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rickud / gel-lanes-fit

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Gel Lanes fit not starting up #5

Open davidgirata opened 5 years ago

davidgirata commented 5 years ago

After restarting Gel Lanes fit, the plugin threw an error and it did not start. The following is the code: [INFO] Gel Lanes Fit [INFO] Gel Lanes Fit 1.0.5 [INFO] Loading gel-lanes-fit\data\2019_2_15\saved-state.bak ... [ERROR] Module threw exception org.apache.commons.math3.exception.NotPositiveException: number of elements should be positive (-5) at org.apache.commons.math3.linear.ArrayRealVector.getSubVector(ArrayRealVector.java:646) at gellanesfit.Ladder.getMolecularWeights(MainDialog.java:1799) at gellanesfit.MainDialog.updateLadderType(MainDialog.java:1153) at gellanesfit.MainDialog.setupMainDialog(MainDialog.java:567) at gellanesfit.MainDialog.(MainDialog.java:253) at gellanesfit.GelLanesFit.init(GelLanesFit.java:87) at gellanesfit.GelLanesFit.run(GelLanesFit.java:107) at org.scijava.command.CommandModule.run(CommandModule.java:199) at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66) at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) at java.lang.Thread.run(Thread.java:748)

This is the "exception" displayed (Fiji Is Just) ImageJ 2.0.0-rc-68/1.52h; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 51MB of 5967MB (<1%)

java.lang.RuntimeException: java.util.concurrent.ExecutionException: org.apache.commons.math3.exception.NotPositiveException: number of elements should be positive (-5) at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:303) at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:163) at ij.IJ.runPlugIn(IJ.java) at ij.Executer.runCommand(Executer.java:137) at ij.Executer.run(Executer.java:66) at java.lang.Thread.run(Thread.java:748) Caused by: java.util.concurrent.ExecutionException: org.apache.commons.math3.exception.NotPositiveException: number of elements should be positive (-5) at java.util.concurrent.FutureTask.report(FutureTask.java:122) at java.util.concurrent.FutureTask.get(FutureTask.java:192) at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:299) ... 5 more Caused by: org.apache.commons.math3.exception.NotPositiveException: number of elements should be positive (-5) at org.apache.commons.math3.linear.ArrayRealVector.getSubVector(ArrayRealVector.java:646) at gellanesfit.Ladder.getMolecularWeights(MainDialog.java:1799) at gellanesfit.MainDialog.updateLadderType(MainDialog.java:1153) at gellanesfit.MainDialog.setupMainDialog(MainDialog.java:567) at gellanesfit.MainDialog.(MainDialog.java:253) at gellanesfit.GelLanesFit.init(GelLanesFit.java:87) at gellanesfit.GelLanesFit.run(GelLanesFit.java:107) at org.scijava.command.CommandModule.run(CommandModule.java:199) at org.scijava.module.ModuleRunner.run(ModuleRunner.java:168) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:66) at org.scijava.thread.DefaultThreadService$3.call(DefaultThreadService.java:238) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ... 1 more

davidgirata commented 5 years ago

After some exploration, it seems that what fixed this issue was to delete the Gel Lane Fits data of that particular gel from the actual computer. The issue may have been caused by accidentally putting a lower band at the first band, and a higher band as the last one (when creating ranges for the HiLo Ladder).

sdlevene commented 5 years ago

I can see how that would trigger an error.

SDL

From: davidgirata [mailto:notifications@github.com] Sent: Friday, February 15, 2019 3:03 PM To: rickud/gel-lanes-fit Cc: Subscribed Subject: Re: [rickud/gel-lanes-fit] Gel Lanes fit not starting up (#5)

After some exploration, it seems that what fixed this issue was to delete the Gel Lane Fits data of that particular gel from the actual computer. The issue may have been caused by accidentally putting a lower band at the first band, and a higher band as the last one (when creating ranges for the HiLo Ladder).

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rickud commented 5 years ago

Actually, let's keep this open. the plug-in should check that this doesn't happen or react to it if it does. Let me look into it.

For future reference, deleting the state file (2019_2_15\saved-state.bak) for the gel that was last opened should fix the problem.