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Wonderful!<br>
<br>
Thanks. <br>
<br>
Paul<br>
<br>
<div class="moz-cite-prefix">On 19/02/2016 09:48, William Moore
wrote:<br>
</div>
<blockquote
cite="mid:FC1CE10B-4312-421A-BDD9-D04DF2227AB2@lifesci.dundee.ac.uk"
type="cite">
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<div>Hi Damir,</div>
<div><br class="">
</div>
<div> In response to your asking about Mask support in OMERO.web,
we currently have a PR open that adds the ability to view</div>
<div>masks: <a moz-do-not-send="true"
href="https://github.com/openmicroscopy/openmicroscopy/pull/4432"
class="">https://github.com/openmicroscopy/openmicroscopy/pull/4432</a></div>
<div><br class="">
</div>
<div>So we expect this to be in the upcoming 5.2.2 release.</div>
<div><br class="">
</div>
<div> Regards,</div>
<div><br class="">
</div>
<div> Will.</div>
<div><br class="">
</div>
<div><br class="">
</div>
<div>
<blockquote type="cite" class="">
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<div class="gmail_extra">
<div class="gmail_quote">
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
> 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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
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 moz-do-not-send="true"
href="mailto:ome-users@lists.openmicroscopy.org.uk"
class="">ome-users@lists.openmicroscopy.org.uk</a><br
class="">
>> <a moz-do-not-send="true"
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 moz-do-not-send="true"
href="tel:%2B44%201223%2049%2044%2022"
value="+441223494422" class="">+44 1223 49 44 22</a><br
class="">
>> F: <a moz-do-not-send="true"
href="tel:%2B44%201223%2049%2044%2068"
value="+441223494468" class="">+44 1223 49 44 68</a><br
class="">
>>
_______________________________________________<br
class="">
>> ome-users mailing list<br class="">
>> <a moz-do-not-send="true"
href="mailto:ome-users@lists.openmicroscopy.org.uk"
class="">ome-users@lists.openmicroscopy.org.uk</a><br
class="">
>> <a moz-do-not-send="true"
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="">
>>
_______________________________________________<br
class="">
>> ome-users mailing list<br class="">
>> <a moz-do-not-send="true"
href="mailto:ome-users@lists.openmicroscopy.org.uk"
class="">ome-users@lists.openmicroscopy.org.uk</a><br
class="">
>> <a moz-do-not-send="true"
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="">
><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 moz-do-not-send="true"
href="tel:510%2F486-5346" value="+15104865346"
class="">510/486-5346</a> - F: <a
moz-do-not-send="true" href="tel:510%2F486-5586"
value="+15104865586" class="">510/486-5586</a> - E:
<a moz-do-not-send="true" 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="">
> ome-users mailing list<br class="">
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class="">ome-users@lists.openmicroscopy.org.uk</a><br
class="">
> <a moz-do-not-send="true"
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rel="noreferrer" target="_blank" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br
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><br class="">
_______________________________________________<br
class="">
ome-users mailing list<br class="">
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</blockquote>
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<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
moz-do-not-send="true"
href="mailto:DSudar@lbl.gov" target="_blank"
class=""><a class="moz-txt-link-abbreviated" href="mailto:DSudar@lbl.gov">DSudar@lbl.gov</a></a><br class="">
<br class="">
</div>
</div>
<div class="">Visiting Scientist, Oregon Health
and Science University</div>
</div>
</div>
</div>
</div>
</div>
</div>
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<br>
<div class="moz-signature">-- <br>
With kind regards,<br>
<br>
<strong>Paul K Korir, PhD</strong><br>
<i>Scientific Programmer</i><br>
EMBL-EBI<br>
Main Building, A2-35,<br>
WTGC, Hinxton, Cambridge CB10 1SD<br>
P: +44 1223 49 44 22<br>
F: +44 1223 49 44 68</div>
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