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mastodon-sc / mastodon

Mastodon – a large-scale tracking and track-editing framework for large, multi-view images.
BSD 2-Clause "Simplified" License
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Compute features option not working in Mastodon #280

Closed sundar07 closed 9 months ago

sundar07 commented 9 months ago

Hi Jean Yves, I have been using Mastodon plugin in FIJI to track cells manually in zebrafish embryos. When I finished tracking and went for “Compute Features” option, I get the following error:

Exception in thread “Feature computation thread” java.lang.NoClassDefFoundError: io/humble/ferry/AtomicInteger at org.mastodon.mamut.feature.SpotTrackIDFeatureComputer.run(SpotTrackIDFeatureComputer.java:77) at org.mastodon.feature.DefaultFeatureComputerService.compute(DefaultFeatureComputerService.java:261) at org.mastodon.mamut.feature.MamutFeatureComputerService.compute(MamutFeatureComputerService.java:96) at org.mastodon.mamut.MamutFeatureComputation$MyFeatureComputerService.compute(MamutFeatureComputation.java:163) at org.mastodon.feature.ui.FeatureComputationController$2.run(FeatureComputationController.java:129) Caused by: java.lang.ClassNotFoundException: io.humble.ferry.AtomicInteger at java.net.URLClassLoader.findClass(URLClassLoader.java:387) at java.lang.ClassLoader.loadClass(ClassLoader.java:419) at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:352) at java.lang.ClassLoader.loadClass(ClassLoader.java:352) … 5 more

I have updated java, updated fiji, tried uninstalling and re-installing Mastodon, but still have the same problem. Any suggestions?

Thanks Sundar

sundar07 commented 9 months ago

Hi Stefan, Thanks for your reply. I am very much an end user and I do not particularly understand how to change what you have suggested. Can you detail this a bit more? Or does this change has to happen from Mastodon's end?

stefanhahmann commented 9 months ago

GIF 21 02 2024 10-16-15

stefanhahmann commented 9 months ago

Currently this dependency is needed: https://sites.imagej.net/Humble-Video/jars/humble-video-noarch-0.3.0.jar-20221115102504

sundar07 commented 9 months ago

It works now! Thanks a lot for the work around!!

tinevez commented 9 months ago

It is an import error. I imported AtomicInteger from humble video, while I should have imported the one in java.lang. I did not see the error because I am distracted and I had humble video in my class path when compiling. I am so sorry >.<

stefanhahmann commented 9 months ago

It is an import error. I imported AtomicInteger from humble video, while I should have imported the one in java.lang. I did not see the error because I am distracted and I had humble video in my class path when compiling. I am so sorry >.<

Cf.: https://github.com/mastodon-sc/mastodon/pull/281