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

[Melissa Linkert]

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
> 
> 
> 

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