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

Tue Feb 25 01:28:18 GMT 2014

Hi Kevin,

> Sorry to bother you again, but looks like this ticket is still shown as
> "open" and not merged? I downloaded the the latest development build of
> loci_tool.jar from the URL above and it still shows the same problem. I
> just want to check if there's any update or I missed something. Thank you
> very much.

That's correct - the fix is still open for the moment, and so is not yet
included in the latest development build.  We've had to slow the review
process for the last couple of weeks to allow for packaging the upcoming
5.0.0 release, but expect to have this merged very soon.

Regards,
-Melissa

On Mon, Feb 24, 2014 at 05:23:28PM -0800, Kevin Chen wrote:
> Hi Melissa,
> Sorry to bother you again, but looks like this ticket is still shown as
> "open" and not merged? I downloaded the the latest development build of
> loci_tool.jar from the URL above and it still shows the same problem. I
> just want to check if there's any update or I missed something. Thank you
> very much.
> Best regards,
> Kevin
> 
> 
> 
> On Mon, Feb 3, 2014 at 12:12 PM, Melissa Linkert <
> melissa at glencoesoftware.com> wrote:
> 
> > 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
> > > >
> > > >
> >