Support importing zarr volumes #75
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manasaV3
approved these changes
May 30, 2024
| return max(self.get_dimensions().values()) | ||
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| def get_center_coords(self) -> List[int]: | ||
| return [np.round(np.mean([getattr(self, f"{d}end"), getattr(self, f"{d}start")])) for d in "xyz"] | ||
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| class ZarrReader: |
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Yeah, the key image generator uses it.
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This adds support for ingesting ome-zarr volumes as well as MRC volumes. I added some basic test coverage and a starting point for the next ingestion config, to test it.
I upgraded to the latest version of ome_zarr_py to support reading/writing zarrs with fsspec parameters, which is necessary to make the library work properly with our moto-based test setup (see ome/ome-zarr-py#349)
I also added a wrapper around reading volume info so that the neuroglancer config importer doesn't read MRC headers directly (it could eventually support zarr volumes instead of MRC volumes). This might be a little too basic, but I'm happy to rethink it!