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  • delgadom · 2 ✖

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  • Writing a a dataset to .zarr in a loop makes all the data NaNs · 2 ✖

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  • CONTRIBUTOR · 2 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
1098574761 https://github.com/pydata/xarray/issues/6456#issuecomment-1098574761 https://api.github.com/repos/pydata/xarray/issues/6456 IC_kwDOAMm_X85Beuup delgadom 3698640 2022-04-13T23:34:16Z 2022-04-13T23:34:48Z CONTRIBUTOR

In the example it's saving every iteration, but in my actual code it's much less frequent

when I said "you're overwriting the file every iteration" I meant to put the emphasis on overwiting. by using mode='w' instead of mode='a' you're telling zarr to delete the file if it exists and the re-create it every time to_zarr is executed.

See the docs on xr.Dataset.to_zarr:

mode ({"w", "w-", "a", "r+", None}, optional) – Persistence mode: “w” means create (overwrite if exists); “w-” means create (fail if exists); “a” means override existing variables (create if does not exist); “r+” means modify existing array values only (raise an error if any metadata or shapes would change). The default mode is “a” if append_dim is set. Otherwise, it is “r+” if region is set and w- otherwise.

This interpretation of mode is consistent across all of python - see the docs for python builtins: open

So I think changing your writes to ds3.to_zarr('zarr_bug.zarr', mode='a') as Max suggested will get you a good part of the way there :)

 
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   Writing a a dataset to .zarr in a loop makes all the data NaNs 1197117301
1094411214 https://github.com/pydata/xarray/issues/6456#issuecomment-1094411214 https://api.github.com/repos/pydata/xarray/issues/6456 IC_kwDOAMm_X85BO2PO delgadom 3698640 2022-04-10T23:40:49Z 2022-04-10T23:40:49Z CONTRIBUTOR

@tbloch1 following up on Max's suggestion - it looks like you might be overwriting the file with every iteration. See the docs on ds.to_zarr - mode='w' will overwrite the file while mode='a' will append. That said, you still would need your indices to not overlap. How are you distinguishing between the files? is each one a different point in time?

To me, this doesn't seem likely to be a bug, but is more of a usage question. Have you tried asking on stackoverflow with the xarray tag?

 
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   Writing a a dataset to .zarr in a loop makes all the data NaNs 1197117301

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