[ome-devel] RuntimeException with ScanR importer.

[Melissa Linkert]

Hi Rubén,

> After a long ScanR conversion with bfconvert. I got this exception. The
> conversion output is complete however.

Given the contents of the stack trace, it's very likely that the TIFF will
not contain any OME-XML, and thus is not a valid OME-TIFF.

> I will try to reproduce it but, do you know if this could be due to having
> recompiled loci_tools.jar during the conversion?

Recompiling during the conversion is almost certainly the cause of this
error.  If it were an actual bug, I would expect to see this error
message at the very beginning of the conversion process.

If you are able to reproduce the error even without recompiling, then please let
me know.

Regards,
-Melissa

On Thu, Sep 23, 2010 at 09:46:32AM +0200, Rubén Muñoz wrote:
> Hi Melissa,
>  
> After a long ScanR conversion with bfconvert. I got this exception. The conversion output is complete however.
> 
> I will try to reproduce it but, do you know if this could be due to having recompiled loci_tools.jar during the conversion?
> 
> Thanks,
> 
> Rubén
> 
> Reading IFDs
> Populating metadata
> 	Series 259: converted 95/95 planes (100%)
> 
> Exception in thread "main" java.lang.RuntimeException: services.properties not found on CLASSPATH
> 	at loci.formats.out.OMETiffWriter.close(OMETiffWriter.java:122)
> 	at loci.formats.ImageWriter.close(ImageWriter.java:408)
> 	at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:284)
> 	at loci.formats.tools.ImageConverter.main(ImageConverter.java:302)
> Caused by: services.properties not found on CLASSPATH
> 	at loci.common.services.ServiceFactory.<init>(ServiceFactory.java:83)
> 	at loci.common.services.ServiceFactory.<init>(ServiceFactory.java:70)
> 	at loci.formats.out.OMETiffWriter.setupServiceAndMetadata(OMETiffWriter.java:213)
> 	at loci.formats.out.OMETiffWriter.close(OMETiffWriter.java:97)
> 	... 3 more