ImgOpener

[Mark Hiner]

Hi Michael,

 Just wanted to let you know that in the latest
commit<https://github.com/scifio/scifio/commit/9a0cd564ae4665697989cf184af7e306cf096fdb>,
I updated ImgOptions to allow discontinuous sub-regions to be specified.

 I don't love the API right now, especially since it's still tied to being
5-D.. so I hope to refine it soon when we switch to an N-D model. But it
does seem to be functional at least!

 I have OME-XML changes ready for SCIFIO-BF-compat, so we just need to fix
the dimension order error. Then we can start testing scifio + the
compatibility layer together and move towards a release.

  I'm out tomorrow so it may not be until early next week.

- Mark


On Wed, Aug 7, 2013 at 10:28 AM, Michael Zinsmaier <michael.zinsmaier at gmx.de
> wrote:

> Hi Mark,
>
> that sound great. We used Snapshot versions because we want to actively
> test the ImgOpener however given your fast release cycle the latest stable
> version should be recent enough.
> Removing the need to depend on OME-XML 4.5 would be great.
>
> Regards Michael
>
>  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/**
>> 677fe7645e26e9e692f0ca823698f5**0349b69ef7<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 <mailto:michael.zinsmaier at gmx.**de<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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