Posted by
Pascal Lorentz-2 on
URL: http://imagej.273.s1.nabble.com/Java-Exceptions-Thrown-When-a-Leica-Confocal-Stack-is-Opened-tp3688177p3688179.html
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)
>>
>>