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  • Unicode strings unexpectedly transformed to byte strings upon `open_dataset` · 7 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
974686019 https://github.com/pydata/xarray/issues/4859#issuecomment-974686019 https://api.github.com/repos/pydata/xarray/issues/4859 IC_kwDOAMm_X846GIdD kmuehlbauer 5821660 2021-11-20T17:48:43Z 2021-11-20T17:48:43Z MEMBER

@mathause This can be closed. 

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   Unicode strings unexpectedly transformed to byte strings upon `open_dataset` 800678839
777612332 https://github.com/pydata/xarray/issues/4859#issuecomment-777612332 https://api.github.com/repos/pydata/xarray/issues/4859 MDEyOklzc3VlQ29tbWVudDc3NzYxMjMzMg== kripnerl 38673295 2021-02-11T16:16:43Z 2021-02-11T16:16:43Z NONE

@kmuehlbauer Thanks a lot, I will check it ASAP. Yop, conversion to object from U4 is, I believe, normal behaviour. However, this does not cause any trouble for me so far. 

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   Unicode strings unexpectedly transformed to byte strings upon `open_dataset` 800678839
777451036 https://github.com/pydata/xarray/issues/4859#issuecomment-777451036 https://api.github.com/repos/pydata/xarray/issues/4859 MDEyOklzc3VlQ29tbWVudDc3NzQ1MTAzNg== kmuehlbauer 5821660 2021-02-11T13:19:43Z 2021-02-11T13:19:43Z MEMBER

@kniperl You can test with #4893. This should fix the bytes issue.

But It seems that converting to string objects is by design (using "netcdf4").

```python coils = np.array(["A", "B", "C", "D", "E"]) test_ds = xr.Dataset() test_ds.coords["coils"] = coils print(test_ds)

<xarray.Dataset> Dimensions: (coils: 5) Coordinates: * coils (coils) <U1 'A' 'B' 'C' 'D' 'E' Data variables: empty

test_ds.to_netcdf("test_netcdf4.nc", engine="netcdf4") del test_ds test_ds = xr.open_dataset("test_netcdf4.nc", engine="netcdf4") print(test_ds)

<xarray.Dataset> Dimensions: (coils: 5) Coordinates: * coils (coils) object 'A' 'B' 'C' 'D' 'E' Data variables: empty

```

 
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   Unicode strings unexpectedly transformed to byte strings upon `open_dataset` 800678839
772827126 https://github.com/pydata/xarray/issues/4859#issuecomment-772827126 https://api.github.com/repos/pydata/xarray/issues/4859 MDEyOklzc3VlQ29tbWVudDc3MjgyNzEyNg== kmuehlbauer 5821660 2021-02-03T21:13:01Z 2021-02-03T21:13:25Z MEMBER

@kripnerl The actual fix is in https://github.com/h5netcdf/h5netcdf/pull/82.

@mathause Would you mind having a look at the proposed changes, also with respect to the implications for xarray? 

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   Unicode strings unexpectedly transformed to byte strings upon `open_dataset` 800678839
772818772 https://github.com/pydata/xarray/issues/4859#issuecomment-772818772 https://api.github.com/repos/pydata/xarray/issues/4859 MDEyOklzc3VlQ29tbWVudDc3MjgxODc3Mg== kripnerl 38673295 2021-02-03T20:59:00Z 2021-02-03T20:59:00Z NONE

Yes, there was a behaviour change in h5py. A fix is on the way but not yet released: h5netcdf/h5netcdf#81

For the time being you can downgrade h5py: conda install h5py=2 which should fix the issue.

Thank you!

 
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   Unicode strings unexpectedly transformed to byte strings upon `open_dataset` 800678839
772818248 https://github.com/pydata/xarray/issues/4859#issuecomment-772818248 https://api.github.com/repos/pydata/xarray/issues/4859 MDEyOklzc3VlQ29tbWVudDc3MjgxODI0OA== kripnerl 38673295 2021-02-03T20:58:07Z 2021-02-03T20:58:07Z NONE

Possible solution to my problem is:

python test_ds.coords["coils"] = test_ds.coils.values.astype(np.unicode_) test_ds

 
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   Unicode strings unexpectedly transformed to byte strings upon `open_dataset` 800678839
772818220 https://github.com/pydata/xarray/issues/4859#issuecomment-772818220 https://api.github.com/repos/pydata/xarray/issues/4859 MDEyOklzc3VlQ29tbWVudDc3MjgxODIyMA== mathause 10194086 2021-02-03T20:58:03Z 2021-02-03T20:58:03Z MEMBER

Yes, there was a behaviour change in h5py. A fix is on the way but not yet released: h5netcdf/h5netcdf#81

For the time being you can downgrade h5py: conda install h5py=2 which should fix the issue.

 
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   Unicode strings unexpectedly transformed to byte strings upon `open_dataset` 800678839

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