ImgOpener

[Mark Hiner]

Hi Michael,

 I'm copying the scifio mailing list, as this could be of general interest.

bioformats, scifio and scifio-bf-compat are the latest snapshot versions
> from the maven repository
>

First of all, I would recommend trying to use the release versions first
(scifio 0.4.1, scifio-bf-compat 1.0.1). Is there some API in the snapshot
versions you need specifically? If so, you could then transition from the
release to snapshots, once you're updated to the SCIFIO 0.4.X API.

Of course, SCIFIO-BF-compat 1.0.0 includes a scifio 0.3.X dependency so
it's not compatible with 0.4.X... so I understand why you had to use
snapshots. :(

 * bioformats 4.4.8
>  * ome-xml 4.5
>

This looks like a limitation of the current SCIFIO-BF-compat project. First
of all, it includes bio-formats and ome-xml 4.4.8 dependencies, so you
shouldn't need to explicitly declare them.

The OME-XML 4.5 with OMEMetadata class isn't really ready for consumption
yet. Having an OME-XML 4.5 on the classpath with the inherited 4.4.8
dependency seems like a bad idea. So I think SCIFIO-BF-compat should have
its own copy of the OMEMetadata class + translators for now, so you can
translate to it to extract the OME-XML.

This would be a temporary solution until our Bio-Formats fork is actually
released (which could be a while, and would still have to resolve the 4.5.X
and 4.4.X dependency issues).

Unless anyone has other suggestions I'll do migrate over the OMEMetadata +
translators this afternoon and release a SCIFIO-BF-compat 1.1.0. That
should resolve your dependency issues, at least, by also updating the
SCIFIO version to 0.4.X, so you can use actual release artifacts.

The error message is "IllegalArgumentException: Invalid dimension order:
> XYC"
>

This is a bug introduced in this
commit<https://github.com/scifio/scifio-bf-compat/commit/677fe7645e26e9e692f0ca823698f50349b69ef7>.
I will resolve it and make sure you can extract OME-XML with
scifio-bf-compat + scifio 0.4.1 before releasing.

Hope that helps! Thanks for testing :)

- Mark


On Tue, Aug 6, 2013 at 4:46 PM, Michael Zinsmaier
<michael.zinsmaier at gmx.de>wrote:

> Hi Mark,
>
> we just started to use the ImgOpener. Unfortunately I can't open .jpg
> images.
> The error message is "IllegalArgumentException: Invalid dimension order:
> XYC"
>
> My last working testversion used
>  * scifio3.1
>  * bioformats 4.4.8
>  * ome-xml 4.5
>  * scifio-bf-compat 1.0.1
>
> and builds from roughly 3 weeks ago
>
>
>
> the new setup uses
> * scifio4.2
>  * bioformats 4.4.8
>  * ome-xml 4.5
>  * scifio-bf-compat 1.0.1
>
> bioformats, scifio and scifio-bf-compat are the latest snapshot versions
> from the maven repository, ome-xml
> is self build updated to the scifio branch from bioformats (last commit
> 12.07)
> (By the way can I add the scifio ome-xml with OMEMetadata as maven
> dependency? If yes how do I do it?)
>
> Any ideas?
>
> Best regards
> Michael
>
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