[OpenSPIM] open SPIM acquisition error

[Ulrik Günther]

  Hello Aurelia and Johannes,


I modified the OMETiffHandler to use the new Units API of BioFormats, you can find the changes at https://github.com/skalarproduktraum/SPIMAcquisition/tree/OMEUnitFixes


Question to Johannes: Do you want a pull request for that? The issue I’m currently having is that it works just fine in Fiji with the MM update site, but not with the latest MM nightly, as it brings an older ome-xml version. Suggestions?


cheers,


ulrik




—
Ulrik Günther, Dipl.-Phys.
PhD Student
MOSAIC Group & Tomancak Lab, Center of Systems Biology Dresden
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108, D-01307 Dresden, Germany



E-Mail: guenther at mpi-cbg.de




> On Apr 17, 2015, at 10:10 PM, Johannes Schindelin <johannes.schindelin at gmx.de> wrote:
> 
> 
> Hi Aurelia,
> 
> 
> On 2015-04-17 16:56, Aurelia Honerkamp-Smith wrote:
> 
> 
>> java.lang.NoSuchMethodError:
>> loci.formats.meta.IMetadata.setPixelsPhysicalSizeX(Lome/xml/model/primitives/PositiveFloat;I)V
>> 
>> 
>> 
> 
> 
> It would appear as if OMERO might have broken Bio-Formats' 
> backwards-compatibility once again... Exceptions like this one mean that 
> the method setPixelsPhysicalSizeX(PositiveFloat) was available at 
> compile time but is no longer available at runtime.
> 
> 
> And indeed, it looks as if IMetadata by virtue of extending 
> ome.xml.meta.MetadataStore defines only the following 
> setPixelsPhysicalSizeX() method:
> 
> 
> public abstract void setPixelsPhysicalSizeX(ome.units.quantity.Length, 
> int);
> 
> 
> I fear that we will have to update the SPIMAcquisition plugin in a hurry 
> to conform with the new Bio-Formats version that was so overzealously 
> uploaded to the Fiji update site despite breaking backwards 
> compatibility in a rather blatant way.
> 
> 
> My calendar is densely packed, though, so I have no idea when I will get 
> around to fix it (hint: help appreciated).
> 
> 
> Ciao,
> Johannes
> 
> 
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