Bug 652 – Z/C/T sliders on images do not work anymore

Bug 652 - Z/C/T sliders on images do not work anymore


Summary:	Z/C/T sliders on images do not work anymore

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:	2013-08-16 09:41 CDT by Stephan Preibisch
Modified:	2013-09-25 15:09 CDT
CC List:	3 users (show)

See Also:

Description Stephan Preibisch 2013-08-16 09:41:52 CDT

After an update, clean build and build the sliders on windows do not work anymore. When opening an image the following exception is thrown in the ImageJ exception window:

java.lang.UnsupportedOperationException: The DummyLegacyService has no LegacyImageMap!
	at imagej.legacy.DummyLegacyService.getImageMap(DummyLegacyService.java:168)
	at imagej.legacy.patches.ImagePlusMethods.updateAndDraw(ImagePlusMethods.java:66)
	at ij.ImagePlus.updateAndDraw(ImagePlus.java:265)
	at ij.ImagePlus.updateAndRepaintWindow(ImagePlus.java:312)
	at ij.ImagePlus.setSlice(ImagePlus.java:1357)
	at ij.gui.StackWindow.<init>(StackWindow.java:42)
	at ij.gui.StackWindow.<init>(StackWindow.java:24)
	at ij.ImagePlus.show(ImagePlus.java:380)
	at ij.io.Opener.open(Opener.java:151)
	at ij.io.Opener.openAndAddToRecent(Opener.java:246)
	at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:176)
	at ij.plugin.DragAndDrop.run(DragAndDrop.java:152)
	at java.lang.Thread.run(Thread.java:662)

Upon startup of Fiji, the following exception is thrown on the command line:

preibisc@myers-pc-8:~/workspace/fiji$ ./ImageJ --mem=60000M
[INFO] Created service: org.scijava.log.StderrLogService
[INFO] Created service: org.scijava.thread.DefaultThreadService
[INFO] Created service: org.scijava.event.DefaultEventService
[INFO] Found 424 plugins.
[INFO] Created service: org.scijava.plugin.DefaultPluginService
[INFO] Created service: imagej.module.DefaultModuleService
[INFO] Created service: imagej.command.DefaultCommandService
[INFO] Created service: org.scijava.object.DefaultObjectService
Exception in thread "AWT-EventQueue-0" java.lang.IllegalArgumentException: Invalid service: imagej.console.DefaultConsoleService
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:235)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:190)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:153)
	at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:131)
	at org.scijava.Context.<init>(Context.java:167)
	at org.scijava.Context.<init>(Context.java:125)
	at org.scijava.Context.<init>(Context.java:86)
	at org.scijava.Context.<init>(Context.java:76)
	at ij.IJ.getContext(IJ.java)
	at ij.IJ.runPlugIn(IJ.java)
	at fiji.Main$1.run(Main.java:116)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:642)
	at java.awt.EventQueue.access$000(EventQueue.java:85)
	at java.awt.EventQueue$1.run(EventQueue.java:603)
	at java.awt.EventQueue$1.run(EventQueue.java:601)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:612)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Caused by: java.lang.IllegalArgumentException: Invalid service: imagej.data.DefaultDatasetService
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:235)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:190)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:286)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:224)
	... 24 more
Caused by: java.lang.IllegalArgumentException: Invalid service: io.scif.services.DefaultFormatService
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:235)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:190)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:286)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:224)
	... 27 more
Caused by: java.lang.IllegalArgumentException: Invalid service: io.scif.services.JAIIIOServiceImpl
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:235)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:190)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:286)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:224)
	... 30 more
Caused by: java.lang.NoClassDefFoundError: io/scif/media/imageioimpl/plugins/jpeg2000/J2KImageReaderSpi
	at java.lang.Class.getDeclaredConstructors0(Native Method)
	at java.lang.Class.privateGetDeclaredConstructors(Class.java:2389)
	at java.lang.Class.getConstructor0(Class.java:2699)
	at java.lang.Class.newInstance0(Class.java:326)
	at java.lang.Class.newInstance(Class.java:308)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:256)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:224)
	... 33 more
Caused by: java.lang.ClassNotFoundException: io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReaderSpi
	at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:307)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:248)
	... 40 more
Done: Checksummer

Any help would be great ...

Nice greetings,
Stephan

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 3.2.0-45-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: REMIND_LATER

Information relevant to JAVA_HOME related problems:

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

Information about the version of each plugin:

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  a77cab39 20130816134916 scripts/importTrackMateTracks.m

Comment 1 Johannes Schindelin 2013-08-18 10:44:45 CDT

Could you try with http://jenkins.imagej.net/job/ImageJ/lastSuccessfulBuild/artifact/core/legacy/target/ij-legacy-2.0.0-SNAPSHOT.jar (you will most likely have to remove ij-legacy-2.0.0-beta-7.2.jar so it does not interfere)?

As to the io.scif.media.imageioimpl.plugins.jpeg2000.J2KImageReaderSpi error... that is a different issue, and I'd like to encourage you to raise this on https://github.com/scifio/scifio/issues -- especially if you can reproduce the issue reliably (which I failed to do).

Comment 2 Stephan Preibisch 2013-08-22 03:42:10 CDT

Hi Johannes,

replacing the jar file makes the sliders work again, however upon startup still a lot of exceptions are thrown (see below). An update via the updater after a clean build removes all problems though ... 

Bye bye,
Steffi

preibischs-lm1:fiji preibischs$ ./ImageJ 
java.lang.NoClassDefFoundError: imagej/service/ImageJService
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
	at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
	at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
	at fiji.IJ1Patcher.run(IJ1Patcher.java:43)
	at imagej.ClassLauncher.patchIJ1(ClassLauncher.java:170)
	at imagej.ClassLauncher.run(ClassLauncher.java:129)
	at imagej.ClassLauncher.main(ClassLauncher.java:72)
Caused by: java.lang.ClassNotFoundException: imagej.service.ImageJService
	at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
	... 28 more
Did not find DefaultLegacyService class: java.lang.NoClassDefFoundError: imagej/service/ImageJService
[ERROR] Invalid service: class='imagej.legacy.DefaultLegacyService', priority=0.0, enabled=true, pluginType=Service
java.lang.NoClassDefFoundError: imagej/service/ImageJService
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
	at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
	at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
	at org.scijava.util.ClassUtils.loadClass(ClassUtils.java:303)
	at org.scijava.plugin.PluginInfo.loadClass(PluginInfo.java:293)
	at org.scijava.service.ServiceHelper.findServiceClasses(ServiceHelper.java:307)
	at org.scijava.service.ServiceHelper.<init>(ServiceHelper.java:104)
	at org.scijava.Context.<init>(Context.java:165)
	at org.scijava.Context.<init>(Context.java:125)
	at org.scijava.Context.<init>(Context.java:86)
	at org.scijava.Context.<init>(Context.java:76)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at java.lang.Class.newInstance0(Class.java:357)
	at java.lang.Class.newInstance(Class.java:310)
	at ij.IJ.runUserPlugIn(IJ.java:194)
	at ij.IJ.runPlugIn(IJ.java:160)
	at ij.IJ.runPlugIn(IJ.java:149)
	at fiji.Main$1.run(Main.java:116)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715)
	at java.awt.EventQueue.access$400(EventQueue.java:82)
	at java.awt.EventQueue$2.run(EventQueue.java:676)
	at java.awt.EventQueue$2.run(EventQueue.java:674)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:685)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Caused by: java.lang.ClassNotFoundException: imagej.service.ImageJService
	at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
	... 56 more
[INFO] Created service: org.scijava.log.StderrLogService
[INFO] Created service: org.scijava.thread.DefaultThreadService
[INFO] Created service: org.scijava.event.DefaultEventService
[INFO] Found 424 plugins.
[INFO] Created service: org.scijava.plugin.DefaultPluginService
[INFO] Created service: imagej.module.DefaultModuleService
[INFO] Created service: imagej.command.DefaultCommandService
[INFO] Created service: org.scijava.object.DefaultObjectService
[INFO] Created service: io.scif.services.JAIIIOServiceImpl
[INFO] Created service: io.scif.services.DefaultFormatService
[INFO] Created service: imagej.data.DefaultDatasetService
[INFO] Created service: imagej.display.DefaultDisplayService
[INFO] Created service: imagej.console.DefaultConsoleService
[INFO] Created service: imagej.data.display.DefaultImageDisplayService
[INFO] Created service: imagej.core.commands.restructure.SplitChannelsContextMonitor
[INFO] Created service: imagej.core.commands.app.CoreAppEventService
[INFO] Configuring platform: imagej.core.platforms.macosx.MacOSXPlatform
[INFO] Configuring platform: imagej.platform.DefaultPlatform
[INFO] Created service: imagej.platform.DefaultPlatformService
[INFO] Found 17 scripts
[INFO] Created service: imagej.script.DefaultScriptService
[INFO] Created service: imagej.io.DefaultRecentFileService
[INFO] Created service: imagej.io.DefaultIOService
[INFO] Found 11 InputWidget plugins.
[INFO] Created service: imagej.widget.DefaultWidgetService
[INFO] Created service: imagej.text.DefaultTextService
[INFO] Created service: imagej.menu.DefaultMenuService
[ERROR] Cannot create plugin: class='imagej.legacy.app.LegacyImageJApp', name='ImageJ', priority=100.0, enabled=true, pluginType=App
java.lang.NoClassDefFoundError: imagej/service/ImageJService
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClassCond(ClassLoader.java:631)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:615)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:141)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:283)
	at java.net.URLClassLoader.access$000(URLClassLoader.java:58)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:197)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
	at java.lang.Class.getDeclaredFields0(Native Method)
	at java.lang.Class.privateGetDeclaredFields(Class.java:2339)
	at java.lang.Class.getDeclaredFields(Class.java:1770)
	at org.scijava.util.ClassUtils.getAnnotatedFields(ClassUtils.java:471)
	at org.scijava.util.ClassUtils.getAnnotatedFields(ClassUtils.java:443)
	at org.scijava.Context.inject(Context.java:221)
	at org.scijava.plugin.DefaultPluginService.createInstance(DefaultPluginService.java:241)
	at org.scijava.app.DefaultAppService.discoverApps(DefaultAppService.java:98)
	at org.scijava.app.DefaultAppService.initialize(DefaultAppService.java:84)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:291)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:224)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:190)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:286)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:224)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:190)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:286)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:224)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:190)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:153)
	at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:131)
	at org.scijava.Context.<init>(Context.java:167)
	at org.scijava.Context.<init>(Context.java:125)
	at org.scijava.Context.<init>(Context.java:86)
	at org.scijava.Context.<init>(Context.java:76)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at java.lang.Class.newInstance0(Class.java:357)
	at java.lang.Class.newInstance(Class.java:310)
	at ij.IJ.runUserPlugIn(IJ.java:194)
	at ij.IJ.runPlugIn(IJ.java:160)
	at ij.IJ.runPlugIn(IJ.java:149)
	at fiji.Main$1.run(Main.java:116)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715)
	at java.awt.EventQueue.access$400(EventQueue.java:82)
	at java.awt.EventQueue$2.run(EventQueue.java:676)
	at java.awt.EventQueue$2.run(EventQueue.java:674)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:685)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Caused by: java.lang.ClassNotFoundException: imagej.service.ImageJService
	at java.net.URLClassLoader$1.run(URLClassLoader.java:202)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:190)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:306)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:247)
	... 60 more
[INFO] Found 3 applications.
[INFO] Created service: org.scijava.app.DefaultAppService
[INFO] Created service: org.scijava.app.DefaultStatusService
[INFO] Found 25 Tool plugins.
[INFO] Created service: imagej.tool.DefaultToolService
[INFO] Created service: imagej.options.DefaultOptionsService
[INFO] Created service: imagej.data.animation.DefaultAnimationService
[INFO] Found 11 DataType plugins.
[INFO] Created service: imagej.data.types.DefaultDataTypeService
[INFO] Created service: imagej.data.operator.DefaultCalculatorService
[INFO] Created service: imagej.ui.common.awt.AWTRenderingService
[ERROR] Cannot create plugin: label='Default Overlay Settings', menu='Image > Overlay > Overlay Options...', priority=0.0, enabled=true, pluginType=Command
java.lang.IllegalArgumentException: Required service is missing: imagej.data.display.OverlayService
	at org.scijava.Context.inject(Context.java:240)
	at org.scijava.plugin.DefaultPluginService.createInstance(DefaultPluginService.java:241)
	at imagej.options.DefaultOptionsService.createInstance(DefaultOptionsService.java:183)
	at imagej.options.DefaultOptionsService.getOptions(DefaultOptionsService.java:97)
	at imagej.data.display.DefaultOverlayService.initialize(DefaultOverlayService.java:332)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:291)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:224)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:190)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:286)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:224)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:190)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:153)
	at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:131)
	at org.scijava.Context.<init>(Context.java:167)
	at org.scijava.Context.<init>(Context.java:125)
	at org.scijava.Context.<init>(Context.java:86)
	at org.scijava.Context.<init>(Context.java:76)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at java.lang.Class.newInstance0(Class.java:357)
	at java.lang.Class.newInstance(Class.java:310)
	at ij.IJ.runUserPlugIn(IJ.java:194)
	at ij.IJ.runPlugIn(IJ.java:160)
	at ij.IJ.runPlugIn(IJ.java:149)
	at fiji.Main$1.run(Main.java:116)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715)
	at java.awt.EventQueue.access$400(EventQueue.java:82)
	at java.awt.EventQueue$2.run(EventQueue.java:676)
	at java.awt.EventQueue$2.run(EventQueue.java:674)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:685)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Exception in thread "AWT-EventQueue-0" java.lang.IllegalArgumentException: Invalid service: imagej.data.threshold.DefaultThresholdService
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:235)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:190)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:153)
	at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:131)
	at org.scijava.Context.<init>(Context.java:167)
	at org.scijava.Context.<init>(Context.java:125)
	at org.scijava.Context.<init>(Context.java:86)
	at org.scijava.Context.<init>(Context.java:76)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:39)
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:27)
	at java.lang.reflect.Constructor.newInstance(Constructor.java:513)
	at java.lang.Class.newInstance0(Class.java:357)
	at java.lang.Class.newInstance(Class.java:310)
	at ij.IJ.runUserPlugIn(IJ.java:194)
	at ij.IJ.runPlugIn(IJ.java:160)
	at ij.IJ.runPlugIn(IJ.java:149)
	at fiji.Main$1.run(Main.java:116)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
	at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:715)
	at java.awt.EventQueue.access$400(EventQueue.java:82)
	at java.awt.EventQueue$2.run(EventQueue.java:676)
	at java.awt.EventQueue$2.run(EventQueue.java:674)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:685)
	at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)
	at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)
Caused by: java.lang.IllegalArgumentException: Invalid service: imagej.data.display.DefaultOverlayService
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:235)
	at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:190)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:286)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:224)
	... 31 more
Caused by: java.lang.NullPointerException
	at imagej.data.display.DefaultOverlayService.initialize(DefaultOverlayService.java:334)
	at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:291)
	at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:224)
	... 34 more

Comment 3 Johannes Schindelin 2013-09-04 10:16:36 CDT

Okay, so these issues all arise due to Fiji being bound to a release version of ImageJ2 that does not contain the bug fixes offered by the updater (i.e. the latest -SNAPSHOT version I was comfortable enough to upload it to the update site).

These issues will be fixed with the next release; in the meantime, please use your expertise to work around the problem by either running the updater after building or binding to IJ2's -SNAPSHOT version (locally only, please).

Comment 4 Curtis Rueden 2013-09-24 11:53:51 CDT

With the 2.0.0-beta-7.3 release, is this problem fixed now?

Comment 5 Stephan Preibisch 2013-09-25 15:09:59 CDT

Yes, just tested it, works like a charm!

Thanks a lot,
Steffi