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Use CF Standard Names for standard_name attribute #74

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Dec 10, 2020
Merged

Use CF Standard Names for standard_name attribute #74

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fc5da1e
Use CF Standard Names for standard_name attribute
DocOtak Dec 2, 2020
e1e057d
Guard against unknown values in teos10 accesssor
DocOtak Dec 9, 2020
b786116
Describe allowed values in teos10 accessor
DocOtak Dec 9, 2020
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43 changes: 35 additions & 8 deletions argopy/xarray.py
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Original file line number Diff line number Diff line change
Expand Up @@ -690,13 +690,33 @@ def interp_std_levels(self, std_lev):
def teos10(self, vlist: list = ['SA', 'CT', 'SIG0', 'N2', 'PV', 'PTEMP'], inplace: bool = True):
""" Add TEOS10 variables to the dataset

By default, add: 'SA', 'CT', 'SIG0', 'N2', 'PV', 'PTEMP'
Rely on the gsw library.
By default, adds: 'SA', 'CT', 'SIG0', 'N2', 'PV', 'PTEMP'
Relies on the gsw library.

If one exists, the correct CF standard name will be added to the attrs.

Parameters
----------
vlist: list(str)
List with the name of variables to add.
Must be a list containing one or more of the following string values:

* `"SA"`
Adds an absolute salinity variable
* `"CT"`
Adds a conservative temperature variable
* `"SIG0"`
Adds a potential density anomaly variable referenced to 0 dbar
* `"N2"`
Adds a buoyancy (Brunt-Vaisala) frequency squared variable.
This variable has been regridded to the original pressure levels in the Dataset using a linear interpolation.
* `"PV"`
Adds a planetary vorticity variable calculated from :math:`\\frac{f N^2}{\\text{gravity}}`.
This is not a TEOS-10 variable from the gsw toolbox, but is provided for convenience.
This variable has been regridded to the original pressure levels in the Dataset using a linear interpolation.
* `"PTEMP"`
Adds a potential temperature variable

inplace: boolean, True by default
If True, return the input :class:`xarray.Dataset` with new TEOS10 variables added as a new :class:`xarray.DataArray`
If False, return a :class:`xarray.Dataset` with new TEOS10 variables
Expand All @@ -709,6 +729,10 @@ def teos10(self, vlist: list = ['SA', 'CT', 'SIG0', 'N2', 'PV', 'PTEMP'], inplac
raise ModuleNotFoundError(
"This functionality requires the gsw library")

allowed = ['SA', 'CT', 'SIG0', 'N2', 'PV', 'PTEMP']
if any(var not in allowed for var in vlist):
raise ValueError(f"vlist must be a subset of {allowed}, instead found {vlist}")

this = self._obj

to_profile = False
Expand Down Expand Up @@ -765,38 +789,41 @@ def mid(x):
that = []
if 'SA' in vlist:
SA = xr.DataArray(sa, coords=this['PSAL'].coords, name='SA')
SA.attrs['standard_name'] = 'Absolute Salinity'
SA.attrs['long_name'] = 'Absolute Salinity'
SA.attrs['standard_name'] = 'sea_water_absolute_salinity'
SA.attrs['unit'] = 'g/kg'
that.append(SA)

if 'CT' in vlist:
CT = xr.DataArray(ct, coords=this['TEMP'].coords, name='CT')
CT.attrs['standard_name'] = 'Conservative Temperature'
CT.attrs['long_name'] = 'Conservative Temperature'
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Thanks for preserving these as long names, it will reduce breakages in case people are relying on those names.

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As much as the various data standards "recommend against it" I think most people rely on the variable name itself (in this case it's CT) rather than things in attributes. I'd like to get some doc string things added before this is merged mainly defining all the options for vlist.

I'll also note the potentially breaking change in the docs themselves.

CT.attrs['standard_name'] = 'sea_water_conservative_temperature'
CT.attrs['unit'] = 'degC'
that.append(CT)

if 'SIG0' in vlist:
SIG0 = xr.DataArray(sig0, coords=this['TEMP'].coords, name='SIG0')
SIG0.attrs['long_name'] = 'Potential density anomaly with reference pressure of 0 dbar'
SIG0.attrs['standard_name'] = 'Potential Density'
SIG0.attrs['standard_name'] = 'sea_water_sigma_theta'
SIG0.attrs['unit'] = 'kg/m^3'
that.append(SIG0)

if 'N2' in vlist:
N2 = xr.DataArray(n2, coords=this['TEMP'].coords, name='N2')
N2.attrs['standard_name'] = 'Squared buoyancy frequency'
N2.attrs['long_name'] = 'Squared buoyancy frequency'
N2.attrs['unit'] = '1/s^2'
that.append(N2)

if 'PV' in vlist:
PV = xr.DataArray(pv, coords=this['TEMP'].coords, name='PV')
PV.attrs['standard_name'] = 'Planetary Potential Vorticity'
PV.attrs['long_name'] = 'Planetary Potential Vorticity'
PV.attrs['unit'] = '1/m/s'
that.append(PV)

if 'PTEMP' in vlist:
PTEMP = xr.DataArray(pt, coords=this['TEMP'].coords, name='PTEMP')
PTEMP.attrs['standard_name'] = 'Potential Temperature'
PTEMP.attrs['long_name'] = 'Potential Temperature'
PTEMP.attrs['standard_name'] = 'sea_water_potential_temperature'
PTEMP.attrs['unit'] = 'degC'
that.append(PTEMP)

Expand Down
4 changes: 4 additions & 0 deletions docs/whats-new.rst
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Expand Up @@ -32,6 +32,10 @@ v0.1.7 (XX Nov. 2020)

**Breaking changes with previous versions**

- In the teos10 xarray accessor, the ``standard_name`` attribute will now be populated using values from the `CF Standard Name table <https://cfconventions.org/Data/cf-standard-names/76/build/cf-standard-name-table.html>`_ if one exists.
The previous values of ``standard_name`` have been moved to the ``long_name`` attribute.
(:pr:`74`) by `A. Barna <https://github.com/docotak>`_.

- The unique resource identifier property is now named ``uri`` for all data fetchers, it is always a list of strings.

**Internals**
Expand Down