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Bug 1010 - All stack tools fail after 2/27 update
All stack tools fail after 2/27 update
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
Macintosh Mac OS
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2015-02-27 10:55 CST by spraguecleghorn
Modified: 2015-03-01 22:31 CST
3 users (show)

See Also:

Description spraguecleghorn 2015-02-27 10:55:09 CST
The following exception is thrown when applying stack tools to a hyperstack:

(Fiji Is Just) ImageJ 2.0.0-rc-25/1.49m; Java 1.6.0_65 [64-bit]; Mac OS X 10.10.2; 154MB of 3497MB (4%)
 
java.lang.NullPointerException
	at net.imagej.legacy.translate.AbstractDisplayCreator.getDataset(AbstractDisplayCreator.java:76)
	at net.imagej.legacy.translate.GrayDisplayCreator.grayCase(GrayDisplayCreator.java:159)
	at net.imagej.legacy.translate.GrayDisplayCreator.makeDisplay(GrayDisplayCreator.java:129)
	at net.imagej.legacy.translate.AbstractDisplayCreator.createDisplay(AbstractDisplayCreator.java:63)
	at net.imagej.legacy.translate.DefaultImageTranslator.createDisplay(DefaultImageTranslator.java:100)
	at net.imagej.legacy.translate.DefaultImageTranslator.createDisplay(DefaultImageTranslator.java:84)
	at net.imagej.legacy.LegacyImageMap.registerLegacyImage(LegacyImageMap.java:271)
	at net.imagej.legacy.DefaultLegacyHooks.registerImage(DefaultLegacyHooks.java:177)
	at ij.gui.ImageWindow.show(ImageWindow.java)
	at ij.gui.ImageWindow.<init>(ImageWindow.java:138)
	at ij.gui.StackWindow.<init>(StackWindow.java:28)
	at ij.gui.StackWindow.<init>(StackWindow.java:24)
	at ij.ImagePlus.show(ImagePlus.java:388)
	at ij.plugin.ZProjector.run(ZProjector.java:156)
	at ij.IJ.runPlugIn(IJ.java:172)
	at ij.Executer.runCommand(Executer.java:131)
	at ij.Executer.run(Executer.java:64)
	at java.lang.Thread.run(Thread.java:695)

Information about your version of Java:

  os.arch => x86_64
  os.name => Mac OS X
  os.version => 10.10.2
  java.version => 1.6.0_65
  java.vendor => Apple Inc.
  java.runtime.name => Java(TM) SE Runtime Environment
  java.runtime.version => 1.6.0_65-b14-466.1-11M4716
  java.vm.name => Java HotSpot(TM) 64-Bit Server VM
  java.vm.version => 20.65-b04-466.1
  java.vm.vendor => Apple Inc.
  java.vm.info => mixed mode
  java.awt.graphicsenv => apple.awt.CGraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => null
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: null
  imagej.dir => /Applications/Fiji.app

Information about the version of each plugin:

Activated update sites:
ImageJ: http://update.imagej.net/ (last check:20150226143217)
Fiji: http://fiji.sc/update/ (last check:20150226143401)

Files not up-to-date:
  1ad3be0d (LOCAL_ONLY) 20140925112353 jars/jpedalSTD.jar
Comment 1 Mark Hiner 2015-02-27 11:09:31 CST
I can only confirm this happens when "Edit > Options > ImageJ2 > Enable ImageJ2 data structures" is checked. If unchecked I am able to apply stack tools without problem.

To reproduce this issue I am doing the following:
1. Open Samples > Mitosis
2. Run Image > Stack > Z Project

If you have a sequence which fails even without "Enable ImageJ2 data structures" checked, please let me know.

Thanks!
Comment 2 Mark Hiner 2015-02-27 11:53:35 CST
Note that this looks to be a general bug in how image titles were being transferred from ImagePlus to Dataset. A tentative fix can be found here:
https://github.com/imagej/imagej-legacy/commit/b660d6754501353b29a1104bd1b0418103357ffe

Until this goes live in Fiji, it should be sufficient to disable "Edit > Options > ImageJ2 > Enable ImageJ2 data structures" as this will cause problems when ImagePluses are generated by commands (such as running Z project... on a stack).
Comment 3 spraguecleghorn 2015-02-27 12:47:53 CST
Thanks for your prompt replies, Mark. Not enabling ImageJ2 data structures does indeed allow normal operation of the stack tools. 

And thank you for proposing a fix as well.
Comment 4 Curtis Rueden 2015-03-01 22:31:08 CST
The fix has been uploaded. Run Help > Update... to receive it.

Note that it is also recommended to disable the "Enable ImageJ2 data structures" option in Edit > Options > ImageJ2, since this feature is still buggy and causes performance problems.