Bug 1182 – 3D Convex Hull plugin uses all available memory and processor but does not complete

Bug 1182 - 3D Convex Hull plugin uses all available memory and processor but does not complete


Summary:	3D Convex Hull plugin uses all available memory and processor but does not co...

Status:	NEEDSINFO

Product:	Fiji
Classification:	Unclassified
Component:	Plugins
Version:	unspecified
Hardware:	PC Windows

Importance:	P4 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2015-11-02 13:26 CST by Nick Galati
Modified:	2015-11-02 15:14 CST
CC List:	2 users (show)

See Also:

Attachments
Thread dump from 3D Convex Hull hang (7.29 KB, text/plain) 2015-11-02 15:14 CST, Nick Galati

Description Nick Galati 2015-11-02 13:26:58 CST

When using the 3D Convex Hull plugin on a binary image stack with ~700 points, the 3D Convex Hull plugin uses all of the processor and slowly consumes all memory but it doesn't ever actually finish. 

I can run the same plugin in IJ1 with the same image and the convex hull is created in ~20 seconds.

Information about your version of Java:

  os.arch => amd64
  os.name => Windows NT (unknown)
  os.version => 6.2
  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: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Users\Nick\Desktop\FIJI~1.APP/java/win64/jdk1.6.0_24//jre
  imagej.dir => C:\Users\Nick\Desktop\FIJI~1.APP

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20151026135651)
Fiji: http://update.fiji.sc/ (last check:20151028093859)
3D ImageJ Suite: http://sites.imagej.net/Tboudier/ (last check:20151008005610)

Files not up-to-date:
  8cb8d89b (LOCAL_ONLY) 20151102112105 plugins/quickhull3d.jar

Comment 1 Curtis Rueden 2015-11-02 13:34:26 CST

You could try analyzing what ImageJ is doing during the processing, according to this guide:

  http://imagej.net/Troubleshooting#If_ImageJ_freezes_or_hangs

While you are not experiencing a "hang" per se, you can still generate stack traces during the processing -- in both IJ1 and IJ2 -- and then compare the differences. It may shed some light on the culprit. If I had to take a wild guess, I'd say you might see something relating to "net.imagej.legacy" doing syncing stuff? But hard to be sure until you actually check.

Alternately, if you create an MCVE such that we can reproduce, we can go from there.

  http://imagej.net/Bug_reporting_best_practices

Comment 2 Nick Galati 2015-11-02 15:12:30 CST

(In reply to Curtis Rueden from comment #1)
> You could try analyzing what ImageJ is doing during the processing,
> according to this guide:
> 
>   http://imagej.net/Troubleshooting#If_ImageJ_freezes_or_hangs
> 
> While you are not experiencing a "hang" per se, you can still generate stack
> traces during the processing -- in both IJ1 and IJ2 -- and then compare the
> differences. It may shed some light on the culprit. If I had to take a wild
> guess, I'd say you might see something relating to "net.imagej.legacy" doing
> syncing stuff? But hard to be sure until you actually check.
> 
> Alternately, if you create an MCVE such that we can reproduce, we can go
> from there.
> 
>   http://imagej.net/Bug_reporting_best_practices

1) I have uploaded the file "Binary_Duplicate.tif" via Help > Upload Sample Data
2) Open the image
3) Run Plugins>3D>3D Convex Hull 
3a)the quickhull3d.jar needs to be installed in the plugins folder
from: http://imagejdocu.tudor.lu/doku.php?id=plugin:stacks:3d_ij_suite:start
4) The plugin does not finish and gradually consumes resources
5) The thread dump is attached from my machine (Windows 8; Java 8 (just updated))


Thanks for your help. I'll work on my bug reporting practices to make life easier.

Comment 3 Nick Galati 2015-11-02 15:14:06 CST

Created attachment 274
Thread dump from 3D Convex Hull hang