Thank you -- it now works with the morphology jar file back where it
belongs.
In addition to updating, I needed to manually remove the launcher.toml
file that was left over from SciJava Ops.
I did that using the updater in the advanced mode by uninstalling it.
Best regards,
--aryeh
On 21/04/2025 7:22 pm, Mark Hiner wrote:
Ahh yes! This is a problem with the SciJava Ops update site. It
initially served Jaunch files, but wasn't updated with the latest
versions, which are now available on Java-8.
I just pushed an update to the SciJava Ops update site removing these
files. The SciJava Ops site itself will become obsolete in the
not-too-distant future, but it's fine to keep it enabled for now.
If you do another Help > Update... round, the updater should update
these files to the Java-8 version. The *.toml.old files are just
backups and can be removed.
Let me know if updating doesn't fix things for you!
Best,
Mark
------------------------------------------------------------------------
*From:* Aryeh Weiss <[email protected]> on behalf of Aryeh Weiss
<[email protected]>
*Sent:* Monday, April 21, 2025 10:54 AM
*To:* Mark Hiner <[email protected]>; ImageJ Interest Group
<[email protected]>
*Subject:* Re: strange problem running morphology_collection classes
Thank you for your reply. I am sure you are correct, as I am using
Jaunch with java-21.
Here is the output of the updater for the *.toml files.
and for fiji-linux
Can you tell me the correct way to fix this (ie, shoudl I remove local
files and have the updater replace them)?
Best regards
--aryeh
On 21/04/2025 6:39 pm, Mark Hiner wrote:
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]> <mailto:[email protected]>
*Sent:* Monday, April 21, 2025 6:40 AM
*To:* [email protected] <mailto:[email protected]>
<[email protected]> <mailto:[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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--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel
Ph: 972-3-5317638
FAX: 972-3-7384051
--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel
Ph: 972-3-5317638
FAX: 972-3-7384051
--
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