Add Plate support to KeyVal_to_csv.py

[will-moore]

I was prompted by the need for test data for #195,
so I have updated KeyVal_to_csv.py to support Plate input.
I seem to remember @abhamacher requested this too somewhere?

I wasn't sure whether to export KV pairs from wells or images for a Plate.
Combining different KV pairs from images and wells could be tricky.
My initial update allows the user to choose, with a boolean input "Export Wells"? for a Plate.

But if we can define how to combine KV pairs from Wells and Images, I could give it a go.

E.g. if you have a Well containing 2 images:

• Well: A1 with KV pairs: key1: value1, key2: value2
• Image: field1 with KV pairs: key1: value10, key2: value20
• Image: field2 with KV pairs: key1: value11, key2: value22

What should the CSV look like? 1 row or 2 rows or even 3?
cc @JensWendt

[JensWendt]

Hi @will-moore ,

I think we should orient ourselves at the same standard that the KV_from_csv script implements.
For every object with KV-pairs one row.
For every Key one column.
Resulting in this output for your above sample:

well	image	key1	key2
A1		value1	value2
A1	field1	value10	value20
A1	field2	value11	value22

In general I assume it is highly unlikely that a well and the "underlying" images have differing KV-pairs.
I personally recommend my users to use the same KV-pairs for both, for a better overview in certain situations.
With the same reasoning it is unlikely that the image names are not unique in a plate and therefore the well name before the image might not be required in a single plate setup. But if we go for multiple plates in one .csv I think the whole "chain" plate-name, well-name and image-name is required.

Nevertheless I think that creating a .csv that would allow the recreation of the same annotation-setup if it immediately gets used for the reverse KV_from_csv is the goal.

I hope that helps (although it comes pretty late, sorry)

[snoopycrimecop]

Conflicting PR. Removed from build OMERO-python-superbuild-push#308. See the console output for more details.
Possible conflicts:

• Upstream changes
  • omero/annotation_scripts/KeyVal_to_csv.py

--conflicts