No save button in Roi Manager 3D 3.83 on mac

Hello,

On my mac I don’t have any button on the bottom part of the “RoiManager3D 3.83” windows (save, load, option, info).

I have try on a windows computer and it works fine… I have try to make a fresh install of Fiji, a Fiji install without the JRE and the JRE-8 from oracle website.

Mac OsX 10.9.5 - MCIB V3.83 - ImageJ1.51h

Thanks.

Hi Antoine,

Oh, very strange, I must admit I never test my plugins on mac. The problem is maybe due to the fact that these 4 buttons are displayed as icons. Do you have problems with icons in other plugins ?

Best,

Thomas

Are the icons bundled with the JAR? If so, there might be an issue with the paths you are providing to ClassLoader.getResourceAsStream(). You might have to remove the first / to make it work on OSX, although I am not sure if it breaks compatibility with other OSs…

Hi,
I never notice icons problems in other plugins…
A.

Hi,

Humm when I change the path, I get an error in Linux, actually the 3Dmanager won´t open and an error will be displayed . Do you have any error message ? The icons are classical png images, any issue with png images on your computer ? like this one ?

Best,

Thomas

Hi,

I haven’t any trouble with png images, i see your folder icon in this discussion.

I have some error message but It isn’t specific of your plugin.
After download the fiji-macosx.dmg file from the FIJI web site and make a update of Fiji I have this error message :

[WARNING] Ignoring obsolete dependency jars/imagescience.jar of plugins/Trainable_Segmentation-3.2.4.jar

After a reboot of Fiji I add “3D ImageJ Suite” and “ImageScience” in the manage udpdates sites. And went I start the 3D manager I have this message:

Getting universes
3D [dev] 1.6.0-scijava-2-pre11-daily-experimental daily
Universes opened 0
Universe ij3d.Image3DUniverse@7e242fce

But if for example if I start the 3D viewer (before or after install “3D ImageJ Suite” and “ImageScience”) I have the same message:

3D [dev] 1.6.0-scijava-2-pre11-daily-experimental daily

I did some tests on my Mac and could reproduce the same issue.

After some digging, I found out that it is not about the icons but about the layout of the 3D Manager. The buttons in the last row are not shown on OS X (no matter if they contain an icon or not). Also, manual resizing of the JFrame is disabled, which would be a solution for now.

In long run, however, the GroupLayout with fixed pixel values will have to go…

Hi,

Thanks @Antoine and @stelfrich for you feedbacks, I modified the code to allow resizeable frame on macOS, can you test it on github https://github.com/mcib3d/mcib3d-plugins ? I am not an expert in GUI but yes one day it should be redesigned :wink: .

Thomas

Hello,

Thanks for your help! I have successfully resized the 3dmanager window with your modified code and now I can see the icons :slight_smile:.
But now when I add the ROI from the 3D counter It doesn’t work and I have this error message: :disappointed:

Exception in thread "Run\$\_AWT-EventQueue-0" java.lang.NoClassDefFoundError: mcib3d/geom/Object3D_IJUtils at mcib_plugins.tools.RoiManager3D_2.computeRois(RoiManager3D_2.java:2665) at mcib_plugins.tools.RoiManager3D_2.listValueChanged(RoiManager3D_2.java:1184) at mcib_plugins.tools.RoiManager3D_2.access\$100(RoiManager3D_2.java:48) at mcib_plugins.tools.RoiManager3D_2\$4.valueChanged(RoiManager3D_2.java:847) at javax.swing.JList.fireSelectionValueChanged(JList.java:1796) at javax.swing.JList\$ListSelectionHandler.valueChanged(JList.java:1810) at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:184) at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:164) at javax.swing.DefaultListSelectionModel.fireValueChanged(DefaultListSelectionModel.java:211) at javax.swing.DefaultListSelectionModel.changeSelection(DefaultListSelectionModel.java:405) at javax.swing.DefaultListSelectionModel.changeSelection(DefaultListSelectionModel.java:415) at javax.swing.DefaultListSelectionModel.setSelectionInterval(DefaultListSelectionModel.java:459) at javax.swing.JList.setSelectionInterval(JList.java:2065) at javax.swing.plaf.basic.BasicListUI\$Handler.adjustSelection(BasicListUI.java:2739) at javax.swing.plaf.basic.BasicListUI\$Handler.mousePressed(BasicListUI.java:2695) at javax.swing.plaf.basic.BasicListUI\$MouseInputHandler.mousePressed(BasicListUI.java:1514) at java.awt.AWTEventMulticaster.mousePressed(AWTEventMulticaster.java:280) at java.awt.Component.processMouseEvent(Component.java:6532) at javax.swing.JComponent.processMouseEvent(JComponent.java:3324) at java.awt.Component.processEvent(Component.java:6300) at java.awt.Container.processEvent(Container.java:2236) at java.awt.Component.dispatchEventImpl(Component.java:4891) at java.awt.Container.dispatchEventImpl(Container.java:2294) at java.awt.Component.dispatchEvent(Component.java:4713) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4888) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4522) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4466) at java.awt.Container.dispatchEventImpl(Container.java:2280) at java.awt.Window.dispatchEventImpl(Window.java:2750) at java.awt.Component.dispatchEvent(Component.java:4713) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:758) at java.awt.EventQueue.access$500(EventQueue.java:97) at java.awt.EventQueue\$3.run(EventQueue.java:709) at java.awt.EventQueue\$3.run(EventQueue.java:703) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain\$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain\$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:86) at java.awt.EventQueue\$4.run(EventQueue.java:731) at java.awt.EventQueue\$4.run(EventQueue.java:729) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain\$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:728) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93) at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

It’s the first time for me I build a .jar so I’m not sure I’m doing this well… I downloaded the code via git, maven and Netbeans to build the .jar.

With NetBeans I created “mcib3d-plugins-master-SNAPSHOT.jar” file. I added this .jar in the Fiji.app/plugins/mcib3d-suite folder.

Antoine.

That sounds right. In addition, you will also have to build the latest version of mcib3d-core and put it in the same location. @ThomasBoudier has added some additional changes that make this move necessary.

@ThomasBoudier: Thanks for the fix! :thumbsup:

Yes ! :smile:

with the new build of mcib3d-core it’s work fine!

Thanks @ThomasBoudier and @stelfrich! Now it’s time to count!

Hi @Antoine and @stelfrich,

Thanks for your feedback, sorry it was live debugging :relaxed: .
Do you mind testing the latest version, with the nimbus LookNFeel, maybe it looks better. Thanks.

Best,

Thomas

Hi,

I have try with this news version and it looks like that :slight_smile:.

Thanks again.

Hi Antoine,

Ok looks good, I think I will release this version soon, thanks for your feedbacks.

Best,

Thomas

Good Evening! I’m afraid I am having a similar problem visualizing the save button in ROI on a Mac and I’m having a difficult time understanding the solution. Would anyone mind clarifying how I need to proceed?

Thanks so much in advance!!
Kristin

Dear @KScaplen,

are you running an up-to-date Fiji with the Tboudier update site activated?

@ThomasBoudier has released a recent version of the plugins. Also take a look at the web page of the 3D suite for more information.

If you are still experiencing the issue, please take a screenshot and upload it to the forum, so that we can actually see if it is the same or just a similar issue.

Best,
Stefan

1 Like

Hi Stefan,

Thanks for responding!

I downloaded 3D suite bundle 3.83 a couple of weeks ago from the wiki that you included in your response. I am running Fiji and have ImageJ, Fiji, Java-8, and ImageScience as activated update sites.

Here is a screenshot of the plugins that were included in the bundle and also a screenshot of what I see in 3D ROI Manager.

Thanks!!

Hi @KScaplen,

As suggested by @stelfrich you need to update to latest version 3.9, the easiest way is to activate the 3D suite update site in Fiji or download latest version here.

Hope this helps

Best

Thomas

2 Likes

My apologizes. I was looking for the latest version in the installation section, not the download section.

I’ve activated the 3D suite to my update sites and this seems to have worked. I very much appreciate the save and settings option (for double checking) in the ROI manager.

Thank you @stelfrich and @ThomasBoudier!!

2 Likes

Hi,

Sorry I did not update the link into installation, it´s done now :slight_smile: .

Best,

Thomas