[ome-users] Slide book files not opening

[Amanda Balaban]

Hi Sebastien,

Seems the Java site was the problem!  Thank you so much for your help!!!!!

Amanda


> On Mar 27, 2017, at 10:06 AM, Sebastien Besson (Staff) <s.besson at dundee.ac.uk> wrote:
> 
> HI Amanda,
> 
> It looks like the legacy reader is still chosen and fails to open the file.
> 
> One additional check/question: can you tell us which update sites are enabled in your
> Fiji distribution? The new Slidebook reader is only available since Bio-Formats 5.2.0 and
> currently requires the Java8 update site to be enabled.
> 
> If your sample file size is lower than 2GB, you should be able to upload it at this URL [1].
> 
> Best,
> Sebastien
> 
> [1] http://qa.openmicroscopy.org.uk/qa/upload/ <http://qa.openmicroscopy.org.uk/qa/upload/>
> 
> 
>> On 27 Mar 2017, at 14:08, Amanda Balaban <nabalab90 at gmail.com <mailto:nabalab90 at gmail.com>> wrote:
>> 
>> Hi Sebasien,
>> 
>> I have enabled the SSlidebook site, but still am getting error messages.  Like the one below:
>> 
>> java.lang.ArrayIndexOutOfBoundsException: 0
>> at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:634)
>> at loci.formats.FormatReader.setId(FormatReader.java:1426)
>> at loci.formats.ImageReader.setId(ImageReader.java:835)
>> at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:424)
>> at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:406)
>> at io.scif.AbstractParser.parse(AbstractParser.java:253)
>> at io.scif.AbstractParser.parse(AbstractParser.java:336)
>> at io.scif.AbstractParser.parse(AbstractParser.java:52)
>> at io.scif.AbstractReader.setSource(AbstractReader.java:270)
>> at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)
>> at io.scif.img.ImgOpener.createReader(ImgOpener.java:562)
>> at io.scif.img.ImgOpener.openImgs(ImgOpener.java:145)
>> 
>> 
>> 
>> or 
>> 
>> Finding offsets to pixel data
>> Determining dimensions
>> [ERROR] Exception during event handling:
>> [Event] org.scijava.platform.event.AppOpenFilesEvent
>> context = org.scijava.Context at 61361166
>> consumed = false
>> [Subscriber] net.imagej.legacy.IJ1Helper$LegacyEventDelegator at 73386d72
>> [Method] private void net.imagej.legacy.IJ1Helper$LegacyEventDelegator.onEvent(org.scijava.platform.event.AppOpenFilesEvent)
>> java.lang.ArrayIndexOutOfBoundsException: 0
>> at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:634)
>> 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:80)
>> 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)
>> 
>> My files are too large to send over email.  Do you have another mechanism by which I cans end you an example data set?
>> 
>> Thank you for your help!!!
>> 
>> Amanda
>> 
>>> On Mar 24, 2017, at 4:21 AM, Sebastien Besson (Staff) <s.besson at dundee.ac.uk <mailto:s.besson at dundee.ac.uk>> wrote:
>>> 
>>> Hi Amanda,
>>> 
>>> thanks for contacting us. 
>>> 
>>> As mentioned in a related ImageJ forum thread [1], modern Slidebook files now require
>>> the enabling of the 3i Slidebook update site to open in Fiji - see their instructions [2].
>>> 
>>> Can you check whether this update site is enabled and the images still fail to open? If this
>>> remains the case, we might need a failing sample file before engaging with 3i to discuss the
>>> issue.
>>> 
>>> Best,
>>> Sebastien
>>> 
>>> 
>>> [1] http://forum.imagej.net/t/slidebook-file-opening-failed/4533 <http://forum.imagej.net/t/slidebook-file-opening-failed/4533>
>>> [2] https://support.intelligent-imaging.com/techanswers.php#SLDinFiji <https://support.intelligent-imaging.com/techanswers.php#SLDinFiji> 
>>> 
>>>> On 23 Mar 2017, at 16:27, Amanda Balaban <nabalab90 at gmail.com <mailto:nabalab90 at gmail.com>> wrote:
>>>> 
>>>> Hello,
>>>> 
>>>> Hello. I have been receiving an error message when attempting to open a slide book file in fiji.
>>>> 
>>>> Exception in thread "DrawAndDrop" java.lang.ArrayIndexOutOfBoundsException: 0
>>>> at loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:634)
>>>> at loci.formats.FormatReader.setId(FormatReader.java:1399)
>>>> at loci.formats.ImageReader.setId(ImageReader.java:839)
>>>> at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:431)
>>>> at io.scif.bf.BioFormatsFormat$Parser.typedParse(BioFormatsFormat.java:413)
>>>> at io.scif.AbstractParser.parse(AbstractParser.java:253)
>>>> at io.scif.AbstractParser.parse(AbstractParser.java:336)
>>>> at io.scif.AbstractParser.parse(AbstractParser.java:52)
>>>> at io.scif.AbstractReader.setSource(AbstractReader.java:270)
>>>> at io.scif.services.DefaultInitializeService.initializeReader(DefaultInitializeService.java:90)
>>>> at io.scif.img.ImgOpener.createReader(ImgOpener.java:562)
>>>> at io.scif.img.ImgOpener.openImgs(ImgOpener.java:145)
>>>> at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:126)
>>>> at io.scif.services.DefaultDatasetIOService.open(DefaultDatasetIOService.java:111)
>>>> at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:75)
>>>> at io.scif.io.DatasetIOPlugin.open(DatasetIOPlugin.java:50)
>>>> at net.imagej.legacy.plugin.DefaultLegacyOpener.open(DefaultLegacyOpener.java:135)
>>>> at net.imagej.legacy.DefaultLegacyHooks.interceptDragAndDropFile(DefaultLegacyHooks.java:363)
>>>> at ij.plugin.DragAndDrop.openFile(DragAndDrop.java)
>>>> at ij.plugin.DragAndDrop.run(DragAndDrop.java:159)
>>>> at java.lang.Thread.run(Thread.java:745)
>>>> 
>>>> 
>>>> I am running this on a Mac. Have updated/reinstalled the latest version of fiji and java.  I have also tried this on other computers/fiji downloads witht he same result.
>>>> 
>>>> Thank you,
>>>> 
>>>> Amanda
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>>> 
>>> 
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>> 
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> 
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