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Bug 688 - interaction between bigdataviewer and bioformats
interaction between bigdataviewer and bioformats
Status: RESOLVED FIXED
Product: Fiji
Classification: Unclassified
Component: Plugins
unspecified
PC Linux
: P4 normal
Assigned To: Tobias Pietzsch
Depends on:
Blocks:
 
Reported: 2013-12-22 08:02 CST by Aryeh Weiss
Modified: 2014-01-10 19:47 CST
3 users (show)

See Also:
Description Aryeh Weiss 2013-12-22 08:02:30 CST 
When bigdataviewwer is fully installed, teh follwoing error occured while trying to read an nd2 file with loci:
There was a problem with the class ome.scifio.xml.XMLTools which can be found here:
/home/hila/Desktop/Fiji.app/jars/scifio-devel-4.5-SNAPSHOT.jar
/home/hila/Desktop/Fiji.app/jars/loci-common.jar

WARNING: multiple locations found!
java.lang.NoSuchMethodError: ome.scifio.xml.XMLTools.createBuilder()Ljavax/xml/parsers/DocumentBuilder;
	at loci.formats.ome.AbstractOMEXMLMetadata.createNewDocument(AbstractOMEXMLMetadata.java:125)
	at loci.formats.ome.AbstractOMEXMLMetadata.dumpXML(AbstractOMEXMLMetadata.java:114)
	at loci.formats.ome.OMEXMLMetadataImpl.dumpXML(OMEXMLMetadataImpl.java:109)
	at loci.formats.services.OMEXMLServiceImpl.getOMEXML(OMEXMLServiceImpl.java:419)
	at loci.plugins.in.ImagePlusReader.createFileInfo(ImagePlusReader.java:518)
	at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:306)
	at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
	at loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
	at loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:114)
	at loci.plugins.in.Importer.readPixels(Importer.java:150)
	at loci.plugins.in.Importer.run(Importer.java:89)
	at loci.plugins.LociImporter.run(LociImporter.java:81)
	at ij.IJ.runUserPlugIn(IJ.java:196)
	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:196)
	at ij.IJ.runPlugIn(IJ.java:160)
	at ij.IJ.runPlugIn(IJ.java:149)
	at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:454)
	at ij.io.Opener.openImage(Opener.java:311)
	at ij.io.Opener.openImage(Opener.java:334)
	at ij.io.Opener.open(Opener.java:144)
	at ij.RecentOpener.run(RecentOpener.java:19)
	at java.lang.Thread.run(Thread.java:662)
Could not find method ome.scifio.xml.XMLTools.createBuilder()Ljavax/xml/parsers/DocumentBuilder;
(See Log for details)

Removal of  scifio-devel.jar enabled LOCI bioformats to properly load the nd2 file.

Information about your version of Java:

  os.arch => amd64
  os.name => Linux
  os.version => 3.1.10-1.29-desktop
  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 => null
  file.separator => /

The up-to-date check says: REMIND_LATER

Information relevant to JAVA_HOME related problems:

  JAVA_HOME is set to: /home/hila/Desktop/Fiji.app/java/linux-amd64/jdk1.6.0_24//jre
  ij.dir => /home/hila/Desktop/Fiji.app

Information about the version of each plugin:

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Comment 1 Curtis Rueden 2014-01-06 15:13:53 CST 
Did you get this problem resolved? If not, what happens if you delete scifio-devel-4.5-SNAPSHOT.jar, then restart Fiji?

In any case, this is a problem with BigDataViewer's dependencies. It shadows a bunch of libraries, and apparently depends on a development version of Bio-Formats 4.5.x too. Tobias, please let me know if I can be of assistance in untangling the mess.
Comment 2 Aryeh Weiss 2014-01-07 02:11:49 CST 
At the time, I noted that removal of  scifio-devel.jar enabled LOCI bioformats to properly load the nd2 file.
I can also add that the problem does not occur on my OSX 9 system. 
I will check the Linux box when I next get to that lab.
Comment 3 Tobias Pietzsch 2014-01-07 02:55:31 CST 
I plan to update the BigDataViewer later this week and I will try to resolve the dependency issue then. Thanks for offering assistance, Curtis! If I cannot manage to solve this on my own, I will get back to you.
Comment 4 Tobias Pietzsch 2014-01-10 19:47:04 CST 
This should be solved now. The BigDataViewer update site no longer updates scifio.