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  • NetCDF coordinates in parent group is not used when reading sub group · 4 ✖

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  • NONE · 4 ✖
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612137754 https://github.com/pydata/xarray/issues/1982#issuecomment-612137754 https://api.github.com/repos/pydata/xarray/issues/1982 MDEyOklzc3VlQ29tbWVudDYxMjEzNzc1NA== lamorton 23484003 2020-04-10T17:38:50Z 2020-04-10T17:38:50Z NONE

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, 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
437988119 https://github.com/pydata/xarray/issues/1982#issuecomment-437988119 https://api.github.com/repos/pydata/xarray/issues/1982 MDEyOklzc3VlQ29tbWVudDQzNzk4ODExOQ== Chiil 110313 2018-11-12T18:45:21Z 2018-11-12T18:45:21Z NONE

How about searching in the parent group until the root group is reached? As far as I can see it, this cannot cause any conflict. It would be really awesome to have this functionality. I really like to idea of nicely organizing NetCDF files while still having the full functionality of xarray at hand.

On 12 Nov 2018, at 18:55, Stephan Hoyer notifications@github.com wrote:

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
437856617 https://github.com/pydata/xarray/issues/1982#issuecomment-437856617 https://api.github.com/repos/pydata/xarray/issues/1982 MDEyOklzc3VlQ29tbWVudDQzNzg1NjYxNw== Chiil 110313 2018-11-12T12:09:55Z 2018-11-12T12:09:55Z NONE

The problem occurs with plotting as well. See the StackOverflow question that I posted a few days ago.

https://stackoverflow.com/questions/53196437/missing-axis-values-in-plotting-of-netcdf-variable-in-group-with-xarray

 
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   NetCDF coordinates in parent group is not used when reading sub group 304314787
372324699 https://github.com/pydata/xarray/issues/1982#issuecomment-372324699 https://api.github.com/repos/pydata/xarray/issues/1982 MDEyOklzc3VlQ29tbWVudDM3MjMyNDY5OQ== jacklovell 4849151 2018-03-12T14:17:01Z 2018-03-12T14:17:01Z NONE

It looks to me like #1092 is about a Dataset-like object which can contain groups and sub-groups. Here we have a simpler issue: the Dataset can still be a flat object containing a single group, but it should respect the scope of netCDF dimensions. This means that any dimensions which are mentioned but not visible in the group being written should be searched for and copied (linked?) from a parent group, up to and including the root group if the dimensions reside there.

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

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