Closing console in Fiji

I updated Fiji and Bioformats about a month ago and since then I have the console opening whenever I initialise Fiji. I want to disable the console.

I understand there’s an issue in Bioformats at the moment which is being fixed:
Ticket https://trac.openmicroscopy.org/ome/ticket/13220

GH issue https://github.com/openmicroscopy/bioformats/issues/2367

I have several additional update sites added into my Fiji, (MIST, NucleusJ, SIMcheck, Cookbook, CellMotility as well as Bioformats). Is one of these contributing to the issue?

Apparently this bug has been submitted to the Bioformats team and doesn’t exist in ‘Vanilla’ Fiji. However its present in my Bioformats version. What I’d like to know is how to switch off the console while the Bioformats guys fix their part of the bug.

Thanks

Ann

Ann Wheeler

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By design, there is no easy way to disable it. See:

Unfortunately, Bio-Formats frequently logs information to the “standard error” stream, which causes the ImageJ console to pop up, because the information on this stream represent errors, not just informational output, which users need to see. The best fix will be on the Bio-Formats side, to reduce the frequency of these messages, not to hide the ImageJ console and thus potentially miss other more critical error messages.

Yep! Actually, they merged the fix 3 days ago already! So the next release of Bio-Formats will contain the fix. And in the meantime, the Bio-Formats update site should be shipping this fix already, or at least imminently. (It is supposed to automatically update itself once per day with the latest development version.)

I am not sure what you mean by ‘Vanilla’ Fiji? The standard Fiji distribution includes the latest release of Bio-Formats.

Could you please copy and paste the exact message in the console? It is difficult to analyze the issue further without knowing exactly what Fiji is complaining about.

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Cheers Curtis, is it ok if I admit that one of the Bioformats team shares an office with me 1/2 the week. I know about the fix merging because we were messing around with Fiji to see what we could do in the interim for people who use Bioformats in Fiji and get it updated via the Fiji hosted update site.These people, including me, will need to temporarily turn off the console window until the Bioformats fix is rolled out I guess.

However the fix you suggest from the previous post (which was also probably complaining about the same thing) will work in the meanwhile.

Vanilla Fiji is one which an end user just downloads from the website and doesn’t check managing any update sites, doesn’t load anything into it and indeed unchecks managed update sites.

Interestingly this issue is not present in Macs or Linux.

I can send on the console message next time I restart. Essentially it’s complaining about not finding certain .dlls including the Slidebook one.

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Ok this is what the console says (i.e. what Fiji is complaining about)

13:32:58,542 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback.groovy]
13:32:58,542 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Could NOT find resource [logback-test.xml]
13:32:58,542 |-INFO in ch.qos.logback.classic.LoggerContext[default] - Found resource [logback.xml] at [jar:file:////Mvm-igmm-h213/z$/FIJI-W~1/Fiji.app/jars/scijava-config-2.0.1.jar!/logback.xml]
13:32:58,542 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs multiple times on the classpath.
13:32:58,542 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:////Mvm-igmm-h213/z$/FIJI-W~1/Fiji.app/jars/Thunder_STORM.jar!/logback.xml]
13:32:58,542 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:////Mvm-igmm-h213/z$/FIJI-W~1/Fiji.app/jars/scijava-config-2.0.1.jar!/logback.xml]
13:32:58,542 |-WARN in ch.qos.logback.classic.LoggerContext[default] - Resource [logback.xml] occurs at [jar:file:////Mvm-igmm-h213/z$/FIJI-W~1/Fiji.app/plugins/Thunder_STORM.jar!/logback.xml]
13:32:58,589 |-INFO in ch.qos.logback.core.joran.spi.ConfigurationWatchList@121f34d0 - URL [jar:file:////Mvm-igmm-h213/z$/FIJI-W~1/Fiji.app/jars/scijava-config-2.0.1.jar!/logback.xml] is not of type file
13:32:58,683 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - debug attribute not set
13:32:58,683 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
13:32:58,698 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [stdout]
13:32:58,730 |-INFO in ch.qos.logback.core.joran.action.NestedComplexPropertyIA - Assuming default type [ch.qos.logback.classic.encoder.PatternLayoutEncoder] for [encoder] property
13:32:58,776 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - About to instantiate appender of type [ch.qos.logback.core.ConsoleAppender]
13:32:58,776 |-INFO in ch.qos.logback.core.joran.action.AppenderAction - Naming appender as [stderr]
13:32:58,776 |-INFO in ch.qos.logback.core.joran.action.NestedComplexPropertyIA - Assuming default type [ch.qos.logback.classic.encoder.PatternLayoutEncoder] for [encoder] property
13:32:58,792 |-INFO in ch.qos.logback.classic.joran.action.RootLoggerAction - Setting level of ROOT logger to INFO
13:32:58,792 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [stdout] to Logger[ROOT]
13:32:58,792 |-INFO in ch.qos.logback.core.joran.action.AppenderRefAction - Attaching appender named [stderr] to Logger[ROOT]
13:32:58,792 |-INFO in ch.qos.logback.classic.joran.action.ConfigurationAction - End of configuration.
13:32:58,792 |-INFO in ch.qos.logback.classic.joran.JoranConfigurator@499a12ee - Registering current configuration as safe fallback point

This bit is in Red

SLF4J: Actual binding is of type [ch.qos.logback.classic.util.ContextSelectorStaticBinder]
05-May-2016 13:32:58 org.scijava.nativelib.BaseJniExtractor extractJni
INFO: Couldn’t find resource META-INF/lib/windows_64/ SlideBook6Reader.dll
05-May-2016 13:32:58 org.scijava.nativelib.NativeLibraryUtil loadNativeLibrary
WARNING: IOException creating DefaultJniExtractor
java.io.IOException: Couldn’t find resource META-INF/lib/windows_64/ SlideBook6Reader.dll
_ at org.scijava.nativelib.BaseJniExtractor.extractJni(BaseJniExtractor.java:158)_
_ at org.scijava.nativelib.NativeLibraryUtil.loadNativeLibrary(NativeLibraryUtil.java:287)_
_ at loci.formats.in.SlideBook6Reader.(SlideBook6Reader.java:93)_
_ at java.lang.Class.forName0(Native Method)_
_ at java.lang.Class.forName(Class.java:169)_
_ at loci.formats.ClassList.(ClassList.java:127)_
_ at loci.formats.ClassList.(ClassList.java:85)_
_ at loci.formats.ImageReader.getDefaultReaderClasses(ImageReader.java:78)_
_ at io.scif.bf.BioFormatsFormat.cacheReaderClasses(BioFormatsFormat.java:479)_
_ at io.scif.bf.BioFormatsFormat.(BioFormatsFormat.java:128)_
_ at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)_
_ at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)_
_ at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)_
_ at java.lang.reflect.Constructor.newInstance(Constructor.java:513)_
_ at java.lang.Class.newInstance0(Class.java:355)_
_ at java.lang.Class.newInstance(Class.java:308)_
_ at org.scijava.plugin.PluginInfo.createInstance(PluginInfo.java:302)_
_ at org.scijava.plugin.DefaultPluginService.createInstance(DefaultPluginService.java:236)_
_ at org.scijava.plugin.DefaultPluginService.createInstances(DefaultPluginService.java:225)_
_ at org.scijava.plugin.DefaultPluginService.createInstancesOfType(DefaultPluginService.java:216)_
_ at io.scif.services.DefaultFormatService$2.run(DefaultFormatService.java:450)_
_ at org.scijava.thread.DefaultThreadService$1.run(DefaultThreadService.java:174)_
_ at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)_
_ at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)_
_ at java.util.concurrent.FutureTask.run(FutureTask.java:138)_
_ at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)_
_ at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)_
_ at java.lang.Thread.run(Thread.java:662)_
Searching for blocks

Hi Ann and Curtis,

Bio-Formats 5.1.10 has been released today and the Fiji update site has been updated accordingly so the console issue reported above should now be mitigated for Windows users. Please let us know if errors persist.

Best,
Sebastien

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