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openforis / opensarkit

Tools for Automatic Preprocessing of SAR Imagery
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GRD processing issues with docker image #4

Open jonas-eberle opened 7 years ago

jonas-eberle commented 7 years ago

Hi Andreas,

I have some issues when starting the processing using the docker image.

The import works fine for single file processing, but not for batch processing. Batch processing seems to use SNAP for import, this might be the reason for failing.

GRD to both, RTC and GTC: log_import for single file processing:

Colums total: 26530 Colums cut left side: 644 Colums cut right side: 993 Amount of columns kept: 25537 Write valid columns of image to disk time elapsed: 7.60805797577

log_cal_ml / log_tc_db / log_ls_mask:

INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters SEVERE: org.esa.s2tbx.dataio.gdal.activator.GDALPlugInActivator: The environment variable LD_LIBRARY_PATH does not contain the current folder '.'. Its value is '/usr/lib/R/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/default-java/jre/lib/amd64/server'. java.lang.IllegalArgumentException: The environment variable LD_LIBRARY_PATH does not contain the current folder '.'. Its value is '/usr/lib/R/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/jvm/default-java/jre/lib/amd64/server'. at org.esa.s2tbx.dataio.gdal.activator.GDALDistributionInstaller.processInstalledLinuxDistribution(GDALDistributionInstaller.java:131) at org.esa.s2tbx.dataio.gdal.activator.GDALDistributionInstaller.install(GDALDistributionInstaller.java:82) at org.esa.s2tbx.dataio.gdal.activator.GDALPlugInActivator.start(GDALPlugInActivator.java:22) at org.esa.snap.runtime.Engine.informActivators(Engine.java:222) at org.esa.snap.runtime.Engine.lambda$start$0(Engine.java:121) at org.esa.snap.runtime.Engine.runClientCode(Engine.java:189) at org.esa.snap.runtime.Engine.start(Engine.java:121) at org.esa.snap.runtime.Engine.start(Engine.java:90) 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:498) at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:62) at com.install4j.runtime.launcher.UnixLauncher.main(UnixLauncher.java:57)

java.lang.NumberFormatException: For input string: "-Pinput=/root/test1/DATA/015A/20170716-015A/TMP/S1B_IW_GRDH_1SDV_20170716T171413_20170716T171438_006516_00B74F_AADC_speckle.dim" at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65) at java.lang.Integer.parseInt(Integer.java:580) at java.lang.Integer.parseInt(Integer.java:615) at org.esa.snap.core.gpf.main.CommandLineArgs.parseOptionArgumentInt(CommandLineArgs.java:271) at org.esa.snap.core.gpf.main.CommandLineArgs.parseArgs(CommandLineArgs.java:136) at org.esa.snap.core.gpf.main.CommandLineArgs.parseArgs(CommandLineArgs.java:70) at org.esa.snap.core.gpf.main.CommandLineTool.run(CommandLineTool.java:112) 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:498) at org.esa.snap.runtime.Launcher.lambda$run$0(Launcher.java:55) at org.esa.snap.runtime.Engine.runClientCode(Engine.java:189) 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:498) at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:62) at com.install4j.runtime.launcher.UnixLauncher.main(UnixLauncher.java:57)

Error: For input string: "-Pinput=/root/test1/DATA/015A/20170716-015A/TMP/S1B_IW_GRDH_1SDV_20170716T171413_20170716T171438_006516_00B74F_AADC_speckle.dim"

By the way the log info says successfully processed file:

Importing S1 GRD data file, applying the precise orbit file and removing thermal noise ... done (0 minutes and 28 seconds elapsed) Removing GRD Border Noise ... done (0 minutes and 16 seconds elapsed) Applying the Lee Sigma Speckle Filter ... done (3 minutes and 7 seconds elapsed) Calibrating to Gamma0 (based on ellipsoid earth model) and multi-look by a factor of 3 ... done (0 minutes and 5 seconds elapsed) Creating a layover/shadow mask ... done (0 minutes and 4 seconds elapsed) Applying the geometric terrain correction and transform backscatter to decibel scale ... done (0 minutes and 4 seconds elapsed) Creating final output file ... done (0 minutes and 0 seconds elapsed) Mask out layover/shadow areas ... done (0 minutes and 0 seconds elapsed) Create a kmz file for Google Earth Visualization ... done (0 minutes and 0 seconds elapsed)

Info: Succesfully processed file: S1B_IW_GRDH_1SDV_20170716T171413_20170716T171438_006516_00B74F_AADC_speckle.dim to a geometrically terrain corrected product.

Creating final output file (Band 1: VV, Band 2: VH, Band 3 VV/VH ratio) ... done (0 minutes and 0 seconds elapsed) Processing failed for some reason.

BuddyVolly commented 7 years ago

Hi Jonas,

unfortunately the SNAP error messages are not quite helpful. However you can ignore the INFO and SEVERE messages. Those should not affect the processing. Also note that error handling has to be improved for the toolkit.

Just for clarification, what are the specifications of your machine? Do you have enough RAM and/or disk space? As far as I can see from the log info posted below, the problem is within the calibration step that should take longer than 5 seconds.