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Bug 410 - java.lang.reflect.InvocationTargetException running pQCT tools
java.lang.reflect.InvocationTargetException running pQCT tools
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2012-03-06 00:10 CST by Michael Doube
Modified: 2012-03-06 12:05 CST
1 user (show)

See Also:

Description Michael Doube 2012-03-06 00:10:07 CST
When running Plugins > pQCT > Density Distribution (from BoneJ plugin), this exception is spewed just after the Results window is displayed (no results shown, though). The plugin works fine in ImageJ 1.46f.

Source of the pQCT plugin is at:
https://github.com/mdoube/BoneJ/tree/testing/src/org/doube/bonej/pqct

java.lang.reflect.InvocationTargetException
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at ij.Command.runPlugIn(Command.java:146)
	at ij.Command.runCommand(Command.java:95)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.NullPointerException
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:47)
	at ij.IJ.runUserPlugIn(IJ.java:183)
	at ij.IJ.runPlugIn(IJ.java:150)
	at ij.IJ.runPlugIn(IJ.java:139)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:411)
	at ij.io.Opener.openImage(Opener.java:288)
	at ij.io.Opener.openImage(Opener.java:307)
	at ij.ImagePlus.<init>(ImagePlus.java:127)
	at org.doube.bonej.pqct.utils.ResultsImage.getRGBResultImage(ResultsImage.java:35)
	at org.doube.bonej.pqct.Distribution_Analysis.run(Distribution_Analysis.java:311)
	at ij.IJ.runUserPlugIn(IJ.java:183)
	at ij.IJ.runPlugIn(IJ.java:150)
	... 8 more


Information about your version of Java - this information is useful for the Fiji developers:

  os.arch => amd64
  os.name => Linux
  os.version => 3.3.0-rc3-vaio
  java.version => 1.6.0_24
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_24-b07
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 19.1-b02
  java.vm.vendor => Sun Microsystems Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => sun.awt.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => gnome
  file.separator => /

The up-to-date check says: You wanted never to be reminded.

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /home/mdoube/Fiji.app/java/linux-amd64/jdk1.6.0_24/jre
  ij.dir => /home/mdoube/Fiji.app

Information about the version of each plugin:

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Comment 1 Johannes Schindelin 2012-03-06 00:40:09 CST
From the code

http://fiji.sc/HandleExtraFileTypes.java:47

it appears as if the path is not passed as an absolute one. Is it possible that line 35 in ResultsImage might be faulty in that respect?
Comment 2 Michael Doube 2012-03-06 11:24:38 CST
> http://fiji.sc/HandleExtraFileTypes.java:47
>  
> it appears as if the path is not passed as an absolute one. Is it possible that
> line 35 in ResultsImage might be faulty in that respect?


I added an absolute path:
https://github.com/mdoube/BoneJ/commit/369a046735533eb22d0f03a79c11319ec71f17fd

But now get another similar exception. Plugin still runs fine in IJ
1.46f, so what is special with Fiji that we are not taking care of?

java.lang.reflect.InvocationTargetException
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at
sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at
sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:597)
	at ij.Command.runPlugIn(Command.java:146)
	at ij.Command.runCommand(Command.java:95)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:662)
Caused by: java.lang.ArrayIndexOutOfBoundsException: Array index out of
range: 0
	at java.util.Vector.get(Vector.java:694)
	at
org.doube.bonej.pqct.selectroi.RoiSelector.selectRoiBiggestBoneDetectedEdges(RoiSelector.java:401)
	at
org.doube.bonej.pqct.selectroi.RoiSelector.getSieve(RoiSelector.java:213)
	at org.doube.bonej.pqct.selectroi.SelectROI.<init>(SelectROI.java:69)
	at
org.doube.bonej.pqct.Distribution_Analysis.run(Distribution_Analysis.java:273)
	at ij.IJ.runUserPlugIn(IJ.java:183)
	at ij.IJ.runPlugIn(IJ.java:150)