Fix cmip6 models

esmvalcore/cmor/_fixes/cmip6/bcc_csm2_mr.py

@@ -17,16 +17,41 @@ class Tos(BaseTos):
 
     def fix_metadata(self, cubes):
         """Rename ``var_name`` of 1D-``latitude`` and 1D-``longitude``.
-
         Parameters
         ----------
         cubes : iris.cube.CubeList
             Input cubes.
-
         Returns
         -------
         iris.cube.CubeList
+        """
+        cube = self.get_cube_from_list(cubes)
+        lat_coord = cube.coord('latitude', dimensions=(1, ))
+        lon_coord = cube.coord('longitude', dimensions=(2, ))
+        lat_coord.standard_name = None
+        lat_coord.long_name = 'grid_latitude'
+        lat_coord.var_name = 'i'
+        lat_coord.units = '1'
+        lon_coord.standard_name = None
+        lon_coord.long_name = 'grid_longitude'
+        lon_coord.var_name = 'j'
+        lon_coord.units = '1'
+        lon_coord.circular = False
+        return cubes
+
+
+class Siconc(BaseTos):
+    """Fixes for siconc."""
 
+    def fix_metadata(self, cubes):
+        """Rename ``var_name`` of 1D-``latitude`` and 1D-``longitude``.
+        Parameters
+        ----------
+        cubes : iris.cube.CubeList
+            Input cubes.
+        Returns
+        -------
+        iris.cube.CubeList
         """
         cube = self.get_cube_from_list(cubes)
         lat_coord = cube.coord('latitude', dimensions=(1, ))

esmvalcore/cmor/_fixes/cmip6/cesm2.py

@@ -2,10 +2,12 @@
 from shutil import copyfile
 
 from netCDF4 import Dataset
+import numpy as np
 
 from ..fix import Fix
 from ..shared import (add_scalar_depth_coord, add_scalar_height_coord,
                       add_scalar_typeland_coord, add_scalar_typesea_coord)
+from .gfdl_esm4 import Siconc as Addtypesi
 
 
 class Cl(Fix):
@@ -107,7 +109,10 @@ class Tas(Fix):
     """Fixes for tas."""
 
     def fix_metadata(self, cubes):
-        """Add height (2m) coordinate.
+        """
+        Add height (2m) coordinate.
+
+        Fix latitude_bounds and longitude_bounds data type and round to 4 d.p.
 
         Parameters
         ----------
@@ -121,6 +126,19 @@ def fix_metadata(self, cubes):
         """
         cube = self.get_cube_from_list(cubes)
         add_scalar_height_coord(cube)
+
+        for cube in cubes:
+            latitude = cube.coord('latitude')
+            if latitude.bounds is None:
+                latitude.guess_bounds()
+            latitude.bounds = latitude.bounds.astype(np.float64)
+            latitude.bounds = np.round(latitude.bounds, 4)
+            longitude = cube.coord('longitude')
+            if longitude.bounds is None:
+                longitude.guess_bounds()
+            longitude.bounds = longitude.bounds.astype(np.float64)
+            longitude.bounds = np.round(longitude.bounds, 4)
+
         return cubes
 
 
@@ -164,3 +182,34 @@ def fix_metadata(self, cubes):
         cube = self.get_cube_from_list(cubes)
         add_scalar_typesea_coord(cube)
         return cubes
+
+
+class Tos(Fix):
+    """Fixes for tos."""
+
+    def fix_metadata(self, cubes):
+        """
+        Round times to 1 d.p. for monthly means.
+
+        Required to get hist-GHG and ssp245-GHG Omon tos to concatenate.
+
+        Parameters
+        ----------
+        cubes : iris.cube.CubeList
+            Input cubes.
+
+        Returns
+        -------
+        iris.cube.CubeList
+
+        """
+        cube = self.get_cube_from_list(cubes)
+
+        for cube in cubes:
+            if cube.attributes['mipTable'] == 'Omon':
+                cube.coord('time').points = \
+                    np.round(cube.coord('time').points, 1)
+        return cubes
+
+
+Siconc = Addtypesi

esmvalcore/cmor/_fixes/cmip6/fgoals_g3.py

@@ -1,5 +1,7 @@
 """Fixes for FGOALS-g3 model."""
 from ..cmip5.fgoals_g2 import Cl as BaseCl
+from ..common import OceanFixGrid
+
 
 Cl = BaseCl
 
@@ -8,3 +10,9 @@
 
 
 Clw = BaseCl
+
+
+Tos = OceanFixGrid
+
+
+Siconc = OceanFixGrid

esmvalcore/cmor/_fixes/cmip6/gfdl_esm4.py

@@ -0,0 +1,32 @@
+"""Fixes for GFDL-ESM4 model."""
+import iris
+from ..fix import Fix
+
+
+class Siconc(Fix):
+    """Fixes for siconc."""
+
+    def fix_metadata(self, cubes):
+        """
+        Fix missing type.
+
+        Parameters
+        ----------
+        cubes: iris CubeList
+            List of cubes to fix
+
+        Returns
+        -------
+        iris.cube.CubeList
+
+        """
+        typesi = iris.coords.AuxCoord(
+            'siconc',
+            standard_name='area_type',
+            long_name='Sea Ice area type',
+            var_name='type',
+            units='1',
+            bounds=None)
+        for cube in cubes:
+            cube.add_aux_coord(typesi)
+        return cubes

esmvalcore/cmor/_fixes/cmip6/noresm2_lm.py

@@ -0,0 +1,33 @@
+"""Fixes for NorESM2-LM model."""
+import numpy as np
+from ..fix import Fix
+
+
+class Siconc(Fix):
+    """Fixes for siconc."""
+
+    def fix_metadata(self, cubes):
+        """
+        Fix metadata.
+
+        Some coordinate points vary for different files of this dataset (for
+        different time range). This fix removes these inaccuracies by rounding
+        the coordinates.
+
+        Parameters
+        ----------
+        cubes: iris.cube.CubeList
+            Input cubes to fix.
+
+        Returns
+        -------
+        iris.cube.CubeList
+
+        """
+        for cube in cubes:
+            latitude = cube.coord('latitude')
+            latitude.bounds = np.round(latitude.bounds, 4)
+            longitude = cube.coord('longitude')
+            longitude.bounds = np.round(longitude.bounds, 4)
+
+        return cubes

esmvalcore/cmor/_fixes/common.py

@@ -1,5 +1,7 @@
 """Common fixes used for multiple datasets."""
 import iris
+import numpy as np
+from scipy.ndimage import map_coordinates
 
 from .fix import Fix
 from .shared import add_plev_from_altitude, fix_bounds
@@ -101,3 +103,96 @@ def fix_metadata(self, cubes):
         cube.coord(var_name='ps').attributes = {}
 
         return iris.cube.CubeList([cube])
+
+
+class OceanFixGrid(Fix):
+    """Fixes for tos, siconc in FGOALS-g3."""
+
+    def fix_data(self, cube):
+        """
+        Fix data.
+
+        Calculate missing latitude/longitude boundaries using interpolation.
+        Based on a similar fix for BCC-CSM2-MR.
+
+        Parameters
+        ----------
+        cube: iris.cube.Cube
+            Input cube to fix.
+
+        Returns
+        -------
+        iris.cube.Cube
+        """
+        rlat = cube.coord('grid_latitude').points
+        rlon = cube.coord('grid_longitude').points
+
+        # Guess coordinate bounds in rlat, rlon (following BCC-CSM2-MR-1).
+        rlat_idx_bnds = np.zeros((len(rlat), 2))
+        rlat_idx_bnds[:, 0] = np.arange(len(rlat)) - 0.5
+        rlat_idx_bnds[:, 1] = np.arange(len(rlat)) + 0.5
+        rlat_idx_bnds[0, 0] = 0.
+        rlat_idx_bnds[len(rlat) - 1, 1] = len(rlat)
+        rlon_idx_bnds = np.zeros((len(rlon), 2))
+        rlon_idx_bnds[:, 0] = np.arange(len(rlon)) - 0.5
+        rlon_idx_bnds[:, 1] = np.arange(len(rlon)) + 0.5
+
+        # Calculate latitude/longitude vertices by interpolation
+        lat_vertices = []
+        lon_vertices = []
+        for (i, j) in [(0, 0), (0, 1), (1, 1), (1, 0)]:
+            (rlat_v, rlon_v) = np.meshgrid(rlat_idx_bnds[:, i],
+                                           rlon_idx_bnds[:, j],
+                                           indexing='ij')
+            lat_vertices.append(
+                map_coordinates(cube.coord('latitude').points,
+                                [rlat_v, rlon_v],
+                                mode='nearest'))
+            lon_vertices.append(
+                map_coordinates(cube.coord('longitude').points,
+                                [rlat_v, rlon_v],
+                                mode='wrap'))
+        lat_vertices = np.array(lat_vertices)
+        lon_vertices = np.array(lon_vertices)
+        lat_vertices = np.moveaxis(lat_vertices, 0, -1)
+        lon_vertices = np.moveaxis(lon_vertices, 0, -1)
+
+        # Copy vertices to cube
+        cube.coord('latitude').bounds = lat_vertices
+        cube.coord('longitude').bounds = lon_vertices
+        return cube
+
+    def fix_metadata(self, cubes):
+        """
+        Rename ``var_name`` of 1D-``latitude`` and 1D-``longitude``.
+
+        Parameters
+        ----------
+        cubes : iris.cube.CubeList
+            Input cubes.
+
+        Returns
+        -------
+        iris.cube.CubeList
+        """
+        cube = self.get_cube_from_list(cubes)
+        lat_coord = cube.coord('cell index along second dimension',
+                               dimensions=(1, ))
+        lon_coord = cube.coord('cell index along first dimension',
+                               dimensions=(2, ))
+        lat_coord.standard_name = None
+        lat_coord.long_name = 'grid_latitude'
+        lat_coord.var_name = 'i'
+        lat_coord.units = '1'
+        lon_coord.standard_name = None
+        lon_coord.long_name = 'grid_longitude'
+        lon_coord.var_name = 'j'
+        lon_coord.units = '1'
+        lon_coord.circular = False
+        # FGOALS-g3 data contain latitude and longitude data set to
+        # >1e30 in some places. Set to 0. to avoid problem in check.py.
+        cube.coord('latitude').points[cube.coord('latitude').points > 1000.]\
+            = 0.
+        cube.coord('longitude').points[cube.coord('longitude').points > 1000.]\
+            = 0.
+        return cubes