Hi Aryeh,
Sorry to hear about the trouble with the Morphology plugins. It sounds like a
classpath problem, probably because of the nested file structure, and not
something wrong with the plugin jar itself.
My first guess is that your installation was converted to the Jaunch launcher
(e.g. fiji-windows-x64.exe) at some point and you have an old copy of
$FIJI_HOME/config/jaunch/fiji.toml. Around lines 104/106 there should be
something along the lines of " '!—plugins|${app-dir}/plugins/*/*.jar'," and
if that's missing then you'll definitely see a ClasNotFoundException when
running Morphology commands.
If I'm correct and you are using Jaunch, I would run Help > Update... >
Advanced and make sure your fiji-xxx launcher and config/jaunch/*.toml files
are up-to-date with the Java-8 update site. I verified that the Morphology
plugins are working for me on Windows with both the Jaunch and original
ImageJ-xxx launchers, on Java 8 and 21.
Let me know if that's not the case or these files are up-to-date for you and
you're still seeing the error.
Best,
- Mark
________________________________
From: Aryeh Weiss <[email protected]>
Sent: Monday, April 21, 2025 6:40 AM
To: [email protected] <[email protected]>
Subject: Re: strange problem running morphology_collection classes
I did not think to try that.
Yes -- it works properly with a freshly downloaded ImageJ (that is not
FIJI).
Best regards
--aryeh
On 21/04/2025 2:18 pm, Gabriel Landini wrote:
> Does it work in IJ (not Fiji)?
> (It works here with IJ and Java 17 as well).
>
> Regards
>
> Gabriel
>
>
> On 21/04/2025 10:54, Aryeh Weiss wrote:
>> Hi Gabriel
>>
>> Thank you for your quick reply. I indeed tried to reinstall from the
>> update site and encountered the same problem.
>>
>> Best regards
>> --aryeh
>>
>> On 21/04/2025 12:40 pm, Gabriel Landini wrote:
>>> Hi Aryeh,
>>> Did you install the collection via the "update site" Morphology?
>>> I have the jar file in the same place as you and it works (linux, Java
>>> 8).
>>>
>>> Maybe remove it and reinstalling it again via:
>>> Help>Update...>Manage Update Sites>Morphology
>>>
>>> Hope this helps
>>>
>>> Gabriel
>>>
>>>
>>> On 21/04/2025 07:11, Aryeh Weiss wrote:
>>>> CAUTION: This email originated from outside the organisation. Do not
>>>> click links or open attachments unless you recognise the sender and
>>>> know the content is safe.
>>>>
>>>>
>>>> I encountered a strange problem using the morphology_collection of
>>>> Gabriel Landini.
>>>>
>>>> I got a class not found error for the classes included in
>>>> morphology_collection.jar.
>>>>
>>>> This file is in $FIJI_HOME/plugins/Morphology , together the many
>>>> *.ijm
>>>> scripts that are part of Gabriel's morphology collection.
>>>>
>>>> The workaround was to copy the morphology_collection.jar file to the
>>>> $FIJI_HOME/jars directory.
>>>>
>>>> I tried this with my current installation of FIJI that runs with java
>>>> 21, and a fresh installation that runs with java 8, and experiences
>>>> the
>>>> same behavior each time.
>>>>
>>>> Is there an option that determines how far down the directory tree the
>>>> program looks to find classes?
>>>>
>>>> tnx in advance
>>>>
>>>> --aryeh
>>>>
--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel
Ph: 972-3-5317638
FAX: 972-3-7384051
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