[trackmate] Trackmate Track analysis broken

[emartini (Emanuele Martini)]

dear all and moreover dear @tinevez,
I think after some updates (really don’t know if of Trackmate, Fiji, os or java) the track analysis extra:

tinevez/TrackMate-TrackAnalysis

throws exception and warning

Exception in thread "Linear track analysis thread 2" Exception in thread "Linear track analysis thread 11" java.lang.NullPointerException
	at fiji.plugin.trackmate.FeatureModel.getTrackFeature(FeatureModel.java:429)
	at fiji.plugin.trackmate.features.track.LinearTrackDescriptor$1.run(LinearTrackDescriptor.java:266)
Exception in thread "Linear track analysis thread 12" java.lang.NullPointerException
	at fiji.plugin.trackmate.FeatureModel.getTrackFeature(FeatureModel.java:429)
	at fiji.plugin.trackmate.features.track.LinearTrackDescriptor$1.run(LinearTrackDescriptor.java:266)
Exception in thread "Linear track analysis thread 10" java.lang.NullPointerException
	at fiji.plugin.trackmate.FeatureModel.getTrackFeature(FeatureModel.java:429)
	at fiji.plugin.trackmate.features.track.LinearTrackDescriptor$1.run(LinearTrackDescriptor.java:266)
Exception in thread "Linear track analysis thread 8" java.lang.NullPointerException
	at fiji.plugin.trackmate.FeatureModel.getTrackFeature(FeatureModel.java:429)
	at fiji.plugin.trackmate.features.track.LinearTrackDescriptor$1.run(LinearTrackDescriptor.java:266)
Exception in thread "Linear track analysis thread 6" java.lang.NullPointerException
	at fiji.plugin.trackmate.FeatureModel.getTrackFeature(FeatureModel.java:429)
	at fiji.plugin.trackmate.features.track.LinearTrackDescriptor$1.run(LinearTrackDescriptor.java:266)
Exception in thread "Linear track analysis thread 9" java.lang.NullPointerException
	at fiji.plugin.trackmate.FeatureModel.getTrackFeature(FeatureModel.java:429)
	at fiji.plugin.trackmate.features.track.LinearTrackDescriptor$1.run(LinearTrackDescriptor.java:266)
Exception in thread "Linear track analysis thread 14" Exception in thread "Linear track analysis thread 15" java.lang.NullPointerException
	at fiji.plugin.trackmate.FeatureModel.getTrackFeature(FeatureModel.java:429)
	at fiji.plugin.trackmate.features.track.LinearTrackDescriptor$1.run(LinearTrackDescriptor.java:266)
Exception in thread "Linear track analysis thread 7" Exception in thread "Linear track analysis thread 5" java.lang.NullPointerException
	at fiji.plugin.trackmate.FeatureModel.getTrackFeature(FeatureModel.java:429)
	at fiji.plugin.trackmate.features.track.LinearTrackDescriptor$1.run(LinearTrackDescriptor.java:266)
Exception in thread "Linear track analysis thread 4" java.lang.NullPointerException
	at fiji.plugin.trackmate.FeatureModel.getTrackFeature(FeatureModel.java:429)
	at fiji.plugin.trackmate.features.track.LinearTrackDescriptor$1.run(LinearTrackDescriptor.java:266)
Exception in thread "Linear track analysis thread 0" java.lang.NullPointerException
	at fiji.plugin.trackmate.FeatureModel.getTrackFeature(FeatureModel.java:429)
	at fiji.plugin.trackmate.features.track.LinearTrackDescriptor$1.run(LinearTrackDescriptor.java:266)
Exception in thread "Linear track analysis thread 1" Exception in thread "Linear track analysis thread 13" Exception in thread "Linear track analysis thread 3" java.lang.NullPointerException
	at fiji.plugin.trackmate.FeatureModel.getTrackFeature(FeatureModel.java:429)
	at fiji.plugin.trackmate.features.track.LinearTrackDescriptor$1.run(LinearTrackDescriptor.java:266)
java.lang.NullPointerException
	at fiji.plugin.trackmate.FeatureModel.getTrackFeature(FeatureModel.java:429)
	at fiji.plugin.trackmate.features.track.LinearTrackDescriptor$1.run(LinearTrackDescriptor.java:266)
java.lang.NullPointerException
	at fiji.plugin.trackmate.FeatureModel.getTrackFeature(FeatureModel.java:429)
	at fiji.plugin.trackmate.features.track.LinearTrackDescriptor$1.run(LinearTrackDescriptor.java:266)
java.lang.NullPointerException
	at fiji.plugin.trackmate.FeatureModel.getTrackFeature(FeatureModel.java:429)
	at fiji.plugin.trackmate.features.track.LinearTrackDescriptor$1.run(LinearTrackDescriptor.java:266)
java.lang.NullPointerException
	at fiji.plugin.trackmate.FeatureModel.getTrackFeature(FeatureModel.java:429)
	at fiji.plugin.trackmate.features.track.LinearTrackDescriptor$1.run(LinearTrackDescriptor.java:266)
java.lang.NullPointerException
	at fiji.plugin.trackmate.FeatureModel.getTrackFeature(FeatureModel.java:429)
	at fiji.plugin.trackmate.features.track.LinearTrackDescriptor$1.run(LinearTrackDescriptor.java:266)
Exception in thread "TrackMate spot feature calculation thread." java.lang.IllegalArgumentException: Stack argument out of range: 1
	at ij.ImageStack.getProcessor(ImageStack.java:275)
	at net.imglib2.img.imageplus.ShortImagePlus.<init>(ShortImagePlus.java:98)
	at net.imglib2.img.ImagePlusAdapter.wrapShort(ImagePlusAdapter.java:172)
	at net.imglib2.img.ImagePlusAdapter.wrapLocal(ImagePlusAdapter.java:102)
	at net.imglib2.img.ImagePlusAdapter.wrap(ImagePlusAdapter.java:74)
	at net.imglib2.img.ImagePlusAdapter.wrapImgPlus(ImagePlusAdapter.java:91)
	at fiji.plugin.trackmate.util.TMUtils.rawWraps(TMUtils.java:115)
	at fiji.plugin.trackmate.features.SpotFeatureCalculator.computeSpotFeaturesAgent(SpotFeatureCalculator.java:156)
	at fiji.plugin.trackmate.features.SpotFeatureCalculator.process(SpotFeatureCalculator.java:93)
	at fiji.plugin.trackmate.TrackMate.computeSpotFeatures(TrackMate.java:125)
	at fiji.plugin.trackmate.gui.descriptors.ViewChoiceDescriptor$1.run(ViewChoiceDescriptor.java:94)
Exception in thread "TrackMate preview detection thread" java.lang.IllegalArgumentException: Stack argument out of range: 1
	at ij.ImageStack.getProcessor(ImageStack.java:275)
	at net.imglib2.img.imageplus.ShortImagePlus.<init>(ShortImagePlus.java:98)
	at net.imglib2.img.ImagePlusAdapter.wrapShort(ImagePlusAdapter.java:172)
	at net.imglib2.img.ImagePlusAdapter.wrapLocal(ImagePlusAdapter.java:102)
	at net.imglib2.img.ImagePlusAdapter.wrap(ImagePlusAdapter.java:74)
	at net.imglib2.img.ImagePlusAdapter.wrapImgPlus(ImagePlusAdapter.java:91)
	at fiji.plugin.trackmate.util.TMUtils.rawWraps(TMUtils.java:115)
	at fiji.plugin.trackmate.TrackMate.execDetection(TrackMate.java:258)
	at fiji.plugin.trackmate.gui.panels.detector.LogDetectorConfigurationPanel$1.run(LogDetectorConfigurationPanel.java:234)
Exception in thread "Linear track analysis thread 0" Exception in thread "Linear track analysis thread 4" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 15" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 9" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 6" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 8" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 7" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 5" java.lang.NullPointerException
java.lang.NullPointerException
Exception in thread "Linear track analysis thread 2" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 3" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 1" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 13" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 14" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 11" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 10" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 12" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 0" Exception in thread "Linear track analysis thread 15" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 12" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 11" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 10" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 9" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 8" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 7" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 5" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 6" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 4" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 2" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 1" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 3" java.lang.NullPointerException
Exception in thread "Linear track analysis thread 13" java.lang.NullPointerException
java.lang.NullPointerException
Exception in thread "Linear track analysis thread 14" java.lang.NullPointerException

and produce a None filled Track Analysis Table in the parameters extracted by the TrackAnalysis plugin.

I am working on Windows 10, with Java 1.8.0_172 and ImageJ 2.1.0/1.53c

I tried with the FAkeTracks in the Fiji samples.

hoping someone could check on it,
thank you
Emanuele

[emartini (Emanuele Martini)]

just an update,
I found the problem but not the solution.

Everything works well with trackmate version 5.2.0
It’s broken with trackmate verison 6.0.0

So as a workaround I am using an “old” trackmate.

If and when someone (maybe @tinevez) has time to check what happened with the newer versions let me know.
But if you don’t have time, I’ll use an old version to do this kind of analysis.

Thanks,
Emanuele

[tinevez (Jean-Yves Tinevez)]

Looking at it.

asfdasfasdfadaf

[tinevez (Jean-Yves Tinevez)]

Ok, where did you download the extra module that generated this error?

[emartini (Emanuele Martini)]

I really don’t remember from where and when unfortunately…
it was long time ago.

for sure I started from here:

TrackMate

[emartini (Emanuele Martini)]

and I think from Nexus, but not sure

[tinevez (Jean-Yves Tinevez)]

Can you try with this one and report?
https://maven.scijava.org/service/local/repositories/releases/content/sc/fiji/TrackMate_TrackAnalysis/1.0.1/TrackMate_TrackAnalysis-1.0.1.jar

[emartini (Emanuele Martini)]

it works!
thank you

Emanuele

[tinevez (Jean-Yves Tinevez)]

Ok this is a problem we had already:

• the ImageJ website is read-only.
• and the TrackMate page links to an outdated version of the extras.
• and we cannot change it.
  Somebody already had the same problem you had, caused by the same issue. We have to wait for the ImageJ website to be writable again.

[emartini (Emanuele Martini)]

ok, so maybe this other problem is related:

Export TrackMate overlay to many individual ROIs

sorry to put back this thread after years, since I am having some troubles with Trackmate-extras track analysis: I was trying to download again and test it. I think the .jar links is not working anymore. could it be possible or is it a problem of my connection? thanks Emanuele