Java Exceptions Thrown When a Leica Confocal Stack is Opened.

[Gary G. Li]

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)

[Melissa Linkert-2]

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)
>

[Gary G. Li]

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)
> >
>

[Pascal Lorentz-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)
>>
>>    

[Melissa Linkert-2]

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)
>>>
>>>
>