Parametric Vertical Coordinates¶

Decoding parametric coordinates¶

from cf_xarray.datasets import romsds

romsds

<xarray.Dataset> Size: 1kB
Dimensions:      (s_rho: 30, ocean_time: 2)
Coordinates:
  * s_rho        (s_rho) float64 240B -0.9833 -0.95 -0.9167 ... -0.05 -0.01667
    hc           float64 8B 20.0
    h            float64 8B 603.9
    Vtransform   float64 8B 2.0
    Cs_r         (s_rho) float64 240B -0.933 -0.8092 ... -0.0005206 -5.758e-05
    z_rho_dummy  (ocean_time, s_rho) float64 480B -0.1464 2.083 ... 0.5933
Dimensions without coordinates: ocean_time
Data variables:
    zeta         (ocean_time) float64 16B -0.1554 -0.1274
    temp         (ocean_time, s_rho) float64 480B 20.0 20.34 ... 29.66 30.0

Now we decode the vertical coordinates in-place. Note the new z_rho variable. cf_xarray sees that s_rho has a formula_terms attribute, looks up the right formula using s_rho.attrs["standard_name"] and computes a new vertical coordinate variable.

romsds.cf.decode_vertical_coords(outnames={'s_rho': 'z_rho'})  # adds new z_rho variable
romsds.z_rho

---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
Cell In[3], line 1
----> 1 romsds.cf.decode_vertical_coords(outnames={'s_rho': 'z_rho'})  # adds new z_rho variable
      2 romsds.z_rho

File ~/checkouts/readthedocs.org/user_builds/cf-xarray/checkouts/latest/cf_xarray/accessor.py:2834, in CFDatasetAccessor.decode_vertical_coords(self, outnames, prefix)
   2828 except KeyError:
   2829     # Should occur since stdname is check before
   2830     raise NotImplementedError(
   2831         f"Coordinate function for {stdname!r} not implmented yet. Contributions welcome!"
   2832     ) from None
-> 2834 ds.coords[zname] = transform.from_terms(terms).decode()

File ~/checkouts/readthedocs.org/user_builds/cf-xarray/checkouts/latest/cf_xarray/parametric.py:636, in OceanSG2.decode(self)
    632 S = (self.depth_c * self.s + self.depth * self.c) / (self.depth_c + self.depth)
    634 z = self.eta + (self.eta + self.depth) * S
--> 636 return z.assign_attrs(standard_name=self.computed_standard_name)

File ~/checkouts/readthedocs.org/user_builds/cf-xarray/checkouts/latest/cf_xarray/parametric.py:641, in OceanSG2.computed_standard_name(self)
    638 @property
    639 def computed_standard_name(self) -> str:
    640     """Computes coordinate standard name."""
--> 641     return _derive_ocean_stdname(eta=self.eta.attrs, depth=self.depth.attrs)

File ~/checkouts/readthedocs.org/user_builds/cf-xarray/checkouts/latest/cf_xarray/parametric.py:81, in _derive_ocean_stdname(zlev, eta, depth)
     77         raise ValueError(
     78             f"The values for {', '.join(sorted(search_vars.keys()))} cannot be `None`."
     79         ) from None
     80     except KeyError:
---> 81         raise ValueError(
     82             f"The standard name for the {x!r} variable is not available."
     83         ) from None
     85 for x, y in OCEAN_STDNAME_MAP.items():
     86     check_term = "".join(
     87         [
     88             y[i]
   (...)     91         ]
     92     )

ValueError: The standard name for the 'depth' variable is not available.

Formula terms¶

To see whether decoding is possible, use the Dataset.cf.formula_terms attribute

romsds.cf.formula_terms