[ome-users] SlideBookReader Error + DEBUG output

[David Gault (Staff)]

Hi Felix,

In order to configure the logging level I can recommend using the following utility class http://downloads.openmicroscopy.org/bio-formats/5.1.4/api/loci/common/DebugTools.html#enableLogging(java.lang.String)
So you can add the following to your code for example:
DebugTools.enableLogging("ERROR");

The exception that you are seeing in the logs is indeed due to a library being unavailable. This particular reader still has further development required, including around the loading of libraries. The exception shown is caught and handled but is output to the logger as a debug level log entry.

With Thanks,
David Gault


On 21 Oct 2015, at 16:15, MEYENHOFER Felix <felix.meyenhofer at unifr.ch<mailto:felix.meyenhofer at unifr.ch>> wrote:

Hi

Whenever I call a bio-formats reader the error further down shows up. It continues to run, but I wonder if this is just an info, that we are missing the license? However as long as we don’t use the slidebookreader, I don’t see why it’s throwing an error instead of a warning.

Also I was wondering how to turn of the DEBUG output of Bio-Formats?


17:04:00.645 [SciJava-35e0c0f9-Thread-2] DEBUG loci.formats.FormatHandler - 3i SlideBook SlideBook6Reader library not found. Please see http://www.openmicroscopy.org/site/support/bio-formats/formats/3i-slidebook.html for details.
java.lang.UnsatisfiedLinkError: null
at loci.formats.in.SlideBook6Reader.<clinit>(SlideBook6Reader.java:90) ~[formats-gpl-5.1.5.jar:5.1.5]
at java.lang.Class.forName0(Native Method) [na:1.8.0_40]
at java.lang.Class.forName(Class.java:264) [na:1.8.0_40]
at loci.formats.ClassList.<init>(ClassList.java:127) [formats-api-5.1.5.jar:5.1.5]
at loci.formats.ClassList.<init>(ClassList.java:85) [formats-api-5.1.5.jar:5.1.5]
at loci.formats.ImageReader.getDefaultReaderClasses(ImageReader.java:78) [formats-api-5.1.5.jar:5.1.5]
at loci.formats.ImageReader.<init>(ImageReader.java:115) [formats-api-5.1.5.jar:5.1.5]
at loci.formats.ReaderWrapper.<init>(ReaderWrapper.java:62) [formats-api-5.1.5.jar:5.1.5]
at loci.formats.ChannelSeparator.<init>(ChannelSeparator.java:78) [formats-bsd-5.1.5.jar:5.1.5]
at NdpiTileColorSeparator.tile2GcStack(NdpiTileColorSeparator.java:219) [classes/:na]
at NdpiTileColorSeparator.run(NdpiTileColorSeparator.java:123) [classes/:na]
at org.scijava.command.CommandModule.run(CommandModule.java:201) [scijava-common-2.47.0.jar:2.47.0]
at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167) [scijava-common-2.47.0.jar:2.47.0]
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126) [scijava-common-2.47.0.jar:2.47.0]
at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65) [scijava-common-2.47.0.jar:2.47.0]
at org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:191) [scijava-common-2.47.0.jar:2.47.0]
at java.util.concurrent.FutureTask.run(FutureTask.java:266) [na:1.8.0_40]
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142) [na:1.8.0_40]
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617) [na:1.8.0_40]
at java.lang.Thread.run(Thread.java:745) [na:1.8.0_40]


Best regards,

-------------------------------------
Felix Meyenhofer
University of Fribourg
Departement of Medicine - Anatomy
1, Rte. Albert Gockel
CH-1700 Fribourg

Tel:  +41 26 300 85 45
Web:  www.unifr.ch/anatomy<http://www.unifr.ch/anatomy>
     www.unifr.ch/bioimage<http://www.unifr.ch/bioimage>
-------------------------------------

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