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Multiscale support #25

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merged 10 commits into from
Sep 7, 2020
Merged

Multiscale support #25

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335e741
Use checked relative path for image link
joshmoore Aug 18, 2020
f38d637
pre-commit: fix formatting
joshmoore Aug 20, 2020
b500e86
Use found 'src' instance
joshmoore Aug 31, 2020
81705b6
Fix output arg in README
joshmoore Aug 31, 2020
8c026d7
Apply pre-commit configuration from ome-zarr-py
joshmoore Aug 31, 2020
d0efb8e
Introduce multiscale labels (dropping 6D support)
joshmoore Aug 31, 2020
32bf5de
Add precommit.yml from ome-zarr-py
joshmoore Aug 31, 2020
f1967d3
Search for ROIs across all groups
joshmoore Sep 1, 2020
00562e8
Correct black formatting thanks to Mark
joshmoore Sep 1, 2020
ee35f93
Change 'Layer' to 'Node'
joshmoore Sep 2, 2020
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2 changes: 1 addition & 1 deletion src/omero_zarr/masks.py
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Expand Up @@ -35,7 +35,7 @@ def image_masks_to_zarr(image: omero.gateway.Image, args: argparse.Namespace) ->

conn = image._conn
roi_service = conn.getRoiService()
result = roi_service.findByImage(image.id, None)
result = roi_service.findByImage(image.id, None, {"omero.group": "-1"})
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This probably fails under group sudo but I expect that nobody will notice.

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So under group sudo one would need to get the group of the image and use that?

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If I recall correctly, one's very much locked into the group, so it's more a case of really hoping that the image is in that group. The server could be fixed to better tolerate all-groups context for group sudo so at least there is no exception if the groups do match but I don't think it's a trivial change.

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(For other CLI all-groups stuff I was thinking the client could simply not attempt to set that context at all if in group sudo.)

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Ok. But there haven't been any changes client-side to implement that, right? If so, I assume this will need to be picked up with the rest.

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Right. Fine with me to have this as-is while it awaits that.

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If there's an existing ticket for that issue, please feel free to register this PR with it.


masks = {}
shape_count = 0
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