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Bug 624 - Latest FIJI won't open Nikon nd2 files, even though it did before update
Latest FIJI won't open Nikon nd2 files, even though it did before update
Status: RESOLVED WORKSFORME
Product: Fiji
Classification: Unclassified
Component: Bio-Formats
unspecified
PC Windows
: P4 normal
Assigned To: ImageJ Bugs Mailing List
Depends on:
Blocks:
 
Reported: 2013-06-19 18:15 CDT by koles
Modified: 2013-07-08 16:03 CDT
2 users (show)

See Also:

Description koles 2013-06-19 18:15:26 CDT
I get the following error upon dragging a Nikon nd2 file to FIJI (and it did not happen before I updated fiji and all the loci files and java):


(Fiji Is Just) ImageJ 1.47t; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 31MB of 6057MB (<1%)
 
java.lang.IllegalArgumentException: 0 must not be null and positive.
	at ome.xml.model.primitives.PositiveInteger.<init>(PositiveInteger.java:56)
	at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:266)
	at loci.formats.MetadataTools.populatePixelsOnly(MetadataTools.java:240)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:267)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:274)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at loci.formats.DimensionSwapper.setId(DimensionSwapper.java:292)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:529)
	at loci.plugins.in.ImportProcess.setId(ImportProcess.java:682)
	at loci.plugins.in.ImportProcess.initializeStack(ImportProcess.java:519)
	at loci.plugins.in.ImportProcess.execute(ImportProcess.java:150)
	at loci.plugins.in.Importer.showDialogs(Importer.java:141)
	at loci.plugins.in.Importer.run(Importer.java:79)
	at loci.plugins.LociImporter.run(LociImporter.java:81)
	at ij.IJ.runUserPlugIn(IJ.java:194)
	at ij.IJ.runPlugIn(IJ.java:160)
	at ij.IJ.runPlugIn(IJ.java:149)
	at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:421)
	at HandleExtraFileTypes.run(HandleExtraFileTypes.java:57)
	at ij.IJ.runUserPlugIn(IJ.java:194)
	at ij.IJ.runPlugIn(IJ.java:160)
	at ij.IJ.runPlugIn(IJ.java:149)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:438)
	at ij.io.Opener.openImage(Opener.java:310)
	at ij.io.Opener.openImage(Opener.java:333)
	at ij.io.Opener.open(Opener.java:143)
	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)

Information about your version of Java:

  os.arch => amd64
  os.name => Windows 7
  os.version => 6.1
  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.Win32GraphicsEnvironment
  java.specification.name => Java Platform API Specification
  java.specification.version => 1.6
  sun.cpu.endian => little
  sun.desktop => windows
  file.separator => \

The up-to-date check says: UP_TO_DATE

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: C:\Users\Kate\Desktop\Fiji.app/java/win64/jdk1.6.0_24//jre
  ij.dir => C:\Users\Kate\Desktop\Fiji.app

Information about the version of each plugin:

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Comment 1 Johannes Schindelin 2013-07-08 09:58:14 CDT
I just opened the .nd2 file attached to http://fiji.sc/bugzilla/﷒0﷓ and it works here... Could you update and try again, and if it still fails, either attach a failing example file here (if it is smaller than five megabyte) or upload it with Help>Upload Sample File? In that case, please reopen this issue.
Comment 2 Johannes Schindelin 2013-07-08 16:03:58 CDT
On Mon, 8 Jul 2013, Kate Koles wrote:

> Hi there,
> 
> After I have updated all the plugins of ImageJ AND removed the Nikon nd2
> file viewer plugin, then it worked.
> 
> Thanks,
> -kate