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

[Josh Moore]

Hi Damir,

On Fri, Jan 15, 2016 at 9:45 PM, Damir Sudar <dsudar at lbl.gov> wrote:
>
> That example is great and came at the right time. I'm just working on
> something needs that functionality.
> But one additional question: my current analysis routines generate output in
> the form of masks and an example how to store and retrieve Mask.roi objects
> (in Python) would be great as well.

There's a mask example now open under:

  https://github.com/openmicroscopy/openmicroscopy/pull/4415

As always, comments welcome!
~Josh.



> 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?
>
> 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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>>
>> --
>> With kind regards,
>>
>> Paul K Korir, PhD
>> Scientific Programmer
>> EMBL-EBI
>> Main Building, A2-35,
>> WTGC, Hinxton, Cambridge CB10 1SD
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>> F: +44 1223 49 44 68
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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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