python3 fixes to Images_From_ROIs.py

ome / omero-scripts

Core OMERO Scripts

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python3 fixes to Images_From_ROIs.py #188

Closed will-moore closed 3 years ago

will-moore commented 3 years ago

This fixes python3 issues with generating Big images from ROIs reported at https://forum.image.sc/t/error-in-images-from-rois-py/53411

To test:

Draw a Rectangle over 3k x 3k on a big image - Save
Run util script Images_From_Rois on the Image
Should get a new Big tiled image

imagesc-bot commented 3 years ago

This pull request has been mentioned on Image.sc Forum. There might be relevant details there:

https://forum.image.sc/t/error-in-images-from-rois-py/53411/2

jburel commented 3 years ago

I have reenabled the workflow. This was not run.

jburel commented 3 years ago

Could the change be captured in a test?

will-moore commented 3 years ago

@jburel This is not trivial to add a test for big images, since testlib create_test_image(size_x=4000, size_y=4000) fails with Non-tile based writing unsupported.. To create big tiled images via the API, we need something like https://github.com/ome/omero-py/pull/276/files, but there are other issues as described there. Maybe this is the incentive we need to find a solution... cc @joshmoore

sbesson commented 3 years ago

Is there any requirement to use the RawPixelsStore API to create a large pyramidal image? Would a classical pyramidal file import work for the purpose of the test?

will-moore commented 3 years ago

populate_metadata tests failing due to OMERO.tables message = null table as argument

will-moore commented 3 years ago

@joshmoore No, I think https://github.com/ome/omero-py/pull/276/ covers everything outstanding and https://github.com/ome/omero-figure/issues/403 is the open issue for that.