Ensure env_params intake for calibration

echopype/calibrate/cal_params.py

@@ -49,10 +49,6 @@
 }
 
 
-# TODO: need a function (something like "_check_param_freq_dep")
-# to check user input cal_params and env_params
-
-
 def param2da(p_val: Union[int, float, list], channel: Union[list, xr.DataArray]) -> xr.DataArray:
     """
     Organize individual parameter in scalar or list to xr.DataArray with channel coordinate.
@@ -88,7 +84,7 @@ def param2da(p_val: Union[int, float, list], channel: Union[list, xr.DataArray])
 
 def sanitize_user_cal_dict(
     sonar_type: Literal["EK60", "EK80", "AZFP"],
-    user_dict: Dict[str, Union[int, float, xr.DataArray]],
+    user_dict: Dict[str, Union[int, float, list, xr.DataArray]],
     channel: Union[List, xr.DataArray],
 ) -> Dict[str, Union[int, float, xr.DataArray]]:
     """
@@ -126,7 +122,7 @@ def sanitize_user_cal_dict(
 
     # Screen parameters: only retain those defined in CAL_PARAMS
     #  -- transform params in scalar or list to xr.DataArray
-    #  -- directly pass through those that are xr.DataArray
+    #  -- directly pass through those that are xr.DataArray and pass the check for coordinates
     out_dict = dict.fromkeys(CAL_PARAMS[sonar_type])
     for p_name, p_val in user_dict.items():
         if p_name in out_dict:

echopype/calibrate/calibrate_azfp.py

@@ -15,7 +15,7 @@ def __init__(self, echodata: EchoData, env_params=None, cal_params=None, **kwarg
         self.sonar_type = "AZFP"
 
         # load env and cal parameters
-        self.env_params = get_env_params_AZFP(echodata=self.echodata, user_env_dict=self.env_params)
+        self.env_params = get_env_params_AZFP(echodata=self.echodata, user_dict=self.env_params)
         self.cal_params = get_cal_params_AZFP(
             beam=self.echodata["Sonar/Beam_group1"],
             vend=self.echodata["Vendor_specific"],

echopype/calibrate/calibrate_ek.py

@@ -9,7 +9,7 @@
 from .cal_params import get_cal_params_EK
 from .calibrate_base import CalibrateBase
 from .ek80_complex import compress_pulse, get_filter_coeff, get_tau_effective, get_transmit_signal
-from .env_params import get_env_params_EK60, get_env_params_EK80
+from .env_params import get_env_params_EK
 from .range import compute_range_EK, range_mod_TVG_EK
 
 logger = _init_logger(__name__)
@@ -130,22 +130,27 @@ class CalibrateEK60(CalibrateEK):
     def __init__(self, echodata, env_params, cal_params, **kwargs):
         super().__init__(echodata, env_params, cal_params)
 
-        # Set sonar_type
+        # Set sonar_type and waveform/encode mode
         self.sonar_type = "EK60"
-
-        # Get env_params
-        self.env_params = get_env_params_EK60(echodata=echodata, user_env_dict=self.env_params)
         self.waveform_mode = "CW"
         self.encode_mode = "power"
 
-        # Compute range
-        self.compute_echo_range()
-
         # Get the right ed_group for CW power samples
         self.ed_group = retrieve_correct_beam_group(
             echodata=self.echodata, waveform_mode=self.waveform_mode, encode_mode=self.encode_mode
         )
 
+        # Get env_params
+        self.env_params = get_env_params_EK(
+            sonar_type=self.sonar_type,
+            beam=self.echodata[self.ed_group],
+            env=self.echodata["Environment"],
+            user_dict=self.env_params,
+        )
+
+        # Compute range
+        self.compute_echo_range()
+
         # Set the channels to calibrate
         # For EK60 this is all channels
         self.chan_sel = self.echodata[self.ed_group]["channel"]
@@ -226,11 +231,12 @@ def __init__(self, echodata, env_params, cal_params, waveform_mode, encode_mode)
             self.freq_center = beam["frequency_nominal"].sel(channel=self.chan_sel)
 
         # Get env_params: depends on waveform mode
-        self.env_params = get_env_params_EK80(
-            echodata=echodata,
+        self.env_params = get_env_params_EK(
+            sonar_type=self.sonar_type,
+            beam=beam,
+            env=self.echodata["Environment"],
+            user_dict=self.env_params,
             freq=self.freq_center,
-            user_env_dict=env_params,
-            ed_group=self.ed_group,
         )
 
         # Get cal_params: depends on waveform and encode mode