TraJ plugin issue: unable to process track files from Trackmate

Hi all,

Does anyone else here use the TraJ plugin by T. Wagner (https://imagej.net/TraJClassifier)?

I’ve been experience issues with it lately as it has been erroring when trying to analyse tracks generated from Trackmate.

The following error message appears:

org.renjin.eval.EvalException: invalid subscript type 'list'
	at org.renjin.primitives.subset.Selections.parseSelection(Selections.java:63)
	at org.renjin.primitives.subset.Subsetting.getSubset(Subsetting.java:270)
	at org.renjin.primitives.R$primitive$$bracket.apply(R$primitive$$bracket.java:66)
	at org.renjin.eval.Context.evaluateCall(Context.java:283)
	at org.renjin.eval.Context.evaluate(Context.java:207)
	at org.renjin.primitives.special.AssignLeftFunction.assignLeft(AssignLeftFunction.java:60)
	at org.renjin.primitives.special.AssignLeftFunction.apply(AssignLeftFunction.java:44)
	at org.renjin.eval.Context.evaluateCall(Context.java:283)
	at org.renjin.eval.Context.evaluate(Context.java:207)
	at org.renjin.eval.Context.evaluateExpressionVector(Context.java:266)
	at org.renjin.eval.Context.evaluate(Context.java:205)
	at org.renjin.script.RenjinScriptEngine.eval(RenjinScriptEngine.java:150)
	at org.renjin.script.RenjinScriptEngine.eval(RenjinScriptEngine.java:109)
	at de.biomedical_imaging.ij.trajectory_classifier.RRFClassifierRenjin.classify(RRFClassifierRenjin.java:224)
	at de.biomedical_imaging.ij.trajectory_classifier.WeightedWindowedClassificationProcess.windowedClassification(WeightedWindowedClassificationProcess.java:62)
	at de.biomedical_imaging.ij.trajectory_classifier.TraJClassifier_.classifyAndSegment(TraJClassifier_.java:636)
	at de.biomedical_imaging.ij.trajectory_classifier.TraJClassifier_.run(TraJClassifier_.java:307)
	at ij.IJ.runUserPlugIn(IJ.java:228)
	at ij.IJ.runPlugIn(IJ.java:192)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:745)
java.lang.InterruptedException
	at java.util.concurrent.FutureTask.awaitDone(FutureTask.java:404)
	at java.util.concurrent.FutureTask.get(FutureTask.java:191)
	at net.imglib2.algorithm.fft2.FFTMethods.complexToComplex(FFTMethods.java:901)
	at net.imglib2.algorithm.fft2.FFT.complexToRealUnpad(FFT.java:322)
	at net.imglib2.algorithm.fft2.FFTConvolution.computeConvolution(FFTConvolution.java:607)
	at net.imglib2.algorithm.fft2.FFTConvolution.convolve(FFTConvolution.java:510)
	at fiji.plugin.trackmate.detection.LogDetector.process(LogDetector.java:145)
	at fiji.plugin.trackmate.TrackMate$1.run(TrackMate.java:377)
java.lang.InterruptedException
	at java.util.concurrent.FutureTask.awaitDone(FutureTask.java:404)
	at java.util.concurrent.FutureTask.get(FutureTask.java:191)
	at net.imglib2.algorithm.fft2.FFTMethods.complexToComplex(FFTMethods.java:901)
	at net.imglib2.algorithm.fft2.FFT.realToComplex(FFT.java:248)
	at net.imglib2.algorithm.fft2.FFT.realToComplex(FFT.java:123)
	at net.imglib2.algorithm.fft2.FFT.realToComplex(FFT.java:335)
	at net.imglib2.algorithm.fft2.FFT.realToComplex(FFT.java:74)
	at net.imglib2.algorithm.fft2.FFTConvolution.computeKernelFFT(FFTConvolution.java:578)
	at net.imglib2.algorithm.fft2.FFTConvolution.convolve(FFTConvolution.java:508)
	at fiji.plugin.trackmate.detection.LogDetector.process(LogDetector.java:145)
	at fiji.plugin.trackmate.TrackMate$1.run(TrackMate.java:377)
java.lang.InterruptedException
	at java.util.concurrent.FutureTask.awaitDone(FutureTask.java:404)
	at java.util.concurrent.FutureTask.get(FutureTask.java:191)
	at net.imglib2.algorithm.fft2.FFTMethods.complexToComplex(FFTMethods.java:901)
	at net.imglib2.algorithm.fft2.FFT.complexToRealUnpad(FFT.java:322)
	at net.imglib2.algorithm.fft2.FFTConvolution.computeConvolution(FFTConvolution.java:607)
	at net.imglib2.algorithm.fft2.FFTConvolution.convolve(FFTConvolution.java:510)
	at fiji.plugin.trackmate.detection.LogDetector.process(LogDetector.java:145)
	at fiji.plugin.trackmate.TrackMate$1.run(TrackMate.java:377)
java.lang.InterruptedException
	at java.util.concurrent.FutureTask.awaitDone(FutureTask.java:404)
	at java.util.concurrent.FutureTask.get(FutureTask.java:191)
	at net.imglib2.algorithm.fft2.FFTMethods.complexToComplex(FFTMethods.java:901)
	at net.imglib2.algorithm.fft2.FFT.realToComplex(FFT.java:248)
	at net.imglib2.algorithm.fft2.FFT.realToComplex(FFT.java:123)
	at net.imglib2.algorithm.fft2.FFT.realToComplex(FFT.java:335)
	at net.imglib2.algorithm.fft2.FFT.realToComplex(FFT.java:74)
	at net.imglib2.algorithm.fft2.FFTConvolution.computeImgFFT(FFTConvolution.java:562)
	at net.imglib2.algorithm.fft2.FFTConvolution.convolve(FFTConvolution.java:504)
	at fiji.plugin.trackmate.detection.LogDetector.process(LogDetector.java:145)
	at fiji.plugin.trackmate.TrackMate$1.run(TrackMate.java:377)
java.lang.InterruptedException
	at java.util.concurrent.FutureTask.awaitDone(FutureTask.java:404)
	at java.util.concurrent.FutureTask.get(FutureTask.java:191)
	at net.imglib2.algorithm.fft2.FFTMethods.complexToComplex(FFTMethods.java:901)
	at net.imglib2.algorithm.fft2.FFT.realToComplex(FFT.java:248)
	at net.imglib2.algorithm.fft2.FFT.realToComplex(FFT.java:123)
	at net.imglib2.algorithm.fft2.FFT.realToComplex(FFT.java:335)
	at net.imglib2.algorithm.fft2.FFT.realToComplex(FFT.java:74)
	at net.imglib2.algorithm.fft2.FFTConvolution.computeKernelFFT(FFTConvolution.java:578)
	at net.imglib2.algorithm.fft2.FFTConvolution.convolve(FFTConvolution.java:508)
	at fiji.plugin.trackmate.detection.LogDetector.process(LogDetector.java:145)
	at fiji.plugin.trackmate.TrackMate$1.run(TrackMate.java:377)
java.lang.InterruptedException
	at java.util.concurrent.FutureTask.awaitDone(FutureTask.java:404)
	at java.util.concurrent.FutureTask.get(FutureTask.java:191)
	at net.imglib2.algorithm.fft2.FFTMethods.complexToComplex(FFTMethods.java:901)
	at net.imglib2.algorithm.fft2.FFT.complexToRealUnpad(FFT.java:322)
	at net.imglib2.algorithm.fft2.FFTConvolution.computeConvolution(FFTConvolution.java:607)
	at net.imglib2.algorithm.fft2.FFTConvolution.convolve(FFTConvolution.java:510)
	at fiji.plugin.trackmate.detection.LogDetector.process(LogDetector.java:145)
	at fiji.plugin.trackmate.TrackMate$1.run(TrackMate.java:377)
java.lang.InterruptedException
	at java.util.concurrent.FutureTask.awaitDone(FutureTask.java:404)
	at java.util.concurrent.FutureTask.get(FutureTask.java:191)
	at net.imglib2.algorithm.fft2.FFTMethods.complexToComplex(FFTMethods.java:901)
	at net.imglib2.algorithm.fft2.FFT.realToComplex(FFT.java:248)
	at net.imglib2.algorithm.fft2.FFT.realToComplex(FFT.java:123)
	at net.imglib2.algorithm.fft2.FFT.realToComplex(FFT.java:335)
	at net.imglib2.algorithm.fft2.FFT.realToComplex(FFT.java:74)
	at net.imglib2.algorithm.fft2.FFTConvolution.computeImgFFT(FFTConvolution.java:562)
	at net.imglib2.algorithm.fft2.FFTConvolution.convolve(FFTConvolution.java:504)
	at fiji.plugin.trackmate.detection.LogDetector.process(LogDetector.java:145)
	at fiji.plugin.trackmate.TrackMate$1.run(TrackMate.java:377)
org.renjin.eval.EvalException: invalid subscript type 'list'
	at org.renjin.primitives.subset.Selections.parseSelection(Selections.java:63)
	at org.renjin.primitives.subset.Subsetting.getSubset(Subsetting.java:270)
	at org.renjin.primitives.R$primitive$$bracket.apply(R$primitive$$bracket.java:66)
	at org.renjin.eval.Context.evaluateCall(Context.java:283)
	at org.renjin.eval.Context.evaluate(Context.java:207)
	at org.renjin.primitives.special.AssignLeftFunction.assignLeft(AssignLeftFunction.java:60)
	at org.renjin.primitives.special.AssignLeftFunction.apply(AssignLeftFunction.java:44)
	at org.renjin.eval.Context.evaluateCall(Context.java:283)
	at org.renjin.eval.Context.evaluate(Context.java:207)
	at org.renjin.eval.Context.evaluateExpressionVector(Context.java:266)
	at org.renjin.eval.Context.evaluate(Context.java:205)
	at org.renjin.script.RenjinScriptEngine.eval(RenjinScriptEngine.java:150)
	at org.renjin.script.RenjinScriptEngine.eval(RenjinScriptEngine.java:109)
	at de.biomedical_imaging.ij.trajectory_classifier.RRFClassifierRenjin.classify(RRFClassifierRenjin.java:224)
	at de.biomedical_imaging.ij.trajectory_classifier.WeightedWindowedClassificationProcess.windowedClassification(WeightedWindowedClassificationProcess.java:62)
	at de.biomedical_imaging.ij.trajectory_classifier.TraJClassifier_.classifyAndSegment(TraJClassifier_.java:636)
	at de.biomedical_imaging.ij.trajectory_classifier.TraJClassifier_.run(TraJClassifier_.java:307)
	at ij.IJ.runUserPlugIn(IJ.java:228)
	at ij.IJ.runPlugIn(IJ.java:192)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:745)
org.renjin.eval.EvalException: invalid subscript type 'list'
	at org.renjin.primitives.subset.Selections.parseSelection(Selections.java:63)
	at org.renjin.primitives.subset.Subsetting.getSubset(Subsetting.java:270)
	at org.renjin.primitives.R$primitive$$bracket.apply(R$primitive$$bracket.java:66)
	at org.renjin.eval.Context.evaluateCall(Context.java:283)
	at org.renjin.eval.Context.evaluate(Context.java:207)
	at org.renjin.primitives.special.AssignLeftFunction.assignLeft(AssignLeftFunction.java:60)
	at org.renjin.primitives.special.AssignLeftFunction.apply(AssignLeftFunction.java:44)
	at org.renjin.eval.Context.evaluateCall(Context.java:283)
	at org.renjin.eval.Context.evaluate(Context.java:207)
	at org.renjin.eval.Context.evaluateExpressionVector(Context.java:266)
	at org.renjin.eval.Context.evaluate(Context.java:205)
	at org.renjin.script.RenjinScriptEngine.eval(RenjinScriptEngine.java:150)
	at org.renjin.script.RenjinScriptEngine.eval(RenjinScriptEngine.java:109)
	at de.biomedical_imaging.ij.trajectory_classifier.RRFClassifierRenjin.classify(RRFClassifierRenjin.java:224)
	at de.biomedical_imaging.ij.trajectory_classifier.WeightedWindowedClassificationProcess.windowedClassification(WeightedWindowedClassificationProcess.java:62)
	at de.biomedical_imaging.ij.trajectory_classifier.TraJClassifier_.classifyAndSegment(TraJClassifier_.java:636)
	at de.biomedical_imaging.ij.trajectory_classifier.TraJClassifier_.run(TraJClassifier_.java:307)
	at ij.IJ.runUserPlugIn(IJ.java:228)
	at ij.IJ.runPlugIn(IJ.java:192)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:745)

Any help appreciated, thanks!