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Greetings,
The following Java Exceptions were thrown when I was trying to open a Leica Confocal stack. What could be the cause? Regards Gary ------ java.lang.ArrayIndexOutOfBoundsException: -1 at java.util.Vector.get(Vector.java:696) at loci.formats.ome.OMEXML200809Metadata.getImageNode(OMEXML200809Metadata.java:5675) at loci.formats.ome.OMEXML200809Metadata.setImageCreationDate(OMEXML200809Metadata.java:3409) at loci.formats.meta.FilterMetadata.setImageCreationDate(FilterMetadata.java:643) at loci.formats.in.LeicaHandler.startElement(LeicaHandler.java:715) at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:501) at com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(AbstractXMLDocumentParser.java:179) at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanStartElement(XMLDocumentFragmentScannerImpl.java:1339) at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2747) at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:648) at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510) at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:807) at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737) at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:107) at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205) at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:522) at javax.xml.parsers.SAXParser.parse(SAXParser.java:395) at javax.xml.parsers.SAXParser.parse(SAXParser.java:198) at loci.common.XMLTools.parseXML(XMLTools.java:277) at loci.common.XMLTools.parseXML(XMLTools.java:252) at loci.formats.in.LIFReader.initMetadata(LIFReader.java:383) at loci.formats.in.LIFReader.initFile(LIFReader.java:315) at loci.formats.FormatReader.setId(FormatReader.java:901) at loci.plugins.importer.Importer.run(Importer.java:267) at loci.plugins.LociImporter.run(LociImporter.java:77) at ij.IJ.runUserPlugIn(IJ.java:175) at ij.IJ.runPlugIn(IJ.java:142) at ij.IJ.runPlugIn(IJ.java:131) at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:241) at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37) at ij.IJ.runUserPlugIn(IJ.java:175) at ij.IJ.runPlugIn(IJ.java:142) at ij.IJ.runPlugIn(IJ.java:131) at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:337) at ij.io.Opener.openImage(Opener.java:245) at ij.io.Opener.openImage(Opener.java:268) at ij.io.Opener.open(Opener.java:124) at ij.io.Opener.open(Opener.java:63) at ij.plugin.Commands.run(Commands.java:23) at ij.IJ.runPlugIn(IJ.java:148) at ij.Executer.runCommand(Executer.java:121) at ij.Executer.run(Executer.java:58) at java.lang.Thread.run(Thread.java:619) |
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Hi Gary,
This problem can be fixed by updating to the latest trunk build of Bio-Formats - see http://loci.wisc.edu/bio-formats/imagej for instructions. Regards, -Melissa On Tue, May 11, 2010 at 8:11 AM, Gary G. Li <[hidden email]> wrote: > Greetings, > > The following Java Exceptions were thrown when I was trying to open a Leica > Confocal stack. > > What could be the cause? > > Regards > > Gary > > > > ------ > > java.lang.ArrayIndexOutOfBoundsException: -1 > > at java.util.Vector.get(Vector.java:696) > > at > loci.formats.ome.OMEXML200809Metadata.getImageNode(OMEXML200809Metadata.java:5675) > > at > loci.formats.ome.OMEXML200809Metadata.setImageCreationDate(OMEXML200809Metadata.java:3409) > > at > loci.formats.meta.FilterMetadata.setImageCreationDate(FilterMetadata.java:643) > > at > loci.formats.in.LeicaHandler.startElement(LeicaHandler.java:715) > > at > com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:501) > > at > com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(AbstractXMLDocumentParser.java:179) > > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanStartElement(XMLDocumentFragmentScannerImpl.java:1339) > > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2747) > > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:648) > > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510) > > at > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:807) > > at > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737) > > at > com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:107) > > at > com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205) > > at > com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:522) > > at javax.xml.parsers.SAXParser.parse(SAXParser.java:395) > > at javax.xml.parsers.SAXParser.parse(SAXParser.java:198) > > at loci.common.XMLTools.parseXML(XMLTools.java:277) > > at loci.common.XMLTools.parseXML(XMLTools.java:252) > > at > loci.formats.in.LIFReader.initMetadata(LIFReader.java:383) > > at loci.formats.in.LIFReader.initFile(LIFReader.java:315) > > at loci.formats.FormatReader.setId(FormatReader.java:901) > > at loci.plugins.importer.Importer.run(Importer.java:267) > > at loci.plugins.LociImporter.run(LociImporter.java:77) > > at ij.IJ.runUserPlugIn(IJ.java:175) > > at ij.IJ.runPlugIn(IJ.java:142) > > at ij.IJ.runPlugIn(IJ.java:131) > > at > HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:241) > > at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37) > > at ij.IJ.runUserPlugIn(IJ.java:175) > > at ij.IJ.runPlugIn(IJ.java:142) > > at ij.IJ.runPlugIn(IJ.java:131) > > at > ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:337) > > at ij.io.Opener.openImage(Opener.java:245) > > at ij.io.Opener.openImage(Opener.java:268) > > at ij.io.Opener.open(Opener.java:124) > > at ij.io.Opener.open(Opener.java:63) > > at ij.plugin.Commands.run(Commands.java:23) > > at ij.IJ.runPlugIn(IJ.java:148) > > at ij.Executer.runCommand(Executer.java:121) > > at ij.Executer.run(Executer.java:58) > > at java.lang.Thread.run(Thread.java:619) > ... [show rest of quote]
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Hi Melissa,
Thank you very much! -- Gary G. Li, Ph.D. On Tue, May 11, 2010 at 9:33 AM, Melissa Linkert < [hidden email]> wrote: > Hi Gary, > > This problem can be fixed by updating to the latest trunk build of > Bio-Formats - see http://loci.wisc.edu/bio-formats/imagej for > instructions. > > Regards, > -Melissa > > On Tue, May 11, 2010 at 8:11 AM, Gary G. Li <[hidden email]> > wrote: > > Greetings, > > > > The following Java Exceptions were thrown when I was trying to open a > Leica > > Confocal stack. > > > > What could be the cause? > > > > Regards > > > > Gary > > > > > > > > ------ > > > > java.lang.ArrayIndexOutOfBoundsException: -1 > > > > at java.util.Vector.get(Vector.java:696) > > > > at > > > loci.formats.ome.OMEXML200809Metadata.getImageNode(OMEXML200809Metadata.java:5675) > > > > at > > > loci.formats.ome.OMEXML200809Metadata.setImageCreationDate(OMEXML200809Metadata.java:3409) > > > > at > > > loci.formats.meta.FilterMetadata.setImageCreationDate(FilterMetadata.java:643) > > > > at > > loci.formats.in.LeicaHandler.startElement(LeicaHandler.java:715) > > > > at > > > com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:501) > > > > at > > > com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(AbstractXMLDocumentParser.java:179) > > > > at > > > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanStartElement(XMLDocumentFragmentScannerImpl.java:1339) > > > > at > > > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2747) > > > > at > > > com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:648) > > > > at > > > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510) > > > > at > > > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:807) > > > > at > > > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737) > > > > at > > > com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:107) > > > > at > > > com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205) > > > > at > > > com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:522) > > > > at javax.xml.parsers.SAXParser.parse(SAXParser.java:395) > > > > at javax.xml.parsers.SAXParser.parse(SAXParser.java:198) > > > > at loci.common.XMLTools.parseXML(XMLTools.java:277) > > > > at loci.common.XMLTools.parseXML(XMLTools.java:252) > > > > at > > loci.formats.in.LIFReader.initMetadata(LIFReader.java:383) > > > > at loci.formats.in.LIFReader.initFile(LIFReader.java:315) > > > > at loci.formats.FormatReader.setId(FormatReader.java:901) > > > > at loci.plugins.importer.Importer.run(Importer.java:267) > > > > at loci.plugins.LociImporter.run(LociImporter.java:77) > > > > at ij.IJ.runUserPlugIn(IJ.java:175) > > > > at ij.IJ.runPlugIn(IJ.java:142) > > > > at ij.IJ.runPlugIn(IJ.java:131) > > > > at > > HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:241) > > > > at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37) > > > > at ij.IJ.runUserPlugIn(IJ.java:175) > > > > at ij.IJ.runPlugIn(IJ.java:142) > > > > at ij.IJ.runPlugIn(IJ.java:131) > > > > at > > ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:337) > > > > at ij.io.Opener.openImage(Opener.java:245) > > > > at ij.io.Opener.openImage(Opener.java:268) > > > > at ij.io.Opener.open(Opener.java:124) > > > > at ij.io.Opener.open(Opener.java:63) > > > > at ij.plugin.Commands.run(Commands.java:23) > > > > at ij.IJ.runPlugIn(IJ.java:148) > > > > at ij.Executer.runCommand(Executer.java:121) > > > > at ij.Executer.run(Executer.java:58) > > > > at java.lang.Thread.run(Thread.java:619) > > > ... [show rest of quote]
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In reply to this post by Melissa Linkert-2
Hi Melissa,
Unfortunately I still have that problem with one of my lif stack even with the latest trunk build. It is a little strange since I can open other stacks from the same microscope. I can also open the mentioned stack with an older version of the loci_tools.jar This is the error log: java.lang.IndexOutOfBoundsException: Index: 3, Size: 1 at java.util.ArrayList.RangeCheck(Unknown Source) at java.util.ArrayList.get(Unknown Source) at ome.xml.r201004.Pixels.getPlane(Pixels.java:577) at loci.formats.ome.OMEXMLMetadataImpl.setPlanePositionX(OMEXMLMetadataImpl.java:10843) at loci.formats.meta.FilterMetadata.setPlanePositionX(FilterMetadata.java:1724) at loci.formats.in.LeicaHandler.startElement(LeicaHandler.java:608) at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(Unknown Source) at com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(Unknown Source) at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown Source) at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(Unknown Source) at com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(Unknown Source) at com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown Source) at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source) at com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown Source) at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown Source) at com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown Source) at com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source) at javax.xml.parsers.SAXParser.parse(Unknown Source) at javax.xml.parsers.SAXParser.parse(Unknown Source) at loci.common.xml.XMLTools.parseXML(XMLTools.java:282) at loci.common.xml.XMLTools.parseXML(XMLTools.java:255) at loci.formats.in.LIFReader.initMetadata(LIFReader.java:340) at loci.formats.in.LIFReader.initFile(LIFReader.java:320) at loci.formats.FormatReader.setId(FormatReader.java:1012) at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:397) at loci.plugins.in.ImportProcess.execute(ImportProcess.java:134) at loci.plugins.in.Importer.showDialogs(Importer.java:124) at loci.plugins.in.Importer.run(Importer.java:77) at loci.plugins.LociImporter.run(LociImporter.java:77) at ij.IJ.runUserPlugIn(IJ.java:184) at ij.IJ.runPlugIn(IJ.java:151) at ij.IJ.runPlugIn(IJ.java:140) at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:241) at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37) at ij.IJ.runUserPlugIn(IJ.java:184) at ij.IJ.runPlugIn(IJ.java:151) at ij.IJ.runPlugIn(IJ.java:140) at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:405) at ij.io.Opener.openImage(Opener.java:282) at ij.io.Opener.openImage(Opener.java:301) at ij.io.Opener.open(Opener.java:137) at ij.io.Opener.openAndAddToRecent(Opener.java:221) at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:172) at ij.plugin.DragAndDrop.run(DragAndDrop.java:148) at java.lang.Thread.run(Unknown Source) Best regards Pascal Melissa Linkert schrieb: > Hi Gary, > > This problem can be fixed by updating to the latest trunk build of > Bio-Formats - see http://loci.wisc.edu/bio-formats/imagej for > instructions. > > Regards, > -Melissa > > On Tue, May 11, 2010 at 8:11 AM, Gary G. Li <[hidden email]> wrote: > >> Greetings, >> >> The following Java Exceptions were thrown when I was trying to open a Leica >> Confocal stack. >> >> What could be the cause? >> >> Regard_ >> >> Gary >> >> >> >> ------ >> >> java.lang.ArrayIndexOutOfBoundsException: -1 >> >> at java.util.Vector.get(Vector.java:696) >> >> at >> loci.formats.ome.OMEXML200809Metadata.getImageNode(OMEXML200809Metadata.java:5675) >> >> at >> loci.formats.ome.OMEXML200809Metadata.setImageCreationDate(OMEXML200809Metadata.java:3409) >> >> at >> loci.formats.meta.FilterMetadata.setImageCreationDate(FilterMetadata.java:643) >> >> at >> loci.formats.in.LeicaHandler.startElement(LeicaHandler.java:715) >> >> at >> com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:501) >> >> at >> com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(AbstractXMLDocumentParser.java:179) >> >> at >> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanStartElement(XMLDocumentFragmentScannerImpl.java:1339) >> >> at >> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2747) >> >> at >> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:648) >> >> at >> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510) >> >> at >> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:807) >> >> at >> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737) >> >> at >> com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:107) >> >> at >> com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205) >> >> at >> com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:522) >> >> at javax.xml.parsers.SAXParser.parse(SAXParser.java:395) >> >> at javax.xml.parsers.SAXParser.parse(SAXParser.java:198) >> >> at loci.common.XMLTools.parseXML(XMLTools.java:277) >> >> at loci.common.XMLTools.parseXML(XMLTools.java:252) >> >> at >> loci.formats.in.LIFReader.initMetadata(LIFReader.java:383) >> >> at loci.formats.in.LIFReader.initFile(LIFReader.java:315) >> >> at loci.formats.FormatReader.setId(FormatReader.java:901) >> >> at loci.plugins.importer.Importer.run(Importer.java:267) >> >> at loci.plugins.LociImporter.run(LociImporter.java:77) >> >> at ij.IJ.runUserPlugIn(IJ.java:175) >> >> at ij.IJ.runPlugIn(IJ.java:142) >> >> at ij.IJ.runPlugIn(IJ.java:131) >> >> at >> HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:241) >> >> at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37) >> >> at ij.IJ.runUserPlugIn(IJ.java:175) >> >> at ij.IJ.runPlugIn(IJ.java:142) >> >> at ij.IJ.runPlugIn(IJ.java:131) >> >> at >> ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:337) >> >> at ij.io.Opener.openImage(Opener.java:245) >> >> at ij.io.Opener.openImage(Opener.java:268) >> >> at ij.io.Opener.open(Opener.java:124) >> >> at ij.io.Opener.open(Opener.java:63) >> >> at ij.plugin.Commands.run(Commands.java:23) >> >> at ij.IJ.runPlugIn(IJ.java:148) >> >> at ij.Executer.runCommand(Executer.java:121) >> >> at ij.Executer.run(Executer.java:58) >> >> at java.lang.Thread.run(Thread.java:619) >> >> ... 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Hi Pascal,
Thank you for mentioning this problem, and my apologies for not replying sooner. In fact, this is a very different problem from the one reported by Gary. Regardless, updating to the very latest trunk build should solve the problem you've reported. If you still see an error message after updating to the latest trunk build of loci_tools.jar, then it would be very helpful if you could send one of the problematic .lif files. If needed, I can provide you with an FTP server on which to place the file. Regards, -Melissa On Mon, May 17, 2010 at 7:29 AM, Pascal Lorentz <[hidden email]> wrote: > Hi Melissa, > > Unfortunately I still have that problem with one of my lif stack even with > the latest trunk build. > It is a little strange since I can open other stacks from the same > microscope. > I can also open the mentioned stack with an older version of the > loci_tools.jar > > This is the error log: > java.lang.IndexOutOfBoundsException: Index: 3, Size: 1 > at java.util.ArrayList.RangeCheck(Unknown Source) > at java.util.ArrayList.get(Unknown Source) > at ome.xml.r201004.Pixels.getPlane(Pixels.java:577) > at > loci.formats.ome.OMEXMLMetadataImpl.setPlanePositionX(OMEXMLMetadataImpl.java:10843) > at > loci.formats.meta.FilterMetadata.setPlanePositionX(FilterMetadata.java:1724) > at loci.formats.in.LeicaHandler.startElement(LeicaHandler.java:608) > at > com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(Unknown > Source) > at > com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(Unknown > Source) > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanStartElement(Unknown > Source) > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(Unknown > Source) > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(Unknown > Source) > at > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown > Source) > at > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown > Source) > at > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(Unknown > Source) > at com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(Unknown > Source) > at > com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(Unknown > Source) > at > com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown > Source) > at javax.xml.parsers.SAXParser.parse(Unknown Source) > at javax.xml.parsers.SAXParser.parse(Unknown Source) > at loci.common.xml.XMLTools.parseXML(XMLTools.java:282) > at loci.common.xml.XMLTools.parseXML(XMLTools.java:255) > at loci.formats.in.LIFReader.initMetadata(LIFReader.java:340) > at loci.formats.in.LIFReader.initFile(LIFReader.java:320) > at loci.formats.FormatReader.setId(FormatReader.java:1012) > at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:397) > at loci.plugins.in.ImportProcess.execute(ImportProcess.java:134) > at loci.plugins.in.Importer.showDialogs(Importer.java:124) > at loci.plugins.in.Importer.run(Importer.java:77) > at loci.plugins.LociImporter.run(LociImporter.java:77) > at ij.IJ.runUserPlugIn(IJ.java:184) > at ij.IJ.runPlugIn(IJ.java:151) > at ij.IJ.runPlugIn(IJ.java:140) > at HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:241) > at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37) > at ij.IJ.runUserPlugIn(IJ.java:184) > at ij.IJ.runPlugIn(IJ.java:151) > at ij.IJ.runPlugIn(IJ.java:140) > at ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:405) > at ij.io.Opener.openImage(Opener.java:282) > at ij.io.Opener.openImage(Opener.java:301) > at ij.io.Opener.open(Opener.java:137) > at ij.io.Opener.openAndAddToRecent(Opener.java:221) > at ij.plugin.DragAndDrop.openFile(DragAndDrop.java:172) > at ij.plugin.DragAndDrop.run(DragAndDrop.java:148) > at java.lang.Thread.run(Unknown Source) > > > Best regards > > Pascal > > > > > Melissa Linkert schrieb: >> >> Hi Gary, >> >> This problem can be fixed by updating to the latest trunk build of >> Bio-Formats - see http://loci.wisc.edu/bio-formats/imagej for >> instructions. >> >> Regards, >> -Melissa >> >> On Tue, May 11, 2010 at 8:11 AM, Gary G. Li <[hidden email]> >> wrote: >> >>> >>> Greetings, >>> >>> The following Java Exceptions were thrown when I was trying to open a >>> Leica >>> Confocal stack. >>> >>> What could be the cause? >>> >>> Regard_ >>> >>> Gary >>> >>> >>> >>> ------ >>> >>> java.lang.ArrayIndexOutOfBoundsException: -1 >>> >>> at java.util.Vector.get(Vector.java:696) >>> >>> at >>> >>> loci.formats.ome.OMEXML200809Metadata.getImageNode(OMEXML200809Metadata.java:5675) >>> >>> at >>> >>> loci.formats.ome.OMEXML200809Metadata.setImageCreationDate(OMEXML200809Metadata.java:3409) >>> >>> at >>> >>> loci.formats.meta.FilterMetadata.setImageCreationDate(FilterMetadata.java:643) >>> >>> at >>> loci.formats.in.LeicaHandler.startElement(LeicaHandler.java:715) >>> >>> at >>> >>> com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.startElement(AbstractSAXParser.java:501) >>> >>> at >>> >>> com.sun.org.apache.xerces.internal.parsers.AbstractXMLDocumentParser.emptyElement(AbstractXMLDocumentParser.java:179) >>> >>> at >>> >>> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanStartElement(XMLDocumentFragmentScannerImpl.java:1339) >>> >>> at >>> >>> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2747) >>> >>> at >>> >>> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:648) >>> >>> at >>> >>> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:510) >>> >>> at >>> >>> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:807) >>> >>> at >>> >>> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737) >>> >>> at >>> >>> com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:107) >>> >>> at >>> >>> com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205) >>> >>> at >>> >>> com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:522) >>> >>> at javax.xml.parsers.SAXParser.parse(SAXParser.java:395) >>> >>> at javax.xml.parsers.SAXParser.parse(SAXParser.java:198) >>> >>> at loci.common.XMLTools.parseXML(XMLTools.java:277) >>> >>> at loci.common.XMLTools.parseXML(XMLTools.java:252) >>> >>> at >>> loci.formats.in.LIFReader.initMetadata(LIFReader.java:383) >>> >>> at loci.formats.in.LIFReader.initFile(LIFReader.java:315) >>> >>> at loci.formats.FormatReader.setId(FormatReader.java:901) >>> >>> at loci.plugins.importer.Importer.run(Importer.java:267) >>> >>> at loci.plugins.LociImporter.run(LociImporter.java:77) >>> >>> at ij.IJ.runUserPlugIn(IJ.java:175) >>> >>> at ij.IJ.runPlugIn(IJ.java:142) >>> >>> at ij.IJ.runPlugIn(IJ.java:131) >>> >>> at >>> HandleExtraFileTypes.openImage(HandleExtraFileTypes.java:241) >>> >>> at HandleExtraFileTypes.run(HandleExtraFileTypes.java:37) >>> >>> at ij.IJ.runUserPlugIn(IJ.java:175) >>> >>> at ij.IJ.runPlugIn(IJ.java:142) >>> >>> at ij.IJ.runPlugIn(IJ.java:131) >>> >>> at >>> ij.io.Opener.openWithHandleExtraFileTypes(Opener.java:337) >>> >>> at ij.io.Opener.openImage(Opener.java:245) >>> >>> at ij.io.Opener.openImage(Opener.java:268) >>> >>> at ij.io.Opener.open(Opener.java:124) >>> >>> at ij.io.Opener.open(Opener.java:63) >>> >>> at ij.plugin.Commands.run(Commands.java:23) >>> >>> at ij.IJ.runPlugIn(IJ.java:148) >>> >>> at ij.Executer.runCommand(Executer.java:121) >>> >>> at ij.Executer.run(Executer.java:58) >>> >>> at java.lang.Thread.run(Thread.java:619) >>> >>> > ... 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