<div dir="ltr">Hi Melissa,<div>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.</div>
<div>Best regards,</div><div>Kevin</div><div> </div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Mon, Feb 3, 2014 at 12:12 PM, Melissa Linkert <span dir="ltr"><<a href="mailto:melissa@glencoesoftware.com" target="_blank">melissa@glencoesoftware.com</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Kevin,<br>
<div class=""><br>
> I have uploaded two files, both are having problems: image1 cannot be open<br>
> at all, image2 can be open but the images from two of the 3 channels are<br>
> not correct. I suspect there're some parsing issues.<br>
<br>
</div>Thank you for uploading example data. We are reviewing a fix for both files<br>
here:<br>
<br>
<a href="https://github.com/openmicroscopy/bioformats/pull/886" target="_blank">https://github.com/openmicroscopy/bioformats/pull/886</a><br>
<br>
Once that is shown as being "merged", you should be able to use the<br>
latest development build of Bio-Formats from:<br>
<br>
<a href="http://ci.openmicroscopy.org/view/5.1/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/" target="_blank">http://ci.openmicroscopy.org/view/5.1/job/BIOFORMATS-5.1-latest/lastSuccessfulBuild/artifact/artifacts/</a><br>
<br>
to verify that both files open correctly.<br>
<br>
Regards,<br>
-Melissa<br>
<div class="HOEnZb"><div class="h5"><br>
On Thu, Jan 30, 2014 at 02:55:27PM -0800, Kevin Chen wrote:<br>
> Hi Melissa,<br>
> I have uploaded two files, both are having problems: image1 cannot be open<br>
> at all, image2 can be open but the images from two of the 3 channels are<br>
> not correct. I suspect there're some parsing issues.<br>
> Thank you so much for your help!<br>
> Regards,<br>
> Kevin<br>
><br>
><br>
> On Thu, Jan 30, 2014 at 2:15 PM, Melissa Linkert <<br>
> <a href="mailto:melissa@glencoesoftware.com">melissa@glencoesoftware.com</a>> wrote:<br>
><br>
> > Hi Kevin,<br>
> ><br>
> > > I have a flex file that can be read correctly in Opera's EvoShell<br>
> > > environment but throws IOException when I try to open it in ImageJ using<br>
> > > the bio-format plug-in. I'm using ImageJ v1.48p, and the Bio-Formats<br>
> > 4.4.10<br>
> > > loci_tools.jar downloaded from<br>
> > > <a href="http://downloads.openmicroscopy.org/bio-formats/4.4.10/" target="_blank">http://downloads.openmicroscopy.org/bio-formats/4.4.10/</a> as an ImageJ<br>
> > > plugin.<br>
> > ><br>
> > > The error log with exception:<br>
> ><br>
> > Thank you for reporting this problem. Could you please upload the<br>
> > problematic file to <a href="http://qa.openmicroscopy.org.uk/qa/upload/" target="_blank">http://qa.openmicroscopy.org.uk/qa/upload/</a>?<br>
> ><br>
> > Regards,<br>
> > -Melissa<br>
> ><br>
> > On Wed, Jan 29, 2014 at 05:51:15PM -0800, Kevin Chen wrote:<br>
> > > Hi all,<br>
> > ><br>
> > > I have a flex file that can be read correctly in Opera's EvoShell<br>
> > > environment but throws IOException when I try to open it in ImageJ using<br>
> > > the bio-format plug-in. I'm using ImageJ v1.48p, and the Bio-Formats<br>
> > 4.4.10<br>
> > > loci_tools.jar downloaded from<br>
> > > <a href="http://downloads.openmicroscopy.org/bio-formats/4.4.10/" target="_blank">http://downloads.openmicroscopy.org/bio-formats/4.4.10/</a> as an ImageJ<br>
> > > plugin.<br>
> > ><br>
> > > The error log with exception:<br>
> > ><br>
> > > java.io.IOException<br>
> > > at loci.common.xml.XMLTools.parseXML(XMLTools.java:373)<br>
> > > at loci.common.xml.XMLTools.parseXML(XMLTools.java:351)<br>
> > > at loci.formats.in.FlexReader.parseFlexFile(FlexReader.java:796)<br>
> > > at loci.formats.in.FlexReader.groupFiles(FlexReader.java:1256)<br>
> > > at loci.formats.in.FlexReader.initFlexFile(FlexReader.java:495)<br>
> > > at loci.formats.in.FlexReader.initFile(FlexReader.java:328)<br>
> > > at loci.formats.FormatReader.setId(FormatReader.java:1244)<br>
> > > at loci.plugins.in.ImportProcess.initializeFile(ImportProcess.java:482)<br>
> > > at loci.plugins.in.ImportProcess.execute(ImportProcess.java:146)<br>
> > > at loci.plugins.in.Importer.showDialogs(Importer.java:141)<br>
> > > at loci.plugins.in.Importer.run(Importer.java:79)<br>
> > > at loci.plugins.LociImporter.run(LociImporter.java:81)<br>
> > > at ij.IJ.runUserPlugIn(IJ.java:196)<br>
> > > at ij.IJ.runPlugIn(IJ.java:160)<br>
> > > at ij.Executer.runCommand(Executer.java:131)<br>
> > > at ij.Executer.run(Executer.java:64)<br>
> > > at java.lang.Thread.run(Thread.java:619)<br>
> > > Caused by: org.xml.sax.SAXParseException: Content is not allowed in<br>
> > > trailing section.<br>
> > > at<br>
> > ><br>
> > com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.createSAXParseException(ErrorHandlerWrapper.java:195)<br>
> > > at<br>
> > ><br>
> > com.sun.org.apache.xerces.internal.util.ErrorHandlerWrapper.fatalError(ErrorHandlerWrapper.java:174)<br>
> > > at<br>
> > ><br>
> > com.sun.org.apache.xerces.internal.impl.XMLErrorReporter.reportError(XMLErrorReporter.java:388)<br>
> > > at<br>
> > ><br>
> > com.sun.org.apache.xerces.internal.impl.XMLScanner.reportFatalError(XMLScanner.java:1414)<br>
> > > at<br>
> > ><br>
> > com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl$TrailingMiscDriver.next(XMLDocumentScannerImpl.java:1459)<br>
> > > at<br>
> > ><br>
> > com.sun.org.apache.xerces.internal.impl.XMLDocumentScannerImpl.next(XMLDocumentScannerImpl.java:648)<br>
> > > at<br>
> > ><br>
> > com.sun.org.apache.xerces.internal.impl.XMLDocumentFragmentScannerImpl.scanDocument(XMLDocumentFragmentScannerImpl.java:511)<br>
> > > at<br>
> > ><br>
> > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:808)<br>
> > > at<br>
> > ><br>
> > com.sun.org.apache.xerces.internal.parsers.XML11Configuration.parse(XML11Configuration.java:737)<br>
> > > at<br>
> > ><br>
> > com.sun.org.apache.xerces.internal.parsers.XMLParser.parse(XMLParser.java:119)<br>
> > > at<br>
> > ><br>
> > com.sun.org.apache.xerces.internal.parsers.AbstractSAXParser.parse(AbstractSAXParser.java:1205)<br>
> > > at<br>
> > ><br>
> > com.sun.org.apache.xerces.internal.jaxp.SAXParserImpl$JAXPSAXParser.parse(SAXParserImpl.java:522)<br>
> > > at javax.xml.parsers.SAXParser.parse(SAXParser.java:395)<br>
> > > at javax.xml.parsers.SAXParser.parse(SAXParser.java:198)<br>
> > > at loci.common.xml.XMLTools.parseXML(XMLTools.java:365)<br>
> > > ... 16 more<br>
> > ><br>
> > > Looks like the Bio-Format code is not parsing the specific flex file<br>
> > > correctly. I can provide the problematic flex file once I know where to<br>
> > > upload it.<br>
> > > Thank you very much in advance for any help.<br>
> > > Best regards,<br>
> > > Kevin<br>
> ><br>
> > > _______________________________________________<br>
> > > ome-users mailing list<br>
> > > <a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
> > > <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
> ><br>
> ><br>
</div></div></blockquote></div><br></div>