Add ocean variable to the ACCESS Live CMORiser

doc/quickstart/find_data.rst

@@ -679,21 +679,24 @@ For some variables, extra facets are necessary; otherwise ESMValCore cannot
 read them properly.
 Supported keys for extra facets are:
 
-==================== ====================================== =================================
-Key                  Description                            Default value if not specified
-==================== ====================================== =================================
-``raw_name``         Variable name of the variable in the   CMOR variable name of the
-                     raw input file                         corresponding variable
-``modeling_realm``   Realm attribute include `atm`, `ice`   No default (needs to be
-                     and `oce`                              specified in extra facets or
-                                                            recipe if default DRS is used)
-```special_attr``    A special attribute in the filename    No default
-                     `ACCESS-ESM` raw data, it's related to
+==================== ========================================== ====================================
+Key                  Description                                Default value if not specified
+==================== ========================================== ====================================
+``raw_name``         Variable name of the variable in the       CMOR variable name of the
+                     raw input file                             corresponding variable
+``modeling_realm``   Realm attribute includes `atm`, `ice`,     No default (needs to be
+                     and `oce`                                  specified in extra facets or
+                                                                recipe if default DRS is used)
+``freq_attribute``   A special attribute in the filename        No default
+                     `ACCESS-ESM` raw data, related to the
                      frequency of raw data
-``sub_dataset``      Part of the ACCESS-ESM raw dataset     No default
-                     root, need to specify if you want to
-                     use the cmoriser
-==================== ====================================== =================================
+``sub_dataset``      Part of the ACCESS-ESM raw dataset root,   No default
+                     needs to be specified if you want to use
+                     the cmoriser
+``ocean_grid_path``  Path to load the grid data for ACCESS      No default
+                     ocean variables
+==================== ========================================== ====================================
+
 
 .. _data-retrieval:
 

esmvalcore/cmor/_fixes/access/_base_fix.py

@@ -1,7 +1,12 @@
 """Fix base classes for ACCESS-ESM on-the-fly CMORizer."""
 
 import logging
+import warnings
+from pathlib import Path
 
+import iris
+import numpy as np
+from cf_units import Unit
 from iris.cube import CubeList
 
 from esmvalcore.cmor._fixes.native_datasets import NativeDatasetFix
@@ -21,8 +26,103 @@ def fix_coord_system(self, cube):
     def get_cubes_from_multivar(self, cubes):
         """Get cube before calculate from multiple variables."""
         name_list = self.extra_facets.get("raw_name", self.vardef.short_name)
+        name_list = self.extra_facets.get("raw_name", self.vardef.short_name)
 
         data_list = []
         for name in name_list:
             data_list.append(self.get_cube(cubes, name))
         return CubeList(data_list)
+
+    def fix_ocean_dim_coords(self, cube):
+        """Fix dim coords of ocean variables."""
+        cube.dim_coords[-2].points = np.array([int(i) for i in range(300)])
+        cube.dim_coords[-2].standard_name = None
+        cube.dim_coords[-2].var_name = "j"
+        cube.dim_coords[-2].long_name = "cell index along second dimension"
+        cube.dim_coords[-2].attributes = None
+
+        cube.dim_coords[-1].points = np.array([int(i) for i in range(360)])
+        cube.dim_coords[-1].standard_name = None
+        cube.dim_coords[-1].var_name = "i"
+        cube.dim_coords[-1].long_name = "cell index along first dimension"
+        cube.dim_coords[-1].attributes = None
+        cube.dim_coords[-1].units = Unit(1)
+
+    def fix_ocean_aux_coords(self, cube):
+        """Fix aux coords of ocean variables."""
+        lat_bounds, lon_bounds = self.load_ocean_grid_data("ocean_grid_path")
+        temp_points = []
+        for i in cube.aux_coords[-1].points:
+            temp_points.append(
+                [j + 360 for j in i if j < 0] + [j for j in i if j >= 0]
+            )
+        cube.aux_coords[-1].points = np.array(temp_points)
+        cube.aux_coords[-1].standard_name = "longitude"
+        cube.aux_coords[-1].long_name = "longitude"
+        cube.aux_coords[-1].var_name = "longitude"
+        cube.aux_coords[-1].attributes = None
+        cube.aux_coords[-1].units = "degrees"
+        cube.aux_coords[-1].bounds = lon_bounds
+
+        temp_points = []
+        for i in cube.aux_coords[-2].points:
+            temp_points.append([j.astype(np.float64) for j in i])
+        cube.aux_coords[-2].points = np.array(temp_points)
+        cube.aux_coords[-2].standard_name = "latitude"
+        cube.aux_coords[-2].long_name = "latitude"
+        cube.aux_coords[-2].var_name = "latitude"
+        cube.aux_coords[-2].attributes = None
+        cube.aux_coords[-2].units = "degrees"
+        cube.aux_coords[-2].bounds = lat_bounds
+
+    def _get_path_from_facet(self, facet):
+        """Try to get path from facet."""
+        path = Path(self.extra_facets[facet])
+        if not path.is_file():
+            raise FileNotFoundError(
+                f"'{path}' given by facet '{facet}' does not exist"
+            )
+        return path
+
+    def load_ocean_grid_data(self, facet):
+        """Load supplementary grid data for ACCESS ocean variable."""
+        path_to_grid_data = self._get_path_from_facet(facet)
+        cubes = self._load_cubes(path_to_grid_data)
+
+        y_vert_t = [cube for cube in cubes if cube.var_name == "y_vert_T"][0]
+        lat_bounds = np.transpose(y_vert_t.data, (1, 2, 0))
+        x_vert_t = [cube for cube in cubes if cube.var_name == "x_vert_T"][0]
+        lon_bounds = np.transpose(x_vert_t.data, (1, 2, 0))
+
+        return lat_bounds, lon_bounds
+
+    @staticmethod
+    def _load_cubes(path: Path | str) -> CubeList:
+        """Load cubes and ignore certain warnings."""
+        with warnings.catch_warnings():
+            warnings.filterwarnings(
+                "ignore",
+                message="Ignoring netCDF variable .* invalid units .*",
+                category=UserWarning,
+                module="iris",
+            )  # iris < 3.8
+            warnings.filterwarnings(
+                "ignore",
+                message="Ignoring invalid units .* on netCDF variable .*",
+                category=UserWarning,
+                module="iris",
+            )  # iris >= 3.8
+            warnings.filterwarnings(
+                "ignore",
+                message="Gracefully filling .* dimension coordinate.*",
+                category=UserWarning,
+                module="iris",
+            )
+            warnings.filterwarnings(
+                "ignore",
+                message="Failed to create .*dimension coordinate.*",
+                category=UserWarning,
+                module="iris",
+            )
+            cubes = iris.load(path)
+        return cubes

esmvalcore/cmor/_fixes/access/access_esm1_5.py

@@ -2,6 +2,7 @@
 
 import logging
 
+from cf_units import Unit
 from iris.cube import CubeList
 
 from ._base_fix import AccessFix
@@ -126,3 +127,63 @@ def fix_height_value(self, cube):
         """Fix height value to make it comparable to other dataset."""
         if cube.coord("height").points[0] != 2:
             cube.coord("height").points = [2]
+
+
+class Tos(AccessFix):
+    """Fixes for Tos."""
+
+    def fix_metadata(self, cubes):
+        """Fix metadata.
+
+        Parameters
+        ----------
+        cubes : iris.cube.CubeList
+            Input cubes.
+
+        Returns
+        -------
+        iris.cube.CubeList
+        """
+        cube = self.get_cube(cubes)
+
+        self.fix_ocean_dim_coords(cube)
+        self.fix_ocean_aux_coords(cube)
+
+        return CubeList([cube])
+
+
+class So(AccessFix):
+    """FIxes for So."""
+
+    def fix_metadata(self, cubes):
+        """Fix metadata.
+
+        Parameters
+        ----------
+        cubes : iris.cube.CubeList
+            Input cubes.
+
+        Returns
+        -------
+        iris.cube.CubeList
+        """
+        cube = self.get_cube(cubes)
+
+        self.fix_ocean_dim_coords(cube)
+        self.fix_ocean_aux_coords(cube)
+        self.fix_depth_metadata(cube)
+        self.fix_so_units(cube)
+
+        return CubeList([cube])
+
+    def fix_depth_metadata(self, cube):
+        """Fix depth metadata."""
+        cube.dim_coords[1].standard_name = "depth"
+        cube.dim_coords[1].long_name = "ocean depth coordinate"
+        cube.dim_coords[1].var_name = "lev"
+        cube.dim_coords[1].attributes = {"positive": "down"}
+
+    def fix_so_units(self, cube):
+        """Fix units of so."""
+        cube.attributes.pop("invalid_units")
+        cube.units = Unit(0.001)

esmvalcore/config-developer.yml

@@ -203,7 +203,9 @@ ACCESS:
     default:
       - '{dataset}/{sub_dataset}/{exp}/{modeling_realm}/netCDF'
   input_file:
-    default: '{sub_dataset}.{special_attr}-*.nc'
-  output_file: '{project}_{dataset}_{mip}_{exp}_{institute}_{sub_dataset}_{special_attr}_{short_name}'
+    default:
+      - '{sub_dataset}.{freq_attribute}-*.nc'
+      - 'ocean_{freq_attribute}.nc-*'
+  output_file: '{project}_{dataset}_{mip}_{exp}_{institute}_{sub_dataset}_{freq_attribute}_{short_name}'
   cmor_type: 'CMIP6'
   cmor_default_table_prefix: 'CMIP6_'

esmvalcore/config/extra_facets/access-mappings.yml

@@ -7,6 +7,7 @@
 ACCESS-ESM1-5:
 
   '*':
+  # atm
 
     tas:
       raw_name: fld_s03i236
@@ -65,3 +66,109 @@ ACCESS-ESM1-5:
         - fld_s01i235
         - fld_s01i201
       modeling_realm: atm
+
+    clivi:
+      raw_name: fld_s30i406
+      modeling_realm: atm
+
+    evspsbl:
+      raw_name: fld_s03i223
+      modeling_realm: atm
+
+    hfls:
+      raw_name: fld_s03i234
+      modeling_realm: atm
+
+    hfss:
+      raw_name: fld_s03i217
+      modeling_realm: atm
+
+    hur:
+      raw_name: fld_s30i206
+      modeling_realm: atm
+
+    hurs:
+      raw_name: fld_s03i245
+      modeling_realm: atm
+
+    huss:
+      raw_name: fld_s03i237
+      modeling_realm: atm
+
+    prsn:
+      raw_name: fld_s05i215
+      modeling_realm: atm
+
+    rldscs:
+      raw_name: fld_s02i208
+      modeling_realm: atm
+
+    rsdt:
+      raw_name: fld_s01i207
+      modeling_realm: atm
+
+    rsuscs:
+      raw_name: fld_s01i211
+      modeling_realm: atm
+
+    rsut:
+      raw_name: fld_s01i208
+      modeling_realm: atm
+
+    rsutcs:
+      raw_name: fld_s01i209
+      modeling_realm: atm
+
+    sci:
+      raw_name: fld_s05i270
+      modeling_realm: atm
+
+    sfcWind:
+      raw_name: fld_s03i230
+      modeling_realm: atm
+
+    sfcWindmax:
+      raw_name: fld_s03i227_max
+      modeling_realm: atm
+
+    tauu:
+      raw_name: fld_s03i460
+      modeling_realm: atm
+
+    tauv:
+      raw_name: fld_s03i461
+      modeling_realm: atm
+
+    ts:
+      raw_name: fld_s00i024
+      modeling_realm: atm
+
+    uas:
+      raw_name: fld_s03i209
+      modeling_realm: atm
+
+    vas:
+      raw_name: fld_s03i210
+      modeling_realm: atm
+
+    wap:
+      raw_name: fld_s30i208
+      modeling_realm: atm
+
+    rls:
+      raw_name: fld_s02i201
+      modeling_realm: atm
+
+    rss:
+      raw_name: fld_s01i201
+      modeling_realm: atm
+
+    # ocean
+
+    tos:
+      raw_name: sst
+      modeling_realm: ocn
+
+    so:
+      raw_name: salt
+      modeling_realm: ocn