[ome-users] Evotec/Opera FLEX file format issue

[Melissa Linkert]

Hi Jeff,

> Yes.  There is a whole plate of images...  For now, I'll upload 1 image...

Thank you for uploading an example files.

> Will it be easier to investigate if I upload more of the images?

I can duplicate the problem with just the one file, so it is not
necessary to send additional files at the moment.

I have filed a ticket on our issue tracking system to fix this problem:

https://trac.openmicroscopy.org.uk/ome/ticket/11286

You have been CC'd on that ticket, and so will receive an automated
email each time we update the status.  If you prefer not to receive
those emails, please let me know.

Regards,
-Melissa

On Tue, Jul 16, 2013 at 09:37:15PM +0000, Jeff C Hanson wrote:
> Yes.  There is a whole plate of images...  For now, I'll upload 1 image...
> Will it be easier to investigate if I upload more of the images?
> 
> Jeff
> 
> -----Original Message-----
> From: Melissa Linkert [mailto:melissa.linkert at gmail.com] On Behalf Of Melissa Linkert
> Sent: Tuesday, July 16, 2013 5:26 PM
> To: Jeff C Hanson
> Cc: ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] Evotec/Opera FLEX file format issue
> 
> Hi Jeff,
> 
> >                 I have flex file that I am having trouble reading in FIJI using the BioFormats reader.  I was able to get read older flex images, but not these newer ones.  I have attached the FIJI error message which includes my OS, Java, ImageJ version #'s.
> >                 The example file I have is 27MB, which is too big for my email system to send.
> >
> 
> Thank you for the bug report.  Could you please upload the file to the OME QA system?  The QA upload page is here:
> 
> http://qa.openmicroscopy.org.uk/qa/upload/
> 
> For the files that cause a problem, are there additional .flex files (e.g. an entire plate of data) in the same folder?
> 
> Regards,
> -Melissa
> 
> On Tue, Jul 16, 2013 at 05:20:47PM +0000, Jeff C Hanson wrote:
> >                 I have flex file that I am having trouble reading in FIJI using the BioFormats reader.  I was able to get read older flex images, but not these newer ones.  I have attached the FIJI error message which includes my OS, Java, ImageJ version #'s.
> >                 The example file I have is 27MB, which is too big for my email system to send.
> > 
> > Thanks,
> > Jeff
> > ---
> > (Fiji Is Just) ImageJ 1.47v; Java 1.6.0_24 [64-bit]; Windows 7 6.1; 
> > 23MB of 2979MB (<1%)
> > 
> > java.lang.reflect.InvocationTargetException
> >                 at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> >                 at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
> >                 at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
> >                 at java.lang.reflect.Method.invoke(Method.java:597)
> >                 at ij.Command.runPlugIn(Command.java:148)
> >                 at ij.Command.runCommand(Command.java:97)
> >                 at ij.Executer.run(Executer.java:64)
> >                 at java.lang.Thread.run(Thread.java:662)
> > Caused by: java.lang.NullPointerException
> >                 at loci.formats.in.FlexReader.populateMetadataStore(FlexReader.java:628)
> >                 at loci.formats.in.FlexReader.initFlexFile(FlexReader.java:502)
> >                 at loci.formats.in.FlexReader.initFile(FlexReader.java:334)
> >                 at loci.formats.FormatReader.setId(FormatReader.java:1183)
> >                 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:195)
> >                 at ij.IJ.runPlugIn(IJ.java:160)
> >                 ... 8 more
> > 
> > 
> > 
> 
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>