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Add methods to export plate to zarr #28

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dominikl
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@dominikl dominikl commented Oct 19, 2020

In progress
Adds an option to export a plate to zarr, see https://github.com/ome/omero-ms-zarr/issues/73#issuecomment-706770955
Doesn't do anything yet wrt resolution levels, labels, metadata, etc. Adds dependency natsort.
Not properly tested yet either.

@dominikl
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And I thought the flake8 harassment was already bad enough...

@manics
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manics commented Oct 19, 2020

The difference is pre-commit will fix most of the errors for you:

pip install pre-commit
pre-commit run -a

commit the updates

@dominikl
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Thanks @will-moore 👍

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I forgot the first hierachy level "PlateAcquisition". Will add that now...

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Note: I'm gonna completely overhaul the plate_to_zarr method, no point in reviewing it yet. After a chat with @sbesson I'm much clearer now about the plate, acquisition, wellsample hierarchy. Right now the method is very inefficient.

@joshmoore
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Feedback from ome/ome-zarr-py#56:

  1. is probably the easiest for the moment. 3. is more verbose but is probably my long-term preference.

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sbesson commented Oct 20, 2020

The contents of the Field_* folder should probably be multiscales. That adds yet another layer to this already pretty deep hierarchy, but it will mean we can always assume a pyramid.

Also assuming multiscales gets increasingly used for thumbnailing, big 👍 for having this a MUST rather than a SHOULD in the spec from my side.

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Closing. Moved to @will-moore 's PR #29 . Comments captured in #31 .

@dominikl dominikl closed this Oct 21, 2020
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5 participants