problems opening files with LOCI Importer

[Katharina Reusch]

Hello,
I used the Mac-version of ImageJ for quite  while now and I have tif-files
from a Nikon TiEclipse micrsocope and used to open them with the
Loci-Importer. Unfortunately it doesn't seem to work anymore and I'm not
sure why. I use the newest ImageJ version 1.44l and the Loci-file is from
this month so it should be up to date.
When I try to open a file two windows are popping up: the first one says:
Sorry, there was an I/O problem during import. and the other one says:

com.sun.org.apache.xerces.internal.impl.io.MalformedByteSequenceException:
Invalid byte 1 of 1-byte UTF-8 sequence.
        at
com.sun.org.apache.xerces.internal.impl.io.UTF8Reader.invalidByte(UTF8Reader.java:684)
        at
com.sun.org.apache.xerces.internal.impl.io.UTF8Reader.read(UTF8Reader.java:554)
        at
com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.load(XMLEntityScanner.java:1742)
        at
com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.scanLiteral(XMLEntityScanner.java:1064)
        at
com.sun.org.apache.xerces.internal.impl.XMLScanner.scanAttributeValue(XMLScanner.java:974)
        at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanAttribute(XMLDocumentFragmentScannerImpl.java:1547)
        at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanStartElement(XMLDocumentFragmentScannerImpl.java:1320)
        at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2755)
        at
com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:648)
        at
com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:511)
        at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:808)
        at
com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737)
        at
com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:119)
        at
com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205)
        at
com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$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.xml.XMLTools.parseXML(XMLTools.java:298)
        at loci.common.xml.XMLTools.parseXML(XMLTools.java:284)
        at loci.common.xml.XMLTools.parseXML(XMLTools.java:263)
        at
loci.formats.in.NikonElementsTiffReader.initStandardMetadata(NikonElementsTiffReader.java:96)
        at loci.formats.in.BaseTiffReader.initMetadata(BaseTiffReader.java:74)
        at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:482)
        at loci.formats.FormatReader.setId(FormatReader.java:1058)
        at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:475)
        at loci.plugins.in.ImportProcess.execute(ImportProcess.java:138)
        at loci.plugins.in.Importer.showDialogs(Importer.java:125)
        at loci.plugins.in.Importer.run(Importer.java:77)
        at loci.plugins.LociImporter.run(LociImporter.java:77)
        at ij.IJ.runUserPlugIn(IJ.java:183)
        at ij.IJ.runPlugIn(IJ.java:150)
        at ij.Executer.runCommand(Executer.java:124)
        at ij.Executer.run(Executer.java:61)
        at java.lang.Thread.run(Thread.java:637)


I honestly have no idea what this means, but it would be great if someone
can help me as I can't do any work at the moment!
Many thanks!

[Melissa Linkert-2]

Hi Katharina,

Thank you very much for reporting this problem.

Fortunately, I think this problem was recently fixed.  Can you please update to
the very latest trunk build of the LOCI plugins and see if that solves the
problem?

Regards,
-Melissa

On Tue, Dec 21, 2010 at 12:23:12PM +0000, Katharina Reusch wrote:

> Hello,
> I used the Mac-version of ImageJ for quite  while now and I have tif-files
> from a Nikon TiEclipse micrsocope and used to open them with the
> Loci-Importer. Unfortunately it doesn't seem to work anymore and I'm not
> sure why. I use the newest ImageJ version 1.44l and the Loci-file is from
> this month so it should be up to date.
> When I try to open a file two windows are popping up: the first one says:
> Sorry, there was an I/O problem during import. and the other one says:
>
> com.sun.org.apache.xerces.internal.impl.io.MalformedByteSequenceException:
> Invalid byte 1 of 1-byte UTF-8 sequence.
> at
> com.sun.org.apache.xerces.internal.impl.io.UTF8Reader.invalidByte(UTF8Reader.java:684)
> at
> com.sun.org.apache.xerces.internal.impl.io.UTF8Reader.read(UTF8Reader.java:554)
> at
> com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.load(XMLEntityScanner.java:1742)
> at
> com.sun.org.apache.xerces.internal.impl.XMLEntityScanner.scanLiteral(XMLEntityScanner.java:1064)
> at
> com.sun.org.apache.xerces.internal.impl.XMLScanner.scanAttributeValue(XMLScanner.java:974)
> at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanAttribute(XMLDocumentFragmentScannerImpl.java:1547)
> at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanStartElement(XMLDocumentFragmentScannerImpl.java:1320)
> at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl$FragmentContentDriver.next(XMLDocumentFragmentScannerImpl.java:2755)
> at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:648)
> at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:511)
> at
> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:808)
> at
> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737)
> at
> com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:119)
> at
> com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205)
> at
> com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$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.xml.XMLTools.parseXML(XMLTools.java:298)
> at loci.common.xml.XMLTools.parseXML(XMLTools.java:284)
> at loci.common.xml.XMLTools.parseXML(XMLTools.java:263)
> at
> loci.formats.in.NikonElementsTiffReader.initStandardMetadata(NikonElementsTiffReader.java:96)
> at loci.formats.in.BaseTiffReader.initMetadata(BaseTiffReader.java:74)
> at loci.formats.in.BaseTiffReader.initFile(BaseTiffReader.java:482)
> at loci.formats.FormatReader.setId(FormatReader.java:1058)
> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:475)
> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:138)
> at loci.plugins.in.Importer.showDialogs(Importer.java:125)
> at loci.plugins.in.Importer.run(Importer.java:77)
> at loci.plugins.LociImporter.run(LociImporter.java:77)
> at ij.IJ.runUserPlugIn(IJ.java:183)
> at ij.IJ.runPlugIn(IJ.java:150)
> at ij.Executer.runCommand(Executer.java:124)
> at ij.Executer.run(Executer.java:61)
> at java.lang.Thread.run(Thread.java:637)
>
>
> I honestly have no idea what this means, but it would be great if someone
> can help me as I can't do any work at the moment!
> Many thanks!