Initial steps to get LRAUV data ready for processing by align.py

.vscode/launch.json

@@ -54,9 +54,12 @@
             "console": "integratedTerminal",
             // A small log_file that has a reasonable amount of data, and known_hash to verify download
             //"args": ["-v", "1", "--log_file", "ahi/missionlogs/2025/20250908_20250912/20250911T201546/202509112015_202509112115.nc4", "--known_hash", "d1235ead55023bea05e9841465d54a45dfab007a283320322e28b84438fb8a85"]
-            // Has bad latitude and longitude values and lots of bad Universal latitude_time values
+            // brizo 20250914T080941 has bad latitude and longitude values and lots of bad Universal latitude_time and longitude_time values
             //"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", "/latitude_time"]
+            //"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_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"]
         },
         {
             "name": "2.0 - calibrate.py",
@@ -112,7 +115,8 @@
             "program": "${workspaceFolder}/src/data/combine.py",
             "console": "integratedTerminal",
             "justMyCode": false,
-            "args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109.nc4"]
+            //"args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250909_20250915/20250914T080941/202509140809_202509150109.nc4"]
+            "args": ["-v", "1", "--log_file", "brizo/missionlogs/2025/20250916_20250922/20250916T230652/202509162306_202509180305.nc4"]
         },
         {
             "name": "3.0 - align.py",
@@ -321,7 +325,8 @@
             "console": "integratedTerminal",
             //"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", "2", "--log_file", "brizo/missionlogs/2025/20250916_20250922/20250916T230652/202509162306_202509180305.nc4", "--no_cleanup"]
             //"args": ["-v", "1", "--auv_name", "tethys", "--start", "20120901", "--end", "20121101", "--noinput"]
         },
 

LRAUV_WORKFLOW.md

@@ -13,24 +13,26 @@ on the local file system's work directory is as follows:
     │   │   ├── <auv_name>           <- e.g.: ahi, brizo, pontus, tethys, ...
     │   │   │   ├── missionlogs/year/dlist_dir
     │   │   │   │   ├── <log_dir>    <- e.g.: ahi/missionlogs/2025/20250908_20250912/20250911T201546/202509112015_202509112115.nc4
-    │   │   │   │   │   ├── <nc4>    <- .nc4 file containing original data
+    │   │   │   │   │   ├── <nc4>    <- .nc4 file containing original data - created by unserialize
     │   │   │   │   │   ├── <nc>     <- .nc files, one for each group from the .nc4 file
-    |   |   |   |   |   |                data identical to original in NETCDF4 format
-    │   │   │   │   │   ├── <_cal>   <- A single NETCDF3 .nc file containing all the
-    |   |   |   |   |   |               varibles from the .nc files along with nudged
-    |   |   |   |   |   |               latitudes and longitudes - created by combine.py
+    |   |   |   |   |   |                data identical to original in NetCDF4 format,
+    |   |   |   |   |   |                but in more interoperable NetCDF3 format 
+    |   |   |   |   |   |                - created by nc42netcdfs.py
+    │   │   │   │   │   ├── <_combined>     <- A single NetCDF3 .nc file containing all the
+    |   |   |   |   |   |                   varibles from the .nc files along with nudged
+    |   |   |   |   |   |                   latitudes and longitudes - created by combine.py
     │   │   │   │   │   ├── <_align> <- .nc file with all measurement variables
     |   |   |   |   |   |               having associated coordinate variables
-    |   |   |   |   |   |               at original instrument sampling rate -
-    |   |   |   |   |   |               created by align.py
+    |   |   |   |   |   |               at original instrument sampling rate
+    |   |   |   |   |   |                - created by align.py
     │   │   │   │   │   ├── <_nS>    <- .nc file with all measurement variables
                                         resampled to a common time grid at n
                                         Second intervals - created by resample.py
 
     nc42netcdfs.py
         Extract the groups and the variables we want from the groups into 
-        individual .nc files. These data are saved using NETCDF4 format as
-        there are many unlimited dimensions that are not allowed in NETCDF3.
+        individual .nc files. These data are saved using NetCDF4 format as
+        there are many unlimited dimensions that are not allowed in NetCDF3.
         The data in the .nc files are identical to what is in the .nc4 groups.
 
     combine.py

README.md

@@ -103,11 +103,11 @@ First time use with Docker on a server using a service account:
 * git clone git@github.com:mbari-org/auv-python.git
 * cd auv-python
 * Create a .env file in `/opt/auv-python` with the following contents:   
-    `M3_VOL=<mount_location>`   
-    `AUVCTD_VOL=<mount_location>`   
-    `CALIBRATION_VOL=<mount_location>`   
-    `WORK_VOL=<auv-python_home>/data`   
-
+    `M3_VOL=<mount_location>`
+    `AUVCTD_VOL=<mount_location>`
+    `CALIBRATION_VOL=<mount_location>`
+    `WORK_VOL=<auv-python_home>/data`
+    `HOST_NAME=<name_of_host>`
 After installation and when logging into the server again mission data can be processed thusly:
 * Setting up environment and printing help message:   
     `sudo -u docker_user -i`  

src/data/AUV.py

@@ -11,6 +11,7 @@
 import logging
 from datetime import datetime
 
+import cf_xarray  # Needed for the .cf accessor  # noqa: F401
 import numpy as np
 import xarray as xr
 
@@ -88,22 +89,23 @@ def nudge_positions(  # noqa: C901, PLR0912, PLR0913, PLR0915
     if lon[:][segi].any():
         lon_nudged_array = lon[segi]
         lat_nudged_array = lat[segi]
-        dt_nudged = lon.get_index("navigation_time")[segi]
+        dt_nudged = lon.cf["T"][segi]
         logger.debug(
             "Filled _nudged arrays with %d values starting at %s "
             "which were before the first GPS fix at %s",
             len(segi),
-            lat.get_index("navigation_time")[0],
-            lat_fix.get_index("gps_time")[0],
+            lat.cf["T"].data[0],
+            lat_fix.cf["T"].data[0],
         )
     else:
         lon_nudged_array = np.array([])
         lat_nudged_array = np.array([])
         dt_nudged = np.array([], dtype="datetime64[ns]")
     if segi.any():
-        seg_min = (
-            lat.get_index("navigation_time")[segi][-1] - lat.get_index("navigation_time")[segi][0]
-        ).total_seconds() / 60
+        # Return difference of numpy timestamps in units of minutes
+        seg_min = (lat.cf["T"].data[segi][-1] - lat.cf["T"].data[segi][0]).astype(
+            "timedelta64[s]"
+        ).astype(float) / 60.0
     else:
         seg_min = 0
     logger.info(