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

[William Moore]

Hi Paul,

 Thanks for the update. I’ve added your comment to the PR at https://github.com/openmicroscopy/openmicroscopy/pull/4412 <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 <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 <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> <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 <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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>> 
>> 
>> 
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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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