[ome-users] SlideBookReader Error + DEBUG output

Thu Oct 22 16:37:50 BST 2015

I Felix,

Just as a follow up to the information provided earlier, if you require a finer level of tuning for your logging then you can also make use of standard Logback configuration.

In order to do so you must first add the logback.xml file to your class path.

Note this will override the DebugTools.enableLogging(...) setting.

In this configuration you can define the level of logging specific to individual components. For example:

<logger name="loci.formats.FormatHandler" level="ERROR" />

<logger name="loci.formats.tiff.TiffParser" level="DEBUG" />

Different appenders can also be configured to write output from specific loggers to various sources.

In the example below all log messages will be sent to the console but only requests from FromatHandler and its children will be sent to the log file.

<configuration>
  <appender name="FILE" class="ch.qos.logback.core.FileAppender">
    <file>formatHandler.log</file>
    <encoder>
      <pattern>%date %level [%thread] %logger{10} [%file:%line] %msg%n</pattern>
    </encoder>
  </appender>

  <appender name="STDOUT" class="ch.qos.logback.core.ConsoleAppender">
    <encoder>
      <pattern>%msg%n</pattern>
    </encoder>
  </appender>

  <logger name="loci.formats.FormatHandler">
    <appender-ref ref="FILE" />
  </logger>

  <root level="debug">
    <appender-ref ref="STDOUT" />
  </root>
</configuration>

Other useful things that can be defined in the LogBack configuration include registering status listeners, setting properties, variables and conditional processing.For further configuration details and more complex examples you can read more at the link below:

http://logback.qos.ch/manual/configuration.html

[http://logback.qos.ch/manual/images/chapters/configuration/lbClassicStatus.jpg]<http://logback.qos.ch/manual/configuration.html>

Chapter 3: Configuration - Logback Home
We start by presenting ways for configuring logback, with many example configuration scripts. Joran, the configuration framework upon which logback relies will ...
Read more...<http://logback.qos.ch/manual/configuration.html>

With Thanks,

David Gault

________________________________
From: ome-users <ome-users-bounces at lists.openmicroscopy.org.uk> on behalf of David Gault (Staff) <d.gault at dundee.ac.uk>
Sent: 22 October 2015 13:49
To: OME User Support List
Subject: Re: [ome-users] SlideBookReader Error + DEBUG output

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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