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  • NetCDF coordinates in parent group is not used when reading sub group · 6 ✖

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1001687725 https://github.com/pydata/xarray/issues/1982#issuecomment-1001687725 https://api.github.com/repos/pydata/xarray/issues/1982 IC_kwDOAMm_X847tIqt alexamici 226037 2021-12-27T18:18:44Z 2021-12-27T18:19:22Z MEMBER

Note that current CF-1.9 now specifies how to read coordinates from any group in file (see spec).

If it is not already one of the goals of the new DataTree structure #4665 it would probably best be added. cc @TomNicholas @aurghs 

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   NetCDF coordinates in parent group is not used when reading sub group 304314787
612140236 https://github.com/pydata/xarray/issues/1982#issuecomment-612140236 https://api.github.com/repos/pydata/xarray/issues/1982 MDEyOklzc3VlQ29tbWVudDYxMjE0MDIzNg== shoyer 1217238 2020-04-10T17:44:48Z 2020-04-10T17:44:48Z MEMBER

I think it would be totally reasonable and consistent with the netcdf data model to read dimension coordinates from parent groups when they are missing on the requested group.

On Fri, Apr 10, 2020 at 10:39 AM Lucas Morton notifications@github.com wrote:

I'm currently working around this by loading the root group & the branch group with two separate calls and then merging the resulting datasets. It's ugly b/c I have to manually associate the 'phony_dim_x' dimensions from one group with the other.

Maybe I can find the time during quarantine to make an attempt at resolving #1092 https://github.com/pydata/xarray/issues/1092, which I think would facilitate resolving this issue as well.

Another option would be to allow the group kwarg to be a tuple of group names, and load_dataset could yield a (flat) Dataset including both the root and the branch variables.

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   NetCDF coordinates in parent group is not used when reading sub group 304314787
437990188 https://github.com/pydata/xarray/issues/1982#issuecomment-437990188 https://api.github.com/repos/pydata/xarray/issues/1982 MDEyOklzc3VlQ29tbWVudDQzNzk5MDE4OA== shoyer 1217238 2018-11-12T18:52:13Z 2018-11-12T18:52:13Z MEMBER

I think it could logically make sense to recursively check parent groups for coordinates referenced by variables in the opened group.

From an implementation perspective, this might be a little tricky. The current backend interface isn't really setup for this. Currently, we open all variables, and do all CF convention decoding afterwards. This would require going back to the dataset to open more variables.

 
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   NetCDF coordinates in parent group is not used when reading sub group 304314787
437972944 https://github.com/pydata/xarray/issues/1982#issuecomment-437972944 https://api.github.com/repos/pydata/xarray/issues/1982 MDEyOklzc3VlQ29tbWVudDQzNzk3Mjk0NA== shoyer 1217238 2018-11-12T17:55:28Z 2018-11-12T17:55:28Z MEMBER

When reading a sub group from a netCDF file with dimensions defined in the root group, the dimensions are not read from the root group. This contradicts the netCDF documentation, which states that dimensions are scoped such that they can be seen by all sub groups.

To be clear, xarray does properly read "dimensions" in parent groups. (This is actually ensured by libraries like netCDF4-Python.)

What xarray doesn't do is read "coordinates" from parent groups. As far as I can tell, this isn't part of either the netCDF4 data model or CF conventions. This might be a usability improvement but the right way to do isn't dictated by the specs.

 
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   NetCDF coordinates in parent group is not used when reading sub group 304314787
372353979 https://github.com/pydata/xarray/issues/1982#issuecomment-372353979 https://api.github.com/repos/pydata/xarray/issues/1982 MDEyOklzc3VlQ29tbWVudDM3MjM1Mzk3OQ== jhamman 2443309 2018-03-12T15:37:48Z 2018-03-12T15:37:48Z MEMBER

but it should respect the scope of netCDF dimensions

Just so we're all using the same terminology, you are actually referring to "coordinates", not dimensions. In your example above, tss is getting the correct dimension (time2) but the corresponding coordinate (time2) is not loaded. In netCDF/xarray dimensions are just names for individual axes.

The fundamental issue is that we don't have any machinery in xarray to look outside of a single netCDF group when opening a dataset. That is the common piece to #1092. 

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   NetCDF coordinates in parent group is not used when reading sub group 304314787
372315058 https://github.com/pydata/xarray/issues/1982#issuecomment-372315058 https://api.github.com/repos/pydata/xarray/issues/1982 MDEyOklzc3VlQ29tbWVudDM3MjMxNTA1OA== jhamman 2443309 2018-03-12T13:47:59Z 2018-03-12T13:47:59Z MEMBER

This seems to be a duplicate of #1092. The short answer is that we don't have a first class solution to working with groups in netCDF files. 

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   NetCDF coordinates in parent group is not used when reading sub group 304314787

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