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Bug 1105 - java.lang.NullPointerException Analyse Skeleton
java.lang.NullPointerException Analyse Skeleton
Status: CONFIRMED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 critical
Assigned To: Ignacio Arganda
Depends on:
Blocks:
 
Reported: 2015-07-02 11:53 CDT by Erick
Modified: 2015-07-02 14:55 CDT
3 users (show)

See Also:
Description Erick 2015-07-02 11:53:18 CDT 
Analyse Skeleton couldn't finish the analyse

It take hours and can't finish.

After close the window, it says:

java.lang.NullPointerException

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  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.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Users\Asus\Desktop\Fiji.app/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Users\Asus\Desktop\Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150623235330)
Fiji: http://fiji.sc/update/ (last check:20150702085244)

Files not up-to-date:
  6d15bb1c (MODIFIED) 20150702115803 jars/ij-1.49v.jar
  1ad3be0d (LOCAL_ONLY) 20141222140600 jars/jpedalSTD.jar
  34e56692 (LOCAL_ONLY) 20150629155033 plugins/BoneJ_.jar
  14f0b2c2 (LOCAL_ONLY) 20150629153853 plugins/Extract_Surface.jar
  0506b2b4 (LOCAL_ONLY) 20150629153858 plugins/Quick3dApplet-1.0.8.jar
  9d331d28 (MODIFIED) 20150428153320 plugins/Volume_Viewer.jar
  f817eddb (LOCAL_ONLY) 20130126230448 plugins/ij-dcraw_.jar
  a53a72ed (LOCAL_ONLY) 20110402233256 plugins/ij-plugins_toolkit-nodep.jar
Comment 1 Mark Hiner 2015-07-02 14:55:12 CDT 
This behavior can be confirmed by running Analyze Skeleton on an large-ish image like the sample MRI Stack.

The tagged skeleton pops up immediately but the results table takes a significant amount of time to appear. If the tagged skeleton image is closed before the results table pops, an NPE is thrown.

I think the perfect world solution would be:

1) reporting progress events, perhaps per plane?

and either:

2a) avoiding the NPE if the tagged skeleton image is closed before the analysis is completed (that is, allowing clean aborts)
or
2b) preventing the tagged skeleton image from being closed before analysis is completed

But how you want to handle this is up to you Ignacio, as I wouldn't call either of these "bugs", just inconveniences.

If you think there's something going on in Fiji that's causing the algorithm to take longer than expected though - let us know!