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

[Josh Moore]

Hi Paul,


Alpha option was added to
https://github.com/openmicroscopy/openmicroscopy/pull/4412
and merged to develop. Thanks for the suggestions!

Cheers,
~Josh.


On Mon, Jan 18, 2016 at 10:36 PM, William Moore
<will at lifesci.dundee.ac.uk> wrote:
> Hi Paul,
>
>  Thanks for the update. I’ve added your comment to the PR at
> https://github.com/openmicroscopy/openmicroscopy/pull/4412
> and the alpha option will be added before merging.
>
>  Regards,
>
>   Will.
>
>
> On 18 Jan 2016, at 09:25, Paul Kibet Korir <pkorir at ebi.ac.uk> wrote:
>
> Thanks very much Will. One step in the right direction.
>
> My particular use-case required that the colours set on ROIs include the
> alpha-channel (which I created) so as not to completely hide the segment
> begin the ROI. You might also want to include that in rgbToRGBInt().
>
> Kind regards,
>
> Paul
>
> On 15/01/2016 11:06, William Moore 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
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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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