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Bug 658 - Fiji reverts preferences back to their defaults
Fiji reverts preferences back to their defaults
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2013-09-03 14:14 CDT by Curtis Rueden
Modified: 2013-09-11 10:33 CDT
3 users (show)

See Also:
Description Curtis Rueden 2013-09-03 14:14:10 CDT 
As reported by an anonymous IRC user today: with a fully updated Fiji, changing a preference in the Edit > Preferences menu, quitting Fiji, and then opening Fiji again resets the preference back to its default value.

The user wrote: "The problem is that it seems that preferences actually are saved, because when I change anything manually in .imagej/IJ_Prefs.txt it gets reverted back to original when I close Fiji. Or better said back to default. If I change anything manually before opening Fiji it is not reflected."

Bug occurs on both Ubuntu Linux 12.04 64-bit and 13.04 64-bit (and very likely other Linuxes), with both OpenJDK 1.7.0 and Fiji's default shipped version of Java 6.

My (very speculative) guess is that the problem might be related to the ImageJ2 legacy layer options synchronization, which is Johannes's *favorite* part of ImageJ!

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 3.2.0-49-generic
  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: CHECK_TURNED_OFF

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /home/curtis/apps/fiji/java/linux-amd64/jdk1.6.0_24//jre
  ij.dir => /home/curtis/apps/fiji

Information about the version of each plugin:

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Comment 1 Curtis Rueden 2013-09-03 15:19:08 CDT 
FWIW, I verified that this bug still occurs with the latest SNAPSHOT builds of ImageJ2 and ImgLib2.
Comment 2 Curtis Rueden 2013-09-03 15:22:23 CDT 
Bug also occurs on the OS X version of Fiji. Bug does *not* occur with the Lifeline version of Fiji.
Comment 3 Johannes Schindelin 2013-09-04 16:59:37 CDT 
I just tested with the current -SNAPSHOT version of ImageJ2 (including that pesky legacy layer) and the issue is fixed, most likely by the OptionPlugin fixes or by disabling the OptionsSynchronizer to run prematurely (and in the wrong direction) in legacy mode.

So it seems this will be fixed when we upload beta 7.3, most likely tomorrow morning (UTC-0500).
Comment 4 Curtis Rueden 2013-09-10 10:01:51 CDT 
We released ImageJ2 2.0.0-beta-7.3 late last week, and can pin Fiji to it now, which should hopefully fix this bug. However, there is one issue with the SLF4J/log4j JARs: they need to be marked obsolete on the ImageJ update site, and reinstated on the Fiji update site. Dscho had an idea for best (i.e., most safely) accomplishing this; we will discuss and implement soon.
Comment 5 Johannes Schindelin 2013-09-10 13:35:17 CDT 
I just uploaded the new version to the update site and documented in https://github.com/imagej/imagej/blob/master/RELEASES.md what needs to be done if files required by Fiji will be marked obsolete on the ImageJ update site.
Comment 6 Curtis Rueden 2013-09-10 15:02:55 CDT 
I tested on my OS X system with vanilla ImageJ v1.47v and the latest Fiji, and I am happy to report the behavior is now the same for both.

That said, I tested with three different preferences, and was surprised that both Fiji and plain ImageJ failed to remember two of the three. They are:

1) Edit > Options > Line Width...
2) Edit > Options > Input/Output..., "Use JFileChooser to open/save"
3) Edit > Options > Appearance, "Open images at 100%"

Of those three, only the third survived a JVM restart. Line Width was reset to 1, and the JFileChooser toggle was reset to unchecked.

I am not sure whether that behavior is intended or a bug, though...
Comment 7 Wayne Rasband 2013-09-11 10:30:41 CDT 
This behavior is intentional. Line width is always reset to 1 on startup and the "Use JFileChooser to open/save" preference is not saved on OS X because the JFileChooser does not work well on OS X.
Comment 8 Curtis Rueden 2013-09-11 10:33:13 CDT 
Thanks for the clarification, Wayne. Sounds like I just got "unlucky" in selecting my test options. Good to know this bug can remain closed.