parse_azfp now parses AZFP pressure data according to given matlab …

…code (#1189)

* added support for parsing azfp pressure data

* fixed failing ci tests

* Revert "fixed failing ci tests"

This reverts commit c378dc0.

* minor changes to tests

* Update test_convert_azfp.py

* Update echopype/tests/convert/test_convert_azfp.py

---------

Co-authored-by: Emilio Mayorga <emiliomayorga@gmail.com>

echopype/convert/parse_azfp.py

@@ -197,6 +197,25 @@ def _compute_battery(self, ping_num, battery_type):
 
         return N * USL5_BAT_CONSTANT
 
+    def _compute_pressure(self, ping_num, is_valid):
+        """
+        Compute pressure in decibar
+
+        Parameters
+        ----------
+        ping_num
+            ping number
+        is_valid
+            whether the associated parameters have valid values
+        """
+        if not is_valid or self.parameters["sensors_flag_pressure_sensor_installed"] == "no":
+            return np.nan
+
+        counts = self.unpacked_data["ancillary"][ping_num][3]
+        v_in = 2.5 * (counts / 65535)
+        P = v_in * self.parameters["a1"] + self.parameters["a0"] - 10.125
+        return P
+
     def parse_raw(self):
         """
         Parse raw data file from AZFP echosounder.
@@ -214,6 +233,7 @@ def _test_valid_params(params):
                 return True
 
         temperature_is_valid = _test_valid_params(["ka", "kb", "kc"])
+        pressure_is_valid = _test_valid_params(["a0", "a1"])
         tilt_x_is_valid = _test_valid_params(["X_a", "X_b", "X_c"])
         tilt_y_is_valid = _test_valid_params(["Y_a", "Y_b", "Y_c"])
 
@@ -235,6 +255,10 @@ def _test_valid_params(params):
                         self.unpacked_data["temperature"].append(
                             self._compute_temperature(ping_num, temperature_is_valid)
                         )
+                        # Compute pressure from unpacked_data[ii]['ancillary'][3]
+                        self.unpacked_data["pressure"].append(
+                            self._compute_pressure(ping_num, pressure_is_valid)
+                        )
                         # compute x tilt from unpacked_data[ii]['ancillary][0]
                         self.unpacked_data["tilt_x"].append(
                             self._compute_tilt(ping_num, "X", tilt_x_is_valid)

echopype/convert/set_groups_azfp.py

@@ -114,7 +114,16 @@ def set_env(self) -> xr.Dataset:
                         "standard_name": "sea_water_temperature",
                         "units": "deg_C",
                     },
-                )
+                ),
+                "pressure": (
+                    ["time1"],
+                    self.parser_obj.unpacked_data["pressure"],
+                    {
+                        "long_name": "Sea water pressure",
+                        "standard_name": "sea_water_pressure_due_to_sea_water",
+                        "units": "dbar",
+                    },
+                ),
             },
             coords={
                 "time1": (

echopype/tests/convert/test_convert_azfp.py

@@ -156,8 +156,8 @@ def test_convert_azfp_01a_different_ranges(azfp_path):
     check_platform_required_scalar_vars(echodata)
 
 
-def test_convert_azfp_01a_notemperature_notilt(azfp_path):
-    """Test converting file with no valid temperature or tilt data."""
+def test_convert_azfp_01a_no_temperature_pressure_tilt(azfp_path):
+    """Test converting file with no valid temperature, pressure and tilt data."""
     azfp_01a_path = azfp_path / 'rutgers_glider_notemperature/22052500.01A'
     azfp_xml_path = azfp_path / 'rutgers_glider_notemperature/22052501.XML'
 
@@ -169,13 +169,35 @@ def test_convert_azfp_01a_notemperature_notilt(azfp_path):
     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()
+
     # Tilt variables are present in the Platform group and their values are all nan
     assert "tilt_x" in echodata["Platform"]
     assert "tilt_y" in echodata["Platform"]
     assert echodata["Platform"]["tilt_x"].isnull().all()
     assert echodata["Platform"]["tilt_y"].isnull().all()
 
 
+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'
+
+    echodata = open_raw(
+        raw_file=azfp_01a_path, sonar_model='AZFP', xml_path=azfp_xml_path
+    )
+
+    # Pressure variable is present in the Environment group and its values are not all nan
+    assert "pressure" in echodata["Environment"]
+    assert not echodata["Environment"]["pressure"].isnull().all()
+
+    # Temperature variable is present in the Environment group and its values are not all nan
+    assert "temperature" in echodata["Environment"]
+    assert not echodata["Environment"]["temperature"].isnull().all()
+
+
 def test_load_parse_azfp_xml(azfp_path):
 
     azfp_xml_path = azfp_path / '23081211.XML'