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

Mon Jan 25 12:17:41 GMT 2016

Thank you very much.

Does this resolve the alpha channel bug? See 
http://lists.openmicroscopy.org.uk/pipermail/ome-users/2016-January/005815.html 
for details.

P

On 24/01/2016 17:06, Josh Moore wrote:
> 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
>> 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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>>
>> --
>> 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
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
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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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