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

[Damir Sudar]

Hi Will,

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.
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>
> <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
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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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