Multiscale support #25
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To have this PR generating the multiscale labels, we will need to add a dependency on |
joshmoore
changed the title
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@will-moore : this has been to generate the label pyramids. It needs by ome-zarr PR though. |
| @@ -35,7 +35,7 @@ def image_masks_to_zarr(image: omero.gateway.Image, args: argparse.Namespace) -> | |||
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| 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.
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| import numpy as np | ||
| import omero.clients # noqa | ||
| from ome_zarr.data import write_multiscale |
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In the same spirit as ome/ome-zarr-py#45 (review), we will likely need to define the minimal version of ome_zarr in setup.py as this depends on upstream API additions.
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Agreed. I wasn't planning on pushing a release of ome_zarr without color unless there's a pressing need in order to prevent intermediate versions from being created. (Note: this repository is still in need of tests & GitHub actions to detect that dependency.)
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Since this PR is needed for the other two PRs (ome/ome-zarr-py#45 and ome/omero-ms-zarr#70), merging. I'll open the follow on immediately for review today. |
ome_zarr.scaleto generate multiscale labels--output(fix Update docs README #26)