coordinate variable not written in netcdf file in some cases

[rafa-guedes]

I came across a situation where my coordinate variable was not dumped as a variable in the output netcdf file using dataset.to_netcdf. In my case I managed to fix it by simply adding variable attributes to this coordinate variable (which didn't have any).

The situation where that happened was while creating a sliced dataset with dataset.isel_points method which automatically defines a new coordinate called points in the sliced dataset. If I dump that dataset as is, the coordinate isn't written as a variable in the netcdf. adding attributes to points however changes that. Here is an example:

In [1]: import xarray as xr

In [2]: ds = xr.open_dataset('netcdf_file_with_longitude_and_latitude.nc')

In [3]: ds
Out[3]: 
<xarray.Dataset>
Dimensions:    (latitude: 576, longitude: 1152, time: 745)
Coordinates:
  * latitude   (latitude) float64 -89.76 -89.45 -89.14 -88.83 -88.52 -88.2 ...
  * longitude  (longitude) float64 0.0 0.3125 0.625 0.9375 1.25 1.562 1.875 ...
  * time       (time) datetime64[ns] 1979-01-01 1979-01-01T01:00:00 ...
Data variables:
    ugrd10m    (time, latitude, longitude) float64 0.2094 0.25 0.2799 0.3183 ...
    vgrd10m    (time, latitude, longitude) float64 -5.929 -5.918 -5.918 ...

In [4]: ds2 = ds.isel_points(longitude=[0], latitude=[0]).reset_coords()

In [5]: ds2
Out[5]: 
<xarray.Dataset>
Dimensions:    (points: 1, time: 745)
Coordinates:
  * time       (time) datetime64[ns] 1979-01-01 1979-01-01T01:00:00 ...
  * points     (points) int64 0
Data variables:
    latitude   (points) float64 -89.76
    vgrd10m    (points, time) float64 -5.929 -6.078 -6.04 -5.958 -5.858 ...
    ugrd10m    (points, time) float64 0.2094 0.109 0.008546 -0.09828 -0.2585 ...
    longitude  (points) float64 0.0

In [6]: ds2['points'].attrs
Out[6]: OrderedDict()

In [7]: ds2.to_netcdf('/home/rafael/ncout1.nc')

In [8]: ds2['points'].attrs.update({'standard_name': 'site'})

In [9]: ds2['points'].attrs
Out[9]: OrderedDict([('standard_name', 'site')])

In [10]: ds2.to_netcdf('/home/rafael/ncout2.nc')

Here is the ncdump output for these two files:

$ ncdump -h /home/rafael/ncout1.nc
netcdf ncout1 {
dimensions:
    time = 745 ;
    points = 1 ;
variables:
    double time(time) ;
        time:_FillValue = 9.999e+20 ;
        string time:long_name = "verification time generated by wgrib2 function verftime()" ;
        time:reference_time = 283996800. ;
        time:reference_time_type = 0 ;
        string time:reference_date = "1979.01.01 00:00:00 UTC" ;
        string time:reference_time_description = "kind of product unclear, reference date is variable, min found reference date is given" ;
        string time:time_step_setting = "auto" ;
        time:time_step = 3600. ;
        string time:units = "seconds since 1970-01-01" ;
        time:calendar = "proleptic_gregorian" ;
    double latitude(points) ;
        string latitude:units = "degrees_north" ;
        string latitude:long_name = "latitude" ;
    double vgrd10m(points, time) ;
        string vgrd10m:short_name = "vgrd10m" ;
        string vgrd10m:long_name = "V-Component of Wind" ;
        string vgrd10m:level = "10 m above ground" ;
        string vgrd10m:units = "m/s" ;
    double ugrd10m(points, time) ;
        string ugrd10m:short_name = "ugrd10m" ;
        string ugrd10m:long_name = "U-Component of Wind" ;
        string ugrd10m:level = "10 m above ground" ;
        string ugrd10m:units = "m/s" ;
    double longitude(points) ;
        string longitude:units = "degrees_east" ;
        string longitude:long_name = "longitude" ;
}

$ ncdump -h /home/rafael/ncout2.nc
netcdf ncout2 {
dimensions:
    time = 745 ;
    points = 1 ;
variables:
    double time(time) ;
        time:_FillValue = 9.999e+20 ;
        string time:long_name = "verification time generated by wgrib2 function verftime()" ;
        time:reference_time = 283996800. ;
        time:reference_time_type = 0 ;
        string time:reference_date = "1979.01.01 00:00:00 UTC" ;
        string time:reference_time_description = "kind of product unclear, reference date is variable, min found reference date is given" ;
        string time:time_step_setting = "auto" ;
        time:time_step = 3600. ;
        string time:units = "seconds since 1970-01-01" ;
        time:calendar = "proleptic_gregorian" ;
    double latitude(points) ;
        string latitude:units = "degrees_north" ;
        string latitude:long_name = "latitude" ;
    double vgrd10m(points, time) ;
        string vgrd10m:short_name = "vgrd10m" ;
        string vgrd10m:long_name = "V-Component of Wind" ;
        string vgrd10m:level = "10 m above ground" ;
        string vgrd10m:units = "m/s" ;
    double ugrd10m(points, time) ;
        string ugrd10m:short_name = "ugrd10m" ;
        string ugrd10m:long_name = "U-Component of Wind" ;
        string ugrd10m:level = "10 m above ground" ;
        string ugrd10m:units = "m/s" ;
    double longitude(points) ;
        string longitude:units = "degrees_east" ;
        string longitude:long_name = "longitude" ;
    int64 points(points) ;
        points:standard_name = "site" ;
}

[shoyer]

This is an unadvertised feature, though I agree that it may be more trouble than it's worth -- xarray implicitly creates coordinates like range(n) when coordinates corresponding to a dimension are missing from the netCDF file.

The original intent (see #245) was for more faithful roundtripping of netCDF files, which may not have all coordinate variables defined. Arguably, it would make more sense to only do this when a certain encoding parameter is found (e.g., {'trivial_index': True}), indicating that xarray created the coordinate itself.

[shoyer]

At the very least, we should advertise this feature in the documentation. But given how surprising people find it, it might be even better to remove it...

[rafa-guedes]

I personally find it useful - maybe not too intuitive though that the behaviour changes depending on whether there are attrs defined for that coordinate variable or not. I agree some documentation on this would be definitely helpful!

[wilhelmsen]

I also find it useful, now that I understand it.

But I also find it useful to know if the xarray coordinate is a netcdf coordinate or netcdf dimension: "A variable with the same name as a dimension is called a coordinate variable". But I guess that is the same as "indicating that xarray created the coordinate itself", as @shoyer mentioned above?

[stale]

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[kmuehlbauer]

Given the age of this issue, let's close it. Please reopen with updated MCVE, if the issue still persists.