Set EK60/80 Platform and NMEA nan timestamp to first ping_time value [all tests ci]

echopype/convert/set_groups_azfp.py

@@ -158,15 +158,22 @@ def set_platform(self) -> xr.Dataset:
         """Set the Platform group."""
         platform_dict = {"platform_name": "", "platform_type": "", "platform_code_ICES": ""}
         unpacked_data = self.parser_obj.unpacked_data
-        time2 = self.parser_obj.ping_time
-        time1 = [time2[0]]
+
+        # Create nan time coordinate for lat/lon (lat/lon do not exist in AZFP 01A data)
+        time1 = [np.nan]
 
         # If tilt_x and/or tilt_y are all nan, create single-value time2 dimension
         # and single-value (np.nan) tilt_x and tilt_y
         tilt_x = [np.nan] if np.isnan(unpacked_data["tilt_x"]).all() else unpacked_data["tilt_x"]
         tilt_y = [np.nan] if np.isnan(unpacked_data["tilt_y"]).all() else unpacked_data["tilt_y"]
         if (len(tilt_x) == 1 and np.isnan(tilt_x)) and (len(tilt_y) == 1 and np.isnan(tilt_y)):
-            time2 = [time2[0]]
+            time2 = [self.parser_obj.ping_time[0]]
+        else:
+            time2 = self.parser_obj.ping_time
+
+        # Handle potential nan timestamp for time1 and time2
+        time1 = self._nan_timestamp_handler(time1)
+        time2 = self._nan_timestamp_handler(time2)  # should not be nan; but add for completeness
 
         ds = xr.Dataset(
             {

echopype/convert/set_groups_base.py

@@ -112,6 +112,23 @@ def set_platform(self) -> xr.Dataset:
         """Set the Platform group."""
         raise NotImplementedError
 
+    def _nan_timestamp_handler(self, time_val) -> List:
+        """
+        Replace nan in time coordinate to avoid xarray warning.
+        """
+        if len(time_val) == 1 and np.isnan(time_val[0]):
+            # set time_val to earliest ping_time among all channels
+            if self.sonar_model in ["EK60", "ES70", "EK80", "ES80", "EA640"]:
+                return [np.array([v[0] for v in self.parser_obj.ping_time.values()]).min()]
+            elif self.sonar_model == "AZFP":
+                return [self.parser_obj.ping_time[0]]
+            else:
+                return NotImplementedError(
+                    f"Nan timestamp handling has not been implemented for {self.sonar_model}!"
+                )
+        else:
+            return time_val
+
     def set_nmea(self) -> xr.Dataset:
         """Set the Platform/NMEA group."""
         # Save nan if nmea data is not encoded in the raw file
@@ -126,6 +143,9 @@ def set_nmea(self) -> xr.Dataset:
             time = [np.nan]
             raw_nmea = [np.nan]
 
+        # Handle potential nan timestamp for time
+        time = self._nan_timestamp_handler(time)
+
         ds = xr.Dataset(
             {
                 "NMEA_datagram": (

echopype/convert/set_groups_ek60.py

@@ -176,9 +176,14 @@ def set_platform(self) -> xr.Dataset:
 
         # NMEA dataset: variables filled with np.nan if they do not exist
         platform_dict = {"platform_name": "", "platform_type": "", "platform_code_ICES": ""}
-        # Values for the variables below having a channel (ch) dependence
+
+        # Values for the variables in ds below having a channel (ch) dependence
         # are identical across channels
         ch = list(self.sorted_channel.keys())[0]
+
+        # Handle potential nan timestamp for time1 and time2
+        time1 = self._nan_timestamp_handler(time1)
+
         ds = xr.Dataset(
             {
                 "latitude": (

echopype/convert/set_groups_ek80.py

@@ -310,6 +310,10 @@ def set_platform(self) -> xr.Dataset:
         time2 = self.parser_obj.mru.get("timestamp", None)
         time2 = np.array(time2) if time2 is not None else [np.nan]
 
+        # Handle potential nan timestamp for time1 and time2
+        time1 = self._nan_timestamp_handler(time1)
+        time2 = self._nan_timestamp_handler(time2)
+
         # Assemble variables into a dataset: variables filled with nan if do not exist
         platform_dict = {"platform_name": "", "platform_type": "", "platform_code_ICES": ""}
         ds = xr.Dataset(