<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Hi Damir, <div class=""><br class=""></div><div class=""> I have created a trello card for this (on our Priorities board) and would love to work on it soon, but can’t say when as we have a bunch of </div><div class="">other web client cards already scheduled for 5.2.2. </div><div class=""><a href="https://trello.com/b/saRkqYnB/omero-5-2-2" class="">https://trello.com/b/saRkqYnB/omero-5-2-2</a></div><div class=""><br class=""></div><div class=""> Regards,</div><div class=""><br class=""></div><div class=""> Will.</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 18 Jan 2016, at 23:29, Damir Sudar <<a href="mailto:dsudar@lbl.gov" class="">dsudar@lbl.gov</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div dir="ltr" class="">Thanks Josh,<div class="gmail_extra"><br class=""><div class="gmail_quote">On Mon, Jan 18, 2016 at 5:16 AM, Josh Moore <span dir="ltr" class=""><<a href="mailto:josh@glencoesoftware.com" target="_blank" class="">josh@glencoesoftware.com</a>></span> wrote:<br class=""><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">> But one additional question: my current analysis routines generate output in<br class="">
> the form of masks and an example how to store and retrieve Mask.roi objects<br class="">
> (in Python) would be great as well.<br class="">
<br class="">
There's a mask example now open under:<br class="">
<br class="">
<a href="https://github.com/openmicroscopy/openmicroscopy/pull/4415" rel="noreferrer" target="_blank" class="">https://github.com/openmicroscopy/openmicroscopy/pull/4415</a><br class="">
<br class="">
As always, comments welcome!<br class="">
~Josh.<br class=""></blockquote><div class=""> </div><div class="">Looks good and will work with it over the next days. </div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<br class="">
<br class="">
> Of course that brings up another question: currently Omero.web doesn't<br class="">
> render Mask.roi objects (while Insight does). Any plans to fix that<br class="">
> shortcoming in Omero.web?<br class=""></blockquote><div class=""><br class=""></div><div class="">Any thoughts/plans on this? I know mask ROIs are not a very efficient method to store but it tends to be the easiest to actually use in analysis software.</div><div class=""><br class=""></div><div class="">Cheers,</div><div class="">- Damir</div><div class=""><br class=""></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
> Thanks,<br class="">
> - Damir<br class="">
><br class="">
> On Fri, Jan 15, 2016 at 3:06 AM, William Moore <<a href="mailto:will@lifesci.dundee.ac.uk" class="">will@lifesci.dundee.ac.uk</a>><br class="">
> wrote:<br class="">
>><br class="">
>> Hi Paul,<br class="">
>><br class="">
>> I have just opened a PR to improve our python ROI examples, adding a<br class="">
>> Polygon example<br class="">
>> and setting the strokeWidth, strokeColor and fillColor.<br class="">
>><br class="">
>> See <a href="https://github.com/openmicroscopy/openmicroscopy/pull/4412" rel="noreferrer" target="_blank" class="">https://github.com/openmicroscopy/openmicroscopy/pull/4412</a><br class="">
>><br class="">
>> The updated ROIs.py file can be viewed at<br class="">
>><br class="">
>> <a href="https://github.com/will-moore/openmicroscopy/blob/polygon_python_training_example/examples/Training/python/ROIs.py" rel="noreferrer" target="_blank" class="">https://github.com/will-moore/openmicroscopy/blob/polygon_python_training_example/examples/Training/python/ROIs.py</a><br class="">
>><br class="">
>> Some changes might be made during the PR review, but hopefully that<br class="">
>> example is enough<br class="">
>> to help you now?<br class="">
>><br class="">
>> Regards,<br class="">
>><br class="">
>> Will.<br class="">
>><br class="">
>><br class="">
>><br class="">
>> On 14 Jan 2016, at 15:37, Paul Kibet Korir <<a href="mailto:pkorir@ebi.ac.uk" class="">pkorir@ebi.ac.uk</a>> wrote:<br class="">
>><br class="">
>> Thanks. I was actually interested in formating arguments for Python (not<br class="">
>> Java).<br class="">
>><br class="">
>> P<br class="">
>><br class="">
>> On 14/01/2016 14:04, Mark Carroll wrote:<br class="">
>><br class="">
>> On 01/14/2016 01:38 PM, Paul Kibet Korir wrote:<br class="">
>><br class="">
>> I'm having a difficult time making sense of OMERO model objects<br class="">
>> described here<br class="">
>><br class="">
>> <<a href="https://www.openmicroscopy.org/site/support/omero5.2/developers/Model/EveryObject.html" rel="noreferrer" target="_blank" class="">https://www.openmicroscopy.org/site/support/omero5.2/developers/Model/EveryObject.html</a>>.<br class="">
>> There seems to be no explicit definition of the argument formats.<br class="">
>><br class="">
>> I'm presently working with omero.model.PolygonI() objects for which I<br class="">
>> need to set a number of attributes e.g. fillColor, strokeColor etc. The<br class="">
>> documentation specifies base types (e.g. int, string, bool) for the<br class="">
>> arguments but no accompanying structure.<br class="">
>><br class="">
>><br class="">
>> Indeed: I am afraid that page does not document value formats. It was<br class="">
>> generated by introspecting into the Hibernate (ORM) model to investigate<br class="">
>> which mapped model objects refer to each other via which properties; it<br class="">
>> doesn't contain anything that Hibernate doesn't know. That page is most<br class="">
>> useful for figuring out how to write the JOINs in HQL to get from what<br class="">
>> one has to what one wants.<br class="">
>><br class="">
>> (snip)<br class="">
>><br class="">
>> Is there any documentation on model arguments that I can refer to? If<br class="">
>> not is there any plan to include this because client programming is nigh<br class="">
>> impossible without it.<br class="">
>><br class="">
>><br class="">
>> The most useful source is<br class="">
>><br class="">
>> <a href="http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2015-01/ome.html" rel="noreferrer" target="_blank" class="">http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2015-01/ome.html</a><br class="">
>> -- click on "Polygon", far down on the left. That tells you the format<br class="">
>> for the "points" property and links you back to "Shape" for the others,<br class="">
>> for instance describing that the stroke color is a signed 32-bit RGBA<br class="">
>> value.<br class="">
>><br class="">
>> To generate examples, one can create the data interactively (e.g., draw<br class="">
>> ROIs in Insight) then query them via HQL. For instance, doing the<br class="">
>> described conversion, a -993737532 integer that I just queried from<br class="">
>> OMERO is #C4C4C4C4 as a color and indeed in Insight's code I see,<br class="">
>><br class="">
>> DEFAULT_STROKE_COLOUR = new Color(196, 196, 196, 196);<br class="">
>><br class="">
>> If you have trouble with any specific properties we'd be happy to take a<br class="">
>> look to see if we can make any sense of them, as it may have been some<br class="">
>> time since anybody read the OME-XML schema documentation carefully for<br class="">
>> the properties you need. The web client code has to deal with some of<br class="">
>> these formats "manually" as well.<br class="">
>><br class="">
>> Cheers,<br class="">
>><br class="">
>> Mark<br class="">
>><br class="">
>> The University of Dundee is a registered Scottish Charity, No: SC015096<br class="">
>> _______________________________________________<br class="">
>> ome-users mailing list<br class="">
>> <a href="mailto:ome-users@lists.openmicroscopy.org.uk" class="">ome-users@lists.openmicroscopy.org.uk</a><br class="">
>> <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" rel="noreferrer" target="_blank" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br class="">
>><br class="">
>><br class="">
>> --<br class="">
>> With kind regards,<br class="">
>><br class="">
>> Paul K Korir, PhD<br class="">
>> Scientific Programmer<br class="">
>> EMBL-EBI<br class="">
>> Main Building, A2-35,<br class="">
>> WTGC, Hinxton, Cambridge CB10 1SD<br class="">
>> P: <a href="tel:%2B44%201223%2049%2044%2022" value="+441223494422" class="">+44 1223 49 44 22</a><br class="">
>> F: <a href="tel:%2B44%201223%2049%2044%2068" value="+441223494468" class="">+44 1223 49 44 68</a><br class="">
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><br class="">
> --<br class="">
> Damir Sudar - Staff Scientist<br class="">
> Lawrence Berkeley Laboratory / Life Sciences Division<br class="">
> One Cyclotron Road, MS 977, Berkeley, CA 94720, USA<br class="">
> T: <a href="tel:510%2F486-5346" value="+15104865346" class="">510/486-5346</a> - F: <a href="tel:510%2F486-5586" value="+15104865586" class="">510/486-5586</a> - E: <a href="mailto:DSudar@lbl.gov" class="">DSudar@lbl.gov</a><br class="">
><br class="">
> Visiting Scientist, Oregon Health and Science University<br class="">
><br class="">
> _______________________________________________<br class="">
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</blockquote></div><br class=""><br clear="all" class=""><div class=""><br class=""></div>-- <br class=""><div class="gmail_signature"><div dir="ltr" class=""><div class=""><div dir="ltr" class=""><div class=""><div dir="ltr" class="">Damir Sudar - Staff Scientist<br class="">Lawrence Berkeley Laboratory / Life Sciences Division<br class="">One Cyclotron Road, MS 977, Berkeley, CA 94720, USA<br class="">T: 510/486-5346 - F: 510/486-5586 - E: <a href="mailto:DSudar@lbl.gov" target="_blank" class="">DSudar@lbl.gov</a><br class=""><br class=""></div></div><div class="">Visiting Scientist, Oregon Health and Science University</div></div></div></div></div>
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