For AZFP Env group, create temperature and pressure only if they have…

… valid data; add missing mandatory absorption_indicative & sound_speed_indicative vars (currently all nan); and update tests (#1226)
OSOceanAcoustics · Nov 20, 2023 · 31e35f7 · 31e35f7
1 parent 3335cae
commit 31e35f7
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Showing 2 changed files with 76 additions and 35 deletions.
diff --git a/echopype/convert/set_groups_azfp.py b/echopype/convert/set_groups_azfp.py
@@ -101,44 +101,90 @@ def _create_unique_channel_name(self):
 
     def set_env(self) -> xr.Dataset:
         """Set the Environment group."""
-        # TODO Look at why this cannot be encoded without the modifications
-        # @ngkavin: what modification?
-        ping_time = self.parser_obj.ping_time
+
+        # Mandatory variables
         ds = xr.Dataset(
             {
-                "temperature": (
-                    ["time1"],
-                    self.parser_obj.unpacked_data["temperature"],
+                "absorption_indicative": (
+                    ["channel"],
+                    [np.nan] * len(self.channel_ids_sorted),
                     {
-                        "long_name": "Water temperature",
-                        "standard_name": "sea_water_temperature",
-                        "units": "deg_C",
+                        "long_name": "Indicative acoustic absorption",
+                        "units": "dB/m",
+                        "valid_min": 0.0,
                     },
                 ),
-                "pressure": (
-                    ["time1"],
-                    self.parser_obj.unpacked_data["pressure"],
+                "sound_speed_indicative": (
+                    [],
+                    np.nan,
                     {
-                        "long_name": "Sea water pressure",
-                        "standard_name": "sea_water_pressure_due_to_sea_water",
-                        "units": "dbar",
+                        "long_name": "Indicative sound speed",
+                        "standard_name": "speed_of_sound_in_sea_water",
+                        "units": "m/s",
+                        "valid_min": 0.0,
                     },
                 ),
-            },
-            coords={
-                "time1": (
-                    ["time1"],
-                    ping_time,
+                "frequency_nominal": (
+                    ["channel"],
+                    self.freq_sorted,
                     {
-                        "axis": "T",
-                        "long_name": "Timestamp of each ping",
-                        "standard_name": "time",
-                        "comment": "Time coordinate corresponding to environmental variables.",
+                        "units": "Hz",
+                        "long_name": "Transducer frequency",
+                        "valid_min": 0.0,
+                        "standard_name": "sound_frequency",
                     },
-                )
+                ),
+            },
+            coords={
+                "channel": (
+                    ["channel"],
+                    self.channel_ids_sorted,
+                    self._varattrs["beam_coord_default"]["channel"],
+                ),
             },
         )
 
+        # Additional variables, if present
+        temp_press = dict()
+        if not np.isnan(self.parser_obj.unpacked_data["temperature"]).all():
+            temp_press["temperature"] = (
+                ["time1"],
+                self.parser_obj.unpacked_data["temperature"],
+                {
+                    "long_name": "Water temperature",
+                    "standard_name": "sea_water_temperature",
+                    "units": "deg_C",
+                },
+            )
+        if not np.isnan(self.parser_obj.unpacked_data["pressure"]).all():
+            temp_press["pressure"] = (
+                ["time1"],
+                self.parser_obj.unpacked_data["pressure"],
+                {
+                    "long_name": "Sea water pressure",
+                    "standard_name": "sea_water_pressure_due_to_sea_water",
+                    "units": "dbar",
+                },
+            )
+
+        if len(temp_press) > 0:
+            ds_temp_press = xr.Dataset(
+                temp_press,
+                coords={
+                    "time1": (
+                        ["time1"],
+                        self.parser_obj.ping_time,
+                        {
+                            "axis": "T",
+                            "long_name": "Timestamp of each ping",
+                            "standard_name": "time",
+                            "comment": "Time coordinate corresponding to environmental variables.",
+                        },
+                    )
+                },
+            )
+            ds = xr.merge([ds, ds_temp_press], combine_attrs="override")
+
         return set_time_encodings(ds)
 
     def set_sonar(self) -> xr.Dataset:

diff --git a/echopype/tests/convert/test_convert_azfp.py b/echopype/tests/convert/test_convert_azfp.py
@@ -165,13 +165,9 @@ def test_convert_azfp_01a_no_temperature_pressure_tilt(azfp_path):
         raw_file=azfp_01a_path, sonar_model='AZFP', xml_path=azfp_xml_path
     )
 
-    # Temperature variable is present in the Environment group and its values are all nan
-    assert "temperature" in echodata["Environment"]
-    assert echodata["Environment"]["temperature"].isnull().all()
-
-    # Pressure variable is present in the Environment group and its values are all nan
-    assert "pressure" in echodata["Environment"]
-    assert echodata["Environment"]["pressure"].isnull().all()
+    # Temperature and pressure variables are not present in the Environment group
+    assert "temperature" not in echodata["Environment"]
+    assert "pressure" not in echodata["Environment"]
 
     # Tilt variables are present in the Platform group and their values are all nan
     assert "tilt_x" in echodata["Platform"]
@@ -182,8 +178,8 @@ def test_convert_azfp_01a_no_temperature_pressure_tilt(azfp_path):
 
 def test_convert_azfp_01a_pressure_temperature(azfp_path):
     """Test converting file with valid pressure and temperature data."""
-    azfp_01a_path = azfp_path / 'pressure' / '22042221.01A'
-    azfp_xml_path = azfp_path / 'pressure' / '22042220.XML'
+    azfp_01a_path = azfp_path / 'pressure/22042221.01A'
+    azfp_xml_path = azfp_path / 'pressure/22042220.XML'
 
     echodata = open_raw(
         raw_file=azfp_01a_path, sonar_model='AZFP', xml_path=azfp_xml_path
@@ -199,7 +195,6 @@ def test_convert_azfp_01a_pressure_temperature(azfp_path):
 
 
 def test_load_parse_azfp_xml(azfp_path):
-
     azfp_xml_path = azfp_path / '23081211.XML'
     parseAZFP = ParseAZFP(None, str(azfp_xml_path))
     parseAZFP.load_AZFP_xml()