Triggered by an IDR submission, the following code exposes the issue
from ome_model.experimental import Plate, Image, create_companion
for i in range(5):
plate = Plate(str(i), 1, 1)
well = plate.add_well(0,0)
image = Image(
str(i), 10, 10, 1, 2, 1,
order="XYZCT", type="uint16")
image.add_tiff(str(i) + '.tif')
well.add_wellsample(0, image)
create_companion(plates=[plate], out=str(i) + '.companion.ome')
While expecting this will create 4 companion OME files with 1 plate/1 well/1 well sample/1 image each, the second companion contains 2 images, the third 3...
Tracing down the source of the issue comes down to the usage of empty lists as default arguments which is a classical Python gotcha as these are mutable. At the moment, a workaround would be to explicitly pass a new empty list.
Triggered by an IDR submission, the following code exposes the issue
While expecting this will create 4 companion OME files with 1 plate/1 well/1 well sample/1 image each, the second companion contains 2 images, the third 3...
Tracing down the source of the issue comes down to the usage of empty lists as default arguments which is a classical Python gotcha as these are mutable. At the moment, a workaround would be to explicitly pass a new empty list.
87f4859 updates all locations using empty lists as default to using
Noneinstead and handles the check within the methodAll the other commits add some unit test coverage of the plate generation scenarios. The tests should be failing without 87f4859 and passing with.