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

Fri Feb 19 16:08:34 GMT 2016

Thanks Will. That's fabulous.
- Damir

Sent from my iPad, please excuse poor spelling

> On Feb 19, 2016, at 01:48, William Moore <will at lifesci.dundee.ac.uk> wrote:
> 
> 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
> 
> 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>
>>> > 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
>>> >>
>>> >> 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
>>> >>
>>> >> 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> 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>.
>>> >> 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
>>> >> -- 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
>>> >> _______________________________________________
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>>> >> ome-users at lists.openmicroscopy.org.uk
>>> >> 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
>>> >> F: +44 1223 49 44 68
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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 - F: 510/486-5586 - E: DSudar at lbl.gov
>>> >
>>> > Visiting Scientist, Oregon Health and Science University
>>> >
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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 - F: 510/486-5586 - E: DSudar at lbl.gov
>> 
>> Visiting Scientist, Oregon Health and Science University
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
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