adding conversion to tensorstore #242
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ziw-liu
reviewed
Sep 2, 2024
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Seems like the new pydantic release is breaking. |
also removed non-standard axis
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@edyoshikun Did you cherry-pick the commit from main? The history is now weird. I would rebase it manually. |
ziw-liu
reviewed
Sep 9, 2024
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| except ValueError as e: | ||
| print(f"Error opening Zarr store: {e}") | ||
| raise |
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What's the purpose of this?
ziw-liu
reviewed
Sep 9, 2024
| "path": str((Path(self._store.path) / self.path).resolve()), | ||
| }, | ||
| "metadata": metadata, | ||
| } |
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There could be a **ts_kwargs here to allow passing in additional configuration, for example a global cache context.
ziw-liu
reviewed
Sep 9, 2024
| ) | ||
| def test_ome_zarr_to_tensorstore(channels_and_random_5d, arr_name): | ||
| """Test `iohub.ngff.Position.data` to tensortore""" | ||
| pytest.importorskip("tensorstore") |
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Maybe add tensorstore to dev requirements and not skip this?
ziw-liu
reviewed
Sep 9, 2024
| @@ -344,7 +345,27 @@ def downscale(self): | |||
| raise NotImplementedError | |||
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| def tensorstore(self): | |||
| raise NotImplementedError | |||
| import tensorstore as ts | |||
ziw-liu
reviewed
Sep 9, 2024
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| with _temp_ome_zarr(random_5d, channel_names, "0") as dataset: | ||
| assert_array_almost_equal(dataset.data.numpy(), random_5d) |
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Is this redundant with another test case?
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This PR makes a zarray into tensorstore object