[ome-users] SlideBookReader Error + DEBUG output

Thu Oct 22 16:39:39 BST 2015

Hi Felix,

>From your stack trace, it looks like you are likely calling Bio-Formats
from ImageJ.

In which case, you may want to read this article as well:

   http://imagej.net/Logging

Contributions to that wiki page are welcome, e.g. if you have success
configuring logging in novel ways.

Regards,
Curtis

On Thu, Oct 22, 2015 at 10:37 AM, David Gault (Staff) <d.gault at dundee.ac.uk>
wrote:

>
> 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/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>
> 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
>      www.unifr.ch/bioimage
> -------------------------------------
>
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>
>
>
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>
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