It would be nice to demo how we could use the character/fixes defined by dachar to fix data with daops and then convert that from an xarray to iris cube for use in the ESMValCore.
Example fixes:
Fix standard name:
class O2 (Fix ):
"""Fixes for o2."""
def fix_metadata (self , cubes ):
"""
Fix standard and long names.
Parameters
----------
cube: iris.cube.CubeList
Returns
-------
iris.cube.CubeList
"""
std = 'mole_concentration_of_dissolved_molecular_oxygen_in_sea_water'
long_name = 'Dissolved Oxygen Concentration'
cubes [0 ].long_name = long_name
cubes [0 ].standard_name = std
return cubes
Fix fill value:
class Gpp (Fix ):
"""Fixes for gpp variable."""
def fix_data (self , cube ):
"""Fix data.
Fix missing values.
Parameters
----------
cube: iris.cube.Cube
Returns
-------
iris.cube.Cube
"""
data = da .ma .masked_equal (cube .core_data (), 1.0e33 )
return cube .copy (data )
Fix hybrid sigma coordinate (more complicated, only if time permits):
class Cl (Fix ):
"""Fixes for ``cl``."""
def _fix_formula_terms (self , filepath , output_dir ):
"""Fix ``formula_terms`` attribute."""
new_path = self .get_fixed_filepath (output_dir , filepath )
copyfile (filepath , new_path )
dataset = Dataset (new_path , mode = 'a' )
dataset .variables ['lev' ].formula_terms = 'p0: p0 a: a b: b ps: ps'
dataset .variables ['lev' ].standard_name = (
'atmosphere_hybrid_sigma_pressure_coordinate' )
dataset .close ()
return new_path
def fix_data (self , cube ):
"""Fix data.
Fixed ordering of vertical coordinate.
Parameters
----------
cube: iris.cube.Cube
Input cube to fix.
Returns
-------
iris.cube.Cube
"""
(z_axis ,) = cube .coord_dims (cube .coord (axis = 'Z' , dim_coords = True ))
indices = [slice (None )] * cube .ndim
indices [z_axis ] = slice (None , None , - 1 )
cube = cube [tuple (indices )]
return cube
def fix_file (self , filepath , output_dir ):
"""Fix hybrid pressure coordinate.
Adds missing ``formula_terms`` attribute to file.
Note
----
Fixing this with :mod:`iris` in ``fix_metadata`` or ``fix_data`` is
**not** possible, since the bounds of the vertical coordinates ``a``
and ``b`` are not present in the loaded :class:`iris.cube.CubeList`,
even when :func:`iris.load_raw` is used.
Parameters
----------
filepath : str
Path to the original file.
output_dir : str
Path of the directory where the fixed file is saved to.
Returns
-------
str
Path to the fixed file.
"""
new_path = self ._fix_formula_terms (filepath , output_dir )
dataset = Dataset (new_path , mode = 'a' )
dataset .variables ['a_bnds' ][:] = dataset .variables ['a_bnds' ][::- 1 , :]
dataset .variables ['b_bnds' ][:] = dataset .variables ['b_bnds' ][::- 1 , :]
dataset .close ()
return new_path
The plan is that:
@agstephens or one of his team members will prepare the character and fix .json files with dachar and possibly implement the fixes mentioned above in daops.Someone from @ESMValGroup/esmvaltool-coreteam (@jvegasbsc would you have time?) Will make a demo how this could be used to load the fixed data into the ESMValCore.
Related to #755
👍 React with 👍 2valeriupredoi and jvegreg
