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StuartLab / MiNA

MiNA (Mitochondrial Network Analysis) is a project aimed at making the analysis and characterization of mitochondrial network morphology more accurate, faster, and objective. This project currently consists of a set of Python scripts (and JAVA for the user interface) for the Fiji distribution of ImageJ.
GNU General Public License v3.0
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Plugin won't run bc of exception window #38

Closed hcha2 closed 3 years ago

hcha2 commented 3 years ago

Hi,

I am having issues on both Windows and a Mac, running the StuartLab-> MiNA Script -> MiNA Analyze Morphology Plug-in. An exception window comes up and says the following:

(Fiji Is Just) ImageJ 2.3.0/1.53f51; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 51MB of 5930MB (<1%)

java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:307) at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:166) at ij.IJ.runPlugIn(IJ.java) at ij.Executer.runCommand(Executer.java:150) at ij.Executer.run(Executer.java:68) at java.lang.Thread.run(Thread.java:748) Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception 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:303) ... 5 more Caused by: java.lang.RuntimeException: Module threw exception at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63) at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ... 1 more Caused by: java.lang.NullPointerException at org.scijava.ui.swing.widget.SwingNumberWidget.lambda$suitableFormat$0(SwingNumberWidget.java:344) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.reduce(ReferencePipeline.java:479) at java.util.stream.ReferencePipeline.max(ReferencePipeline.java:515) at org.scijava.ui.swing.widget.SwingNumberWidget.suitableFormat(SwingNumberWidget.java:344) at org.scijava.ui.swing.widget.SwingNumberWidget.set(SwingNumberWidget.java:127) at org.scijava.ui.swing.widget.SwingNumberWidget.set(SwingNumberWidget.java:74) at org.scijava.plugin.WrapperService.create(WrapperService.java:65) at org.scijava.widget.AbstractInputHarvester.addInput(AbstractInputHarvester.java:110) at org.scijava.widget.AbstractInputHarvester.buildPanel(AbstractInputHarvester.java:84) at org.scijava.widget.InputHarvester.harvest(InputHarvester.java:67) at org.scijava.ui.AbstractInputHarvesterPlugin.process(AbstractInputHarvesterPlugin.java:74) at org.scijava.module.ModuleRunner.preProcess(ModuleRunner.java:102) at org.scijava.module.ModuleRunner.run(ModuleRunner.java:152) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124) ... 6 more

I keep seeing "Module threw exception" and was wondering what I could do. I have tried uninstalling and installing Fiji and also updated Java to the latest version. Would appreciate any help or advice!

RodoVJ commented 3 years ago

Hello, how are you downloading MiNA?

hcha2 commented 3 years ago

Hi, I downloaded FiJi, and in Help -> Update... -> Manage Update sites -> added Biomedgroup & StuartLab. Then I restarted Fiji. This is when I started getting the 'Module threw exception' window.

I then to download MiNA another way. I downloaded the contents of the folders in https://github.com/StuartLab/MiNA as a zipped folder and followed the instructions below.

  1. Go to your FIJI installation and go to the "Fiji.app" folder. If you're using mac, right click on the FIJI icon and select "Show Package Contents".
  2. Move the folder with the name "mina" located in "src" of this repository to jars>Lib (create the folder Lib if it does not already exist).
  3. Move the file "MiNA_Analyze_Morphology.py" located at "src>scripts" to "scripts".
  4. Move the folder "mina_icons" inside "images".
  5. In the "build" folder of this repository you will see a jar file. Move it inside "plugins".
  6. Finally, start ImageJ and if you don't have the Biomedroup site installed then click on Help->Update... Navigate to the update site manager (Manage update sites). Add the "Biomedgroup" site by checking the checkbox beside the site. Close the site manager dialog (Close) and apply the changes (Apply changes)

Now I get notifications that there are duplicate commands on Fiji and I still get the same 'Module threw exception' window when I try to run the MiNA plug-in.

RomainPe commented 3 years ago

Hi,

Im just having the same problem and I dont know how to resolve it, when i run Mina Analyse an exception window open

(Fiji Is Just) ImageJ 2.3.0/1.53f51; Java 1.8.0_172 [64-bit]; Windows 10 10.0; 82MB of 9096MB (<1%)

java.lang.RuntimeException: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception at net.imagej.legacy.LegacyService.runLegacyCompatibleCommand(LegacyService.java:307) at net.imagej.legacy.DefaultLegacyHooks.interceptRunPlugIn(DefaultLegacyHooks.java:166) at ij.IJ.runPlugIn(IJ.java) at ij.Executer.runCommand(Executer.java:150) at ij.Executer.run(Executer.java:68) at java.lang.Thread.run(Thread.java:748) Caused by: java.util.concurrent.ExecutionException: java.lang.RuntimeException: Module threw exception 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:303) ... 5 more Caused by: java.lang.RuntimeException: Module threw exception at org.scijava.module.ModuleRunner.call(ModuleRunner.java:127) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:63) at org.scijava.thread.DefaultThreadService.lambda$wrap$2(DefaultThreadService.java:225) at java.util.concurrent.FutureTask.run(FutureTask.java:266) at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1149) at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:624) ... 1 more Caused by: java.lang.NullPointerException at org.scijava.ui.swing.widget.SwingNumberWidget.lambda$suitableFormat$0(SwingNumberWidget.java:344) at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193) at java.util.Spliterators$ArraySpliterator.forEachRemaining(Spliterators.java:948) at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481) at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471) at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708) at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.util.stream.ReferencePipeline.reduce(ReferencePipeline.java:479) at java.util.stream.ReferencePipeline.max(ReferencePipeline.java:515) at org.scijava.ui.swing.widget.SwingNumberWidget.suitableFormat(SwingNumberWidget.java:344) at org.scijava.ui.swing.widget.SwingNumberWidget.set(SwingNumberWidget.java:127) at org.scijava.ui.swing.widget.SwingNumberWidget.set(SwingNumberWidget.java:74) at org.scijava.plugin.WrapperService.create(WrapperService.java:65) at org.scijava.widget.AbstractInputHarvester.addInput(AbstractInputHarvester.java:110) at org.scijava.widget.AbstractInputHarvester.buildPanel(AbstractInputHarvester.java:84) at org.scijava.widget.InputHarvester.harvest(InputHarvester.java:67) at org.scijava.ui.AbstractInputHarvesterPlugin.process(AbstractInputHarvesterPlugin.java:74) at org.scijava.module.ModuleRunner.preProcess(ModuleRunner.java:102) at org.scijava.module.ModuleRunner.run(ModuleRunner.java:152) at org.scijava.module.ModuleRunner.call(ModuleRunner.java:124) ... 6 more

I thank you in advance if you have the solution

hcha2 commented 3 years ago

Hi, I resolved this issue by downloading MiNA through these steps:

  1. If you by chance added StuartLab through Help -> Update... -> Manage Update sites, then you must undo that. Go to Help -> Update... -> Manage Update sites and UNCHECK StuartLab.

  2. After unchecking StuartLab, go to https://github.com/StuartLab/MiNA as a zipped folder and download the contents of the folders in the website.

  3. Go to your FIJI installation and go to the "Fiji.app" folder. If you're using mac, right click on the FIJI icon and select "Show Package Contents".

  4. Move the folder with the name "mina" located in "src" of this repository to jars>Lib (create the folder Lib if it does not already exist).

  5. Move the file "MiNA_Analyze_Morphology.py" located at "src>scripts" to "scripts".

  6. Move the folder "mina_icons" inside "images".

  7. In the "build" folder of this repository you will see a jar file. Move it inside "plugins".

  8. Finally, start ImageJ and if you don't have the Biomedroup site installed then click on Help->Update... Navigate to the update site manager (Manage update sites). Add the "Biomedgroup" site by checking the checkbox beside the site.

  9. Close the site manager dialog (Close) and apply the changes (Apply changes)

  10. Restart Fiji

pguptabhm commented 2 years ago

Did as mentioned above. Plug-in still didn't work! Please advise. Thanks