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Re: Problems executing Fiji plugins in ImageJ

Posted by Mark Hiner on Feb 16, 2015; 1:52pm
URL: http://imagej.273.s1.nabble.com/Potential-updates-to-ImageJ-a-question-tp5011598p5011610.html

Hi Peter,

>The question I still have is if plugins written in the Fiji environment
are thought to be (easily) available as ImageJ plugins too or if - because
of the complex library
>dependencies - this compatibility is achievable only with time and expert
knowhow?

It depends on the plugin. In the case of Stitching, for example, there is
an ImageJ 1.x download[1] provided by the author.

But yes as a general rule a you need to consider any dependencies. All the
Fiji plugins are Mavenized for dependency management[2].
Also, the ImageJ updater (Help > Update...) that ships with Fiji will show
you the dependencies it knows of for any library if you go to Advanced Mode.

Best,
Mark

[1] http://fiji.sc/Image_Stitching#Download_for_ImageJ_.26_Acknowledgements
[2] https://github.com/fiji/Stitching/blob/master/pom.xml#L42-121

On Mon, Feb 16, 2015 at 2:02 AM, Peter Haub <[hidden email]> wrote:

> Hi,
> I have to correct my statement.
>
> After writing a SSCCE I found that ImageJ and Fiji both do access plugins
> located in subdirectories of jar archives in the same way.
>
> After all - my problem  arises because of missing libraries when using the
> original plugin jar in ImageJ.
>
> The message
>     Plugin or class not found: "Stitching Grid"
>     (java.lang.ClassNotFoundException: Stitching_Grid)
> was misleading.
> There is no problem in the class file and no problem in the class handling
> in ImageJ/Fiji.
>
> The question I still have is if plugins written in the Fiji environment
> are thought to be (easily) available as ImageJ plugins too or if - because
> of the complex library dependencies - this compatibility is achievable only
> with time and expert knowhow?
>
> Regards,
> Peter
>
>
> On 14.02.2015 21:13, Peter Haub wrote:
>
>> Dear list,
>>
>> I thought that Fiji is just ImageJ.
>> It seems as if there are slight differences in the way plugins (packed in
>> jar archives) are treated.
>> Maybe someone can point to a place where I can find some information
>> regarding the necessary structure of plugin jar archives - for ImageJ and
>> for Fiji.
>>
>> My problem:
>> I would like to use a Fiji plugin in an ImageJ installation (Stitching
>> plugin, S. Preibisch).
>> The plugin is encapsulated in a jar archive.
>> The main classes to be accessed as plugin are located in a subdirectory
>> (\pluin) inside the jar file.
>> The classes are made available to Fiji/ImageJ by a plugin.config file.
>> I can run this (jar packed) plugin in Fiji without problems.
>> In ImageJ the plugin command is available and the plugin user interface
>> (UI) can be started. But when the UI is closed with OK an error is shown:
>> Plugin or class not found: "Stitching Grid"
>> (java.lang.ClassNotFoundException: Stitching_Grid)
>>
>> There is no conflict with additional libraries or wrong configurations.
>>
>> If I recompile the source code by placing the relevant class files in the
>> default package instead of the plugin package the relevant class files are
>> located in the root of the jar archive. This recompiled plugin packed as
>> jar archive can be executed without error message in ImageJ.
>>
>> My questions are:
>> Is there a difference in the handling of plugin jar archives in ImageJ
>> and Fiji?
>> Should it be possible to us plugin jar archives from Fiji without changes
>> in ImageJ?
>> Do I miss something in my specific case?
>> Or do I have to recompile the classes in the way described above?
>>
>> A personal comment:
>> These kinds of differences of complex dependencies are confusing and are
>> challenging the close connection of the two project streams.
>>
>> I would be happy for any hint.
>>
>> Regards
>> Peter
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
>>
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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