http://imagej.273.s1.nabble.com/Java-Exceptions-Thrown-When-a-Leica-Confocal-Stack-is-Opened-tp3688177p3688180.html
replying sooner. In fact, this is a very different problem from the
one reported by Gary. Regardless, updating to the very latest trunk
send one of the problematic .lif files. If needed, I can provide you
> 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)
>>>
>>>
>