[ome-users] Format for arguments for OMERO model objects

Fri Feb 19 09:48:46 GMT 2016

Hi Damir,

 In response to your asking about Mask support in OMERO.web, we currently have a PR open that adds the ability to view
masks: https://github.com/openmicroscopy/openmicroscopy/pull/4432 <https://github.com/openmicroscopy/openmicroscopy/pull/4432>

So we expect this to be in the upcoming 5.2.2 release.

 Regards,

  Will.

> > Of course that brings up another question: currently Omero.web doesn't
> > render Mask.roi objects (while Insight does). Any plans to fix that
> > shortcoming in Omero.web?
> 
> 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.
> 
> Cheers,
> - Damir
> 
> > Thanks,
> > - Damir
> >
> > On Fri, Jan 15, 2016 at 3:06 AM, William Moore <will at lifesci.dundee.ac.uk <mailto:will at lifesci.dundee.ac.uk>>
> > wrote:
> >>
> >> Hi Paul,
> >>
> >>  I have just opened a PR to improve our python ROI examples, adding a
> >> Polygon example
> >> and setting the strokeWidth, strokeColor and fillColor.
> >>
> >> See https://github.com/openmicroscopy/openmicroscopy/pull/4412 <https://github.com/openmicroscopy/openmicroscopy/pull/4412>
> >>
> >> The updated ROIs.py file can be viewed at
> >>
> >> https://github.com/will-moore/openmicroscopy/blob/polygon_python_training_example/examples/Training/python/ROIs.py <https://github.com/will-moore/openmicroscopy/blob/polygon_python_training_example/examples/Training/python/ROIs.py>
> >>
> >> Some changes might be made during the PR review, but hopefully that
> >> example is enough
> >> to help you now?
> >>
> >>  Regards,
> >>
> >>   Will.
> >>
> >>
> >>
> >> On 14 Jan 2016, at 15:37, Paul Kibet Korir <pkorir at ebi.ac.uk <mailto:pkorir at ebi.ac.uk>> wrote:
> >>
> >> Thanks. I was actually interested in formating arguments for Python (not
> >> Java).
> >>
> >> P
> >>
> >> On 14/01/2016 14:04, Mark Carroll wrote:
> >>
> >> On 01/14/2016 01:38 PM, Paul Kibet Korir wrote:
> >>
> >> I'm having a difficult time making sense of OMERO model objects
> >> described here
> >>
> >> <https://www.openmicroscopy.org/site/support/omero5.2/developers/Model/EveryObject.html <https://www.openmicroscopy.org/site/support/omero5.2/developers/Model/EveryObject.html>>.
> >> There seems to be no explicit definition of the argument formats.
> >>
> >> I'm presently working with omero.model.PolygonI() objects for which I
> >> need to set a number of attributes e.g. fillColor, strokeColor etc. The
> >> documentation specifies base types (e.g. int, string, bool) for the
> >> arguments but no accompanying structure.
> >>
> >>
> >> Indeed: I am afraid that page does not document value formats. It was
> >> generated by introspecting into the Hibernate (ORM) model to investigate
> >> which mapped model objects refer to each other via which properties; it
> >> doesn't contain anything that Hibernate doesn't know. That page is most
> >> useful for figuring out how to write the JOINs in HQL to get from what
> >> one has to what one wants.
> >>
> >> (snip)
> >>
> >> Is there any documentation on model arguments that I can refer to? If
> >> not is there any plan to include this because client programming is nigh
> >> impossible without it.
> >>
> >>
> >> The most useful source is
> >>
> >> http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2015-01/ome.html <http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2015-01/ome.html>
> >> -- click on "Polygon", far down on the left. That tells you the format
> >> for the "points" property and links you back to "Shape" for the others,
> >> for instance describing that the stroke color is a signed 32-bit RGBA
> >> value.
> >>
> >> To generate examples, one can create the data interactively (e.g., draw
> >> ROIs in Insight) then query them via HQL. For instance, doing the
> >> described conversion, a -993737532 integer that I just queried from
> >> OMERO is #C4C4C4C4 as a color and indeed in Insight's code I see,
> >>
> >>     DEFAULT_STROKE_COLOUR = new Color(196, 196, 196, 196);
> >>
> >> If you have trouble with any specific properties we'd be happy to take a
> >> look to see if we can make any sense of them, as it may have been some
> >> time since anybody read the OME-XML schema documentation carefully for
> >> the properties you need. The web client code has to deal with some of
> >> these formats "manually" as well.
> >>
> >> Cheers,
> >>
> >> Mark
> >>
> >> The University of Dundee is a registered Scottish Charity, No: SC015096
> >> _______________________________________________
> >> ome-users mailing list
> >> ome-users at lists.openmicroscopy.org.uk <mailto:ome-users at lists.openmicroscopy.org.uk>
> >> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users <http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users>
> >>
> >>
> >> --
> >> With kind regards,
> >>
> >> Paul K Korir, PhD
> >> Scientific Programmer
> >> EMBL-EBI
> >> Main Building, A2-35,
> >> WTGC, Hinxton, Cambridge CB10 1SD
> >> P: +44 1223 49 44 22 <tel:%2B44%201223%2049%2044%2022>
> >> F: +44 1223 49 44 68 <tel:%2B44%201223%2049%2044%2068>
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> >>
> >>
> >>
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> >>
> >
> >
> >
> > --
> > Damir Sudar - Staff Scientist
> > Lawrence Berkeley Laboratory / Life Sciences Division
> > One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
> > T: 510/486-5346 <tel:510%2F486-5346> - F: 510/486-5586 <tel:510%2F486-5586> - E: DSudar at lbl.gov <mailto:DSudar at lbl.gov>
> >
> > Visiting Scientist, Oregon Health and Science University
> >
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> 
> 
> -- 
> Damir Sudar - Staff Scientist
> Lawrence Berkeley Laboratory / Life Sciences Division
> One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
> T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov <mailto:DSudar at lbl.gov>
> 
> Visiting Scientist, Oregon Health and Science University
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