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Bug 140 - 3d viewer freezes without generating anything
3d viewer freezes without generating anything
Status: RESOLVED WORKSFORME
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2010-02-18 16:59 CST by Christian
Modified: 2011-03-23 15:52 CDT
3 users (show)

See Also:

Description Christian 2010-02-18 16:59:35 CST
When I select 'show in 3d' in TrakEM2 3d-Viewer opens with an empty white bar inthe lower part of the window. I am asked to confirm resampling N which i do. No content shows after that. Windows task manager shows virtually idle CPU for long time. I can look at different Menus of 3d-Viewer but after a while it freezes showing funny effects when i drag it on the desktop. When frozen i can only kill it by task manager, killing FIJI at the same time. Fiji is installed in a different place on C:\ from other programs including a JAVA environment that was already on the computer.
Information about your version of Java - this information is useful for the Fiji developers:
  os.arch => x86
  os.name => Windows XP
  os.version => 5.1
  java.version => 1.6.0_16
  java.vendor => Sun Microsystems Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_16-b01
  java.vm.name => Java HotSpot(TM) Client VM
  java.vm.version => 14.2-b01
  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 => \
Comment 1 Albert Cardona 2010-02-18 18:12:07 CST
Thank you for reporting this error. I saw a similar error to what you are describing recently, and a fix was released.

So first question: have you updated Fiji recently? If not, please call "Help - Update Fiji" to get the latest version of all packages.
Comment 2 Albert Cardona 2010-02-23 09:55:19 CST
>Hello Sapristi,
>yes, my Fiji says it is up to date (as per automatic update).
>In advanced mode of the updater though, the following items
>show as uninstalled :
>SIOX plugin
>RATS plugin
>fiji-lib.jar
>weka.jar
>Why these are not installed, i have no clue. Would these solve my problem?


I have no clue either, for I don't have any Windows machine to test on. If anything, these jar files should be installed. weka.jar is a dependency of TrakEM2--perhaps its absence is causing problems.
Please check if the weka.jar really isn't in the Fiji.app/jars/ folder.

Please reply to the bug report at bugzilla webpage, otherwise I may overlook it.
Comment 3 Christian 2010-02-23 12:03:48 CST
Thank you for following up.
Sorry for not using the bugzilla webpage for the last communication (attached below)
I installed weka.jar and fiji-lib.jar and no improvement.
I then noticed that after starting 3dViewer I have an error message in System-Log that reads: \\fileserver\profiles$\Desktop\.ImageJ_3D_Viewer.props (Zugriff verweigert)
Now i searched for files named "ImageJ_3D_Viewer.props" but i did not find any.
Any hints?

> Hello Sapristi,
> >yes, my Fiji says it is up to date (as per automatic update).
> >In advanced mode of the updater though, the following items
> >show as uninstalled :
> >SIOX plugin
> >RATS plugin
> >fiji-lib.jar
> >weka.jar
> >Why these are not installed, i have no clue. Would these solve my problem?


I have no clue either, for I don't have any Windows machine to test on. If
anything, these jar files should be installed. weka.jar is a dependency of
TrakEM2--perhaps its absence is causing problems.
Please check if the weka.jar really isn't in the Fiji.app/jars/ folder.

Please reply to the bug report at bugzilla webpage, otherwise I may overlook
it.

Comment 4 Johannes Schindelin 2010-02-23 12:19:00 CST
Just a wild shot in the dark (I do not have enough information to make an educated guess): maybe the object you are trying to visualize is very, very large? Or your graphics adapter has little texture memory? That would explain the freeze after a delay.
Comment 5 Christian 2010-02-23 16:13:29 CST
Hello Johannes,
I just tried with the ImageJ Sample "Bat Cochlea" scaled up by 2x. Now that is really not such a big structure. After using 'Show as Volume' which started the 3d_viewer i got no content in the viewer window but this error message in the Log:
ERROR:
java.lang.IllegalArgumentException: Argument out of range: 1

	at ij.ImageStack.getPixels(ImageStack.java:159)

	at ini.trakem2.persistence.FSLoader.fetchImage(FSLoader.java:479)

	at ini.trakem2.persistence.FSLoader.fetchImagePlus(FSLoader.java:449)

	at ini.trakem2.imaging.PatchStack$VirtualStack.getPixels(PatchStack.java:681)

	at ij3d.Volume$ByteLoader.<init>(Volume.java:238)

	at voltex.VoltexVolume$ByteLoader.<init>(VoltexVolume.java:368)

	at voltex.VoltexVolume.initLoader2(VoltexVolume.java:163)

	at voltex.VoltexVolume.<init>(VoltexVolume.java:102)

	at voltex.VoltexVolume.<init>(VoltexVolume.java:68)

	at voltex.VolumeRenderer.<init>(VolumeRenderer.java:72)

	at voltex.VoltexGroup.<init>(VoltexGroup.java:72)

	at ij3d.Content.displayAs(Content.java:119)

	at ij3d.Image3DUniverse.addContent(Image3DUniverse.java:506)

	at ij3d.Image3DUniverse.addVoltex(Image3DUniverse.java:572)

	at ini.trakem2.display.Display3D.showVolume(Display3D.java:569)

	at ini.trakem2.display.Display$22.run(Display.java:3977)

	at ini.trakem2.utils.Dispatcher$Task.run(Dispatcher.java:46)

	at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:441)

	at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)

	at java.util.concurrent.FutureTask.run(FutureTask.java:138)

	at java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)

	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)

	at java.lang.Thread.run(Thread.java:619)
Does this explain anything?
Comment 6 Albert Cardona 2010-02-23 20:29:29 CST
Christian, this bug is in trakem2 as your Exception stack trace indicates. I will fix it after March 1st -- hard deadline for a grant application.
Comment 7 Johannes Schindelin 2011-03-23 15:13:03 CDT
Albert, was this fixed yet?
Comment 8 Albert Cardona 2011-03-23 15:52:04 CDT
(In reply to comment #7)
> Albert, was this fixed yet?


As far as I know it is fixed.