Fixes for problems found processing brizo for sep2025.

.vscode/launch.json

@@ -60,7 +60,7 @@
             //"args": ["-v", "2", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109.nc4"]
             //"args": ["-v", "2", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109.nc4", "--plot_time", "/longitude_time"]
             //"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109.nc4", "--plot_universals"]
-            "args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109.nc4", "--plot_time", "/latitude_time"]
+            //"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109.nc4", "--plot_time", "/latitude_time"]
             // brizo 20250916T230652 has several ESP Samples from stoqs_lrauv_sep2025
             //"args": ["-v", "2", "--log_file", "brizo/missionlogs/2025/20250916_20250922/20250916T230652/202509162306_202509180305.nc4", "--plot_time", "/longitude_time"]
             //"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109_cleaned_by_quinn.nc4", "--plot_time", "/longitude_time"]
@@ -69,6 +69,9 @@
             //"args": ["-v", "1", "--log_file", "tethys/missionlogs/2012/20120908_20120920/20120917T025522/201209170255_201209171110.nc4", "--plot_time", "/longitude_time"]
             // Single spike in longitude_time
             //"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109.nc4", "--plot_time", "/NAL9602/longitude_fix_time"]
+            // Fails in nudge_positions - bad time removed by outlier detection, then that index re-appears in longitude_fix_time
+            //"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250911T073640/202509110736_202509120809.nc4", "--plot_universals"]
+            "args": ["-v", "2", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250911T073640/202509110736_202509120809.nc4", "--plot_time", "/NAL9602/longitude_fix_time"]
         },
         {
             "name": "2.0 - calibrate.py",
@@ -125,11 +128,13 @@
             "program": "${workspaceFolder}/src/data/combine.py",
             "console": "integratedTerminal",
             "justMyCode": false,
-            "args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109.nc4", "--plot"]
+            //"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109.nc4", "--plot"]
             //"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250916_20250922/20250916T230652/202509162306_202509180305.nc4", "--plot"]
             //"args": ["-v", "1", "--log_file", "tethys/missionlogs/2012/20120908_20120920/20120909T010636/201209090106_201209091521.nc4", "--plot"]
             // Conflicting sizes for nudged_time and data - fixed by filtering GPS fixes to be monotonically increasing
             //"args": ["-v", "1", "--log_file", "tethys/missionlogs/2012/20120908_20120920/20120917T025522/201209170255_201209171110.nc4", "--plot"]
+            // Fails in nudge_positions, maybe bad GPS data?
+            "args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250911T073640/202509110736_202509120809.nc4", "--plot"]
 
         },
         {
@@ -348,7 +353,7 @@
             // Lots bad time values in brizo 20250914T080941 due to memory corruption on the vehicle
             //"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109.nc4"]
             //"args": ["-v", "2", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109.nc4", "--clobber"]
-            "args": ["-v", "2", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109.nc4", "--clobber", "--no_cleanup"]
+            //"args": ["-v", "2", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109.nc4", "--clobber", "--no_cleanup"]
             //"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250916_20250922/20250916T230652/202509162306_202509180305.nc4", "--no_cleanup"]
             //"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250916_20250922/20250916T230652/202509162306_202509180305.nc4", "--no_cleanup", "--clobber"]
             // Has different universals time coodinates for longitude/latitude and depth
@@ -366,6 +371,12 @@
             //"args": ["-v", "1", "--auv_name", "pontus", "--start", "20250601T000000", "--end", "20250721T000000", "--noinput", "--num_cores", "1", "--no_cleanup"]
             //"args": ["-v", "1", "--auv_name", "pontus", "--start", "20250601T000000", "--end", "20250702T000000", "--noinput", "--num_cores", "1", "--no_cleanup", "--clobber"]
             //"args": ["-v", "1", "--log_file", "pontus/missionlogs/2025/20250623_20250707/20250707T043011/slate.nc4", "--no_cleanup"]
+            //"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250903_20250903/20250903T202626/202509032026_202509032030.nc4", "--no_cleanup"]
+            // Does not have ctdseabird data, hence no coordinates for resampling
+            //"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250903_20250903/20250903T202626/202509032026_202509032030.nc4", "--no_cleanup"]
+            // Fails in nudge_positions, maybe bad GPS data?
+            //"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250911T073640/202509110736_202509120809.nc4", "--no_cleanup"]
+            "args": ["-v", "1", "--auv_name", "brizo", "--start", "20250901T000000", "--end", "20251001T000000", "--noinput", "--num_cores", "1", "--no_cleanup"]
         },
 
     ]

src/data/align.py

@@ -568,66 +568,67 @@ def process_combined(self) -> Path:  # noqa: C901, PLR0912, PLR0915
                 np.mean(np.diff(self.combined_nc[timevar])) / np.timedelta64(1, "s")
             )
 
-            time_coord = variable_time_coord_mapping.get(variable)
-            depth_coord = (
-                time_coord[:-5] + "_depth"
-                if time_coord and time_coord.endswith("_time")
-                else f"{group_name}_depth"
-            )
-            lat_coord = (
-                time_coord[:-5] + "_latitude"
-                if time_coord and time_coord.endswith("_time")
-                else f"{group_name}_latitude"
-            )
-            lon_coord = (
-                time_coord[:-5] + "_longitude"
-                if time_coord and time_coord.endswith("_time")
-                else f"{group_name}_longitude"
-            )
-
-            # Add interpolated depth, latitude, and longitude variables
-            if depth_coord in self.combined_nc:
-                self.aligned_nc[depth_coord].attrs = self.combined_nc[depth_coord].attrs
-            self.aligned_nc[depth_coord] = xr.DataArray(
-                depth_interp(var_time).astype(np.float64).tolist(),
-                dims={timevar},
-                coords=[self.combined_nc[variable].get_index(timevar)],
-                name=depth_coord,
-            )
-            self.aligned_nc[depth_coord].attrs["long_name"] = "Depth"
-            self.aligned_nc[depth_coord].attrs["comment"] = "depth from Group_Universals.nc"
+            # Determine coordinate variable names based on group
+            depth_coord = f"{group_name}_depth"
+            lat_coord = f"{group_name}_latitude"
+            lon_coord = f"{group_name}_longitude"
+
             TINY_SAMPLE_RATE = 10e-2
-            self.aligned_nc[depth_coord].attrs["instrument_sample_rate_hz"] = (
+            sample_rate_str = (
                 f"{sample_rate:.2f}" if sample_rate > TINY_SAMPLE_RATE else f"{sample_rate:.6f}"
             )
 
-            self.aligned_nc[lat_coord] = xr.DataArray(
-                lat_interp(var_time).astype(np.float64).tolist(),
-                dims={timevar},
-                coords=[self.combined_nc[variable].get_index(timevar)],
-                name=lat_coord,
-            )
-            self.aligned_nc[lat_coord].attrs = self.combined_nc["nudged_latitude"].attrs
-            self.aligned_nc[lat_coord].attrs["comment"] += (
-                f". Variable nudged_latitude linearly"
-                f" interpolated onto {variable.split('_')[0]} time values."
-            )
-            self.aligned_nc[lat_coord].attrs["long_name"] = "Latitude"
-            self.aligned_nc[lat_coord].attrs["instrument_sample_rate_hz"] = sample_rate
-
-            self.aligned_nc[lon_coord] = xr.DataArray(
-                lon_interp(var_time).astype(np.float64).tolist(),
-                dims={timevar},
-                coords=[self.combined_nc[variable].get_index(timevar)],
-                name=lon_coord,
-            )
-            self.aligned_nc[lon_coord].attrs = self.combined_nc["nudged_longitude"].attrs
-            self.aligned_nc[lon_coord].attrs["comment"] += (
-                f". Variable nudged_longitude linearly"
-                f" interpolated onto {variable.split('_')[0]} time values."
-            )
-            self.aligned_nc[lon_coord].attrs["long_name"] = "Longitude"
-            self.aligned_nc[lon_coord].attrs["instrument_sample_rate_hz"] = sample_rate
+            # Create depth coordinate - only if not already created for this group
+            if depth_coord not in self.aligned_nc:
+                self.aligned_nc[depth_coord] = xr.DataArray(
+                    depth_interp(var_time).astype(np.float64).tolist(),
+                    dims={timevar},
+                    coords=[self.combined_nc[variable].get_index(timevar)],
+                    name=depth_coord,
+                )
+                # Copy attributes from combined_nc if they exist - ensusre proper standard_name
+                if depth_coord in self.combined_nc:
+                    self.aligned_nc[depth_coord].attrs = self.combined_nc[depth_coord].attrs.copy()
+                self.aligned_nc[depth_coord].attrs["long_name"] = "Depth"
+                self.aligned_nc[depth_coord].attrs["standard_name"] = "depth"
+                self.aligned_nc[depth_coord].attrs["comment"] = "depth from Group_Universals.nc"
+                self.aligned_nc[depth_coord].attrs["instrument_sample_rate_hz"] = sample_rate_str
+
+            # Create latitude coordinate - only if not already created for this group
+            if lat_coord not in self.aligned_nc:
+                self.aligned_nc[lat_coord] = xr.DataArray(
+                    lat_interp(var_time).astype(np.float64).tolist(),
+                    dims={timevar},
+                    coords=[self.combined_nc[variable].get_index(timevar)],
+                    name=lat_coord,
+                )
+                self.aligned_nc[lat_coord].attrs = self.combined_nc["nudged_latitude"].attrs.copy()
+                self.aligned_nc[lat_coord].attrs["comment"] += (
+                    f". Variable nudged_latitude linearly"
+                    f" interpolated onto {group_name} time values."
+                )
+                # Ensure proper standard_name
+                self.aligned_nc[lat_coord].attrs["long_name"] = "Latitude"
+                self.aligned_nc[lat_coord].attrs["standard_name"] = "latitude"
+                self.aligned_nc[lat_coord].attrs["instrument_sample_rate_hz"] = sample_rate_str
+
+            # Create longitude coordinate - only if not already created for this group
+            if lon_coord not in self.aligned_nc:
+                self.aligned_nc[lon_coord] = xr.DataArray(
+                    lon_interp(var_time).astype(np.float64).tolist(),
+                    dims={timevar},
+                    coords=[self.combined_nc[variable].get_index(timevar)],
+                    name=lon_coord,
+                )
+                self.aligned_nc[lon_coord].attrs = self.combined_nc["nudged_longitude"].attrs.copy()
+                self.aligned_nc[lon_coord].attrs["comment"] += (
+                    f". Variable nudged_longitude linearly"
+                    f" interpolated onto {group_name} time values."
+                )
+                # Ensure proper standard_name
+                self.aligned_nc[lon_coord].attrs["long_name"] = "Longitude"
+                self.aligned_nc[lon_coord].attrs["standard_name"] = "longitude"
+                self.aligned_nc[lon_coord].attrs["instrument_sample_rate_hz"] = sample_rate_str
 
             # Update spatial temporal bounds for global metadata
             if pd.to_datetime(self.aligned_nc[timevar][0].values).tz_localize(UTC) < pd.to_datetime(
@@ -661,13 +662,13 @@ def process_combined(self) -> Path:  # noqa: C901, PLR0912, PLR0915
             )
             self.aligned_nc[variable].attrs = self.combined_nc[variable].attrs
             if (
-                time_coord in self.aligned_nc
+                timevar in self.aligned_nc
                 and depth_coord in self.aligned_nc
                 and lat_coord in self.aligned_nc
                 and lon_coord in self.aligned_nc
             ):
                 self.aligned_nc[variable].attrs["coordinates"] = (
-                    f"{time_coord} {depth_coord} {lat_coord} {lon_coord}"
+                    f"{timevar} {depth_coord} {lat_coord} {lon_coord}"
                 )
             else:
                 self.logger.info("Skipping setting coordinates attribute for %s", variable)

src/data/nc42netcdfs.py

@@ -199,7 +199,7 @@ def extract_groups_to_files_netcdf4(self, log_file: str) -> Path:
 
             # Extract all other groups
             all_groups = list(src_dataset.groups.keys())
-            for group_name in SCIENG_PARMS:
+            for group_name in sorted(SCIENG_PARMS):
                 if group_name == "/" or group_name not in all_groups:
                     if group_name != "/" and group_name not in all_groups:
                         self.logger.warning("Group %s not found in %s", group_name, input_file)
@@ -555,11 +555,44 @@ def _process_single_time_coordinate(  # noqa: PLR0913
 
         # Get the valid time subset
         valid_time_data = original_time_data[spike_removed_indices]
+        self.logger.debug(
+            "Before monotonic: len(valid_time_data)=%d, len(spike_removed_indices)=%d, "
+            "type(spike_removed_indices)=%s",
+            len(valid_time_data),
+            len(spike_removed_indices),
+            type(spike_removed_indices).__name__,
+        )
+        self.logger.debug(
+            "valid_time_data shape/size: %s",
+            getattr(valid_time_data, "shape", len(valid_time_data)),
+        )
 
         # Apply monotonic filtering
         mono_indices_in_filtered = self._get_monotonic_indices(valid_time_data)
+        self.logger.debug(
+            "After monotonic: len(mono_indices)=%d, max(mono_indices)=%s, type(mono_indices)=%s",
+            len(mono_indices_in_filtered),
+            max(mono_indices_in_filtered) if len(mono_indices_in_filtered) > 0 else "N/A",
+            type(mono_indices_in_filtered).__name__,
+        )
 
         # Convert monotonic indices back to original array indices
+        if len(mono_indices_in_filtered) > 0 and max(mono_indices_in_filtered) >= len(
+            spike_removed_indices
+        ):
+            self.logger.error(
+                "BUG: monotonic indices out of range! max(mono_indices)=%d >= "
+                "len(spike_removed)=%d",
+                max(mono_indices_in_filtered),
+                len(spike_removed_indices),
+            )
+            self.logger.error("mono_indices_in_filtered: %s", mono_indices_in_filtered[:20])
+            self.logger.error("spike_removed_indices: %s", spike_removed_indices[:20])
+            # Clamp to valid range to prevent crash
+            mono_indices_in_filtered = [
+                i for i in mono_indices_in_filtered if i < len(spike_removed_indices)
+            ]
+
         final_indices = [spike_removed_indices[i] for i in mono_indices_in_filtered]
 
         # Store data for plotting if requested (do this before early return)

src/data/process.py

@@ -106,6 +106,10 @@ def wrapper(self, log_file: str):
             return func(self, log_file)
         except (TestMission, FailedMission, EOFError) as e:
             self.logger.info(str(e))
+        except Exception:
+            # Catch all other exceptions and log full traceback
+            self.logger.exception("Exception occurred while processing %s", log_file)
+            raise
         finally:
             if hasattr(self, "log_handler"):
                 # Cleanup and archiving logic
@@ -545,9 +549,14 @@ def align(self, mission: str = "", log_file: str = "") -> None:
                 netcdf_dir = align_netcdf.process_cal()
                 align_netcdf.write_combined_netcdf(netcdf_dir)
         except (FileNotFoundError, EOFError) as e:
-            align_netcdf.logger.error("%s %s", mission, e)  # noqa: TRY400
-            error_message = f"{mission} {e}"
+            align_netcdf.logger.error("%s %s", mission or log_file, e)  # noqa: TRY400
+            error_message = f"{mission or log_file} {e}"
             raise InvalidCalFile(error_message) from e
+        except Exception:
+            align_netcdf.logger.exception(
+                "Exception occurred during alignment of %s", mission or log_file
+            )
+            raise
         finally:
             align_netcdf.logger.removeHandler(self.log_handler)
 
@@ -601,9 +610,14 @@ def resample(self, mission: str = "", log_file: str = "") -> None:
                 raise ValueError(error_message)
             subprocess.run([wget_path, dap_file_str, "-O", nc_file_str], check=True)  # noqa: S603
         try:
-            resamp.resample_mission(nc_file)
+            resamp.resample_align_file(nc_file)
         except (FileNotFoundError, InvalidAlignFile) as e:
             self.logger.error("%s %s", nc_file, e)  # noqa: TRY400
+        except Exception:
+            resamp.logger.exception(
+                "Exception occurred during resampling of %s", mission or log_file
+            )
+            raise
         finally:
             resamp.logger.removeHandler(self.log_handler)
 
@@ -981,11 +995,17 @@ def extract(self, log_file: str) -> None:
         extract.logger.setLevel(self._log_levels[self.config["verbose"]])
         extract.logger.addHandler(self.log_handler)
 
-        url = os.path.join(BASE_LRAUV_WEB, log_file)  # noqa: PTH118
-        output_dir = Path(BASE_LRAUV_PATH, Path(log_file).parent)
-        extract.logger.info("Downloading %s", url)
-        input_file = extract.download_with_pooch(url, output_dir)
-        return extract.extract_groups_to_files_netcdf4(input_file)
+        try:
+            url = os.path.join(BASE_LRAUV_WEB, log_file)  # noqa: PTH118
+            output_dir = Path(BASE_LRAUV_PATH, Path(log_file).parent)
+            extract.logger.info("Downloading %s", url)
+            input_file = extract.download_with_pooch(url, output_dir)
+            return extract.extract_groups_to_files_netcdf4(input_file)
+        except Exception:
+            extract.logger.exception("Exception occurred during extraction of %s", log_file)
+            raise
+        finally:
+            extract.logger.removeHandler(self.log_handler)
 
     def combine(self, log_file: str) -> None:
         self.logger.info("Combining netCDF files for log file: %s", log_file)
@@ -1002,8 +1022,14 @@ def combine(self, log_file: str) -> None:
         combine.logger.setLevel(self._log_levels[self.config["verbose"]])
         combine.logger.addHandler(self.log_handler)
 
-        combine.combine_groups()
-        combine.write_netcdf()
+        try:
+            combine.combine_groups()
+            combine.write_netcdf()
+        except Exception:
+            combine.logger.exception("Exception occurred during combine of %s", log_file)
+            raise
+        finally:
+            combine.logger.removeHandler(self.log_handler)
 
     @log_file_processor
     def process_log_file(self, log_file: str) -> None: