Fix rotated coordinate grids and tas and pr for CORDEX datasets (#…

…1765)

Co-authored-by: Pep Cos <[email protected]>
Co-authored-by: Klaus Zimmermann <[email protected]>

environment.yml

@@ -30,6 +30,7 @@ dependencies:
   - pip!=21.3
   - prov
   - psutil
+  - py-cordex
   - pybtex
   - python>=3.8
   - python-stratify

esmvalcore/cmor/_fixes/cordex/__init__ .py

@@ -0,0 +1 @@
+"""Fixes for CORDEX data."""

esmvalcore/cmor/_fixes/cordex/cnrm_cerfacs_cnrm_cm5/__init__.py

@@ -0,0 +1 @@
+"""Fixes for CORDEX data."""

esmvalcore/cmor/_fixes/cordex/cnrm_cerfacs_cnrm_cm5/cnrm_aladin63.py

@@ -0,0 +1,33 @@
+"""Fixes for rcm CNRM-ALADIN63 driven by CNRM-CERFACS-CNRM-CM5."""
+import numpy as np
+
+from esmvalcore.cmor._fixes.cordex.cordex_fixes import TimeLongName as BaseFix
+from esmvalcore.cmor._fixes.shared import add_scalar_height_coord
+from esmvalcore.cmor.fix import Fix
+
+
+class Tas(Fix):
+    """Fixes for tas."""
+
+    def fix_metadata(self, cubes):
+        """Add height (2m) coordinate and correct long_name for time.
+
+        Parameters
+        ----------
+        cubes : iris.cube.CubeList
+            Input cubes.
+
+        Returns
+        -------
+        iris.cube.CubeList
+        """
+        for cube in cubes:
+            add_scalar_height_coord(cube)
+            if cube.coord('height').points != 2.:
+                cube.coord('height').points = np.ma.array([2.0])
+            cube.coord('time').long_name = 'time'
+
+        return cubes
+
+
+Pr = BaseFix

esmvalcore/cmor/_fixes/cordex/cnrm_cerfacs_cnrm_cm5/mohc_hadrem3_ga7_05.py

@@ -0,0 +1,7 @@
+"""Fixes for rcm MOHC-HadREM3-GA7-05 driven by CNRM-CERFACS-CNRM-CM5."""
+from esmvalcore.cmor._fixes.cordex.cordex_fixes import (
+    MOHCHadREM3GA705 as BaseFix)
+
+Tas = BaseFix
+
+Pr = BaseFix

esmvalcore/cmor/_fixes/cordex/cordex_fixes.py

@@ -0,0 +1,206 @@
+"""Fixes that are shared between datasets and drivers."""
+import logging
+from functools import lru_cache
+
+import cordex as cx
+import iris
+import numpy as np
+from cf_units import Unit
+from iris.coord_systems import LambertConformal, RotatedGeogCS
+
+from esmvalcore.cmor.fix import Fix
+from esmvalcore.exceptions import RecipeError
+
+logger = logging.getLogger(__name__)
+
+
+@lru_cache
+def _get_domain(data_domain):
+    domain = cx.cordex_domain(data_domain, add_vertices=True)
+    return domain
+
+
+@lru_cache
+def _get_domain_info(data_domain):
+    domain_info = cx.domain_info(data_domain)
+    return domain_info
+
+
+class MOHCHadREM3GA705(Fix):
+    """General fix for MOHC-HadREM3-GA7-05."""
+
+    def fix_metadata(self, cubes):
+        """Fix time long_name, and latitude and longitude var_name.
+
+        Parameters
+        ----------
+        cubes : iris.cube.CubeList
+            Input cubes.
+
+        Returns
+        -------
+        iris.cube.CubeList
+        """
+        for cube in cubes:
+            cube.coord('latitude').var_name = 'lat'
+            cube.coord('longitude').var_name = 'lon'
+            cube.coord('time').long_name = 'time'
+
+        return cubes
+
+
+class TimeLongName(Fix):
+    """Fixes for time coordinate."""
+
+    def fix_metadata(self, cubes):
+        """Fix time long_name.
+
+        Parameters
+        ----------
+        cubes : iris.cube.CubeList
+            Input cubes.
+
+        Returns
+        -------
+        iris.cube.CubeList
+        """
+        for cube in cubes:
+            cube.coord('time').long_name = 'time'
+
+        return cubes
+
+
+class CLMcomCCLM4817(Fix):
+    """Fixes for CLMcom-CCLM4-8-17."""
+
+    def fix_metadata(self, cubes):
+        """Fix calendars.
+
+        Set calendar to 'proleptic_gregorian' to avoid
+        concatenation issues between historical and
+        scenario runs.
+
+        Fix dtype value of coordinates and coordinate bounds.
+
+        Parameters
+        ----------
+        cubes : iris.cube.CubeList
+            Input cubes.
+
+        Returns
+        -------
+        iris.cube.CubeList
+        """
+        for cube in cubes:
+            time_unit = cube.coord('time').units
+            if time_unit.calendar == 'standard':
+                new_unit = time_unit.change_calendar('proleptic_gregorian')
+                cube.coord('time').units = new_unit
+            for coord in cube.coords():
+                if coord.dtype in ['>f8', '>f4']:
+                    coord.points = coord.core_points().astype(
+                        np.float64, casting='same_kind')
+                    if coord.bounds is not None:
+                        coord.bounds = coord.core_bounds().astype(
+                            np.float64, casting='same_kind')
+        return cubes
+
+
+class AllVars(Fix):
+    """General CORDEX grid fix."""
+
+    def _check_grid_differences(self, old_coord, new_coord):
+        """Check differences between coords."""
+        diff = np.max(np.abs(old_coord.points - new_coord.points))
+        logger.debug(
+            "Maximum difference between original %s"
+            "points and standard %s domain points  "
+            "for dataset %s and driver %s is: %s.", new_coord.var_name,
+            self.extra_facets['domain'], self.extra_facets['dataset'],
+            self.extra_facets['driver'], str(diff))
+
+        if diff > 10e-4:
+            raise RecipeError(
+                "Differences between the original grid and the "
+                f"standardised grid are above 10e-4 {new_coord.units}.")
+
+    def _fix_rotated_coords(self, cube, domain, domain_info):
+        """Fix rotated coordinates."""
+        for dim_coord in ['rlat', 'rlon']:
+            old_coord = cube.coord(domain[dim_coord].standard_name)
+            old_coord_dims = old_coord.cube_dims(cube)
+            points = domain[dim_coord].data
+            coord_system = iris.coord_systems.RotatedGeogCS(
+                grid_north_pole_latitude=domain_info['pollat'],
+                grid_north_pole_longitude=domain_info['pollon'])
+            new_coord = iris.coords.DimCoord(
+                points,
+                var_name=dim_coord,
+                standard_name=domain[dim_coord].standard_name,
+                long_name=domain[dim_coord].long_name,
+                units=Unit('degrees'),
+                coord_system=coord_system,
+            )
+            self._check_grid_differences(old_coord, new_coord)
+            new_coord.guess_bounds()
+            cube.remove_coord(old_coord)
+            cube.add_dim_coord(new_coord, old_coord_dims)
+
+    def _fix_geographical_coords(self, cube, domain):
+        """Fix geographical coordinates."""
+        for aux_coord in ['lat', 'lon']:
+            old_coord = cube.coord(domain[aux_coord].standard_name)
+            cube.remove_coord(old_coord)
+            points = domain[aux_coord].data
+            bounds = domain[f'{aux_coord}_vertices'].data
+            new_coord = iris.coords.AuxCoord(
+                points,
+                var_name=aux_coord,
+                standard_name=domain[aux_coord].standard_name,
+                long_name=domain[aux_coord].long_name,
+                units=Unit(domain[aux_coord].units),
+                bounds=bounds,
+            )
+            self._check_grid_differences(old_coord, new_coord)
+            aux_coord_dims = (cube.coord(var_name='rlat').cube_dims(cube) +
+                              cube.coord(var_name='rlon').cube_dims(cube))
+            cube.add_aux_coord(new_coord, aux_coord_dims)
+
+    def fix_metadata(self, cubes):
+        """Fix CORDEX rotated grids.
+
+        Set rotated and geographical coordinates to the
+        values given by each domain specification.
+
+        The domain specifications are retrieved from the
+        py-cordex package.
+
+        Parameters
+        ----------
+        cubes : iris.cube.CubeList
+            Input cubes.
+
+        Returns
+        -------
+        iris.cube.CubeList
+        """
+        data_domain = self.extra_facets['domain']
+        domain = _get_domain(data_domain)
+        domain_info = _get_domain_info(data_domain)
+        for cube in cubes:
+            coord_system = cube.coord_system()
+            if isinstance(coord_system, RotatedGeogCS):
+                self._fix_rotated_coords(cube, domain, domain_info)
+                self._fix_geographical_coords(cube, domain)
+            elif isinstance(coord_system, LambertConformal):
+                logger.warning(
+                    "Support for CORDEX datasets in a Lambert Conformal "
+                    "coordinate system is ongoing. Certain preprocessor "
+                    "functions may fail.")
+            else:
+                raise RecipeError(
+                    f"Coordinate system {coord_system.grid_mapping_name} "
+                    "not supported in CORDEX datasets. Must be "
+                    "rotated_latitude_longitude or lambert_conformal_conic.")
+
+        return cubes

esmvalcore/cmor/_fixes/cordex/ichec_ec_earth/__init__.py

@@ -0,0 +1 @@
+"""Fixes for CORDEX data."""

esmvalcore/cmor/_fixes/cordex/ichec_ec_earth/clmcom_cclm4_8_17.py

@@ -0,0 +1,5 @@
+"""Fixes for rcm CLMcom-CCLM4-8-17 driven by ICHEC-EC-EARTH."""
+from esmvalcore.cmor._fixes.cordex.cordex_fixes import (
+    CLMcomCCLM4817 as BaseFix)
+
+AllVars = BaseFix

esmvalcore/cmor/_fixes/cordex/ichec_ec_earth/gerics_remo2015.py

@@ -0,0 +1,5 @@
+"""Fixes for rcm GERICS-REMO2015 driven by ICHEC-EC-EARTH."""
+from esmvalcore.cmor._fixes.cordex.cordex_fixes import (
+    TimeLongName as BaseFix)
+
+Pr = BaseFix

esmvalcore/cmor/_fixes/cordex/ichec_ec_earth/knmi_racmo22e.py

@@ -0,0 +1,5 @@
+"""Fixes for rcm KNMI-RACMO22E driven by ICHEC-EC-EARTH."""
+from esmvalcore.cmor._fixes.cordex.cordex_fixes import (
+    TimeLongName as BaseFix)
+
+Pr = BaseFix

esmvalcore/cmor/_fixes/cordex/ichec_ec_earth/mohc_hadrem3_ga7_05.py

@@ -0,0 +1,7 @@
+"""Fixes for rcm MOHC-HadREM3-GA7-05 driven by ICHEC-EC-EARTH."""
+from esmvalcore.cmor._fixes.cordex.cordex_fixes import (
+    MOHCHadREM3GA705 as BaseFix)
+
+Tas = BaseFix
+
+Pr = BaseFix

esmvalcore/cmor/_fixes/cordex/ichec_ec_earth/smhi_rca4.py

@@ -0,0 +1,7 @@
+"""Fixes for rcm SMHI-RCA4 driven by ICHEC-EC-EARTH."""
+from esmvalcore.cmor._fixes.cordex.cordex_fixes import (
+    TimeLongName as BaseFix)
+
+Pr = BaseFix
+
+Tas = BaseFix

esmvalcore/cmor/_fixes/cordex/miroc_miroc5/__init__.py

@@ -0,0 +1 @@
+"""Fixes for CORDEX data."""

esmvalcore/cmor/_fixes/cordex/miroc_miroc5/clmcom_cclm4_8_17.py

@@ -0,0 +1,5 @@
+"""Fixes for rcm CLMcom-CCLM4-8-17 driven by MIROC-MIROC5."""
+from esmvalcore.cmor._fixes.cordex.cordex_fixes import (
+    CLMcomCCLM4817 as BaseFix)
+
+AllVars = BaseFix

esmvalcore/cmor/_fixes/cordex/miroc_miroc5/gerics_remo2015.py

@@ -0,0 +1,5 @@
+"""Fixes for rcm GERICS-REMO2015 driven by MIROC-MIROC5."""
+from esmvalcore.cmor._fixes.cordex.cordex_fixes import (
+    TimeLongName as BaseFix)
+
+Pr = BaseFix

esmvalcore/cmor/_fixes/cordex/miroc_miroc5/uhoh_wrf361h.py

@@ -0,0 +1,34 @@
+"""Fixes for rcm UHOH-WRF361H driven by MIROC-MIROC5."""
+import iris
+from esmvalcore.cmor.fix import Fix
+
+
+class Tas(Fix):
+    """Fixes for tas."""
+
+    def fix_metadata(self, cubes):
+        """Fix tas coordinates.
+
+        Set height as an auxiliary coordinate instead
+        of as a dimensional coordinate.
+
+        Parameters
+        ----------
+        cubes : iris.cube.CubeList
+            Input cubes.
+
+        Returns
+        -------
+        iris.cube.CubeList
+
+        """
+        fixed_cubes = iris.cube.CubeList()
+        for cube in cubes:
+            height = cube.coord('height')
+            if isinstance(height, iris.coords.DimCoord):
+                iris.util.demote_dim_coord_to_aux_coord(
+                    cube,
+                    height
+                )
+            fixed_cubes.append(iris.util.squeeze(cube))
+        return fixed_cubes

esmvalcore/cmor/_fixes/cordex/mohc_hadgem2_es/__init__.py

@@ -0,0 +1 @@
+"""Fixes for CORDEX data."""

esmvalcore/cmor/_fixes/cordex/mohc_hadgem2_es/dmi_hirham5.py

@@ -0,0 +1,25 @@
+"""Fixes for rcm DMI-HIRHAM driven by MOHC-HadGEM2."""
+from esmvalcore.cmor.fix import Fix
+
+
+class Pr(Fix):
+    """Fixes for pr."""
+
+    def fix_metadata(self, cubes):
+        """Remove latitude and longitude attributes.
+
+        Parameters
+        ----------
+        cubes : iris.cube.CubeList
+            Input cubes.
+
+        Returns
+        -------
+        iris.cube.CubeList
+
+        """
+        for cube in cubes:
+            cube.coord('latitude').attributes = {}
+            cube.coord('longitude').attributes = {}
+
+        return cubes

esmvalcore/cmor/_fixes/cordex/mohc_hadgem2_es/gerics_remo2015.py

@@ -0,0 +1,7 @@
+"""Fixes for rcm GERICS-REMO2015 driven by MOHC-HadGEM2."""
+from esmvalcore.cmor._fixes.cordex.cordex_fixes import (
+    TimeLongName as BaseFix)
+
+Pr = BaseFix
+
+Tas = BaseFix

esmvalcore/cmor/_fixes/cordex/mohc_hadgem2_es/mohc_hadrem3_ga7_05.py

@@ -0,0 +1,7 @@
+"""Fixes for rcm MOHC-HadREM3-GA7-05 driven by MOHC-HadGEM2-ES."""
+from esmvalcore.cmor._fixes.cordex.cordex_fixes import (
+    MOHCHadREM3GA705 as BaseFix)
+
+Tas = BaseFix
+
+Pr = BaseFix

esmvalcore/cmor/_fixes/cordex/mohc_hadgem2_es/smhi_rca4.py

@@ -0,0 +1,7 @@
+"""Fixes for rcm SMHI-RCA4 driven by MOHC-HadGEM2-ES."""
+from esmvalcore.cmor._fixes.cordex.cordex_fixes import (
+    TimeLongName as BaseFix)
+
+Pr = BaseFix
+
+Tas = BaseFix

esmvalcore/cmor/_fixes/cordex/mpi_m_mpi_esm_lr/__init__.py

@@ -0,0 +1 @@
+"""Fixes for CORDEX data."""