Bug 81 – 3D Viewer can't take an 8-bit color image

Bug 81 - 3D Viewer can't take an 8-bit color image


Summary:	3D Viewer can't take an 8-bit color image

Status:	RESOLVED FIXED

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

Importance:	P4 normal
Assigned To:	ImageJ Bugs Mailing List

URL:

Depends on:
Blocks:

Reported:	2009-09-26 13:12 CDT by Albert Cardona
Modified:	2011-02-06 16:01 CST
CC List:	1 user (show)

See Also:

Description Albert Cardona 2009-09-26 13:12:10 CDT

Useful Java System Properties:
  os.arch => i386
  os.name => Linux
  os.version => 2.6.27-14-generic
  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.X11GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => gnome
  file.separator => /

Bug Report Text:

On opening a template.labels amira file, and then trying
to see it in the 3D Viewer, it asks me: "Convert to 8-bit?"
I say yes. Then it announces: "Format not supported" and ... crashes!

Exception in thread "Thread-46" java.lang.NullPointerException
	at voltex.VoltexVolume.updateData(VoltexVolume.java:119)
	at voltex.VoltexVolume.<init>(VoltexVolume.java:104)
	at voltex.VoltexVolume.<init>(VoltexVolume.java:68)
	at voltex.VolumeRenderer.<init>(VolumeRenderer.java:71)
	at voltex.VoltexGroup.<init>(VoltexGroup.java:71)
	at ij3d.Content.displayAs(Content.java:119)
	at ij3d.Image3DUniverse.addContent(Image3DUniverse.java:505)
	at ij3d.Executer.addC(Executer.java:194)
	at ij3d.Executer.access$000(Executer.java:53)
	at ij3d.Executer$1.run(Executer.java:104)
./run-debug-gnome: line 2:  7981 Segmentation fault      JAVA_HOME=/home/albert/Programming/fiji/java/linux/jdk1.6.0_16 ./fiji -cp ./TrakEM2/clj -Xincgc -XX:+DisableExplicitGC -agentlib:jdwp=transport=dt_socket,address=8010,server=y,suspend=n -- "$@"

Comment 1 Johannes Schindelin 2009-11-12 02:21:06 CST

Could you please try opening it with Plugins>Process>Show Color Surfaces?  At the moment, this is very slow, due to an inefficient implementation of a 3D Gaussian blur, but if this plugin works for you, I will work on improving the performance, and on integrating it into Plugins>3D Viewer.

Comment 2 Albert Cardona 2009-11-24 16:59:17 CST

I tried with the Fly Brain sample stack, converting it to 8-bit color. Then run the Show color surfaces with default parameters. The resulting 3D image looks broken up into a myriad of pieces, but at least it didn't fail with an exception. And it refined it for several minutes until I gave up on it.

An easier cure would be to convert 8-bit color to RGB stacks prior to adding them to the 3D viewer.


Some observations:

 - the plugin uses lots of progress bars: it's hard to tell how far it has really progressed.

- in debug mode, ImageJ freezes when running "Show Color Surfaces" without an image open, i.e. after the "No images are open" dialog pops up.