[SCIFIO] Some small bugs / feature requests

[Mark Hiner]

Hi Michael,

 You're using the scifio-bf-compat snapshot right?

    - we had to add two services to our Scifio Context
> OMEXMLMetadataService.class, OMEXMLService.class
>

 Curtis and I talked about a Service solution.. it should be fairly
straightforward, just have to do it!


One other small bug: the OMEMetadata empty constructor is broken
>
>

 Yeah, Curtis made the @Parameter injection smarter for Scijava-common, but
it means no more null contexts allowed. I will fix that, thanks for
pointing it out!

- but this does not work for jpg images (index out of bounds)
>

where do you get this exception? I'll write some calibration unit tests
today to try and cover these scenarios.

Also, where is your calibration data coming from exactly? I don't believe
there's any metadata in JPEG that's explicitly being translated to
calibration values. So currently the expected behavior would be to see
default calibration (1.0um) for each axis.

Still, setting the calibration after initializing Metadata should work..
can you share the code snippet that's doing the setting?

    - and I have at least one .lsm image that fails with a null pointer if
> I load it with .openImg.
>       This error is not related to our attemps to get callibration working
>       (img in the appendix)
>

Thanks for providing the failing image. I'll test that today.

I looked today at the interval selection code. Could you add a long[]
> constructor for DimRange? I think a simple one that just lists all included
> indices should be enough (equivalent to the string constructor with
> "a,b,c,d"   long[] {a,b,c,d})
>

Yep, that sounds reasonable :) I may release a 0.5.2 today because of some
ImgSaver bug fixes I made yesterday.. so if so, this will be included as
well.

Thanks for the feedback,
Mark


On Thu, Aug 15, 2013 at 7:48 AM, Michael Zinsmaier <michael.zinsmaier at gmx.de
> wrote:

> Hi Mark,
>
> yay the new libs (currently scifio-bf-compat 1.0.1 / scifio-0.5.1 /
> scijava-common-2.0.2) are working (-:
>
> Callibration still makes some trouble (I know that is super early
> implementation stage but anyways)
>     - we had to add two services to our Scifio Context
> OMEXMLMetadataService.class, OMEXMLService.class
>     - the ImgPlus returned by ImgOpener.openImg does not contain
> callibration values
>
>     because of the 2nd point we added a small hack: we currently add the
> calibration values after loading of the image (calibration values
>     come from metadata -> ome metadata)
>
>     - but this does not work for jpg images (index out of bounds)
>
>     - and I have at least one .lsm image that fails with a null pointer if
> I load it with .openImg.
>       This error is not related to our attemps to get callibration working
>       (img in the appendix)
>
>
>
> One other small bug: the OMEMetadata empty constructor is broken
>
>   OMEMEtadata()     ->     this(null)
>         OMEMetadata(final Context context)       -> this(context, null);
>             OMEMetadata(final Context context, final OMEXMLMetadata root)
>      ->    setContext(context)
>                     context.inject(this);
>
>     => NullPointer
>
>
> And finally a feature request:
> I looked today at the interval selection code. Could you add a long[]
> constructor for DimRange? I think a simple one that just lists all included
> indices should be enough (equivalent to the string constructor with
> "a,b,c,d"   long[] {a,b,c,d})
>
> Best regards
> Michael
>
>
>
>
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