From 90d36305971b8ffb3ed1e561ec378b2ca301cd5a Mon Sep 17 00:00:00 2001
From: Wu-Jung Lee <leewujung@gmail.com>
Date: Wed, 5 Jul 2023 15:41:47 -0700
Subject: [PATCH] Handling problematic NMEA messages when setting lat/lon in
 Platform group (#1067)

* add handling of problematic NMEA strings

* fix bug re no lat/lon scenario

* add warning for problematic lat/lon entry

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* fix dimension mismatches

* remove conversion to numpy array for msg_type

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>
---
 echopype/convert/set_groups_base.py | 34 +++++++++++++++++++----------
 1 file changed, 23 insertions(+), 11 deletions(-)

diff --git a/echopype/convert/set_groups_base.py b/echopype/convert/set_groups_base.py
index 7c520d17b..f2144c268 100644
--- a/echopype/convert/set_groups_base.py
+++ b/echopype/convert/set_groups_base.py
@@ -1,4 +1,5 @@
 import abc
+import warnings
 from typing import List, Set, Tuple
 
 import dask.array
@@ -173,18 +174,29 @@ def _extract_NMEA_latlon(self):
                 pynmea2.ParseError,
             ):
                 nmea_msg.append(None)
-        lat = (
-            np.array([x.latitude if hasattr(x, "latitude") else np.nan for x in nmea_msg])
-            if nmea_msg
-            else [np.nan]
-        )
-        lon = (
-            np.array([x.longitude if hasattr(x, "longitude") else np.nan for x in nmea_msg])
-            if nmea_msg
-            else [np.nan]
-        )
+        if nmea_msg:
+            lat, lon = [], []
+            for x in nmea_msg:
+                try:
+                    lat.append(x.latitude if hasattr(x, "latitude") else np.nan)
+                except ValueError as ve:
+                    lat.append(np.nan)
+                    warnings.warn(
+                        "At least one latitude entry is problematic and "
+                        f"are assigned None in the converted data: {str(ve)}"
+                    )
+                try:
+                    lon.append(x.longitude if hasattr(x, "longitude") else np.nan)
+                except ValueError as ve:
+                    lon.append(np.nan)
+                    warnings.warn(
+                        f"At least one longitude entry is problematic and "
+                        f"are assigned None in the converted data: {str(ve)}"
+                    )
+        else:
+            lat, lon = [np.nan], [np.nan]
         msg_type = (
-            np.array([x.sentence_type if hasattr(x, "sentence_type") else np.nan for x in nmea_msg])
+            [x.sentence_type if hasattr(x, "sentence_type") else np.nan for x in nmea_msg]
             if nmea_msg
             else [np.nan]
         )