Until now it works fine and we do not see any problems. But we haven't
done any specific testing e.g. of the Micro-Managers logging feature.
> Hi Peter,
>
> Apologies for the delay in my reply.
>
>> 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?
> Three options:
>
> 1) Use Fiji [1]. It comes with the stitching plugins, and is already
> structured to avoid this sort of problem.
>
> 2) Stop using loci_tools.jar and instead put all the individual component
> JAR files of Bio-Formats [1] into your plugins folder. This is what Fiji
> does.
>
> 3) Remove slf4j-api-1.7.1.jar, as you have done. This is actually OK as
> long as Micro-Manager does not use any new API introduced since
> slf4j-api-1.5.10. (But I am really not sure whether it does! Does
> Micro-Manager's logging still work for you with that library removed?)
>
>> Which version of slf4j is used in loci_tools.jar?
> Version 4.4.8 of loci_tools.jar uses SLF4J 1.5.10.
>
>> Is there any plan to update this to the latest version 1.7.1?
> The latest development version of Bio-Formats has already been upgraded to
> 1.7.2 [3], which will be the version used for the next releases: 4.4.9 and
> 5.0.0-beta2.
>
>> Would there be a conflict during Java class loading if the same
>> version of slf4j would be available twice?
> It should work, as long as the two versions really are the same.
>
> Regards,
> Curtis
>
> [1]
http://fiji.sc/> [2]
https://www.openmicroscopy.org/site/products/bio-formats/downloads> [3]
>
https://github.com/openmicroscopy/bioformats/commit/5b8b5ff83d23012c5805a8420681085244934cb6>
>
> On Wed, Aug 21, 2013 at 3:25 AM, Peter Haub <
[hidden email]> wrote:
>
>> 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<
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<
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
>>>>>
>>>>> --
>>>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.**html<
http://imagej.nih.gov/ij/list.html>
>>>>>
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>>>> ImageJ mailing list:
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http://imagej.nih.gov/ij/list.html>
>>>>
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>>> ImageJ mailing list:
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http://imagej.nih.gov/ij/list.html>
>>>
>>>
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>>
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