[ome-users] Fiji error - opening certain .czi files

Wed Aug 31 15:28:47 BST 2016

Hi Cecilia,

Thank you for sending this report, we also received the sample file you sent via QA and have since tested it and were able to reproduce the same error that you discovered.
This error appears to be related to an existing issue for which we have a bug tracking ticket - https://trac.openmicroscopy.org/ome/ticket/13239

I have updated the ticket to with this information as well as the sample QA file which you provided for testing.

With Thanks,
David Gault

On 31 Aug 2016, at 09:29, Domínguez Conde Cecilia <Cecilia.DominguezConde at rud.lbg.ac.at<mailto:Cecilia.DominguezConde at rud.lbg.ac.at>> wrote:

Dear all,

I want to report an error in Fiji when trying to open certain .czi files (I tried uploading a 62MB file to your QA system but did not succeed, let me know if I should send it via FTP server, although from the size QA should have worked).

Error message below.

Looking forward to your feedback and thank you in advance,
Cecilia

ERROR MESSAGE:

[ERROR] Exception during event handling:
[Event] org.scijava.platform.event.AppOpenFilesEvent
context = org.scijava.Context at 4a0de467
consumed = false
[Subscriber] net.imagej.legacy.IJ1Helper$LegacyEventDelegator at 7ba63fe5
[Method] private void net.imagej.legacy.IJ1Helper$LegacyEventDelegator.onEvent(org.scijava.platform.event.AppOpenFilesEvent)
java.lang.IllegalArgumentException: Invalid C index: 1/1
at loci.formats.FormatTools.getIndex(FormatTools.java:413)
at loci.formats.FormatTools.getIndex(FormatTools.java:340)
at loci.formats.FormatReader.getIndex(FormatReader.java:1113)
at loci.formats.in.ZeissCZIReader.assignPlaneIndices(ZeissCZIReader.java:1296)
at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:773)
at loci.formats.FormatReader.setId(FormatReader.java:1426)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.IJ.runPlugIn(IJ.java:170)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.IJ.runPlugIn(IJ.java:170)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)
at ij.io.Opener.openImage(Opener.java:369)
at ij.io.Opener.openImage(Opener.java:243)
at ij.io.Opener.open(Opener.java:110)
at ij.io.Opener.openAndAddToRecent(Opener.java:292)
at net.imagej.legacy.IJ1Helper.openAndAddToRecent(IJ1Helper.java:465)
at net.imagej.legacy.IJ1Helper$LegacyEventDelegator.onEvent(IJ1Helper.java:591)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.scijava.event.DefaultEventService$ProxySubscriber.onEvent(DefaultEventService.java:302)
at org.scijava.event.DefaultEventService$ProxySubscriber.onEvent(DefaultEventService.java:276)
at org.bushe.swing.event.ThreadSafeEventService.publish(ThreadSafeEventService.java:971)
at org.scijava.event.DefaultEventBus.access$101(DefaultEventBus.java:56)
at org.scijava.event.DefaultEventBus$1.run(DefaultEventBus.java:190)
at org.scijava.thread.DefaultThreadService.invoke(DefaultThreadService.java:107)
at org.scijava.event.DefaultEventBus.publishNow(DefaultEventBus.java:184)
at org.scijava.event.DefaultEventBus.publishNow(DefaultEventBus.java:75)
at org.scijava.event.DefaultEventService.publish(DefaultEventService.java:104)
at org.scijava.plugins.platforms.osx.OSXAppEventDispatcher.openFiles(OSXAppEventDispatcher.java:205)
at com.apple.eawt._AppEventHandler$_OpenFileDispatcher.performUsing(_AppEventHandler.java:361)
at com.apple.eawt._AppEventHandler$_OpenFileDispatcher.performUsing(_AppEventHandler.java:352)
at com.apple.eawt._AppEventHandler$_AppEventDispatcher$1.run(_AppEventHandler.java:516)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)
[ERROR] Exception during event handling:
[Event] org.scijava.platform.event.AppOpenFilesEvent
context = org.scijava.Context at 4a0de467
consumed = false
[Subscriber] net.imagej.legacy.IJ1Helper$LegacyEventDelegator at 7ba63fe5
[Method] private void net.imagej.legacy.IJ1Helper$LegacyEventDelegator.onEvent(org.scijava.platform.event.AppOpenFilesEvent)
java.lang.IllegalArgumentException: Invalid C index: 1/1
at loci.formats.FormatTools.getIndex(FormatTools.java:413)
at loci.formats.FormatTools.getIndex(FormatTools.java:340)
at loci.formats.FormatReader.getIndex(FormatReader.java:1113)
at loci.formats.in.ZeissCZIReader.assignPlaneIndices(ZeissCZIReader.java:1296)
at loci.formats.in.ZeissCZIReader.initFile(ZeissCZIReader.java:773)
at loci.formats.FormatReader.setId(FormatReader.java:1426)
at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:505)
at loci.plugins.in.ImportProcess.execute(ImportProcess.java:143)
at loci.plugins.in.Importer.showDialogs(Importer.java:140)
at loci.plugins.in.Importer.run(Importer.java:76)
at loci.plugins.LociImporter.run(LociImporter.java:78)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.IJ.runPlugIn(IJ.java:170)
at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:499)
at HandleExtraFileTypes.run(HandleExtraFileTypes.java:72)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.IJ.runPlugIn(IJ.java:170)
at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:515)
at ij.io.Opener.openImage(Opener.java:369)
at ij.io.Opener.openImage(Opener.java:243)
at ij.io.Opener.open(Opener.java:110)
at ij.io.Opener.openAndAddToRecent(Opener.java:292)
at net.imagej.legacy.IJ1Helper.openAndAddToRecent(IJ1Helper.java:465)
at net.imagej.legacy.IJ1Helper$LegacyEventDelegator.onEvent(IJ1Helper.java:591)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.scijava.event.DefaultEventService$ProxySubscriber.onEvent(DefaultEventService.java:302)
at org.scijava.event.DefaultEventService$ProxySubscriber.onEvent(DefaultEventService.java:276)
at org.bushe.swing.event.ThreadSafeEventService.publish(ThreadSafeEventService.java:971)
at org.scijava.event.DefaultEventBus.access$101(DefaultEventBus.java:56)
at org.scijava.event.DefaultEventBus$1.run(DefaultEventBus.java:190)
at org.scijava.thread.DefaultThreadService.invoke(DefaultThreadService.java:107)
at org.scijava.event.DefaultEventBus.publishNow(DefaultEventBus.java:184)
at org.scijava.event.DefaultEventBus.publishNow(DefaultEventBus.java:75)
at org.scijava.event.DefaultEventService.publish(DefaultEventService.java:104)
at org.scijava.plugins.platforms.osx.OSXAppEventDispatcher.openFiles(OSXAppEventDispatcher.java:205)
at com.apple.eawt._AppEventHandler$_OpenFileDispatcher.performUsing(_AppEventHandler.java:361)
at com.apple.eawt._AppEventHandler$_OpenFileDispatcher.performUsing(_AppEventHandler.java:352)
at com.apple.eawt._AppEventHandler$_AppEventDispatcher$1.run(_AppEventHandler.java:516)
at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)
at java.awt.EventQueue.access$500(EventQueue.java:97)
at java.awt.EventQueue$3.run(EventQueue.java:709)
at java.awt.EventQueue$3.run(EventQueue.java:703)
at java.security.AccessController.doPrivileged(Native Method)
at java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)
at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)
at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)
at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)
at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)

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