Fill value

improver/utilities/save.py

@@ -57,6 +57,7 @@ def save_netcdf(
     filename: str,
     compression_level: int = 1,
     least_significant_digit: Optional[int] = None,
+    fill_value: Optional[float] = None,
 ) -> None:
     """Save the input Cube or CubeList as a NetCDF file and check metadata
     where required for integrity.
@@ -80,7 +81,11 @@ def save_netcdf(
             http://www.esrl.noaa.gov/psd/data/gridded/conventions/cdc_netcdf_standard.shtml
             for details. When used with `compression level`, this will result in lossy
             compression.
-
+        fill_value:
+            If specified, will set the fill value for missing data. If not specified,
+            the default fill value for the data type will be used. If the data is not masked then
+            the numpy array's fill value will retain the default value while the _FillValue attribute
+            in the NetCDF file will be updated.
     Raises:
         warning if cubelist contains cubes of varying dimensions.
     """
@@ -144,5 +149,6 @@ def save_netcdf(
         zlib=compression_level > 0,
         chunksizes=chunksizes,
         least_significant_digit=least_significant_digit,
+        fill_value=fill_value,
     )
     os.rename(ftmp, filename)

improver_tests/utilities/test_save.py

@@ -228,6 +228,45 @@ def test_remove_least_significant_digit(self):
         cube = load_cube(self.filepath)
         self.assertNotIn("least_significant_digit", cube.attributes)
 
+    def test_fill_value_no_mask(self):
+        """Test that the default fill_value is not overriden if there
+        is no masked data."""
+        save_netcdf(self.cube, self.filepath)
+        cube = load_cube(self.filepath)
+        self.assertEqual(
+            cube.data.get_fill_value(), 1e20
+        )  # Default fill value for float32
+
+    def test_fill_value_no_mask_integer_data(self):
+        """Test that the default fill_value is not overriden if there is
+        no masked data and integer data is provided."""
+        cube = self.cube.copy()
+        cube.data = np.array(cube.data.astype(int))
+
+        save_netcdf(cube, self.filepath)
+        cube = load_cube(self.filepath)
+        self.assertEqual(
+            cube.data.get_fill_value(), 999999
+        )  # default fill value for int32
+
+    def test_fill_value_with_mask(self):
+        """Test that fill_value can be overriden."""
+        cube = self.cube.copy()
+        mask = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
+        cube.data = np.ma.masked_array(cube.data, mask=mask)
+        save_netcdf(cube, self.filepath, fill_value=99)
+        cube = load_cube(self.filepath)
+        self.assertEqual(cube.data.get_fill_value(), 99)
+
+    def test_fill_value_with_mask_integer_data(self):
+        """Test that fill_value can be overriden when integer data is provided."""
+        cube = self.cube.copy()
+        mask = [[1, 0, 0], [0, 1, 0], [0, 0, 1]]
+        cube.data = np.ma.masked_array(cube.data.astype(int), mask=mask)
+        save_netcdf(cube, self.filepath, fill_value=99)
+        cube = load_cube(self.filepath)
+        self.assertEqual(cube.data.get_fill_value(), 99)
+
 
 @pytest.fixture(name="bitshaving_cube")
 def bitshaving_cube_fixture():