[ome-users] Format for arguments for OMERO model objects
Paul Kibet Korir
pkorir at ebi.ac.uk
Fri Feb 19 10:04:10 GMT 2016
Wonderful!
Thanks.
Paul
On 19/02/2016 09:48, William Moore 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 <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
>> >>
>> >> 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
>> <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>.
>> >> 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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>> >>
>> >>
>> >> --
>> >> 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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--
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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