[ome-users] Problem reading Evotec Flex file using Bio-Formats plugin in ImageJ

[Melissa Linkert]

Hi Kevin,

> I have a flex file that can be read correctly in Opera's EvoShell
> environment but throws IOException when I try to open it in ImageJ using
> the bio-format plug-in. I'm using ImageJ v1.48p, and the Bio-Formats 4.4.10
> loci_tools.jar downloaded from
> http://downloads.openmicroscopy.org/bio-formats/4.4.10/ as an ImageJ
> plugin.
> 
> The error log with exception:

Thank you for reporting this problem.  Could you please upload the
problematic file to http://qa.openmicroscopy.org.uk/qa/upload/?

Regards,
-Melissa

On Wed, Jan 29, 2014 at 05:51:15PM -0800, Kevin Chen wrote:
> Hi all,
> 
> I have a flex file that can be read correctly in Opera's EvoShell
> environment but throws IOException when I try to open it in ImageJ using
> the bio-format plug-in. I'm using ImageJ v1.48p, and the Bio-Formats 4.4.10
> loci_tools.jar downloaded from
> http://downloads.openmicroscopy.org/bio-formats/4.4.10/ as an ImageJ
> plugin.
> 
> The error log with exception:
> 
> java.io.IOException
> at loci.common.xml.XMLTools.parseXML(XMLTools.java:373)
> at loci.common.xml.XMLTools.parseXML(XMLTools.java:351)
> at loci.formats.in.FlexReader.parseFlexFile(FlexReader.java:796)
> at loci.formats.in.FlexReader.groupFiles(FlexReader.java:1256)
> at loci.formats.in.FlexReader.initFlexFile(FlexReader.java:495)
> at loci.formats.in.FlexReader.initFile(FlexReader.java:328)
> at loci.formats.FormatReader.setId(FormatReader.java:1244)
> at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)
> at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)
> at loci.plugins.in.Importer.showDialogs(Importer.java:141)
> at loci.plugins.in.Importer.run(Importer.java:79)
> at loci.plugins.LociImporter.run(LociImporter.java:81)
> at ij.IJ.runUserPlugIn(IJ.java:196)
> at ij.IJ.runPlugIn(IJ.java:160)
> at ij.Executer.runCommand(Executer.java:131)
> at ij.Executer.run(Executer.java:64)
> at java.lang.Thread.run(Thread.java:619)
> Caused by: org.xml.sax.SAXParseException: Content is not allowed in
> trailing section.
> at
> com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)
> at
> com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:174)
> at
> com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:388)
> at
> com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1414)
> at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$TrailingMiscDriver.next(XMLDocumentScannerImpl.java:1459)
> at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:648)
> at
> com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:511)
> at
> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:808)
> at
> com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737)
> at
> com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:119)
> at
> com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205)
> at
> com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$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:365)
> ... 16 more
> 
> Looks like the Bio-Format code is not parsing the specific flex file
> correctly. I can provide the problematic flex file once I know where to
> upload it.
> Thank you very much in advance for any help.
> Best regards,
> Kevin

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