Mhs/das 2216/quick fixes

CHANGELOG.md

@@ -1,6 +1,14 @@
 # Changelog
 
+## [v1.2.0] - 2024-10-10
+
+### 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. 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
+
 ### Changed
 
 - [[TRT-558](https://bugs.earthdata.nasa.gov/browse/TRT-558)]
@@ -12,6 +20,7 @@
   also been renamed to `earthdata_varinfo_config.json`.
 
 ## [v1.1.0] - 2024-08-29
+
 ### Changed
 
 - [[DAS-1934](https://bugs.earthdata.nasa.gov/browse/DAS-1934)]
@@ -37,14 +46,15 @@ include updated documentation and files outlined by the
 
 Repository structure changes include:
 
-* Migrating `pymods` directory to `swath_projector`.
-* Migrating `swotrepr.py` to `swath_projector/adapter.py`.
-* Addition of `swath_projector/main.py`.
+- Migrating `pymods` directory to `swath_projector`.
+- Migrating `swotrepr.py` to `swath_projector/adapter.py`.
+- Addition of `swath_projector/main.py`.
 
 For more information on internal releases prior to NASA open-source approval,
 see legacy-CHANGELOG.md.
 
-[v1.1.1]:(https://github.com/nasa/harmony-swath-projector/releases/tag/1.1.0)
-[v1.1.0]:(https://github.com/nasa/harmony-swath-projector/releases/tag/1.0.1)
-[v1.0.1]:(https://github.com/nasa/harmony-swath-projector/releases/tag/1.0.1)
-[v1.0.0]:(https://github.com/nasa/harmony-swath-projector/releases/tag/1.0.0)
+[v1.2.0]: (https://github.com/nasa/harmony-swath-projector/releases/tag/1.2.0)
+[v1.1.1]: (https://github.com/nasa/harmony-swath-projector/releases/tag/1.1.1)
+[v1.1.0]: (https://github.com/nasa/harmony-swath-projector/releases/tag/1.1.0)
+[v1.0.1]: (https://github.com/nasa/harmony-swath-projector/releases/tag/1.0.1)
+[v1.0.0]: (https://github.com/nasa/harmony-swath-projector/releases/tag/1.0.0)

bin/project_local_granule.py

@@ -125,8 +125,8 @@ def project_granule(
                         {
                             'url': local_file_path,
                             'temporal': {
-                                'start': '2021-01-03T23:45:00.000Z',
-                                'end': '2020-01-04T00:00:00.000Z',
+                                'start': '2020-01-03T23:45:00.000Z',
+                                'end': '2025-01-04T00:00:00.000Z',
                             },
                             'bbox': [-180, -90, 180, 90],
                         }
@@ -141,5 +141,5 @@ def project_granule(
 
     reprojector = SwathProjectorAdapter(message, config=config(False))
 
-    with patch('swotrepr.shutil.rmtree', side_effect=rmtree_side_effect):
+    with patch('swath_projector.adapter.shutil.rmtree', side_effect=rmtree_side_effect):
         reprojector.invoke()

docker/service_version.txt

@@ -1 +1 @@
-1.1.1
+1.2.0

swath_projector/earthdata_varinfo_config.json

@@ -1,12 +1,35 @@
 {
   "Identification": "Swath Projector VarInfo configuration",
-  "Version": 3,
+  "Version": 4,
   "CollectionShortNamePath": [
-    "ShortName"
+    "ShortName",
+    "collection_shortname"
   ],
   "Mission": {
-    "VNP10": "VIIRS"
+    "VNP10": "VIIRS",
+    "TEMPO_O3TOT_L2": "TEMPO"
   },
+  "ExcludedScienceVariables": [
+    {
+      "Applicability": {
+        "Mission": "TEMPO",
+        "ShortNamePath": "TEMPO_O3TOT_L2"
+      },
+      "VariablePattern": [
+        "/support_data/a_priori_layer_o3",
+        "/support_data/cal_adjustment",
+        "/support_data/dNdR",
+        "/support_data/layer_efficiency",
+        "/support_data/lut_wavelength",
+        "/support_data/N_value",
+        "/support_data/N_value_residual",
+        "/support_data/ozone_sensitivity_ratio",
+        "/support_data/step_1_N_value_residual",
+        "/support_data/step_2_N_value_residual",
+        "/support_data/temp_sensitivity_ratio"
+      ]
+    }
+  ],
   "MetadataOverrides": [
     {
       "Applicability": {
@@ -21,6 +44,20 @@
         }
       ],
       "_Description": "VNP10 SnowData variables have incorrect relative paths for coordinates."
+    },
+    {
+      "Applicability": {
+        "Mission": "TEMPO",
+        "ShortNamePath": "TEMPO_O3TOT_L2",
+        "VariablePattern": "^/product/.*|^/support_data/.*"
+      },
+      "Attributes": [
+        {
+          "Name": "coordinates",
+          "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. Some variables in these groups are excluded via 'ExcludedScienceVariables'"
     }
   ]
 }

swath_projector/interpolation.py

@@ -268,6 +268,7 @@ def get_ewa_results(
         ewa_information['target_area'],
         variable['values'],
         maximum_weight_mode=maximum_weight_mode,
+        rows_per_scan=2,  # Added in QuickFix DAS-2216 to be fixed in DAS-2220
     )
 
     if variable['fill_value'] is not None:

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

@@ -31,7 +31,8 @@ def get_variable_values(
     As the variable data are returned as a `numpy.ma.MaskedArray`, the will
     return no data in the filled pixels. To ensure that the data are
     correctly handled, the fill value is applied to masked pixels using the
-    `filled` method.
+    `filled` method. The variable values are transposed if the `along-track`
+    dimension size is less than the `across-track` dimension size.
 
     """
     # TODO: Remove in favour of apply2D or process_subdimension.
@@ -42,27 +43,38 @@ def get_variable_values(
     if len(variable[:].shape) == 1:
         return make_array_two_dimensional(variable[:])
     elif 'time' in input_file.variables and 'time' in variable.dimensions:
-        # Assumption: Array = (1, y, x)
-        return variable[0][:].filled(fill_value=fill_value)
+        # Assumption: Array = (time, along-track, across-track)
+        return transpose_if_xdim_less_than_ydim(variable[0][:]).filled(
+            fill_value=fill_value
+        )
     else:
-        # Assumption: Array = (y, x)
-        return variable[:].filled(fill_value=fill_value)
+        # Assumption: Array = (along-track, across-track)
+        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:
         if coordinate_substring in coordinate.split('/')[-1] and variable_in_dataset(
             coordinate, dataset
         ):
-            return dataset[coordinate]
+            # QuickFix (DAS-2216) for short and wide swaths
+            if dataset[coordinate].ndim == 1:
+                return dataset[coordinate][:]
+
+            return transpose_if_xdim_less_than_ydim(dataset[coordinate][:])
+
     raise MissingCoordinatesError(coordinates_tuple)
 
 
@@ -216,3 +228,21 @@ 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_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 len(variable_values.shape) != 2:
+        raise ValueError(
+            f'Input variable must be 2 dimensional, but got {len(variable_values.shape)} dimensions.'
+        )
+    if variable_values.shape[0] < variable_values.shape[1]:
+        return np.ma.transpose(variable_values).copy()
+
+    return variable_values

tests/unit/test_interpolation.py

@@ -384,6 +384,7 @@ def test_resample_ewa(
                 self.mock_target_area,
                 mock_values,
                 maximum_weight_mode=False,
+                rows_per_scan=2,  # Added in QuickFix DAS-2216 to be fixed in DAS-2220
             )
             mock_write_output.assert_called_once_with(
                 self.mock_target_area,
@@ -423,6 +424,7 @@ def test_resample_ewa(
                 self.mock_target_area,
                 mock_values,
                 maximum_weight_mode=False,
+                rows_per_scan=2,  # Added in QuickFix DAS-2216 to be fixed in DAS-2220
             )
             mock_write_output.assert_called_once_with(
                 self.mock_target_area,
@@ -491,6 +493,7 @@ def test_resample_ewa_nn(
                 self.mock_target_area,
                 mock_values,
                 maximum_weight_mode=True,
+                rows_per_scan=2,  # Added in QuickFix DAS-2216 to be fixed in DAS-2220
             )
             mock_write_output.assert_called_once_with(
                 self.mock_target_area,
@@ -530,6 +533,7 @@ def test_resample_ewa_nn(
                 self.mock_target_area,
                 mock_values,
                 maximum_weight_mode=True,
+                rows_per_scan=2,  # Added in QuickFix DAS-2216 to be fixed in DAS-2220
             )
             mock_write_output.assert_called_once_with(
                 self.mock_target_area,
@@ -581,6 +585,7 @@ def test_resample_ewa_nn(
                 harmony_target_area,
                 mock_values,
                 maximum_weight_mode=True,
+                rows_per_scan=2,  # Added in QuickFix DAS-2216 to be fixed in DAS-2220
             )
 
             # The Harmony target area should be given to the output function

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)