Scale dict #103
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Scale dict #103
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@sbesson I think this is ready to review now, with latest ome/ome-zarr-py#162 (both updated to use |
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Used this PR in it's current state to export from IDR: https://minio-dev.openmicroscopy.org/idr/v0.4/2022-02-03/idr0062/6001240.zarr (with labels). |
sbesson
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Feb 11, 2022
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Merging to keep the omero-cli-zarr implementation in sync with the API of the latest pre-release of ome-zarr-py as well as the final layout of the OME-NGFF 0.4 specification.At minimum the pixel size metadata should be transformed into the new scale transformation.
I propose to carry out some more testing as we start creating official samples for the specification and capture various RFEs as issues. Immediate thoughts:
translatecoordinate transformations: is there existing OME/OMERO metadata that could be turned into translation elements- image labels: at the moment, the label image create by
omero zarr masksis expanded to match the image size. It should be possible to create labels using the mask width/height and use the transformation to represent the transformation - storing datasets vs multiscales coordinateTransformations: this will requires some upstream
ome-zarrAPI - improve the programmatic edition of metadata: in the context of coordinateTransformations scale list napari-ome-zarr#32, translated images were created by editing manually the
.zattrsbut this could be facilitated by some utilities e.g.ome_zarr translate
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As discussed in #93 (comment) the API for
write_multiscales_metadata()has changed in ome/ome-zarr-py#162 and this PR uses that new API.Also, this now exports
scalesmetadata as a list[1, 1, 0.5, 0.3, 0.3]instead of usingaxesIndices.