CODEWITHSUNDEEP
pythonpython-xarray
Dan
Dan

Reputation: 1175

Writing xarray list-type attributes to netCDF

I wish to have a list of strings as an attribute in an xarray Dataset that survives serialization to netCDF. I believe this is possible with the NC_STRING type in netCDF-4. xarray supports this but I can't get it to persist after writing to and reading from a netCDF file. After the roundtrip, the attr comes back with the list elements concatenated. I'm thinking I might have to set an encoding parameter, and although I know how to do this for variables, I don't know how for attributes.

import xarray as xr
ds = xr.Dataset()
ds.attrs['testing'] = ['a', 'b']
print(ds)

Gives:

<xarray.Dataset>
Dimensions:  ()
Data variables:
    *empty*
Attributes:
    testing:  ['a', 'b']

Now, 

ds.to_netcdf('asdf.nc')
ds = xr.open_dataset('asdf.nc', autoclose=True)
print(ds)

Gives:

<xarray.Dataset>
Dimensions:  ()
Data variables:
    *empty*
Attributes:
    testing:  ab

Update

In response to @jhamman's comment, this behavior is supported using netCDF4's netncattr_string method:

import netCDF4 as nc
rg = nc.Dataset('test_string.nc', 'w', format='NETCDF4')
rg.setncattr_string('testing', ['a', 'b'])
rg.close()

Running ncdump on test_string.nc produces:

$ ncdump test_string.nc
netcdf test_string {

// global attributes:
        string :testing = "a", "b" ;
}

as opposed to setting an attribute in the usual way, which results in a concatenated attribute, as when the nc is created by xarray above:

rg = nc.Dataset('test_normal.nc', 'w', format='NETCDF4')
rg.testing = ['a', 'b']
rg.close()

ncdump results:

$ ncdump test_normal.nc
netcdf test_normal {

// global attributes:
        :testing = "ab" ;
}

Reading the .nc file created using setncattr_string properly imports a list of strings as the attributes in an xarray Dataset:

ds = xr.open_dataset('test_string.nc')
print(ds)

gives:

<xarray.Dataset>
Dimensions:  ()
Data variables:
    *empty*
Attributes:
    testing:  ['a', 'b']

So I guess something like setncattr_string could be implemented in xarray to achieve this?

Upvotes: 2

Views: 2118

Answers (1)

Dan
Dan

Reputation: 1175

Encoding lists of strings as attributes has been implemented in xarray and should be in the next release (0.10.4).

Upvotes: 1

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