<div dir="ltr"><div><div><div><div>Hi Michael,<br><br> Just wanted to let you know that in the <a href="https://github.com/scifio/scifio/commit/9a0cd564ae4665697989cf184af7e306cf096fdb">latest commit</a>, I updated ImgOptions to allow discontinuous sub-regions to be specified.<br>
<br></div> 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!<br><br></div> 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.<br>
<br></div> I'm out tomorrow so it may not be until early next week.<br><br></div>- Mark<br></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Aug 7, 2013 at 10:28 AM, Michael Zinsmaier <span dir="ltr"><<a href="mailto:michael.zinsmaier@gmx.de" target="_blank">michael.zinsmaier@gmx.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Mark,<br>
<br>
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.<br>
Removing the need to depend on OME-XML 4.5 would be great.<br>
<br>
Regards Michael<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div><div class="h5">
Hi Michael,<br>
<br>
I'm copying the scifio mailing list, as this could be of general<br>
interest.<br>
<br>
bioformats, scifio and scifio-bf-compat are the latest snapshot<br>
versions from the maven repository<br>
<br>
<br>
First of all, I would recommend trying to use the release versions<br>
first (scifio 0.4.1, scifio-bf-compat 1.0.1). Is there some API in the<br>
snapshot versions you need specifically? If so, you could then<br>
transition from the release to snapshots, once you're updated to the<br>
SCIFIO 0.4.X API.<br>
<br>
Of course, SCIFIO-BF-compat 1.0.0 includes a scifio 0.3.X dependency<br>
so it's not compatible with 0.4.X... so I understand why you had to<br>
use snapshots. :(<br>
<br>
* bioformats 4.4.8<br>
* ome-xml 4.5<br>
<br>
<br>
This looks like a limitation of the current SCIFIO-BF-compat project.<br>
First of all, it includes bio-formats and ome-xml 4.4.8 dependencies,<br>
so you shouldn't need to explicitly declare them.<br>
<br>
The OME-XML 4.5 with OMEMetadata class isn't really ready for<br>
consumption yet. Having an OME-XML 4.5 on the classpath with the<br>
inherited 4.4.8 dependency seems like a bad idea. So I think<br>
SCIFIO-BF-compat should have its own copy of the OMEMetadata class +<br>
translators for now, so you can translate to it to extract the OME-XML.<br>
<br>
This would be a temporary solution until our Bio-Formats fork is<br>
actually released (which could be a while, and would still have to<br>
resolve the 4.5.X and 4.4.X dependency issues).<br>
<br>
Unless anyone has other suggestions I'll do migrate over the<br>
OMEMetadata + translators this afternoon and release a<br>
SCIFIO-BF-compat 1.1.0. That should resolve your dependency issues, at<br>
least, by also updating the SCIFIO version to 0.4.X, so you can use<br>
actual release artifacts.<br>
<br>
The error message is "IllegalArgumentException: Invalid dimension<br>
order: XYC"<br>
<br>
<br>
This is a bug introduced in this commit<br></div></div>
<<a href="https://github.com/scifio/scifio-bf-compat/commit/677fe7645e26e9e692f0ca823698f50349b69ef7" target="_blank">https://github.com/scifio/<u></u>scifio-bf-compat/commit/<u></u>677fe7645e26e9e692f0ca823698f5<u></u>0349b69ef7</a>>.<div class="im">
<br>
I will resolve it and make sure you can extract OME-XML with<br>
scifio-bf-compat + scifio 0.4.1 before releasing.<br>
<br>
Hope that helps! Thanks for testing :)<br>
<br>
- Mark<br>
<br>
<br>
On Tue, Aug 6, 2013 at 4:46 PM, Michael Zinsmaier<br></div><div><div class="h5">
<<a href="mailto:michael.zinsmaier@gmx.de" target="_blank">michael.zinsmaier@gmx.de</a> <mailto:<a href="mailto:michael.zinsmaier@gmx.de" target="_blank">michael.zinsmaier@gmx.<u></u>de</a>>> wrote:<br>
<br>
Hi Mark,<br>
<br>
we just started to use the ImgOpener. Unfortunately I can't open<br>
.jpg images.<br>
The error message is "IllegalArgumentException: Invalid dimension<br>
order: XYC"<br>
<br>
My last working testversion used<br>
* scifio3.1<br>
* bioformats 4.4.8<br>
* ome-xml 4.5<br>
* scifio-bf-compat 1.0.1<br>
<br>
and builds from roughly 3 weeks ago<br>
<br>
<br>
<br>
the new setup uses<br>
* scifio4.2<br>
* bioformats 4.4.8<br>
* ome-xml 4.5<br>
* scifio-bf-compat 1.0.1<br>
<br>
bioformats, scifio and scifio-bf-compat are the latest snapshot<br>
versions from the maven repository, ome-xml<br>
is self build updated to the scifio branch from bioformats (last<br>
commit 12.07)<br>
(By the way can I add the scifio ome-xml with OMEMetadata as maven<br>
dependency? If yes how do I do it?)<br>
<br>
Any ideas?<br>
<br>
Best regards<br>
Michael<br>
<br>
<br>
</div></div></blockquote>
<br>
<br>
</blockquote></div><br></div>