re-add correctly region-extracted cell measures and ancillary variables after extract_region (for Changelog v2.10: authors: @valeriupredoi and @schlunma)

esmvalcore/preprocessor/_area.py

@@ -65,6 +65,10 @@ def extract_region(cube, start_longitude, end_longitude, start_latitude,
     iris.cube.Cube
         smaller cube.
     """
+    # first examine if any cell_measures are present
+    cell_measures = cube.cell_measures()
+    ancil_vars = cube.ancillary_variables()
+
     if abs(start_latitude) > 90.:
         raise ValueError(f"Invalid start_latitude: {start_latitude}")
     if abs(end_latitude) > 90.:
@@ -87,6 +91,56 @@ def extract_region(cube, start_longitude, end_longitude, start_latitude,
             start_latitude,
             end_latitude,
         )
+
+    # put back cell measures and ancillary_variables;
+    # iris.Cube.cube.intersection removes them both.
+    # This is a workaround resulting from opening upstream
+    # https://github.com/SciTools/iris/issues/5413
+    # When removing this block after iris have a fix, make sure to remove the
+    # test too tests/integration/preprocessor/_extract_region/
+
+    def _extract_region_from_dim_metadata(dim_metadata, dim_metadata_dims):
+        """Extract region from dimensional metadata."""
+        idx = tuple((
+            slice(None) if d in dim_metadata_dims else 0
+            for d in range(cube.ndim)
+        ))
+        subcube = cube[idx].copy(dim_metadata.core_data())
+        for sub_cm in subcube.cell_measures():
+            subcube.remove_cell_measure(sub_cm)
+        for sub_av in subcube.ancillary_variables():
+            subcube.remove_ancillary_variable(sub_av)
+        subcube = extract_region(
+            subcube,
+            start_longitude,
+            end_longitude,
+            start_latitude,
+            end_latitude,
+        )
+        return dim_metadata.copy(subcube.core_data())
+
+    # Step 1: cell measures
+    if cell_measures and not region_subset.cell_measures():
+        for cell_measure in cell_measures:
+            cell_measure_dims = cube.cell_measure_dims(cell_measure)
+            cell_measure_subset = _extract_region_from_dim_metadata(
+                cell_measure, cell_measure_dims
+            )
+            region_subset.add_cell_measure(
+                cell_measure_subset, cell_measure_dims
+            )
+
+    # Step 2: ancillary variables
+    if ancil_vars and not region_subset.ancillary_variables():
+        for ancil_var in ancil_vars:
+            ancil_var_dims = cube.ancillary_variable_dims(ancil_var)
+            ancil_var_subset = _extract_region_from_dim_metadata(
+                ancil_var, ancil_var_dims
+            )
+            region_subset.add_ancillary_variable(
+                ancil_var_subset, ancil_var_dims
+            )
+
     return region_subset
 
 

tests/integration/preprocessor/_extract_region/test_intersect.py

@@ -0,0 +1,98 @@
+"""
+Temporary test.
+
+Remove this test and test file after iris fixes this
+https://github.com/SciTools/iris/issues/5413 .
+"""
+import iris
+import numpy as np
+from cf_units import Unit
+from iris.fileformats.pp import EARTH_RADIUS
+
+from esmvalcore.preprocessor._area import extract_region
+from esmvalcore.preprocessor._shared import guess_bounds
+
+
+def make_cube():
+    """Make a realistic cube with cell measure and ancil var."""
+    coord_sys = iris.coord_systems.GeogCS(EARTH_RADIUS)
+    data = np.ones((10, 192, 288), dtype=np.float32)
+    time = iris.coords.DimCoord(
+        np.arange(0., 10., 1.),
+        standard_name='time',
+        units=Unit('days since 1950-01-01 00:00:00',
+                   calendar='360_day'))
+    lons = iris.coords.DimCoord(
+        [i + .5 for i in range(288)],
+        standard_name='longitude',
+        bounds=[[i, i + 1.] for i in range(288)],
+        units='degrees_east',
+        coord_system=coord_sys)
+    lats = iris.coords.DimCoord(
+        [i + .5 for i in range(192)],
+        standard_name='latitude',
+        bounds=[[i, i + 1.] for i in range(192)],
+        units='degrees_north',
+        coord_system=coord_sys,
+    )
+    coords_spec = [(time, 0), (lats, 1), (lons, 2)]
+    simple_cube = iris.cube.Cube(data, dim_coords_and_dims=coords_spec)
+
+    # add a cell measure
+    simple_cube = guess_bounds(simple_cube, ['longitude', 'latitude'])
+    grid_areas = iris.analysis.cartography.area_weights(simple_cube)
+    measure = iris.coords.CellMeasure(
+        grid_areas,
+        standard_name='cell_area',
+        units='m2',
+        measure='area')
+    simple_cube.add_cell_measure(measure, range(0, measure.ndim))
+
+    # add ancillary variable
+    ancillary_var = iris.coords.AncillaryVariable(
+        simple_cube.data,
+        standard_name='land_ice_area_fraction',
+        var_name='sftgif',
+        units='%')
+    simple_cube.add_ancillary_variable(ancillary_var,
+                                       range(0, simple_cube.ndim))
+
+    return simple_cube
+
+
+def test_extract_region_cell_ancil():
+    """Test re-adding cell measures ancil variables after extract region."""
+    cube = make_cube()
+
+    # intersection cube loses cellmeas/ancillary variables
+    # under normal (unpatched) conditions of extract_region
+    ex1 = extract_region(cube,
+                         start_longitude=-90,
+                         end_longitude=40,
+                         start_latitude=20,
+                         end_latitude=80)
+
+    # intersection cube doesn't lose cellmeas/ancillary variables
+    # under normal (unpatched) conditions of extract_region
+    # so duplication must be avoided
+    ex2 = extract_region(cube,
+                         start_longitude=160,
+                         end_longitude=280,
+                         start_latitude=-5,
+                         end_latitude=5)
+
+    expected_cm = cube.cell_measures()[0]
+    result_cm = ex1.cell_measures()
+    assert result_cm
+    assert expected_cm.measure == result_cm[0].measure
+    assert expected_cm.var_name == result_cm[0].var_name
+    np.testing.assert_array_equal(result_cm[0].shape, (10, 60, 58))
+    assert expected_cm.standard_name == result_cm[0].standard_name
+    expected_ancil = cube.ancillary_variables()[0]
+    result_ancil = ex1.ancillary_variables()
+    assert result_ancil
+    assert expected_ancil.var_name == result_ancil[0].var_name
+    assert expected_ancil.standard_name == result_ancil[0].standard_name
+    np.testing.assert_array_equal(result_ancil[0].shape, (10, 60, 58))
+    assert len(ex2.cell_measures()) == 1
+    assert len(ex2.ancillary_variables()) == 1