Fix CMIP5 MRI-ESM1 grid

esmvalcore/cmor/_fixes/cmip5/mri_esm1.py

@@ -1,8 +1,50 @@
 """Fixes for MRI-ESM1 model."""
 
+from typing import Sequence
+
+import iris.coords
+import iris.cube
+import iris.exceptions
+import numpy as np
 from dask import array as da
 
-from ..fix import Fix
+from esmvalcore.cmor._fixes.fix import Fix
+
+
+class AllVars(Fix):
+    def fix_metadata(
+        self, cubes: Sequence[iris.cube.Cube]
+    ) -> Sequence[iris.cube.Cube]:
+        """Replace rlat and rlon by index coordinates."""
+        # In file fgco2_Omon_MRI-ESM1_historical_r1i1p1_185101-200512.nc
+        # (v20130307) the usual horizontal index coordinates appear to have
+        # been replaced by rotated pole coordinates.
+        #
+        # This leads to iris-esmf-regrid selecting the wrong coordinate when
+        # regridding.
+        for cube in cubes:
+            for coord_name, index_var_name, index_long_name in [
+                ("latitude", "i", "cell index along first dimension"),
+                ("longitude", "j", "cell index along second dimension"),
+            ]:
+                try:
+                    rotated_coord = cube.coord(f"grid_{coord_name}")
+                    horizontal_coord = cube.coord(coord_name)
+                except iris.exceptions.CoordinateNotFoundError:
+                    pass
+                else:
+                    if len(horizontal_coord.shape) == 2:
+                        (dim,) = cube.coord_dims(rotated_coord)
+                        (size,) = rotated_coord.shape
+                        cube.remove_coord(rotated_coord)
+                        index_coord = iris.coords.DimCoord(
+                            points=np.arange(1, size + 1),
+                            var_name=index_var_name,
+                            long_name=index_long_name,
+                            units="1",
+                        )
+                        cube.add_dim_coord(index_coord, dim)
+        return cubes
 
 
 class Msftmyz(Fix):

tests/integration/cmor/_fixes/cmip5/test_mri_esm1.py

@@ -1,18 +1,51 @@
 """Test MRI-ESM1 fixes."""
 
-import unittest
+import iris.coords
+import iris.cube
+import numpy as np
+import pytest
 
-from esmvalcore.cmor._fixes.cmip5.mri_esm1 import Msftmyz
-from esmvalcore.cmor._fixes.fix import GenericFix
+from esmvalcore.cmor._fixes.cmip5.mri_esm1 import AllVars, Msftmyz
 from esmvalcore.cmor.fix import Fix
 
 
-class TestMsftmyz(unittest.TestCase):
-    """Test msftmyz fixes."""
+def test_get_allvars_fix():
+    assert AllVars(None) in Fix.get_fixes("CMIP5", "MRI-ESM1", "Amon", "fgco2")
 
-    def test_get(self):
-        """Test fix get."""
-        self.assertListEqual(
-            Fix.get_fixes("CMIP5", "MRI-ESM1", "Amon", "msftmyz"),
-            [Msftmyz(None), GenericFix(None)],
+
+@pytest.mark.parametrize("has_rotated_coord", [True, False])
+def test_grid_fix(has_rotated_coord):
+    """Test fix for using rotated pole grid coords instead of index coords."""
+    cube = iris.cube.Cube(np.arange(4).reshape((2, 2)))
+    if has_rotated_coord:
+        r_coord = iris.coords.DimCoord(
+            np.arange(2).astype(np.float64),
+            var_name="rlat",
+            standard_name="grid_latitude",
+            long_name="latitude in rotated pole grid",
+            units="degrees",
+        )
+        cube.add_dim_coord(r_coord, 0)
+        h_coord = iris.coords.AuxCoord(
+            np.arange(4).astype(np.float64).reshape((2, 2)),
+            var_name="lat",
+            standard_name="latitude",
+            units="degrees",
         )
+        cube.add_aux_coord(h_coord, (0, 1))
+
+    cubes = [cube]
+    for fix in Fix.get_fixes("CMIP5", "MRI-ESM1", "Omon", "fgco2"):
+        cubes = fix.fix_metadata(cubes)
+
+    assert len(cubes) == 1
+    if has_rotated_coord:
+        assert not cube.coords("grid_latitude")
+        assert cube.coords(var_name="i")
+        assert cube.coords("latitude")
+
+
+def test_get_msftmyz_fix():
+    assert Msftmyz(None) in Fix.get_fixes(
+        "CMIP5", "MRI-ESM1", "Amon", "msftmyz"
+    )