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

[Melissa Linkert]

Hi Kevin,

> I have uploaded two files, both are having problems: image1 cannot be open
> at all, image2 can be open but the images from two of the 3 channels are
> not correct. I suspect there're some parsing issues.

Thank you for uploading example data.  We are reviewing a fix for both files
here:

https://github.com/openmicroscopy/bioformats/pull/886

Once that is shown as being "merged", you should be able to use the
latest development build of Bio-Formats from:

http://ci.openmicroscopy.org/view/5.1/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/

to verify that both files open correctly.

Regards,
-Melissa

On Thu, Jan 30, 2014 at 02:55:27PM -0800, Kevin Chen wrote:
> Hi Melissa,
> I have uploaded two files, both are having problems: image1 cannot be open
> at all, image2 can be open but the images from two of the 3 channels are
> not correct. I suspect there're some parsing issues.
> Thank you so much for your help!
> Regards,
> Kevin
> 
> 
> On Thu, Jan 30, 2014 at 2:15 PM, Melissa Linkert <
> melissa at glencoesoftware.com> wrote:
> 
> > 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
> >
> > > _______________________________________________
> > > ome-users mailing list
> > > ome-users at lists.openmicroscopy.org.uk
> > > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> >
> >