INFO 2025-06-26 14:44:28,012 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 14:44:28,012 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Autonomy mission - ctdToUse = ctd2 INFO 2025-06-26 14:44:28,013 process.py process_mission():449 [1] Processing AUVCTD mission 2009.124.03 by user docker_user on host eae60d30a712 INFO 2025-06-26 14:44:28,013 process.py download_process():165 [1] Download and processing steps for 2009.124.03 INFO 2025-06-26 14:44:28,013 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2009/2009124/2009.124.03 INFO 2025-06-26 14:44:28,013 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2009/2009124/2009.124.03 to /data/auv_data/dorado/missionlogs/2009.124.03 INFO 2025-06-26 14:44:35,561 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2009.124.03 INFO 2025-06-26 14:44:35,561 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.124.03/ctdDriver.log (24633268 bytes) INFO 2025-06-26 14:44:37,705 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.124.03/ctdDriver.log: [ 235 459 647 730 822 3297 3350 4699 5272 11432 11699 16872 17607 23213 26552 26588 28063 34834 34856 35484 35897 36389 39855 44000 47994 66953 74397 77636 81957 91355 97395 106742 113790 116680 118209 133274 151181 157098 159815 163889 165197 173566 180934 190412 190551 193430 201440 203452 210834 212186 212737 216231 216375 223344 225612 225621 228601 229543 230817 231373 238875 250771 257215 258255 265888 271120 272601 273121 276360 276370 277257] INFO 2025-06-26 14:44:37,824 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.124.03/ctdDriver2.log (24633173 bytes) INFO 2025-06-26 14:44:39,781 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.124.03/ctdDriver2.log: [ 6 234 458 646 729 821 3296 3349 4698 5271 6128 11431 11698 13263 17606 23212 26551 26587 31219 34855 35483 35896 43999 47993 54079 55695 56343 66952 72804 74396 77635 91354 95147 97394 101521 106741 123790 138625 141397 151180 178620 187788 200737 212311 218047 223872 232326 234554 239039 259176 262836 265977 273253] INFO 2025-06-26 14:44:39,903 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.124.03/gps.log (408308 bytes) INFO 2025-06-26 14:44:39,956 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.124.03/hydroscatlog.log (23509858 bytes) INFO 2025-06-26 14:44:42,529 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.124.03/hydroscatlog.log: [ 630 759 1097 1221 1237 2307 2342 3468 4333 4680 7592 9477 11330 11496 11514 11632 13947 16040 31004 35985 37117 45627 47245 51454 56890 58249 65016 73952 74760 77980 79147 85652 87914 88279 96088 98109 103115 106777 123817 128313 137516 138030 151782 173170 194887 204289 205459 212295 225597 230391 239427 244646 252427 257175 259137] INFO 2025-06-26 14:44:42,642 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.124.03/navigation.log (82540182 bytes) INFO 2025-06-26 14:44:49,404 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.124.03/isuslog.log (1621365 bytes) INFO 2025-06-26 14:44:49,580 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.124.03/parosci.log (28653302 bytes) INFO 2025-06-26 14:44:52,201 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.124.03/tailCone.log (3444139 bytes) INFO 2025-06-26 14:44:52,673 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.124.03/biolume.log (19046940 bytes) INFO 2025-06-26 14:44:54,679 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 14:44:55,787 logs2netcdfs.py download_process_logs():807 [1] Time to process: 20.23 seconds INFO 2025-06-26 14:44:55,787 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2009.124.03/lopc.bin (206461099 bytes) INFO 2025-06-26 14:44:55,788 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 14:44:55 2025 INFO 2025-06-26 14:44:55,788 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2009.124.03/parosci.nc INFO 2025-06-26 14:44:55,788 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 14:44:55,788 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2009.124.03/parosci.nc INFO 2025-06-26 14:44:55,792 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1241463609.2, sensor_off_time = 1241533614.8 INFO 2025-06-26 14:44:55,793 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 70005 seconds. Expecting to read 140010 L frames from the lopc.bin file. INFO 2025-06-26 14:44:55,793 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 140010 records from the lopc.bin file. INFO 2025-06-26 14:44:56,658 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2009-05-04 19:00:09 Z and endTime = 2009-05-05 14:26:54 Z with 140010 records expected to be read from lopc.bin INFO 2025-06-26 14:44:56,658 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2009.124.03/lopc.bin INFO 2025-06-26 14:44:56,658 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2009.124.03/lopc.nc INFO 2025-06-26 14:44:56,659 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2009.124.03/lopc.nc INFO 2025-06-26 14:44:56,659 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2009.124.03 INFO 2025-06-26 14:44:56,660 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 14:44:56,739 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 14:44:56,739 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 14:44:56,739 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 14:44:56,928 lopcToNetCDF.py main():2340 [1] UnicodeDecodeError: 'utf-8' codec can't decode byte 0xc1 in position 0: invalid start byte INFO 2025-06-26 14:44:56,929 lopcToNetCDF.py main():2341 [1] Failed to decode all of lopc.bin - resulting lopc.nc file likely incomplete INFO 2025-06-26 14:44:56,929 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2009.124.03/parosci.nc INFO 2025-06-26 14:44:56,929 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 14:44:56,929 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2009.124.03/parosci.nc INFO 2025-06-26 14:44:56,933 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1241463609.2, sensor_off_time = 1241533614.8 INFO 2025-06-26 14:44:56,933 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 70005 seconds. Expecting to read 140010 L frames from the lopc.bin file. INFO 2025-06-26 14:44:56,933 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 140010 records from the lopc.bin file. INFO 2025-06-26 14:44:56,933 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 1440 and len(sampleCountList) = 150 INFO 2025-06-26 14:44:56,933 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [] INFO 2025-06-26 14:44:56,934 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [ 1440 1441 1442 1443 1444 1445 1446 31755 31756 31757 31758 31759 31760 31761 31762 31763 31764 31765 31766 31767 31768 31769 31770 31771 31772 31773 31774 31775 31776 31777 31778 31779 31780 31781 31782 31783 31784 31785 31786 31787 31788 31789 31790 31791 31792 31793 31794 31795 31796 31797 31798 31799 31800 31801 31802 31803 31804 31805 31806 31807 31808 31809 31810 31811 31812 31813 31814 31815 31816 31817 31818 31819 31820 31821 31822 31823 31824 31825 31826 31827 31828 31829 31830 31831 31832 31833 31834 31835 31836 31837 31838 31839 31840 31841 31842 31843 31844 31845 31846 31847 31848 31849 31850 31851 31852 31853 31854 31855 31856 31857 31858 31859 31860 31861 31862 31863 31864 31865 31866 31867 31868 31869 31870 31871 31872 31873 31874 31875 31876 31877 31878 31879 31880 31881 31882 31883 31884 31885 31886 31887 31888 31889 31890 31891 31892 31893 31894 31895 31896 31897] INFO 2025-06-26 14:44:56,934 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 14:44:56,934 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-26 14:44:56,934 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [ 1 1 1 1 1 1 30309 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1] INFO 2025-06-26 14:44:56,935 lopcToNetCDF.py deSpike():1590 [1] Found 1 spike indicators at indices: [7] INFO 2025-06-26 14:44:56,935 lopcToNetCDF.py deSpike():1595 [1] Identifying nature of spike value = 31755 at index = 7 INFO 2025-06-26 14:44:56,935 lopcToNetCDF.py deSpike():1714 [1] This is the last element in spike_indx. No need to deSpike(). INFO 2025-06-26 14:44:56,935 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [ 1440 1441 1442 1443 1444 1445 1446 31755 31756 31757 31758 31759 31760 31761 31762 31763 31764 31765 31766 31767 31768 31769 31770 31771 31772 31773 31774 31775 31776 31777 31778 31779 31780 31781 31782 31783 31784 31785 31786 31787 31788 31789 31790 31791 31792 31793 31794 31795 31796 31797 31798 31799 31800 31801 31802 31803 31804 31805 31806 31807 31808 31809 31810 31811 31812 31813 31814 31815 31816 31817 31818 31819 31820 31821 31822 31823 31824 31825 31826 31827 31828 31829 31830 31831 31832 31833 31834 31835 31836 31837 31838 31839 31840 31841 31842 31843 31844 31845 31846 31847 31848 31849 31850 31851 31852 31853 31854 31855 31856 31857 31858 31859 31860 31861 31862 31863 31864 31865 31866 31867 31868 31869 31870 31871 31872 31873 31874 31875 31876 31877 31878 31879 31880 31881 31882 31883 31884 31885 31886 31887 31888 31889 31890 31891 31892 31893 31894 31895 31896 31897] INFO 2025-06-26 14:44:56,936 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [ 1440 1441 1442 1443 1444 1445 1446 31755 31756 31757 31758 31759 31760 31761 31762 31763 31764 31765 31766 31767 31768 31769 31770 31771 31772 31773 31774 31775 31776 31777 31778 31779 31780 31781 31782 31783 31784 31785 31786 31787 31788 31789 31790 31791 31792 31793 31794 31795 31796 31797 31798 31799 31800 31801 31802 31803 31804 31805 31806 31807 31808 31809 31810 31811 31812 31813 31814 31815 31816 31817 31818 31819 31820 31821 31822 31823 31824 31825 31826 31827 31828 31829 31830 31831 31832 31833 31834 31835 31836 31837 31838 31839 31840 31841 31842 31843 31844 31845 31846 31847 31848 31849 31850 31851 31852 31853 31854 31855 31856 31857 31858 31859 31860 31861 31862 31863 31864 31865 31866 31867 31868 31869 31870 31871 31872 31873 31874 31875 31876 31877 31878 31879 31880 31881 31882 31883 31884 31885 31886 31887 31888 31889 31890 31891 31892 31893 31894 31895 31896 31897] with len(correctedSampleCountList) = 150 INFO 2025-06-26 14:44:56,937 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 1440 from all values of correctedSampleCountList INFO 2025-06-26 14:44:56,937 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 14:44:56,937 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [0.00000e+00 5.00000e-01 1.00000e+00 1.50000e+00 2.00000e+00 2.50000e+00 3.00000e+00 1.51575e+04 1.51580e+04 1.51585e+04 1.51590e+04 1.51595e+04 1.51600e+04 1.51605e+04 1.51610e+04 1.51615e+04 1.51620e+04 1.51625e+04 1.51630e+04 1.51635e+04 1.51640e+04 1.51645e+04 1.51650e+04 1.51655e+04 1.51660e+04 1.51665e+04 1.51670e+04 1.51675e+04 1.51680e+04 1.51685e+04 1.51690e+04 1.51695e+04 1.51700e+04 1.51705e+04 1.51710e+04 1.51715e+04 1.51720e+04 1.51725e+04 1.51730e+04 1.51735e+04 1.51740e+04 1.51745e+04 1.51750e+04 1.51755e+04 1.51760e+04 1.51765e+04 1.51770e+04 1.51775e+04 1.51780e+04 1.51785e+04 1.51790e+04 1.51795e+04 1.51800e+04 1.51805e+04 1.51810e+04 1.51815e+04 1.51820e+04 1.51825e+04 1.51830e+04 1.51835e+04 1.51840e+04 1.51845e+04 1.51850e+04 1.51855e+04 1.51860e+04 1.51865e+04 1.51870e+04 1.51875e+04 1.51880e+04 1.51885e+04 1.51890e+04 1.51895e+04 1.51900e+04 1.51905e+04 1.51910e+04 1.51915e+04 1.51920e+04 1.51925e+04 1.51930e+04 1.51935e+04 1.51940e+04 1.51945e+04 1.51950e+04 1.51955e+04 1.51960e+04 1.51965e+04 1.51970e+04 1.51975e+04 1.51980e+04 1.51985e+04 1.51990e+04 1.51995e+04 1.52000e+04 1.52005e+04 1.52010e+04 1.52015e+04 1.52020e+04 1.52025e+04 1.52030e+04 1.52035e+04 1.52040e+04 1.52045e+04 1.52050e+04 1.52055e+04 1.52060e+04 1.52065e+04 1.52070e+04 1.52075e+04 1.52080e+04 1.52085e+04 1.52090e+04 1.52095e+04 1.52100e+04 1.52105e+04 1.52110e+04 1.52115e+04 1.52120e+04 1.52125e+04 1.52130e+04 1.52135e+04 1.52140e+04 1.52145e+04 1.52150e+04 1.52155e+04 1.52160e+04 1.52165e+04 1.52170e+04 1.52175e+04 1.52180e+04 1.52185e+04 1.52190e+04 1.52195e+04 1.52200e+04 1.52205e+04 1.52210e+04 1.52215e+04 1.52220e+04 1.52225e+04 1.52230e+04 1.52235e+04 1.52240e+04 1.52245e+04 1.52250e+04 1.52255e+04 1.52260e+04 1.52265e+04 1.52270e+04 1.52275e+04 1.52280e+04 1.52285e+04] INFO 2025-06-26 14:44:56,938 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.24146361e+09 1.24146361e+09 1.24146361e+09 1.24146361e+09 1.24146361e+09 1.24146361e+09 1.24146361e+09 1.24147877e+09 1.24147877e+09 1.24147877e+09 1.24147877e+09 1.24147877e+09 1.24147877e+09 1.24147877e+09 1.24147877e+09 1.24147877e+09 1.24147877e+09 1.24147877e+09 1.24147877e+09 1.24147877e+09 1.24147877e+09 1.24147877e+09 1.24147877e+09 1.24147877e+09 1.24147878e+09 1.24147878e+09 1.24147878e+09 1.24147878e+09 1.24147878e+09 1.24147878e+09 1.24147878e+09 1.24147878e+09 1.24147878e+09 1.24147878e+09 1.24147878e+09 1.24147878e+09 1.24147878e+09 1.24147878e+09 1.24147878e+09 1.24147878e+09 1.24147878e+09 1.24147878e+09 1.24147878e+09 1.24147878e+09 1.24147879e+09 1.24147879e+09 1.24147879e+09 1.24147879e+09 1.24147879e+09 1.24147879e+09 1.24147879e+09 1.24147879e+09 1.24147879e+09 1.24147879e+09 1.24147879e+09 1.24147879e+09 1.24147879e+09 1.24147879e+09 1.24147879e+09 1.24147879e+09 1.24147879e+09 1.24147879e+09 1.24147879e+09 1.24147879e+09 1.24147880e+09 1.24147880e+09 1.24147880e+09 1.24147880e+09 1.24147880e+09 1.24147880e+09 1.24147880e+09 1.24147880e+09 1.24147880e+09 1.24147880e+09 1.24147880e+09 1.24147880e+09 1.24147880e+09 1.24147880e+09 1.24147880e+09 1.24147880e+09 1.24147880e+09 1.24147880e+09 1.24147880e+09 1.24147880e+09 1.24147881e+09 1.24147881e+09 1.24147881e+09 1.24147881e+09 1.24147881e+09 1.24147881e+09 1.24147881e+09 1.24147881e+09 1.24147881e+09 1.24147881e+09 1.24147881e+09 1.24147881e+09 1.24147881e+09 1.24147881e+09 1.24147881e+09 1.24147881e+09 1.24147881e+09 1.24147881e+09 1.24147881e+09 1.24147881e+09 1.24147882e+09 1.24147882e+09 1.24147882e+09 1.24147882e+09 1.24147882e+09 1.24147882e+09 1.24147882e+09 1.24147882e+09 1.24147882e+09 1.24147882e+09 1.24147882e+09 1.24147882e+09 1.24147882e+09 1.24147882e+09 1.24147882e+09 1.24147882e+09 1.24147882e+09 1.24147882e+09 1.24147882e+09 1.24147882e+09 1.24147883e+09 1.24147883e+09 1.24147883e+09 1.24147883e+09 1.24147883e+09 1.24147883e+09 1.24147883e+09 1.24147883e+09 1.24147883e+09 1.24147883e+09 1.24147883e+09 1.24147883e+09 1.24147883e+09 1.24147883e+09 1.24147883e+09 1.24147883e+09 1.24147883e+09 1.24147883e+09 1.24147883e+09 1.24147883e+09 1.24147884e+09 1.24147884e+09 1.24147884e+09 1.24147884e+09 1.24147884e+09 1.24147884e+09] INFO 2025-06-26 14:44:56,940 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1241463609.2 1241463609.7, ..., timestampArray[-2:] = 1241478837.2 1241478837.7] INFO 2025-06-26 14:44:56,940 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1241463609.2099407), np.float64(1241463609.7099407)], ..., timestampList[-2:] = [np.float64(1241478837.2099407), np.float64(1241478837.7099407)]] INFO 2025-06-26 14:44:56,941 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 150) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 14:44:56,941 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [125, 146] INFO 2025-06-26 14:44:56,941 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 7 INFO 2025-06-26 14:44:56,941 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 150 INFO 2025-06-26 14:44:56,941 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1241463609.2099407), np.float64(1241463609.7099407)], ..., timestampList[-2:] = [np.float64(1241478837.2099407), np.float64(1241478837.7099407)]] INFO 2025-06-26 14:44:56,941 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 150) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 14:44:56,941 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(124), np.int32(145)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 14:44:56,941 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 7 INFO 2025-06-26 14:44:56,941 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 ERROR 2025-06-26 14:44:56,941 lopcToNetCDF.py constructTimestampList():1501 [1] Cannot interpolate to cFrameEsecsListInterpolated: array of sample points is empty INFO 2025-06-26 14:44:56,943 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 7 INFO 2025-06-26 14:44:56,943 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1241478772.7099407)], ..., tsList[-2:] = [np.float64(1241478825.2099407), np.float64(1241478835.7099407)] INFO 2025-06-26 14:44:56,943 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2009-05-04 23:12:52 Z INFO 2025-06-26 14:44:56,943 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2009-05-04 23:13:55 Z INFO 2025-06-26 14:44:56,943 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 150 INFO 2025-06-26 14:44:56,943 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [-9999], ..., cFrameEsecsList[-2:] = [-9999, -9999] INFO 2025-06-26 14:44:56,943 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 1969-12-31 21:13:21 Z INFO 2025-06-26 14:44:56,943 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 1969-12-31 21:13:21 Z INFO 2025-06-26 14:44:56,947 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2009.124.03/lopc.nc INFO 2025-06-26 14:44:56,947 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 14:44:56 2025 Elapsed processing time from start of processing = 1 seconds INFO 2025-06-26 14:44:56,950 process.py calibrate():227 [1] Calibration steps for 2009.124.03 INFO 2025-06-26 14:44:57,833 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 14:44:57,836 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 14:44:58,495 calibrate.py _nudge_pos():1806 [1] 85: 0.030 -0.0000717 0.0001492 6466 21.61 -0.492 1.280 2009-05-04T19:23:05.785638912 INFO 2025-06-26 14:44:59,372 calibrate.py _nudge_pos():1806 [1] 165: 0.030 -0.0000732 0.0000330 8203 27.38 -0.397 0.223 2009-05-04T19:51:47.787673600 INFO 2025-06-26 14:45:00,207 calibrate.py _nudge_pos():1806 [1] 240: 0.040 -0.0000231 0.0000048 6435 21.46 -0.160 0.042 2009-05-04T20:14:29.784370432 INFO 2025-06-26 14:45:01,041 calibrate.py _nudge_pos():1806 [1] 311: 0.040 -0.0000842 -0.0000349 9064 30.23 -0.413 -0.214 2009-05-04T20:45:53.785307392 INFO 2025-06-26 14:45:01,901 calibrate.py _nudge_pos():1806 [1] 383: 0.050 -0.0000801 -0.0000445 8491 28.31 -0.419 -0.291 2009-05-04T21:15:23.784054272 INFO 2025-06-26 14:45:02,702 calibrate.py _nudge_pos():1806 [1] 452: 0.050 -0.0000045 -0.0000270 5299 17.66 -0.038 -0.283 2009-05-04T21:34:11.786780928 INFO 2025-06-26 14:45:03,549 calibrate.py _nudge_pos():1806 [1] 525: 0.050 -0.0000159 -0.0000251 3299 11.00 -0.214 -0.422 2009-05-04T21:46:23.936624896 INFO 2025-06-26 14:45:04,408 calibrate.py _nudge_pos():1806 [1] 600: 0.060 -0.0001122 -0.0000862 9196 30.66 -0.542 -0.521 2009-05-04T22:18:17.785517568 INFO 2025-06-26 14:45:05,270 calibrate.py _nudge_pos():1806 [1] 674: 0.060 -0.0001454 -0.0001661 6981 23.28 -0.925 -1.322 2009-05-04T22:42:47.784815616 INFO 2025-06-26 14:45:06,136 calibrate.py _nudge_pos():1806 [1] 748: 0.070 -0.0001256 -0.0001823 5785 19.28 -0.965 -1.753 2009-05-04T23:03:17.780555008 INFO 2025-06-26 14:45:07,057 calibrate.py _nudge_pos():1806 [1] 824: 0.070 -0.0000314 -0.0003914 5562 18.55 -0.251 -3.910 2009-05-04T23:23:05.779171584 INFO 2025-06-26 14:45:07,982 calibrate.py _nudge_pos():1806 [1] 896: 0.080 0.0001412 -0.0004343 3993 13.31 1.570 -6.045 2009-05-04T23:37:35.779572480 INFO 2025-06-26 14:45:08,927 calibrate.py _nudge_pos():1806 [1] 973: 0.070 0.0000047 -0.0001367 2139 7.13 0.097 -3.553 2009-05-04T23:45:59.785045760 INFO 2025-06-26 14:45:09,612 calibrate.py _nudge_pos():1806 [1] 1029: 0.080 0.0007253 0.0009469 10938 36.48 2.944 4.810 2009-05-05T00:23:23.781321472 INFO 2025-06-26 14:45:10,336 calibrate.py _nudge_pos():1806 [1] 1097: 0.080 0.0007676 0.0009543 9023 30.08 3.780 5.879 2009-05-05T00:54:35.783080704 INFO 2025-06-26 14:45:11,116 calibrate.py _nudge_pos():1806 [1] 1172: 0.080 0.0006057 0.0002412 2450 8.16 10.991 5.475 2009-05-05T01:03:59.784443904 INFO 2025-06-26 14:45:11,128 calibrate.py _nudge_pos():1806 [1] 1173: 0.080 -0.0000067 0.0000051 115 0.38 -2.592 2.492 2009-05-05T01:04:22.782868480 INFO 2025-06-26 14:45:11,771 calibrate.py _nudge_pos():1806 [1] 1234: 0.090 0.0059787 -0.0021394 15000 50.01 17.714 -7.926 2009-05-05T01:55:23.783175424 INFO 2025-06-26 14:45:12,564 calibrate.py _nudge_pos():1806 [1] 1309: 0.100 0.0052421 -0.0027804 14385 47.96 16.202 -10.742 2009-05-05T02:44:35.780949760 INFO 2025-06-26 14:45:13,298 calibrate.py _nudge_pos():1806 [1] 1379: 0.100 0.0031017 -0.0019499 8982 29.95 15.357 -12.066 2009-05-05T03:15:41.783119872 INFO 2025-06-26 14:45:14,090 calibrate.py _nudge_pos():1806 [1] 1454: 0.100 0.0036020 -0.0019020 9529 31.76 16.819 -11.096 2009-05-05T03:48:41.787480320 INFO 2025-06-26 14:45:14,852 calibrate.py _nudge_pos():1806 [1] 1527: 0.100 0.0027399 -0.0016417 8039 26.80 15.168 -11.352 2009-05-05T04:16:41.782392832 INFO 2025-06-26 14:45:15,615 calibrate.py _nudge_pos():1806 [1] 1600: 0.110 0.0048625 -0.0022489 13616 45.40 15.895 -9.180 2009-05-05T05:03:17.780853760 INFO 2025-06-26 14:45:16,683 calibrate.py _nudge_pos():1806 [1] 1700: 0.120 0.0032227 -0.0007144 10452 34.85 13.728 -3.799 2009-05-05T05:39:47.780828416 INFO 2025-06-26 14:45:17,375 calibrate.py _nudge_pos():1806 [1] 1766: 0.120 0.0023928 0.0003722 5584 18.61 19.084 3.705 2009-05-05T05:59:29.779855872 INFO 2025-06-26 14:45:18,140 calibrate.py _nudge_pos():1806 [1] 1839: 0.120 0.0027590 0.0004796 5487 18.30 22.388 4.857 2009-05-05T06:18:59.779705600 INFO 2025-06-26 14:45:18,876 calibrate.py _nudge_pos():1806 [1] 1905: 0.130 0.0065103 0.0053891 13562 45.21 21.383 22.086 2009-05-05T07:05:17.779399424 INFO 2025-06-26 14:45:19,654 calibrate.py _nudge_pos():1806 [1] 1977: 0.140 0.0055107 0.0035592 13683 45.61 17.947 14.459 2009-05-05T07:52:05.787037952 INFO 2025-06-26 14:45:20,415 calibrate.py _nudge_pos():1806 [1] 2048: 0.130 0.0035536 0.0016276 10148 33.83 15.608 8.915 2009-05-05T08:27:05.783177984 INFO 2025-06-26 14:45:21,143 calibrate.py _nudge_pos():1806 [1] 2117: 0.140 0.0016111 0.0006739 4248 14.16 16.903 8.817 2009-05-05T08:42:23.780291072 INFO 2025-06-26 14:45:22,045 calibrate.py _nudge_pos():1806 [1] 2201: 0.150 0.0031574 0.0022657 13561 45.21 10.380 9.286 2009-05-05T09:28:59.778752000 INFO 2025-06-26 14:45:22,889 calibrate.py _nudge_pos():1806 [1] 2279: 0.150 0.0003678 -0.0016016 13171 43.91 1.245 -6.758 2009-05-05T10:14:11.782967040 INFO 2025-06-26 14:45:23,689 calibrate.py _nudge_pos():1806 [1] 2353: 0.150 0.0002550 -0.0005749 4883 16.28 2.328 -6.544 2009-05-05T10:31:41.781037312 INFO 2025-06-26 14:45:24,426 calibrate.py _nudge_pos():1806 [1] 2421: 0.160 0.0004308 -0.0000060 10010 33.38 1.918 -0.034 2009-05-05T11:06:11.779232768 INFO 2025-06-26 14:45:25,167 calibrate.py _nudge_pos():1806 [1] 2489: 0.150 0.0003827 -0.0000468 8603 28.68 1.982 -0.303 2009-05-05T11:35:59.786745856 INFO 2025-06-26 14:45:25,929 calibrate.py _nudge_pos():1806 [1] 2559: 0.160 0.0003885 -0.0000186 9347 31.16 1.852 -0.110 2009-05-05T12:08:18.783915264 INFO 2025-06-26 14:45:26,648 calibrate.py _nudge_pos():1806 [1] 2625: 0.160 0.0003979 -0.0000310 9179 30.60 1.931 -0.188 2009-05-05T12:39:59.783688192 INFO 2025-06-26 14:45:27,397 calibrate.py _nudge_pos():1806 [1] 2694: 0.160 0.0003032 -0.0000217 8328 27.76 1.621 -0.145 2009-05-05T13:08:53.784900608 INFO 2025-06-26 14:45:28,127 calibrate.py _nudge_pos():1806 [1] 2760: 0.170 0.0014111 0.0009894 8584 28.61 7.317 6.408 2009-05-05T13:38:35.782825472 INFO 2025-06-26 14:45:59,705 calibrate.py _nudge_pos():1862 [1] 5625: - - - 5 0.01 - - INFO 2025-06-26 14:45:59,705 calibrate.py _nudge_pos():1868 [1] Points in final series = 349736 WARNING 2025-06-26 14:46:00,174 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 14:46:36,952 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:46:56,923 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:46:58,992 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:46:58,997 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2009.124.03/ctd1.nc INFO 2025-06-26 14:46:58,998 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 14:46:58,998 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 14:46:58,999 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 14:47:14,322 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:47:16,404 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 14:47:16,408 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2009.124.03/ctd2.nc INFO 2025-06-26 14:47:16,410 calibrate.py _range_qc_combined_nc():898 [1] Setting 82 ctd2_salinity values to NaN INFO 2025-06-26 14:47:16,410 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 14:47:16,410 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 14:47:16,506 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 14:47:19,784 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 4191962 4191963 4191964] INFO 2025-06-26 14:47:20,448 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 14:47:20,456 calibrate.py process_logs():3548 [1] Error processing biolume: missing variable "No variable named 'avg_biolume'. Variables on the dataset include ['time', 'rrr', 'cal_striing', 'pump', 'flow', 'humidity', 'temperature', 'time60hz', 'raw']" ERROR 2025-06-26 14:47:20,468 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2009.124.03 INFO 2025-06-26 14:47:20,527 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2009.124.03/dorado_2009.124.03_cal.nc INFO 2025-06-26 14:47:42,088 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_depth, biolume_flow, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, lopc_LCcount, lopc_countListSum, lopc_flowSpeed, lopc_nonTransCount, lopc_time, lopc_transCount, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 14:47:42,097 process.py align():251 [1] Alignment steps for 2009.124.03 INFO 2025-06-26 14:47:42,139 align.py process_cal():139 [1] Processing dorado_2009.124.03_cal.nc from /data/auv_data/dorado/missionnetcdfs/2009.124.03 INFO 2025-06-26 14:47:42,233 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:47:42,242 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:47:42,476 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:47:42,489 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:47:42,708 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:47:42,724 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:47:42,858 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 14:47:42,859 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 14:47:42,943 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 14:47:42,956 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 14:47:43,174 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.124.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:47:43,185 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:47:43,381 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.124.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:47:43,392 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:47:43,587 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.124.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:47:43,602 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:47:43,792 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.124.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:47:43,803 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:47:43,993 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.124.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:47:44,005 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:47:44,193 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.124.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:47:44,204 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:47:44,388 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.124.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:47:44,399 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:47:44,583 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.124.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:47:44,593 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:47:44,781 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.124.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:47:44,791 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:47:44,977 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.124.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:47:44,990 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:47:45,179 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.124.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:47:45,190 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:47:45,375 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.124.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:47:45,385 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:47:45,573 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.124.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:47:45,583 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:47:45,770 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.124.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:47:45,780 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:47:45,967 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.124.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:47:45,979 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:47:46,166 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.124.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:47:46,176 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:47:46,370 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.124.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:47:46,380 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:47:46,569 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.124.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:47:46,582 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:47:46,775 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.124.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:47:46,786 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:47:46,971 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.124.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 14:47:46,981 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 14:47:47,214 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.72 INFO 2025-06-26 14:47:47,352 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.72 INFO 2025-06-26 14:47:47,492 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.72 INFO 2025-06-26 14:47:47,645 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 14:47:47,799 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 14:47:47,920 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 14:47:48,050 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 14:47:48,178 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 14:47:48,306 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 14:47:48,433 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.02 INFO 2025-06-26 14:47:48,476 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2009.124.03/dorado_2009.124.03_align.nc INFO 2025-06-26 14:47:48,642 align.py write_netcdf():342 [1] Data variables written: biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, lopc_LCcount, lopc_countListSum, lopc_depth, lopc_flowSpeed, lopc_latitude, lopc_longitude, lopc_nonTransCount, lopc_time, lopc_transCount, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 14:47:48,645 process.py resample():273 [1] Resampling steps for 2009.124.03 INFO 2025-06-26 14:47:48,645 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 14:47:48,681 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.124.03/dorado_2009.124.03_align.nc mission netCDF file INFO 2025-06-26 14:47:48,690 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.124.03/dorado_2009.124.03_align.nc mission netCDF file INFO 2025-06-26 14:47:48,692 resample.py get_mission_start_end():1145 [1] navigation: 2009-05-04T19:00:39.707851520 to 2009-05-05T14:26:54.784230144 (0 days 00:00:00 before mission_end) INFO 2025-06-26 14:47:48,694 resample.py get_mission_start_end():1145 [1] hs2 : 2009-05-04T19:00:15.799489280 to 2009-05-05T14:26:54.694236416 (0 days 00:00:00.089993728 before mission_end) INFO 2025-06-26 14:47:48,697 resample.py get_mission_start_end():1145 [1] ctd1 : 2009-05-04T19:00:35.688126720 to 2009-05-05T14:26:54.744233216 (0 days 00:00:00.039996928 before mission_end) INFO 2025-06-26 14:47:48,700 resample.py get_mission_start_end():1145 [1] ctd2 : 2009-05-04T19:00:35.678127616 to 2009-05-05T14:26:54.634240512 (0 days 00:00:00.149989632 before mission_end) INFO 2025-06-26 14:47:48,701 resample.py get_mission_start_end():1145 [1] isus : 2009-05-04T19:01:23.104878336 to 2009-05-05T14:26:53.674306304 (0 days 00:00:01.109923840 before mission_end) INFO 2025-06-26 14:47:48,703 resample.py get_mission_start_end():1145 [1] biolume : 2009-05-04T19:00:07.710009088 to 2009-05-05T14:26:53.304297472 (0 days 00:00:01.479932672 before mission_end) INFO 2025-06-26 14:47:48,704 resample.py get_mission_start_end():1145 [1] lopc : 2009-05-04T23:12:52.709940736 to 2009-05-04T23:13:55.709940736 (0 days 15:12:59.074289408 before mission_end) WARNING 2025-06-26 14:47:48,705 resample.py get_mission_start_end():1156 [1] Instrument lopc has a gap > 5 minutes at the end of the mission: 0 days 15:12:59.074289408 INFO 2025-06-26 14:47:48,706 resample.py get_mission_start_end():1145 [1] tailcone : 2009-05-04T19:00:11.829761280 to 2009-05-05T14:26:54.114276096 (0 days 00:00:00.669954048 before mission_end) INFO 2025-06-26 14:47:48,707 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.124.03/dorado_2009.124.03_align.nc mission netCDF file INFO 2025-06-26 14:47:48,707 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:49,406 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:49,518 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:49,627 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:49,738 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:49,831 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:49,921 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:50,012 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:50,101 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:50,188 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:50,274 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:50,359 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:50,444 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:50,530 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:50,616 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:50,702 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:50,787 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:50,876 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:50,964 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:51,058 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:51,146 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:51,232 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:51,320 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:51,352 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:51,382 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:51,409 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:51,442 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:51,458 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:51,458 resample.py resample_variable():1038 [1] Padding lopc_countListSum with 0 days 15:12:59.074289408 of NaNs to the end of mission INFO 2025-06-26 14:47:51,470 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:51,470 resample.py resample_variable():1038 [1] Padding lopc_transCount with 0 days 15:12:59.074289408 of NaNs to the end of mission INFO 2025-06-26 14:47:51,480 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:51,480 resample.py resample_variable():1038 [1] Padding lopc_nonTransCount with 0 days 15:12:59.074289408 of NaNs to the end of mission INFO 2025-06-26 14:47:51,491 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:51,491 resample.py resample_variable():1038 [1] Padding lopc_LCcount with 0 days 15:12:59.074289408 of NaNs to the end of mission INFO 2025-06-26 14:47:51,501 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:51,501 resample.py resample_variable():1038 [1] Padding lopc_flowSpeed with 0 days 15:12:59.074289408 of NaNs to the end of mission INFO 2025-06-26 14:47:51,530 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 14:47:52,027 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2009.124.03/dorado_2009.124.03_1S.nc INFO 2025-06-26 14:47:55,326 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd2 INFO 2025-06-26 14:48:06,309 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2009.124.03/dorado_2009.124.03_1S_Gulper.txt INFO 2025-06-26 14:48:06,309 process.py archive():337 [1] Archiving steps for 2009.124.03 INFO 2025-06-26 14:48:06,310 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2009.124.03/dorado_2009.124.03, BASE_PATH = /data/auv_data INFO 2025-06-26 14:48:06,311 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2009.124.03/dorado_2009.124.03 files to /Volumes/AUVCTD/surveys/2009/netcdf INFO 2025-06-26 14:48:06,312 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.124.03_1S.nc INFO 2025-06-26 14:48:06,366 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.124.03/dorado_2009.124.03_1S.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 14:48:06,367 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.124.03_cal.nc INFO 2025-06-26 14:48:06,629 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.124.03/dorado_2009.124.03_cal.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 14:48:06,631 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.124.03_align.nc INFO 2025-06-26 14:48:06,862 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.124.03/dorado_2009.124.03_align.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 14:48:06,934 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.124.03/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009124/2009.124.03 done. INFO 2025-06-26 14:48:07,005 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.124.03/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009124/2009.124.03 done. INFO 2025-06-26 14:48:07,011 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.124.03/gps.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009124/2009.124.03 done. INFO 2025-06-26 14:48:07,073 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.124.03/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009124/2009.124.03 done. INFO 2025-06-26 14:48:07,268 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.124.03/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009124/2009.124.03 done. INFO 2025-06-26 14:48:07,278 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.124.03/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009124/2009.124.03 done. INFO 2025-06-26 14:48:07,357 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.124.03/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009124/2009.124.03 done. INFO 2025-06-26 14:48:07,373 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.124.03/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009124/2009.124.03 done. INFO 2025-06-26 14:48:07,550 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.124.03/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009124/2009.124.03 done. INFO 2025-06-26 14:48:07,556 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.124.03/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009124/2009.124.03 done. INFO 2025-06-26 14:48:07,556 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 14:48:07,557 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2009/odv/dorado_2009.124.03_1S_Gulper.txt INFO 2025-06-26 14:48:07,562 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2009.124.03/dorado_2009.124.03_1S_Gulper.txt /Volumes/AUVCTD/surveys/2009/odv done. INFO 2025-06-26 14:48:07,562 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.124.03/dorado_2009.124.03_processing.log /Volumes/AUVCTD/surveys/2009/netcdf