Polygon python training example

[will-moore]

Improve ROIs examples in python with new Polygon example and setting of strokeWidth and stroke + fill colours. See http://lists.openmicroscopy.org.uk/pipermail/ome-users/2016-January/005804.html

To test, review and run the example.

[mtbc]

If you need to set it to something other than what's described at http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2015-01/ROI_xsd.html#Polygon_Points then we probably need a card.

[joshmoore]

@mtbc : I think this is the older format. @jburel / @dominikl : is the support for the newer available / carded?

[joshmoore]

Objections to my adding a mask example here?

[will-moore]

Please do! (in another PR you mean)?

[joshmoore]

Yup, I'll build on this commit but re-use the ROIs.py file unless we think there should be a Masks.py one.

[sbesson]

I would reuse ROIs.py minimally to stay consistent with the other training languages (https://github.com/openmicroscopy/openmicroscopy/blob/v5.2.1/examples/Training/java/src/training/ROIs.java, https://github.com/openmicroscopy/openmicroscopy/blob/v5.2.1/examples/Training/matlab/ROIs.m) where ROIs.ext is the generic script demonstrating how to create available shapes.

[will-moore]

Comment from http://lists.openmicroscopy.org.uk/pipermail/ome-users/2016-January/005807.html
"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()."

[will-moore]

The previous commit added support for Alpha, but if I try to set alpha > 127 (50%) for strokeColor then I get this error:

Traceback (most recent call last):
  File "ROIs.py", line 128, in <module>
    createROI(image, [polygon])
  File "ROIs.py", line 56, in createROI
    updateService.saveObject(roi)
  File "/Users/wmoore/Desktop/OMERO/openmicroscopy/dist/lib/python/omero/gateway/__init__.py", line 4205, in __call__
    return self.handle_exception(e, *args, **kwargs)
  File "/Users/wmoore/Desktop/OMERO/openmicroscopy/dist/lib/python/omero/gateway/__init__.py", line 4202, in __call__
    return self.f(*args, **kwargs)
  File "/Users/wmoore/Desktop/OMERO/openmicroscopy/dist/lib/python/omero_api_IUpdate_ice.py", line 107, in saveObject
    return _M_omero.api.IUpdate._op_saveObject.invoke(self, ((obj, ), _ctx))
ValueError: invalid value for ::omero::RInt member `_val'

Any ideas what I'm doing wrong here?

[mtbc]

http://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2015-01/ROI_xsd.html#Shape_FillColor and its kin specify a signed 32 bit value: if alpha > 127 then do you need to subtract to make the most significant bit act like a sign bit? Just as my example from http://lists.openmicroscopy.org.uk/pipermail/ome-users/2016-January/005803.html had #C4C4C4C4 represented by -993737532.

[will-moore]

Hmmm - I wonder if anyone knows straight off how to convert from unsigned 32 bit to signed? Don't really want to spend a day trying to research 2's complement (or whatever) and work it out in python. Do we have code to do this in Java anywhere?

[mtbc]

If the number is larger than 2^31-1 then subtract 2^32 from it.

[will-moore]

Thanks @mtbc. Script is working now with range of alpha values.

[joshmoore]

Makes sense to me and works for me locally. Merging and I'll 1) remark on the list thread and 2) update by PR to not include your commits.