Simplify variable transposal, update effected typehints and unit tests

CHANGELOG.md

@@ -5,7 +5,7 @@
 ### Changed
 
 - [[DAS-2216](https://bugs.earthdata.nasa.gov/browse/DAS-2216)]
-  The Swath Projector has been updated with quick fixes to add support for TEMPO level 2 data.
+  The Swath Projector has been updated with quick fixes to add support for TEMPO level 2 data. These changes include optional transposing of arrays based on dimension sizes and updates to the configuration file for TEMPO_O3TOT_L2 to correctly locate coordinate variables and exclude science variables with dimensions that do no match those of the coordinate variables.
 
 ## [v1.1.1] - 2024-09-16
 

swath_projector/earthdata_varinfo_config.json

@@ -57,7 +57,7 @@
           "Value": "/geolocation/latitude, /geolocation/longitude"
         }
       ],
-      "_Description": "TEMPO_O3TOT_L2 variables only contain basenames for coordinates, which are found in sibling hierarchical groups. This rule fully qualifies the paths to these coordinates."
+      "_Description": "TEMPO_O3TOT_L2 variables only contain basenames for coordinates, which are found in sibling hierarchical groups. This rule fully qualifies the paths to these coordinates. Some variables in these groups are excluded via 'ExcludedScienceVariables'"
     }
   ]
 }

swath_projector/swath_geometry.py

@@ -13,7 +13,7 @@
 
 
 def get_projected_resolution(
-    projection: Proj, longitudes: Variable, latitudes: Variable
+    projection: Proj, longitudes: np.ma.MaskedArray, latitudes: np.ma.MaskedArray
 ) -> Tuple[float]:
     """Find the resolution of the target grid in the projected coordinates, x
     and y. First the perimeter points are found. These are then projected
@@ -40,7 +40,7 @@ def get_projected_resolution(
 
 
 def get_extents_from_perimeter(
-    projection: Proj, longitudes: Variable, latitudes: Variable
+    projection: Proj, longitudes: np.ma.MaskedArray, latitudes: np.ma.MaskedArray
 ) -> Tuple[float]:
     """Find the swath extents in the target CRS. First the perimeter points of
     unfilled valid pixels are found. These are then projected to the target
@@ -59,19 +59,17 @@ def get_extents_from_perimeter(
 def get_projected_coordinates(
     coordinates_mask: np.ma.core.MaskedArray,
     projection: Proj,
-    longitudes: Variable,
-    latitudes: Variable,
+    longitudes: np.ma.MaskedArray,
+    latitudes: np.ma.MaskedArray,
 ) -> Tuple[np.ndarray]:
     """Get the required coordinate points projected in the target Coordinate
     Reference System (CRS).
 
     """
     if len(longitudes.shape) == 1:
-        coordinates = get_all_coordinates(longitudes[:], latitudes[:], coordinates_mask)
+        coordinates = get_all_coordinates(longitudes, latitudes, coordinates_mask)
     else:
-        coordinates = get_perimeter_coordinates(
-            longitudes[:], latitudes[:], coordinates_mask
-        )
+        coordinates = get_perimeter_coordinates(longitudes, latitudes, coordinates_mask)
 
     return reproject_coordinates(coordinates, projection)
 
@@ -135,7 +133,7 @@ def get_absolute_resolution(polygon_area: float, n_pixels: int) -> float:
 
 
 def get_valid_coordinates_mask(
-    longitudes: Variable, latitudes: Variable
+    longitudes: np.ma.MaskedArray, latitudes: np.ma.MaskedArray
 ) -> np.ma.core.MaskedArray:
     """Get a `numpy` N-d array containing boolean values (0 or 1) indicating
     whether the elements of both longitude and latitude are valid at that

swath_projector/utilities.py

@@ -44,23 +44,25 @@ def get_variable_values(
         return make_array_two_dimensional(variable[:])
     elif 'time' in input_file.variables and 'time' in variable.dimensions:
         # Assumption: Array = (time, along-track, across-track)
-        return transpose_if_xdim_less_than_ydim(
-            variable[0][:].filled(fill_value=fill_value)
+        return transpose_if_xdim_less_than_ydim(variable[0][:]).filled(
+            fill_value=fill_value
         )
     else:
         # Assumption: Array = (along-track, across-track)
-        return transpose_if_xdim_less_than_ydim(
-            variable[:].filled(fill_value=fill_value)
+        return transpose_if_xdim_less_than_ydim(variable[:]).filled(
+            fill_value=fill_value
         )
 
 
 def get_coordinate_variable(
     dataset: Dataset, coordinates_tuple: Tuple[str], coordinate_substring
-) -> Optional[Variable]:
+) -> Optional[np.ma.MaskedArray]:
     """Search the coordinate dataset names for a match to the substring,
     which will be either "lat" or "lon". Return the corresponding variable
-    from the dataset. Only the base variable name is used, as the group
-    path may contain either of the strings as part of other words.
+    data from the dataset. Only the base variable name is used, as the group
+    path may contain either of the strings as part of other words. The
+    coordinate variables are transposed if the `along-track`dimension size is
+    less than the `across-track` dimension size.
 
     """
     for coordinate in coordinates_tuple:
@@ -69,9 +71,9 @@ def get_coordinate_variable(
         ):
             # QuickFix (DAS-2216) for short and wide swaths
             if dataset[coordinate].ndim == 1:
-                return dataset[coordinate]
+                return dataset[coordinate][:]
 
-            return transpose_if_xdim_less_than_ydim(dataset[coordinate])
+            return transpose_if_xdim_less_than_ydim(dataset[coordinate][:])
 
     raise MissingCoordinatesError(coordinates_tuple)
 
@@ -228,21 +230,19 @@ def make_array_two_dimensional(one_dimensional_array: np.ndarray) -> np.ndarray:
     return np.expand_dims(one_dimensional_array, 1)
 
 
-def transpose_if_xdim_less_than_ydim(variable: np.ndarray) -> np.ndarray:
+def transpose_if_xdim_less_than_ydim(
+    variable_values: np.ma.MaskedArray,
+) -> np.ma.MaskedArray:
     """Return transposed variable when variable is wider than tall.
 
     QuickFix (DAS-2216): We presume that a swath has more rows than columns and
     if that's not the case we transpose it so that it does.
     """
-    if variable.ndim != 2:
+    if len(variable_values.shape) != 2:
         raise ValueError(
-            f'Input variable must be 2 dimensional, but got {variable.ndim} dimensions.'
+            f'Input variable must be 2 dimensional, but got {len(variable_values.shape)} dimensions.'
         )
-    if variable.shape[0] < variable.shape[1]:
-        transposed_variable = np.ma.transpose(variable).copy()
-        if hasattr(variable, 'mask'):
-            transposed_variable.mask = np.ma.transpose(variable[:].mask)
+    if variable_values.shape[0] < variable_values.shape[1]:
+        return np.ma.transpose(variable_values).copy()
 
-        return transposed_variable
-
-    return variable
+    return variable_values

tests/unit/test_swath_geometry.py

@@ -65,8 +65,8 @@ def setUpClass(cls):
 
     def setUp(self):
         self.test_dataset = Dataset(self.test_path)
-        self.longitudes = self.test_dataset['lon']
-        self.latitudes = self.test_dataset['lat']
+        self.longitudes = self.test_dataset['lon'][:]
+        self.latitudes = self.test_dataset['lat'][:]
 
     def tearDown(self):
         self.test_dataset.close()
@@ -101,8 +101,8 @@ def test_get_projected_resolution_1d(self):
         """Ensure the calculated one-dimensional resolution is correct."""
         resolution = get_projected_resolution(
             self.geographic_projection,
-            self.test_dataset['lon_1d'],
-            self.test_dataset['lat_1d'],
+            self.test_dataset['lon_1d'][:],
+            self.test_dataset['lat_1d'][:],
         )
 
         self.assertAlmostEqual(resolution, 5.0)
@@ -167,9 +167,7 @@ def test_get_perimeter_coordinates(self):
             np.logical_not(valid_pixels), np.ones(self.longitudes.shape)
         )
 
-        coordinates = get_perimeter_coordinates(
-            self.longitudes[:], self.latitudes[:], mask
-        )
+        coordinates = get_perimeter_coordinates(self.longitudes, self.latitudes, mask)
 
         self.assertCountEqual(coordinates, expected_points)
 

tests/unit/test_utilities.py

@@ -138,7 +138,7 @@ def test_get_coordinate_variables(self):
                     dataset, coordinates_tuple, coordinate
                 )
 
-                self.assertIsInstance(coordinates, Variable)
+                self.assertIsInstance(coordinates, np.ma.MaskedArray)
 
         with self.subTest(
             'Non existent coordinate variable "latitude" returns MissingCoordinatesError'