf.NhFileWriter.close(NhFileWriter.java:515)
at org.esa.snap.dataio.netcdf.nc.N4FileWriteable.close(N4FileWriteable.java:183)
at org.esa.snap.dataio.netcdf.DefaultNetCdfWriter.close(DefaultNetCdfWriter.java:123)
at org.esa.snap.core.gpf.common.WriteOp.dispose(WriteOp.java:428)
at org.esa.snap.core.gpf.common.WriteOp.writeProduct(WriteOp.java:230)
at org.esa.snap.core.gpf.GPF.writeProduct(GPF.java:404)
at org.esa.snap.core.gpf.main.DefaultCommandLineContext.writeProduct(DefaultCommandLineContext.java:63)
at org.esa.snap.core.gpf.main.CommandLineTool.writeProduct(CommandLineTool.java:501)
at org.esa.snap.core.gpf.main.CommandLineTool.runOperator(CommandLineTool.java:281)
at org.esa.snap.core.gpf.main.CommandLineTool.runGraphOrOperator(CommandLineTool.java:247)
at org.esa.snap.core.gpf.main.CommandLineTool.run(CommandLineTool.java:151)
at org.esa.snap.core.gpf.main.CommandLineTool.run(CommandLineTool.java:123)
at org.esa.snap.core.gpf.main.GPT.run(GPT.java:54)
at org.esa.snap.core.gpf.main.GPT.main(GPT.java:34)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at org.esa.snap.runtime.Launcher.lambda$run$12(Launcher.java:55)
at org.esa.snap.runtime.Engine.runClientCode(Engine.java:186)
at org.esa.snap.runtime.Launcher.run(Launcher.java:51)
at org.esa.snap.runtime.Launcher.main(Launcher.java:31)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:497)
at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:62)
at com.install4j.runtime.launcher.UnixLauncher.main(UnixLauncher.java:57)
org.esa.snap.core.gpf.OperatorException: Cannot construct DataBuffer.
at org.esa.snap.core.gpf.internal.OperatorExecutor$GPFImagingListener.errorOccurred(OperatorExecutor.java:375)
at com.sun.media.jai.util.SunTileScheduler.sendExceptionToListener(SunTileScheduler.java:1646)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:921)
at javax.media.jai.OpImage.getTile(OpImage.java:1129)
at com.sun.media.jai.util.RequestJob.compute(SunTileScheduler.java:247)
at com.sun.media.jai.util.WorkerThread.run(SunTileScheduler.java:468)
Caused by: java.lang.RuntimeException: Cannot construct DataBuffer.
at com.sun.media.jai.util.DataBufferUtils.constructDataBuffer(DataBufferUtils.java:132)
at com.sun.media.jai.util.DataBufferUtils.createDataBufferFloat(DataBufferUtils.java:214)
at javax.media.jai.ComponentSampleModelJAI.createDataBuffer(ComponentSampleModelJAI.java:271)
at javax.media.jai.RasterFactory.createWritableRaster(RasterFactory.java:691)
at javax.media.jai.PlanarImage.createWritableRaster(PlanarImage.java:1982)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2160)
at javax.media.jai.PlanarImage.getData(PlanarImage.java:2016)
at com.bc.ceres.glevel.MultiLevelImage.getData(MultiLevelImage.java:59)
at org.esa.snap.dataio.netcdf.metadata.profiles.cf.CfTiePointGridPart.encode(CfTiePointGridPart.java:50)
at org.esa.snap.dataio.netcdf.NetCdfWriteProfile.writeProduct(NetCdfWriteProfile.java:52)
at org.esa.snap.dataio.netcdf.DefaultNetCdfWriter.writeProductNodesImpl(DefaultNetCdfWriter.java:62)
at org.esa.snap.core.dataio.AbstractProductWriter.writeProductNodes(AbstractProductWriter.java:109)
at org.esa.snap.core.gpf.common.WriteOp.doExecute(WriteOp.java:287)
at org.esa.snap.core.gpf.internal.OperatorContext.executeOperator(OperatorContext.java:1272)
at org.esa.snap.core.gpf.internal.OperatorImage.computeRect(OperatorImage.java:65)
at javax.media.jai.SourcelessOpImage.computeTile(SourcelessOpImage.java:137)
at com.sun.media.jai.util.SunTileScheduler.scheduleTile(SunTileScheduler.java:904)
… 3 more