Posted by
Peter Haub on
URL: http://imagej.273.s1.nabble.com/segmentation-tp5004436p5004516.html
Hi Stephan,
Hi Curtis,
Thanks for your answers.
I found the reason for the error message.
Stephans stitching plugin comes with a copy of the loci_tools.jar (if
manually installed into a IJ configuration).
This loci_tools.jar contains a version of slf4j (in \org\slf4j\ in the
latest loci_tools.jar, downloaded from the loci web page).
This slf4j seems to be in conflict with another version of that library
(slf4j-api-1.7.1.jar), located in the ..\plugins\Micro-Manager folder in
a default microManager configuration.
Removing this slf4j-api-1.7.1.jar solves the problem. The stitching
plugin can be used then without error messages.
I would prefer to not remove this slf4j-api-1.7.1.jar permanently.
Does anyone has an idea how to deal with this conflict?
Which version of slf4j is used in loci_tools.jar?
Is there any plan to update this to the latest version 1.7.1?
Would there be a conflict during Java class loading if the same version
of slf4j would be available twice?
Maybe someone has a hint.
Thanks,
Peter
On 20.08.2013 16:24, Curtis Rueden wrote:
> Hi Peter,
>
>> After switching from 32bit to a 64bit Windows I get an error always
>> when I try to run the plugin out of my IJ installation.
> As Stephan says, something is missing. But it should definitely not be
> necessary to download anything manually.
>
> If you run Help > Update Fiji, then click "Advanced mode" and change the
> "View Options" to "View uninstalled files only" do you see any entries
> ending in ".jar"?
>
>> java.lang.NoSuchMethodError: org.slf4j.helpers.MessageFormatter.format
> Your error message suggests you are missing slf4j-api-1.5.10.jar.
>
> If indeed you are missing that file (or other JAR files), click the
> "Status/Action" and change it to "Install / Update".
>
> If that doesn't work, you can also try downloading a fresh & up-to-date
> Fiji from:
http://fiji.sc/Downloads.
>
> Regards,
> Curtis
>
>
> On Tue, Aug 20, 2013 at 8:28 AM, Stephan Preibisch <
[hidden email]>wrote:
>
>> Hi Peter,
>>
>> you miss something from the LOCI bioformats to open the stacks ... it is
>> available for download here
http://loci.wisc.edu/bio-formats/downloads>>
>> Hope that helps,
>> Stephan
>>
>> On Aug 20, 2013, at 12:25 , Peter Haub wrote:
>>
>>> Hi List,
>>> I use the stitching plugin of S. Preibisch (Grid/Collection mode).
>>> After switching from 32bit to a 64bit Windows I get an error always when
>> I try to run the plugin out of my IJ installation.
>>> The error message is:
>>> java.lang.NoSuchMethodError:
>> org.slf4j.helpers.MessageFormatter.format(Ljava/lang/String;Ljava/lang/Object;Ljava/lang/Object;)Ljava/lang/String;
>>> at
>> org.slf4j.impl.Log4jLoggerAdapter.debug(Log4jLoggerAdapter.java:246)
>>> at loci.common.IniParser.parseINI(IniParser.java:114)
>>> at loci.common.IniParser.parseINI(IniParser.java:98)
>>> at loci.plugins.prefs.OptionsList.<init>(OptionsList.java:64)
>>> at loci.plugins.in.ImporterOptions.<init>(ImporterOptions.java:156)
>>> at
>> mpicbg.stitching.ImageCollectionElement.open(ImageCollectionElement.java:81)
>>> at Stitching_Grid.run(Stitching_Grid.java:342)
>>> at ij.IJ.runUserPlugIn(IJ.java:185)
>>> at ij.IJ.runPlugIn(IJ.java:152)
>>> at ij.Executer.runCommand(Executer.java:127)
>>> at ij.Executer.run(Executer.java:64)
>>> at java.lang.Thread.run(Unknown Source)
>>> IJ version is 1.47f7
>>> Java version is 1.6.0_31(64bit) - included in the IJ installation
>>> I have update the stitching plugin (from
>>
http://fly.mpi-cbg.de/~preibisch/software.html#Stitching).
>>> The data is ok. (I used a current FIJI installation where everything
>> work as expected.)
>>> Does anyone has an idea what to do?
>>> Thanks,
>>> Peter
>>>
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>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
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