INFO 2025-06-26 20:14:23,131 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 20:14:23,131 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ Spring 2014 in Soquel Bight - ctdToUse = ctd1 INFO 2025-06-26 20:14:23,132 process.py process_mission():449 [1] Processing SIMZ Spring 2014 mission 2014.071.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:14:23,132 process.py download_process():165 [1] Download and processing steps for 2014.071.02 INFO 2025-06-26 20:14:23,132 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014071/2014.071.02 INFO 2025-06-26 20:14:23,132 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014071/2014.071.02 to /data/auv_data/dorado/missionlogs/2014.071.02 INFO 2025-06-26 20:14:26,243 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.071.02 INFO 2025-06-26 20:14:26,243 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.071.02/ctdDriver.log (5383398 bytes) INFO 2025-06-26 20:14:26,643 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.071.02/ctdDriver2.log (5383391 bytes) INFO 2025-06-26 20:14:27,021 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.071.02/gps.log (61340 bytes) INFO 2025-06-26 20:14:27,035 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.071.02/hydroscatlog.log (4716454 bytes) INFO 2025-06-26 20:14:27,510 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.071.02/navigation.log (20166210 bytes) INFO 2025-06-26 20:14:28,906 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.071.02/parosci.log (6623798 bytes) INFO 2025-06-26 20:14:29,445 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2014.071.02/parosci.log: [1] INFO 2025-06-26 20:14:29,461 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.071.02/tailCone.log (3371803 bytes) INFO 2025-06-26 20:14:29,869 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.071.02/biolume.log (3925870 bytes) INFO 2025-06-26 20:14:30,254 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:14:30,447 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.20 seconds INFO 2025-06-26 20:14:30,447 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.071.02/lopc.bin (49610907 bytes) INFO 2025-06-26 20:14:30,447 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:14:30 2025 INFO 2025-06-26 20:14:30,448 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.071.02/parosci.nc INFO 2025-06-26 20:14:30,448 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:14:30,448 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.071.02/parosci.nc INFO 2025-06-26 20:14:30,451 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1394648154.7, sensor_off_time = 1394662200.7 INFO 2025-06-26 20:14:30,451 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 14045 seconds. Expecting to read 28090 L frames from the lopc.bin file. INFO 2025-06-26 20:14:30,451 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 28090 records from the lopc.bin file. INFO 2025-06-26 20:14:30,629 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-03-12 18:15:54 Z and endTime = 2014-03-12 22:10:00 Z with 28090 records expected to be read from lopc.bin INFO 2025-06-26 20:14:30,629 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.071.02/lopc.bin INFO 2025-06-26 20:14:30,629 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.071.02/lopc.nc INFO 2025-06-26 20:14:30,631 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.071.02/lopc.nc INFO 2025-06-26 20:14:30,631 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.071.02 INFO 2025-06-26 20:14:30,631 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 20:14:30,636 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 20:14:30,857 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:14:30,857 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:14:30,857 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:14:30,972 lopcToNetCDF.py main():2340 [1] UnicodeDecodeError: 'utf-8' codec can't decode byte 0x84 in position 0: invalid start byte INFO 2025-06-26 20:14:30,972 lopcToNetCDF.py main():2341 [1] Failed to decode all of lopc.bin - resulting lopc.nc file likely incomplete INFO 2025-06-26 20:14:30,973 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.071.02/parosci.nc INFO 2025-06-26 20:14:30,973 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:14:30,973 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.071.02/parosci.nc INFO 2025-06-26 20:14:30,977 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1394648154.7, sensor_off_time = 1394662200.7 INFO 2025-06-26 20:14:30,977 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 14045 seconds. Expecting to read 28090 L frames from the lopc.bin file. INFO 2025-06-26 20:14:30,977 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 28090 records from the lopc.bin file. INFO 2025-06-26 20:14:30,977 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 19634 and len(sampleCountList) = 138 INFO 2025-06-26 20:14:30,978 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [] INFO 2025-06-26 20:14:30,978 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [19634 19635 19636 19637 19638 19639 19640 19641 19642 19643 19644 19645 19646 19647 19648 19649 19650 19651 19652 19653 19654 19655 19656 19657 19658 19659 19660 19661 19662 19663 19664 19665 19666 19667 19668 19669 19670 19671 19672 19673 19674 19675 19676 19677 19678 19679 19680 19681 19682 19683 19684 19685 19686 19687 19688 19689 19690 19691 19692 19693 19694 19695 19696 19697 19698 19699 19700 19701 19702 19703 19704 19705 19706 19707 19708 19709 19710 19711 19712 19713 19714 19715 19716 19717 19718 19719 19720 19721 19722 19723 19724 19725 19726 19727 19728 19729 19730 19731 19732 19733 19734 19735 19736 19737 19738 19739 19740 19741 19742 19743 19744 19745 19746 19747 19748 19749 19750 19751 19752 19753 19754 19755 19756 19757 19758 19759 19760 19761 19762 19763 19764 19765 19766 19767 19768 19769 19770 19771] INFO 2025-06-26 20:14:30,978 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 20:14:30,978 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-26 20:14:30,979 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [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 20:14:30,979 lopcToNetCDF.py deSpike():1590 [1] Found 0 spike indicators at indices: [] INFO 2025-06-26 20:14:30,979 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [19634 19635 19636 19637 19638 19639 19640 19641 19642 19643 19644 19645 19646 19647 19648 19649 19650 19651 19652 19653 19654 19655 19656 19657 19658 19659 19660 19661 19662 19663 19664 19665 19666 19667 19668 19669 19670 19671 19672 19673 19674 19675 19676 19677 19678 19679 19680 19681 19682 19683 19684 19685 19686 19687 19688 19689 19690 19691 19692 19693 19694 19695 19696 19697 19698 19699 19700 19701 19702 19703 19704 19705 19706 19707 19708 19709 19710 19711 19712 19713 19714 19715 19716 19717 19718 19719 19720 19721 19722 19723 19724 19725 19726 19727 19728 19729 19730 19731 19732 19733 19734 19735 19736 19737 19738 19739 19740 19741 19742 19743 19744 19745 19746 19747 19748 19749 19750 19751 19752 19753 19754 19755 19756 19757 19758 19759 19760 19761 19762 19763 19764 19765 19766 19767 19768 19769 19770 19771] INFO 2025-06-26 20:14:30,980 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [19634 19635 19636 19637 19638 19639 19640 19641 19642 19643 19644 19645 19646 19647 19648 19649 19650 19651 19652 19653 19654 19655 19656 19657 19658 19659 19660 19661 19662 19663 19664 19665 19666 19667 19668 19669 19670 19671 19672 19673 19674 19675 19676 19677 19678 19679 19680 19681 19682 19683 19684 19685 19686 19687 19688 19689 19690 19691 19692 19693 19694 19695 19696 19697 19698 19699 19700 19701 19702 19703 19704 19705 19706 19707 19708 19709 19710 19711 19712 19713 19714 19715 19716 19717 19718 19719 19720 19721 19722 19723 19724 19725 19726 19727 19728 19729 19730 19731 19732 19733 19734 19735 19736 19737 19738 19739 19740 19741 19742 19743 19744 19745 19746 19747 19748 19749 19750 19751 19752 19753 19754 19755 19756 19757 19758 19759 19760 19761 19762 19763 19764 19765 19766 19767 19768 19769 19770 19771] with len(correctedSampleCountList) = 138 INFO 2025-06-26 20:14:30,981 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 19634 from all values of correctedSampleCountList INFO 2025-06-26 20:14:30,981 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 20:14:30,981 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [ 0. 0.5 1. 1.5 2. 2.5 3. 3.5 4. 4.5 5. 5.5 6. 6.5 7. 7.5 8. 8.5 9. 9.5 10. 10.5 11. 11.5 12. 12.5 13. 13.5 14. 14.5 15. 15.5 16. 16.5 17. 17.5 18. 18.5 19. 19.5 20. 20.5 21. 21.5 22. 22.5 23. 23.5 24. 24.5 25. 25.5 26. 26.5 27. 27.5 28. 28.5 29. 29.5 30. 30.5 31. 31.5 32. 32.5 33. 33.5 34. 34.5 35. 35.5 36. 36.5 37. 37.5 38. 38.5 39. 39.5 40. 40.5 41. 41.5 42. 42.5 43. 43.5 44. 44.5 45. 45.5 46. 46.5 47. 47.5 48. 48.5 49. 49.5 50. 50.5 51. 51.5 52. 52.5 53. 53.5 54. 54.5 55. 55.5 56. 56.5 57. 57.5 58. 58.5 59. 59.5 60. 60.5 61. 61.5 62. 62.5 63. 63.5 64. 64.5 65. 65.5 66. 66.5 67. 67.5 68. 68.5] INFO 2025-06-26 20:14:30,982 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.39464815e+09 1.39464816e+09 1.39464816e+09 1.39464816e+09 1.39464816e+09 1.39464816e+09 1.39464816e+09 1.39464816e+09 1.39464816e+09 1.39464816e+09 1.39464816e+09 1.39464816e+09 1.39464816e+09 1.39464816e+09 1.39464816e+09 1.39464816e+09 1.39464816e+09 1.39464816e+09 1.39464816e+09 1.39464816e+09 1.39464816e+09 1.39464817e+09 1.39464817e+09 1.39464817e+09 1.39464817e+09 1.39464817e+09 1.39464817e+09 1.39464817e+09 1.39464817e+09 1.39464817e+09 1.39464817e+09 1.39464817e+09 1.39464817e+09 1.39464817e+09 1.39464817e+09 1.39464817e+09 1.39464817e+09 1.39464817e+09 1.39464817e+09 1.39464817e+09 1.39464817e+09 1.39464818e+09 1.39464818e+09 1.39464818e+09 1.39464818e+09 1.39464818e+09 1.39464818e+09 1.39464818e+09 1.39464818e+09 1.39464818e+09 1.39464818e+09 1.39464818e+09 1.39464818e+09 1.39464818e+09 1.39464818e+09 1.39464818e+09 1.39464818e+09 1.39464818e+09 1.39464818e+09 1.39464818e+09 1.39464818e+09 1.39464819e+09 1.39464819e+09 1.39464819e+09 1.39464819e+09 1.39464819e+09 1.39464819e+09 1.39464819e+09 1.39464819e+09 1.39464819e+09 1.39464819e+09 1.39464819e+09 1.39464819e+09 1.39464819e+09 1.39464819e+09 1.39464819e+09 1.39464819e+09 1.39464819e+09 1.39464819e+09 1.39464819e+09 1.39464819e+09 1.39464820e+09 1.39464820e+09 1.39464820e+09 1.39464820e+09 1.39464820e+09 1.39464820e+09 1.39464820e+09 1.39464820e+09 1.39464820e+09 1.39464820e+09 1.39464820e+09 1.39464820e+09 1.39464820e+09 1.39464820e+09 1.39464820e+09 1.39464820e+09 1.39464820e+09 1.39464820e+09 1.39464820e+09 1.39464820e+09 1.39464821e+09 1.39464821e+09 1.39464821e+09 1.39464821e+09 1.39464821e+09 1.39464821e+09 1.39464821e+09 1.39464821e+09 1.39464821e+09 1.39464821e+09 1.39464821e+09 1.39464821e+09 1.39464821e+09 1.39464821e+09 1.39464821e+09 1.39464821e+09 1.39464821e+09 1.39464821e+09 1.39464821e+09 1.39464821e+09 1.39464822e+09 1.39464822e+09 1.39464822e+09 1.39464822e+09 1.39464822e+09 1.39464822e+09 1.39464822e+09 1.39464822e+09 1.39464822e+09 1.39464822e+09 1.39464822e+09 1.39464822e+09 1.39464822e+09 1.39464822e+09 1.39464822e+09 1.39464822e+09 1.39464822e+09] INFO 2025-06-26 20:14:30,983 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1394648154.7 1394648155.2, ..., timestampArray[-2:] = 1394648222.7 1394648223.2] INFO 2025-06-26 20:14:30,984 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1394648154.6829221), np.float64(1394648155.1829221)], ..., timestampList[-2:] = [np.float64(1394648222.6829221), np.float64(1394648223.1829221)]] INFO 2025-06-26 20:14:30,984 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 138) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 20:14:30,984 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [104, 125] INFO 2025-06-26 20:14:30,984 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 6 INFO 2025-06-26 20:14:30,984 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 138 INFO 2025-06-26 20:14:30,984 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1394648154.6829221), np.float64(1394648155.1829221)], ..., timestampList[-2:] = [np.float64(1394648222.6829221), np.float64(1394648223.1829221)]] INFO 2025-06-26 20:14:30,984 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 138) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 20:14:30,984 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(103), np.int32(124)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 20:14:30,984 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 6 INFO 2025-06-26 20:14:30,984 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 ERROR 2025-06-26 20:14:30,984 lopcToNetCDF.py constructTimestampList():1501 [1] Cannot interpolate to cFrameEsecsListInterpolated: array of sample points is empty INFO 2025-06-26 20:14:30,986 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 6 INFO 2025-06-26 20:14:30,986 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1394648164.1829221)], ..., tsList[-2:] = [np.float64(1394648206.1829221), np.float64(1394648216.6829221)] INFO 2025-06-26 20:14:30,986 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2014-03-12 18:16:04 Z INFO 2025-06-26 20:14:30,986 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2014-03-12 18:16:56 Z INFO 2025-06-26 20:14:30,986 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 138 INFO 2025-06-26 20:14:30,986 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [-9999], ..., cFrameEsecsList[-2:] = [-9999, -9999] INFO 2025-06-26 20:14:30,986 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 1969-12-31 21:13:21 Z INFO 2025-06-26 20:14:30,986 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 1969-12-31 21:13:21 Z INFO 2025-06-26 20:14:30,990 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2014.071.02/lopc.nc INFO 2025-06-26 20:14:30,990 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 20:14:30 2025 Elapsed processing time from start of processing = 0 seconds INFO 2025-06-26 20:14:30,991 process.py calibrate():227 [1] Calibration steps for 2014.071.02 INFO 2025-06-26 20:14:31,145 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 20:14:31,147 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:14:31,934 calibrate.py _nudge_pos():1806 [1] 119: 0.020 -0.0007646 0.0044310 8355 27.85 -4.069 29.485 2014-03-12T18:45:40.030617600 INFO 2025-06-26 20:14:32,471 calibrate.py _nudge_pos():1806 [1] 175: 0.020 0.0013113 0.0043042 8665 28.88 6.730 27.616 2014-03-12T19:15:28.038130432 INFO 2025-06-26 20:14:32,888 calibrate.py _nudge_pos():1806 [1] 219: 0.030 0.0018138 0.0047674 9295 30.98 8.679 28.515 2014-03-12T19:47:10.037834752 INFO 2025-06-26 20:14:33,405 calibrate.py _nudge_pos():1806 [1] 275: 0.030 0.0003630 -0.0002409 1945 6.48 8.304 -6.889 2014-03-12T19:54:34.037418496 INFO 2025-06-26 20:14:33,886 calibrate.py _nudge_pos():1806 [1] 327: 0.030 0.0005243 0.0006038 4455 14.85 5.236 7.536 2014-03-12T20:10:16.032887552 INFO 2025-06-26 20:14:34,369 calibrate.py _nudge_pos():1806 [1] 379: 0.030 -0.0005654 -0.0000919 4425 14.75 -5.684 -1.155 2014-03-12T20:25:52.038766592 INFO 2025-06-26 20:14:34,807 calibrate.py _nudge_pos():1806 [1] 426: 0.030 -0.0012242 -0.0005165 6340 21.13 -8.588 -4.530 2014-03-12T20:47:46.038751488 INFO 2025-06-26 20:14:35,342 calibrate.py _nudge_pos():1806 [1] 483: 0.050 -0.0011565 -0.0006769 6830 22.76 -7.530 -5.510 2014-03-12T21:11:28.031338496 INFO 2025-06-26 20:14:35,786 calibrate.py _nudge_pos():1806 [1] 529: 0.040 -0.0009106 -0.0008646 7545 25.15 -5.366 -6.371 2014-03-12T21:37:22.034881792 INFO 2025-06-26 20:14:36,274 calibrate.py _nudge_pos():1806 [1] 581: 0.040 -0.0003582 -0.0005246 5235 17.45 -3.042 -5.571 2014-03-12T21:55:40.039663360 INFO 2025-06-26 20:14:36,771 calibrate.py _nudge_pos():1806 [1] 633: 0.050 0.0001256 -0.0002536 3015 10.05 1.852 -4.678 2014-03-12T22:06:34.034861568 INFO 2025-06-26 20:14:38,692 calibrate.py _nudge_pos():1862 [1] 793: - - - 3 0.01 - - INFO 2025-06-26 20:14:38,693 calibrate.py _nudge_pos():1868 [1] Points in final series = 70013 INFO 2025-06-26 20:14:41,410 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:14:41,940 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 29 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:14:42,355 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 29 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:14:42,357 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.071.02/ctd1.nc INFO 2025-06-26 20:14:42,358 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:14:42,359 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 20:14:42,359 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:14:42,868 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 29 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:14:43,281 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 29 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:14:43,283 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.071.02/ctd2.nc INFO 2025-06-26 20:14:43,284 calibrate.py _range_qc_combined_nc():898 [1] Setting 40 ctd2_salinity values to NaN INFO 2025-06-26 20:14:43,285 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 20:14:43,285 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 20:14:43,285 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.071.02 INFO 2025-06-26 20:14:43,296 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:14:43,977 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94] INFO 2025-06-26 20:14:44,105 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:14:56,773 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.071.02 INFO 2025-06-26 20:14:56,829 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.071.02/dorado_2014.071.02_cal.nc INFO 2025-06-26 20:14:56,942 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, 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, 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 20:14:56,948 process.py align():251 [1] Alignment steps for 2014.071.02 INFO 2025-06-26 20:14:56,983 align.py process_cal():139 [1] Processing dorado_2014.071.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.071.02 INFO 2025-06-26 20:14:57,005 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:14:57,008 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:14:57,058 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:14:57,062 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:14:57,111 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:14:57,115 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:14:57,144 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:14:57,144 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:14:57,163 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:14:57,167 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:14:57,214 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:57,218 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:57,261 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:57,265 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:57,311 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:57,314 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:57,357 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:57,361 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:57,405 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:57,409 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:57,453 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:57,456 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:57,502 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:57,506 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:57,550 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:57,554 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:57,599 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:57,603 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:57,647 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:57,651 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:57,697 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:57,701 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:57,745 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:57,749 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:57,794 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:57,798 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:57,842 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:57,845 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:57,891 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:57,895 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:57,940 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:57,944 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:57,991 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:57,995 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:58,041 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:58,045 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:58,092 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:58,096 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:58,141 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:58,146 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:58,191 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:58,195 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:58,239 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.071.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:14:58,242 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:14:58,300 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:14:58,343 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:14:58,411 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 20:14:58,771 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:14:58,808 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:14:58,843 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:14:58,878 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:14:58,913 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:14:58,950 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:14:58,988 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.071.02/dorado_2014.071.02_align.nc INFO 2025-06-26 20:14:59,105 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_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 20:14:59,108 process.py resample():273 [1] Resampling steps for 2014.071.02 INFO 2025-06-26 20:14:59,108 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:14:59,140 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.071.02/dorado_2014.071.02_align.nc mission netCDF file INFO 2025-06-26 20:14:59,146 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.071.02/dorado_2014.071.02_align.nc mission netCDF file INFO 2025-06-26 20:14:59,147 resample.py get_mission_start_end():1145 [1] navigation: 2014-03-12T18:16:38.249937664 to 2014-03-12T22:10:00.630708992 (0 days 00:00:00.039996928 before mission_end) INFO 2025-06-26 20:14:59,149 resample.py get_mission_start_end():1145 [1] hs2 : 2014-03-12T18:16:00.982490624 to 2014-03-12T22:10:00.670705920 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:14:59,150 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-03-12T18:16:23.720932864 to 2014-03-12T22:10:00.650707456 (0 days 00:00:00.019998464 before mission_end) INFO 2025-06-26 20:14:59,152 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-03-12T18:16:23.690935040 to 2014-03-12T22:10:00.630708992 (0 days 00:00:00.039996928 before mission_end) INFO 2025-06-26 20:14:59,153 resample.py get_mission_start_end():1145 [1] biolume : 2014-03-12T18:15:53.172991232 to 2014-03-12T22:10:00.000717824 (0 days 00:00:00.669988096 before mission_end) INFO 2025-06-26 20:14:59,155 resample.py get_mission_start_end():1145 [1] lopc : 2014-03-12T18:16:04.182922240 to 2014-03-12T18:16:56.682922240 (0 days 03:53:03.987783680 before mission_end) WARNING 2025-06-26 20:14:59,156 resample.py get_mission_start_end():1156 [1] Instrument lopc has a gap > 5 minutes at the end of the mission: 0 days 03:53:03.987783680 INFO 2025-06-26 20:14:59,157 resample.py get_mission_start_end():1145 [1] tailcone : 2014-03-12T18:15:53.652992768 to 2014-03-12T22:10:00.530715648 (0 days 00:00:00.139990272 before mission_end) INFO 2025-06-26 20:14:59,157 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.071.02/dorado_2014.071.02_align.nc mission netCDF file INFO 2025-06-26 20:14:59,158 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,318 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,347 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,376 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,405 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,432 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,458 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,483 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,507 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,529 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,551 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,573 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,596 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,619 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,642 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,664 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,686 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,708 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,732 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,755 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,779 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,802 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,824 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,847 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,870 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,881 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,892 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:14:59,896 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:14:59,896 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:15:00,390 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:15:00,493 resample.py add_biolume_proxies():633 [1] Zero flow values found: 14048 of 14048 - replaced with 350 ml/s INFO 2025-06-26 20:15:00,493 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:15:00,542 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:15:00,563 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:15:00,582 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:15:00,582 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:15:00,597 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:00,597 resample.py resample_variable():1038 [1] Padding lopc_countListSum with 0 days 03:53:03.987783680 of NaNs to the end of mission INFO 2025-06-26 20:15:00,607 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:00,607 resample.py resample_variable():1038 [1] Padding lopc_transCount with 0 days 03:53:03.987783680 of NaNs to the end of mission INFO 2025-06-26 20:15:00,616 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:00,616 resample.py resample_variable():1038 [1] Padding lopc_nonTransCount with 0 days 03:53:03.987783680 of NaNs to the end of mission INFO 2025-06-26 20:15:00,625 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:00,625 resample.py resample_variable():1038 [1] Padding lopc_LCcount with 0 days 03:53:03.987783680 of NaNs to the end of mission INFO 2025-06-26 20:15:00,634 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:00,634 resample.py resample_variable():1038 [1] Padding lopc_flowSpeed with 0 days 03:53:03.987783680 of NaNs to the end of mission INFO 2025-06-26 20:15:00,663 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:15:00,858 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.071.02/dorado_2014.071.02_1S.nc INFO 2025-06-26 20:15:02,480 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:15:12,439 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.071.02/dorado_2014.071.02_1S_Gulper.txt INFO 2025-06-26 20:15:12,440 process.py archive():337 [1] Archiving steps for 2014.071.02 INFO 2025-06-26 20:15:12,440 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.071.02/dorado_2014.071.02, BASE_PATH = /data/auv_data INFO 2025-06-26 20:15:12,440 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.071.02/dorado_2014.071.02 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:15:12,441 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.071.02_1S.nc INFO 2025-06-26 20:15:12,459 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.02/dorado_2014.071.02_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:15:12,460 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.071.02_cal.nc INFO 2025-06-26 20:15:12,559 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.02/dorado_2014.071.02_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:15:12,560 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.071.02_align.nc INFO 2025-06-26 20:15:12,695 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.02/dorado_2014.071.02_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:15:12,713 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014071/2014.071.02 done. INFO 2025-06-26 20:15:12,732 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014071/2014.071.02 done. INFO 2025-06-26 20:15:12,736 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014071/2014.071.02 done. INFO 2025-06-26 20:15:12,752 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014071/2014.071.02 done. INFO 2025-06-26 20:15:12,806 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014071/2014.071.02 done. INFO 2025-06-26 20:15:12,827 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014071/2014.071.02 done. INFO 2025-06-26 20:15:12,842 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014071/2014.071.02 done. INFO 2025-06-26 20:15:12,879 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014071/2014.071.02 done. INFO 2025-06-26 20:15:12,885 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.02/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014071/2014.071.02 done. INFO 2025-06-26 20:15:12,885 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:15:12,887 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.071.02_1S_Gulper.txt INFO 2025-06-26 20:15:12,892 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.071.02/dorado_2014.071.02_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:15:12,892 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.071.02/dorado_2014.071.02_processing.log /Volumes/AUVCTD/surveys/2014/netcdf