Cannot open a zvi file. Why?

zvi
bio-formats
Tags: #<Tag:0x00007fd54036f9f8> #<Tag:0x00007fd54036f8b8>

#1

I am using the latest version of fiji (md5sum):

5d5c9b236323446e16e549033dd956a0 fiji-linux64.zip

On an Arch Linux box, using Java 8.

When I go to Plugins::Bio-Formats::‘Bio-Formats Importer’ and try to open a zvi file I get (log file):

java.io.IOException: Cannot remove block[ 190606 ]; out of range
	at loci.poi.poifs.storage.BlockListImpl.remove(BlockListImpl.java:126)
	at loci.poi.poifs.storage.RawDataBlockList.remove(RawDataBlockList.java:56)
	at loci.poi.poifs.storage.BlockAllocationTableReader.<init>(BlockAllocationTableReader.java:147)
	at loci.poi.poifs.filesystem.POIFSFileSystem.<init>(POIFSFileSystem.java:126)
	at loci.formats.services.POIServiceImpl.initialize(POIServiceImpl.java:86)
	at loci.formats.services.POIServiceImpl.initialize(POIServiceImpl.java:72)
	at loci.formats.in.ZeissZVIReader.initPOIService(ZeissZVIReader.java:219)
	at loci.formats.in.ZeissZVIReader.initVars(ZeissZVIReader.java:207)
	at loci.formats.in.BaseZeissReader.initFileMain(BaseZeissReader.java:136)
	at loci.formats.in.ZeissZVIReader.initFile(ZeissZVIReader.java:181)
	at loci.formats.FormatReader.setId(FormatReader.java:1397)
	at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:498)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:141)
	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.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:745)

#2

@bug

Perhaps you can check if you have the Java-8 update site enabled?

Also - if the problem persists… you can always report it to the Bio-Formats team.

eta


#3

I did not have the Java-8 update site enabled. I did it and restarted ImageJ. Now it won’t even start…

java.lang.UnsupportedClassVersionError: net/imagej/Main : Unsupported major.minor version 52.0
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:803)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:442)
	at java.net.URLClassLoader.access$100(URLClassLoader.java:64)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:354)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:348)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:347)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
	at net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:252)
	at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:186)
	at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:77)
Falling back to remote updater at http://update.imagej.net/bootstrap.js
java.lang.UnsupportedClassVersionError: org/scijava/plugins/scripting/beanshell/BeanshellScriptLanguage : Unsupported major.minor version 52.0
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:803)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:442)
	at java.net.URLClassLoader.access$100(URLClassLoader.java:64)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:354)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:348)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:347)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
	at java.lang.Class.forName0(Native Method)
	at java.lang.Class.forName(Class.java:278)
	at sun.misc.Service$LazyIterator.next(Service.java:289)
	at javax.script.ScriptEngineManager.initEngines(ScriptEngineManager.java:123)
	at javax.script.ScriptEngineManager.access$000(ScriptEngineManager.java:53)
	at javax.script.ScriptEngineManager$1.run(ScriptEngineManager.java:91)
	at javax.script.ScriptEngineManager$1.run(ScriptEngineManager.java:89)
	at java.security.AccessController.doPrivileged(Native Method)
	at javax.script.ScriptEngineManager.init(ScriptEngineManager.java:88)
	at javax.script.ScriptEngineManager.<init>(ScriptEngineManager.java:65)
	at net.imagej.launcher.RemoteUpdater.runAsJavascript(RemoteUpdater.java:86)
	at net.imagej.launcher.RemoteUpdater.runRemote(RemoteUpdater.java:71)
	at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:189)
	at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:77)

#4

@bug

Can you try downloading/reinstalling Fiji again? And try the .zvi import (File > Import > Bio-Formats) without the update site enabled first after the fresh installation… but again:

… as I said above if the problem persists with Bio-Formats.

eta


#5

@etarena: Thanks anyways. The problem persists so I will contact the Bio-Formats team.