mastodon-sc/mastodon

Feature "Spot intensity" calculation error

Closed this issue · 17 comments

drchrisch commented

Spot intensity calculation error

I analyze a two-channel dataset (20 timepoints, 3D images 20x1024x1024) with Mastodon (Fiji v1.53o, everything updated). It works fine to extract spots and links. But when I run "compute features" I get a java error for feature "Spot intensity" and only for this feature.

Exception in thread "Feature computation thread" java.lang.ArrayIndexOutOfBoundsException: 76
at org.mastodon.mamut.feature.SpotIntensityFeatureComputer.run(SpotIntensityFeatureComputer.java:200)
at org.mastodon.feature.DefaultFeatureComputerService.compute(DefaultFeatureComputerService.java:253)
at org.mastodon.mamut.feature.MamutFeatureComputerService.compute(MamutFeatureComputerService.java:79)
at org.mastodon.mamut.MamutFeatureComputation$MyFeatureComputerService.compute(MamutFeatureComputation.java:138)
at org.mastodon.feature.ui.FeatureComputationController$2.run(FeatureComputationController.java:128)

I did analyze a few other dataset earlier whithout getting this error. Were there some changes in the feature calculation part recently?

tinevez commented

Hello @drchrisch

Not super recently this is suspect.

Can share the image and the files?

drchrisch commented

Sharing image is a bit difficult, I could send a link to the mastodon file.
The procedure is a follows: I load the two-channel bdv image set, run tracking detection and linking on channel 1, start feature computation, then I (without reloading) repeat tracking and linking but now on channel 2, feature computation then gives the error just as shown above.

tinevez commented

Ok I will try to reproduce. Thanks for the procedure.

tinevez commented

Hello @drchrisch
Well I could not reproduce with a 2-channel image I have at hand. I would need the image, or even a portion of it small enough to reproduce the error. If it is very big you can use our FEX instance to send it to me (see your PMs).

drchrisch commented

Well, 200 MB is not that small. Sorry, silly question, but how does this FEX works and how do I restrict access to the data?

tinevez commented
tinevez commented

@drchrisch Thank you for the data.
I could open it and test Mastodon with it.
But I could not reproduce the error. When I start from scratch and do detection with sensible parameters, I have no bug. When I try to compute features on your Mastodon file, again I have no error.
So I have to ask, what is the version of mastodon you use?

drchrisch commented

That's really weird, but matches expectation. I had this problem on two computers (Windows) with Fiji.app/jars/mastodon-1.0.0-beta-20.jar.

tinevez commented

Ok we run the same. Can you give me the parameters with which you run the detection and linking steps?

drchrisch commented

DoG (diameter 4.0, threshold 100), simple LAP (15, 15, 2) (there should be a *.mastodon file as well?).

tinevez commented

Yes. And the mastodon file does not give an error :)
this is interesting.

tinevez commented

Yes I got the bug! On the 2nd channel results.

drchrisch commented

Cool! It's all in the data, right?

tinevez commented

Could you try to replace the core mastodon .jar file in your Fiji.app/jars by this one?
https://dl.pasteur.fr/fop/8R1jRnNN/mastodon-1.0.0-beta-22-SNAPSHOT.jar

drchrisch commented

Great, looks conving. Many thanks!

tinevez commented

So the bug is fixed? If yes I will do a release but not immediately.

drchrisch commented

Yes, solved. That's it for me and I will close the issue.

  • 👍1