Fiji layout bug fix

[Rdornier]

Hello,

As reported in this forum post, MosaicJ plugin is not working anymore, at least for windows users.

I found that the bug was coming from a mixing of java swing / java awt elements. This mixing is apparently not supported by the new FlatLaf layout of Fiji.

All Menu, MenuItem and MenuBar objects have been replaced by JMenu, JMenuItem and JMenuBar objects and the plugin is now working. I tried to keep all keyBoard shortcuts the same but some commands were assigned to the same shortcut and I just change them (I leave a comment next to the ones I changed). Feel free to change them again if you want.

In the meantime, I also updated the pom.xml file with a new parent pom and added the plugin into a package ch.epfl.big.

A Introduce a test method to be able to launch MosaicJ directly in the IDE.

Hope it will help having a new version of MosaicJ working on new Fiji.
Best,

Rémy.

[ctrueden]

@Rdornier This is amazing, thank you!

Unfortunately, the plugins in this fiji-BIG organization are not open source, and the rights to modification have not been granted by the original authors at BIG-EPFL... 😞

@dasv74 What can be done to change this? Valuable contributions from the community like this one are being lost, because I cannot legally accept them here.

[steko]

There is some confusion over the MosaicJ and TurboReg license. The web page at http://bigwww.epfl.ch/thevenaz/mosaicj/ has a clear statement at the bottom:

© 2023 Philippe Thévenaz
This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.
You should have received a copy of the GNU General Public License along with this program. If not, see https://www.gnu.org/licenses/.
You undertake to include a citation or acknowledgment whenever you present or publish results that are based on this program. EPFL makes no warranties of any kind on this software and shall in no event be liable for damages of any kind in connection with the use and exploitation of this technology.

However the ZIP files with the actual software contain no license and the source files have a proprietary license:

You'll be free to use this software for research purposes, but you
should not redistribute it without our consent. In addition, we expect
you to include a citation or acknowledgment whenever you present or
publish results that are based on it.

🫤

[ctrueden]

I am delighted to report that since I wrote the above comment, I have been in communication with @dasv74 as well as the head of the BIG-EPFL group, Michael Unser, who later sent me the following message via private email:

From: Michaël Unser
Date: Mon, Apr 3, 2023 at 5:54 AM
Subject: BIG's plugins for FIJI / licenses
To: Curtis Rueden
Cc: Philippe Thévenaz, Daniel Sage

Dear Curtis,

We wanted to follow up on the recent discussions about the distribution of ImageJ/Fiji plugins produced by the Biomedical Imaging Group at EPFL.

I am pleased to confirm that all of our software are open-source, in line with the FAIR principles promoted by EPFL. Our licensing follows the GPLv3 and we are currently updating our terms to reflect this.

In addition, we also strongly encourage users to properly cite our research papers in any publications that make use of our software.

If you have any further questions or concerns, please don't hesitate to contact Daniel Sage (cc'ed) or Philippe Thévenaz (cc'ed) to discuss the implementation of this term.

Best regards,

Michael

---

Michael Unser, Professor
Biomedical Imaging Group
Ecole Polytechnique Fédérale de Lausanne

I would like to thank Michael and all the BIG-EPFL ImageJ plugin authors for their willingness to do this relicensing.

I was swamped with other priorities over the summer, but my plan is to update the repositories in this organization, as well as the ImageJ wiki to reflect the change of project license to GPLv3.

This means we can start accepting PRs now—thanks a lot @Rdornier for your work on this! 🎉

There is still however the question of governance. I would like to establish a clear statement of who is involved in project decision making and effort for these BIG-EPFL projects, according to the SciJava team roles. Then we'll know who to ping about pending PRs, bug reports and fixes, and new releases of the component.

@dasv74 Could you please comment on who might be available to take on the team role responsibilities? The roles are as follows:

• Founder - Created the project. Does not imply any current participation or responsibility.
• Lead - Has decision-making authority: timing of releases, inclusion of features, etc.
• Developer - Adds new features or enhancements. Can be assigned to address feature requests.
• Debugger - Fixes bugs. Can be assigned open issues to solve.
• Reviewer - Reviews patch submissions.
• Support - Responds to community questions and issue reports. Keeps the issue tracker organized.
• Maintainer - Merges patch submissions. Cuts releases.
• Contributor - Contributed code to the project. Does not imply any current participation or responsibility.

If no one else has time to do it, I volunteer to act as a minimal maintainer and reviewer of PRs, but: 1) I don't want to overstep, since this is a BIG-EPFL project, not a LOCI project; and 2) I act in this capacity for hundreds of other Fiji-related repositories, so relying on me means things will move very slowly. 😅