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  • netcdf roundtrip fails to preserve the shape of numpy arrays in attributes · 5 ✖
id html_url issue_url node_id user created_at updated_at ▲ author_association body reactions performed_via_github_app issue
417008887 https://github.com/pydata/xarray/issues/2251#issuecomment-417008887 https://api.github.com/repos/pydata/xarray/issues/2251 MDEyOklzc3VlQ29tbWVudDQxNzAwODg4Nw== shoyer 1217238 2018-08-29T16:06:28Z 2018-08-29T16:06:28Z MEMBER

I filed a bug report for netCDF4-Python: https://github.com/Unidata/netcdf4-python/issues/841

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  netcdf roundtrip fails to preserve the shape of numpy arrays in attributes 335608017
416994400 https://github.com/pydata/xarray/issues/2251#issuecomment-416994400 https://api.github.com/repos/pydata/xarray/issues/2251 MDEyOklzc3VlQ29tbWVudDQxNjk5NDQwMA== hmaarrfk 90008 2018-08-29T15:24:07Z 2018-08-29T15:24:07Z CONTRIBUTOR

@shoyer, @fmaussion thank you for your answers. I'm OK with this issue being closed. I'm no expert on netcdf4, so I don't know if I could express the issue in a concise manner there.

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  netcdf roundtrip fails to preserve the shape of numpy arrays in attributes 335608017
400428831 https://github.com/pydata/xarray/issues/2251#issuecomment-400428831 https://api.github.com/repos/pydata/xarray/issues/2251 MDEyOklzc3VlQ29tbWVudDQwMDQyODgzMQ== shoyer 1217238 2018-06-26T19:08:57Z 2018-06-26T19:08:57Z MEMBER

If I remember correctly, netCDF intentionally does not support multi-dimensional array attributes. I'm not sure why it silently changes shape, though. An error message would seem much more user-friendly to me. Possibly this is worth raising on the netCDF4 issue tracker: https://github.com/unidata/netcdf4-python

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  netcdf roundtrip fails to preserve the shape of numpy arrays in attributes 335608017
400415380 https://github.com/pydata/xarray/issues/2251#issuecomment-400415380 https://api.github.com/repos/pydata/xarray/issues/2251 MDEyOklzc3VlQ29tbWVudDQwMDQxNTM4MA== hmaarrfk 90008 2018-06-26T18:24:35Z 2018-06-26T18:24:35Z CONTRIBUTOR

@fmaussion, I am in fact now storing them as coordinates as a work around. in fact, for my particular application, I think the array was meant more as the time the particular index was taken at, in which case a coordinate seems perfect, that said, I am mutating the coordinate array through data acquisition.

I think an acceptable solution would be to state this limitation in the description of what attributes are.

in learning how to use xarray, I ran into the fact that boolean variables cannot be stored in netcdf4, and the array limitation reported. I worked around the boolean problem by replacing it with a more descriptive (and ultimately more forward compatible) string.

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  netcdf roundtrip fails to preserve the shape of numpy arrays in attributes 335608017
400411869 https://github.com/pydata/xarray/issues/2251#issuecomment-400411869 https://api.github.com/repos/pydata/xarray/issues/2251 MDEyOklzc3VlQ29tbWVudDQwMDQxMTg2OQ== fmaussion 10050469 2018-06-26T18:12:45Z 2018-06-26T18:16:53Z MEMBER

I have some metadata that is in the form of numpy arrays.

The short answer is: storing arrays (or other objects) as attributes is not easy. When you do so, xarray has to convert them at serialization, and the roundtrip conserving the shape cannot be achieved because it isn't available in the datamodel of NetCDF.

What is it you are storing as 2D arrays? Would a coordinate variable be an option?

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  netcdf roundtrip fails to preserve the shape of numpy arrays in attributes 335608017

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