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  • xarray · 1 ✖
id node_id number title user state locked assignee milestone comments created_at updated_at ▲ closed_at author_association active_lock_reason draft pull_request body reactions performed_via_github_app state_reason repo type
1643408278 I_kwDOAMm_X85h9GuW 7691 `nan` values appearing when saving and loading from `netCDF` due to encoding euronion 42553970 closed 0     11 2023-03-28T07:58:21Z 2024-03-15T16:31:06Z 2024-03-15T16:31:05Z NONE      

What happened?

When writing to and reading my dataset from netCDF using ds.to_netcdf() and xr.open_dataset(...), xarray creates nan values where previously number values (float32) where.

The issue seems related to the encoding used for the original dataset, which causes the data to be stored as short. During loading, the stored values then collide with _FillValue leading to the numbers being interpreted as nan.

What did you expect to happen?

Values after saving & loading should be the same as before saving.

Minimal Complete Verifiable Example

```Python We had a back-and-forth on SO about this, I hope it's fine to just refer to it here:

https://stackoverflow.com/a/75806771/11318472 ```

MVCE confirmation

  • [ ] Minimal example — the example is as focused as reasonably possible to demonstrate the underlying issue in xarray.
  • [ ] Complete example — the example is self-contained, including all data and the text of any traceback.
  • [ ] Verifiable example — the example copy & pastes into an IPython prompt or Binder notebook, returning the result.
  • [X] New issue — a search of GitHub Issues suggests this is not a duplicate.

Relevant log output

Python See the SO link above.

Anything else we need to know?

I'm not sure whether this should be considered a bug or just a combination of conflicting features. My current workaround is resetting the encoding and letting xarray decide to store as float instead of short (cf. https://github.com/pydata/xarray/issues/7686).

Environment

INSTALLED VERSIONS ------------------ commit: None python: 3.11.0 | packaged by conda-forge | (main, Oct 25 2022, 06:24:40) [GCC 10.4.0] python-bits: 64 OS: Linux OS-release: 5.15.90.1-microsoft-standard-WSL2 machine: x86_64 processor: x86_64 byteorder: little LC_ALL: None LANG: C.UTF-8 LOCALE: ('en_US', 'UTF-8') libhdf5: 1.12.2 libnetcdf: 4.8.1 xarray: 2022.11.0 pandas: 1.5.2 numpy: 1.23.5 scipy: 1.10.0 netCDF4: 1.6.2 pydap: None h5netcdf: 1.1.0 h5py: 3.8.0 Nio: None zarr: 2.13.6 cftime: 1.6.2 nc_time_axis: None PseudoNetCDF: None rasterio: 1.3.3 cfgrib: None iris: None bottleneck: 1.3.5 dask: 2022.02.1 distributed: 2022.2.1 matplotlib: 3.6.2 cartopy: None seaborn: None numbagg: None fsspec: 2022.11.0 cupy: None pint: None sparse: None flox: None numpy_groupies: None setuptools: 65.5.1 pip: 22.3.1 conda: None pytest: 7.2.0 IPython: 8.11.0 sphinx: None 
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   completed xarray 13221727 issue

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