INFO 2025-06-26 15:28:10,927 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 15:28:10,927 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Kanna mission - ctdToUse = ctd1 INFO 2025-06-26 15:28:10,927 process.py process_mission():449 [1] Processing AUVCTD mission 2009.313.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 15:28:10,927 process.py download_process():165 [1] Download and processing steps for 2009.313.02 INFO 2025-06-26 15:28:10,928 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2009/2009313/2009.313.02 INFO 2025-06-26 15:28:10,928 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2009/2009313/2009.313.02 to /data/auv_data/dorado/missionlogs/2009.313.02 INFO 2025-06-26 15:28:14,990 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2009.313.02 INFO 2025-06-26 15:28:14,990 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.313.02/ctdDriver.log (6766278 bytes) INFO 2025-06-26 15:28:15,525 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.313.02/ctdDriver.log: [24557 36614] INFO 2025-06-26 15:28:15,548 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.313.02/ctdDriver2.log (6766093 bytes) INFO 2025-06-26 15:28:16,035 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.313.02/ctdDriver2.log: [12814 24555 25295 36612 37941 57271] INFO 2025-06-26 15:28:16,060 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.313.02/gps.log (125636 bytes) INFO 2025-06-26 15:28:16,082 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.313.02/hydroscatlog.log (6463906 bytes) INFO 2025-06-26 15:28:16,742 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.313.02/hydroscatlog.log: [ 1 2 2318 27441 65043 74154 75229] INFO 2025-06-26 15:28:16,761 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.313.02/navigation.log (22663206 bytes) INFO 2025-06-26 15:28:18,374 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.313.02/isuslog.log (450037 bytes) INFO 2025-06-26 15:28:18,420 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.313.02/parosci.log (7872614 bytes) INFO 2025-06-26 15:28:19,092 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.313.02/tailCone.log (955387 bytes) INFO 2025-06-26 15:28:19,216 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.313.02/biolume.log (5239132 bytes) INFO 2025-06-26 15:28:19,711 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 15:28:19,981 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.99 seconds INFO 2025-06-26 15:28:19,981 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2009.313.02/lopc.bin (11379946 bytes) INFO 2025-06-26 15:28:19,982 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 15:28:19 2025 INFO 2025-06-26 15:28:19,982 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2009.313.02/parosci.nc INFO 2025-06-26 15:28:19,982 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 15:28:19,982 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2009.313.02/parosci.nc INFO 2025-06-26 15:28:19,985 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1257783054.1, sensor_off_time = 1257802301.5 INFO 2025-06-26 15:28:19,986 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 19247 seconds. Expecting to read 38494 L frames from the lopc.bin file. INFO 2025-06-26 15:28:19,986 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 38494 records from the lopc.bin file. INFO 2025-06-26 15:28:20,228 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2009-11-09 16:10:54 Z and endTime = 2009-11-09 21:31:41 Z with 38494 records expected to be read from lopc.bin INFO 2025-06-26 15:28:20,228 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2009.313.02/lopc.bin INFO 2025-06-26 15:28:20,228 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2009.313.02/lopc.nc INFO 2025-06-26 15:28:20,228 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2009.313.02/lopc.nc INFO 2025-06-26 15:28:20,229 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2009.313.02 INFO 2025-06-26 15:28:20,229 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 15:28:20,267 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 15:28:20,267 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 15:28:20,267 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-26 15:28:23,328 lopcToNetCDF.py unpackLOPCbin():1013 [1] 10000 16028 4330 1 0 0 0 90 3.1 seconds, last L Frame: 38494 INFO 2025-06-26 15:28:26,405 lopcToNetCDF.py unpackLOPCbin():1013 [1] 20000 26108 8590 1 0 0 0 170 3.1 seconds, last L Frame: 38494 INFO 2025-06-26 15:28:29,518 lopcToNetCDF.py unpackLOPCbin():1013 [1] 30000 36190 12872 1 0 0 0 252 3.1 seconds, last L Frame: 38494 INFO 2025-06-26 15:28:31,988 lopcToNetCDF.py main():2345 [1] >>> Done reading file. INFO 2025-06-26 15:28:31,988 lopcToNetCDF.py main():2346 [1] lFrameCount = 38186, mFrameCount = 15619 INFO 2025-06-26 15:28:31,988 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2009.313.02/parosci.nc INFO 2025-06-26 15:28:31,988 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 15:28:31,988 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2009.313.02/parosci.nc INFO 2025-06-26 15:28:31,991 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1257783054.1, sensor_off_time = 1257802301.5 INFO 2025-06-26 15:28:31,991 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 19247 seconds. Expecting to read 38494 L frames from the lopc.bin file. INFO 2025-06-26 15:28:31,991 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 38494 records from the lopc.bin file. INFO 2025-06-26 15:28:31,991 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 3004 and len(sampleCountList) = 38503 INFO 2025-06-26 15:28:31,995 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [] INFO 2025-06-26 15:28:31,995 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [ 3004 3005 3006 ... 44439 44440 44441] INFO 2025-06-26 15:28:31,995 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 15:28:31,995 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-26 15:28:31,995 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [1 1 1 ... 1 1 1] INFO 2025-06-26 15:28:31,996 lopcToNetCDF.py deSpike():1590 [1] Found 1 spike indicators at indices: [7] INFO 2025-06-26 15:28:31,996 lopcToNetCDF.py deSpike():1595 [1] Identifying nature of spike value = 5946 at index = 7 INFO 2025-06-26 15:28:31,996 lopcToNetCDF.py deSpike():1714 [1] This is the last element in spike_indx. No need to deSpike(). INFO 2025-06-26 15:28:31,996 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [ 3004 3005 3006 ... 44439 44440 44441] INFO 2025-06-26 15:28:31,996 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [ 3004 3005 3006 ... 44439 44440 44441] with len(correctedSampleCountList) = 38503 INFO 2025-06-26 15:28:31,996 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 3004 from all values of correctedSampleCountList INFO 2025-06-26 15:28:31,996 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 15:28:31,996 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [0.00000e+00 5.00000e-01 1.00000e+00 ... 2.07175e+04 2.07180e+04 2.07185e+04] INFO 2025-06-26 15:28:31,997 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.25778305e+09 1.25778305e+09 1.25778306e+09 ... 1.25780377e+09 1.25780377e+09 1.25780377e+09] INFO 2025-06-26 15:28:31,997 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1257783054.1 1257783054.6, ..., timestampArray[-2:] = 1257803772.1 1257803772.6] INFO 2025-06-26 15:28:32,036 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1257783054.1403556), np.float64(1257783054.6403556)], ..., timestampList[-2:] = [np.float64(1257803772.1403556), np.float64(1257803772.6403556)]] INFO 2025-06-26 15:28:32,036 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 38503) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 15:28:32,036 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [38156, 38177] INFO 2025-06-26 15:28:32,037 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 1818 INFO 2025-06-26 15:28:32,037 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 38503 INFO 2025-06-26 15:28:32,037 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1257783054.1403556), np.float64(1257783054.6403556)], ..., timestampList[-2:] = [np.float64(1257803772.1403556), np.float64(1257803772.6403556)]] INFO 2025-06-26 15:28:32,037 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 38503) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 15:28:32,037 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(38155), np.int32(38176)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 15:28:32,039 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 1818 INFO 2025-06-26 15:28:32,039 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 ERROR 2025-06-26 15:28:32,043 lopcToNetCDF.py constructTimestampList():1501 [1] Cannot interpolate to cFrameEsecsListInterpolated: array of sample points is empty INFO 2025-06-26 15:28:32,057 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 1818 INFO 2025-06-26 15:28:32,057 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1257784531.1403556)], ..., tsList[-2:] = [np.float64(1257803599.1403556), np.float64(1257803609.6403556)] INFO 2025-06-26 15:28:32,057 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2009-11-09 16:35:31 Z INFO 2025-06-26 15:28:32,057 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2009-11-09 21:53:29 Z INFO 2025-06-26 15:28:32,058 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 38186 INFO 2025-06-26 15:28:32,058 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [-9999], ..., cFrameEsecsList[-2:] = [-9999, -9999] INFO 2025-06-26 15:28:32,058 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 1969-12-31 21:13:21 Z INFO 2025-06-26 15:28:32,058 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 1969-12-31 21:13:21 Z INFO 2025-06-26 15:28:32,062 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2009.313.02/lopc.nc INFO 2025-06-26 15:28:32,062 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 15:28:32 2025 Elapsed processing time from start of processing = 12 seconds INFO 2025-06-26 15:28:32,063 process.py calibrate():227 [1] Calibration steps for 2009.313.02 INFO 2025-06-26 15:28:32,317 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 15:28:32,318 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 15:28:33,001 calibrate.py _nudge_pos():1806 [1] 99: 0.040 -0.0000370 -0.0000024 25 0.08 -68.649 -5.567 2009-11-09T16:12:35.703397888 INFO 2025-06-26 15:28:33,012 calibrate.py _nudge_pos():1806 [1] 100: 0.030 0.0038506 -0.0000929 9944 33.18 17.224 -0.519 2009-11-09T16:45:46.707004928 INFO 2025-06-26 15:28:33,071 calibrate.py _nudge_pos():1806 [1] 106: 0.040 0.0000781 -0.0000059 105 0.35 33.425 -3.160 2009-11-09T16:46:12.705223936 INFO 2025-06-26 15:28:34,603 calibrate.py _nudge_pos():1806 [1] 266: 0.050 0.0021255 0.0000811 9780 32.61 9.673 0.461 2009-11-09T17:21:28.700268544 INFO 2025-06-26 15:28:35,894 calibrate.py _nudge_pos():1806 [1] 400: 0.050 0.0000070 0.0000026 55 0.18 5.749 2.649 2009-11-09T17:23:52.700403712 INFO 2025-06-26 15:28:35,994 calibrate.py _nudge_pos():1806 [1] 410: 0.050 0.0031296 0.0001391 9853 32.85 14.139 0.785 2009-11-09T17:56:52.704764160 INFO 2025-06-26 15:28:37,607 calibrate.py _nudge_pos():1806 [1] 574: 0.050 0.0041431 -0.0009862 9952 33.18 18.534 -5.508 2009-11-09T18:32:46.707204864 INFO 2025-06-26 15:28:37,684 calibrate.py _nudge_pos():1806 [1] 582: 0.060 0.0000849 0.0000069 185 0.61 20.559 2.071 2009-11-09T18:33:30.704190976 INFO 2025-06-26 15:28:39,030 calibrate.py _nudge_pos():1806 [1] 722: 0.060 0.0001160 0.0000069 75 0.25 69.801 5.204 2009-11-09T18:36:04.703641088 INFO 2025-06-26 15:28:39,078 calibrate.py _nudge_pos():1806 [1] 727: 0.060 0.0022893 -0.0003377 9515 31.73 10.707 -1.972 2009-11-09T19:07:52.702934272 INFO 2025-06-26 15:28:39,127 calibrate.py _nudge_pos():1806 [1] 732: 0.060 0.0000451 -0.0000140 165 0.55 12.238 -4.759 2009-11-09T19:08:29.700399872 INFO 2025-06-26 15:28:40,700 calibrate.py _nudge_pos():1806 [1] 891: 0.070 0.0035695 -0.0007235 10242 34.15 15.516 -3.926 2009-11-09T19:45:16.699209984 INFO 2025-06-26 15:28:42,234 calibrate.py _nudge_pos():1806 [1] 1048: 0.070 0.0012701 0.0009664 9717 32.40 5.818 5.528 2009-11-09T20:20:16.705349632 INFO 2025-06-26 15:28:42,661 calibrate.py _nudge_pos():1806 [1] 1090: 0.080 0.0000077 0.0000084 65 0.21 5.356 7.305 2009-11-09T20:21:10.701650688 INFO 2025-06-26 15:28:43,707 calibrate.py _nudge_pos():1806 [1] 1195: 0.080 0.0031001 -0.0001877 10185 33.96 13.549 -1.024 2009-11-09T20:56:52.704913408 INFO 2025-06-26 15:28:44,753 calibrate.py _nudge_pos():1806 [1] 1300: 0.010 0.0000251 -0.0000017 81 0.27 13.997 -1.195 2009-11-09T20:58:52.906679040 INFO 2025-06-26 15:28:45,113 calibrate.py _nudge_pos():1806 [1] 1336: 0.080 -0.0008700 0.0009838 7680 25.61 -5.042 7.117 2009-11-09T21:25:04.699003904 INFO 2025-06-26 15:28:49,090 calibrate.py _nudge_pos():1862 [1] 1699: - - - 4 0.01 - - INFO 2025-06-26 15:28:49,090 calibrate.py _nudge_pos():1868 [1] Points in final series = 96021 WARNING 2025-06-26 15:28:49,219 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 15:28:58,895 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1 of 76932 INFO 2025-06-26 15:28:59,479 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 15:29:05,012 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:29:05,605 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:29:05,607 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2009.313.02/ctd1.nc INFO 2025-06-26 15:29:05,608 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 15:29:05,608 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 15:29:05,608 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 15:29:09,845 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:29:10,438 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:29:10,440 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2009.313.02/ctd2.nc INFO 2025-06-26 15:29:10,441 calibrate.py _range_qc_combined_nc():898 [1] Setting 171 ctd2_salinity values to NaN INFO 2025-06-26 15:29:10,442 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 15:29:10,442 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 15:29:10,473 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 15:29:11,365 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 65 66 67 68 240 241 242 243 244 245 246 1800 1801 1802 1803 1804 1805 1806 8700 8701 8702 8703 8704 8705 8706 8707 8708 8709 12960 12961 12962 12963 12964 12965 14580 14581 14582 14583 14584 14585 14586 14587 14588 24000 24001 24002 24003 24004 24005 24006 24007 24420 24421 24422 24423 24424 24425 24426 24427 24428 24429 24430 24431 24432 43620 43621 43622 47040 47041 47042 47400 47401 47402 47403 47640 47641 47642 47643 48360 51840 51841 51842 51843 51844 51845 51846 51847 51848 51849 51850 51851 63780 63781 63782 63783 63784 63785 63786 81840 81841 81842 95400 95401 95402 95403 95404 95405 95406 107400 107401 107402 107403 107404 107405 107406 107407 107408 107409 112020 112021 112022 112023 112024 112025 112026 112027 112028 112029 112030 112031 116040 116041 116042 116043 116044 116045 116046 116047 116048 116049 116050 116051 117180 117181 117182 117183 117184 117185 125280 125281 125282 125283 125284 125285 125286 125287 125288 125289 125290 125291 125460 125461 125462 125463 125464 125465 125466 125467 125468 125469 125470 125471 125472 134820 134821 134822 134823 134824 134825 134826 134827 134828 134829 134830 134831 134832 134833 134834 135000 135001 135002 135003 135004 135005 135006 135007 135008 135009 135010 135011 135012 135013 135014 141900 141901 141902 141903 141904 141905 141906 141907 141908 141909 141910 141911 141912 141913 141914 146400 146401 146402 162780 162781 162782 162783 171780 171781 171782 171783 171784 193980 193981 193982 193983 193984 193985 193986 193987 193988 213300 213301 213302 213303 240900 240901 240902 240903 240904 240905 240906 240907 240908 242760 242761 242762 242763 244020 244021 244022 244023 244024 244025 244026 244027 253560 262140 262320 262321 262322 262323 262500 268800 268801 268802 268803 268804 268805 268806 268807 268808 268809 289320 289321 289322 289323 311640 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521228 547380 547381 547382 547383 547384 547385 547386 547387 547388 547389 550980 550981 550982 550983 550984 550985 550986 550987 550988 578520 578521 578522 578523 578524 578525 578526 578527 578528 578529 578530 578531 579600 579601 579602 579603 579604 579605 579606 579607 579608 579609 579610 579611 579612 581640 581641 581642 581643 581644 581645 594960 594961 594962 594963 594964 594965 594966 594967 594968 594969 628980 628981 628982 628983 628984 628985 628986 638820 638821 638822 638823 638824 638825 638826 638827 638828 638829 638830 638831 638832 654060 654061 654062 654063 654064 654065 654066 654067 659460 659461 659462 659463 659464 659465 659466 659467 659468 659469 664380 664381 664382 664383 664384 664385 664386 664387 664388 690540 690541 690542 690543 690544 690545 690546 690547 690548 690549 690550 691860 691861 691862 691863 691864 691865 691866 691867 694320 694321 694322 694323 694324 694325 694326 703680 703681 703682 703683 703684 703685 703686 704280 723600 723601 723602 771240 771241 771242 771243 771244 771245 771246 771420 771421 771422 771423 771424 771425 771426 773220 779880 779881 779882 779883 779884 779885 780060 780061 786600 786601 786602 786603 786604 786605 786606 807060 807061 807062 810540 810541 810542 836280 856740 856741 856742 856743 856744 856745 856746 856747 856748 856749 856980 897360 897361 897362 897363 897364 897365 897366 897367 897368 897369 897480 897481 897482 897483 897484 897485 897486 897487 897488 897489 897490 897491 897492 905880 905881 905882 905883 905884 905885 905886 905887 905888 905889 956040 956041 1032300 1032301 1032302 1032303 1032304 1032305 1044300 1044301 1044302 1061040 1061041 1061042 1061043 1065420 1065421 1065422 1065423 1068060 1068061 1068062 1068063 1068064 1068065 1068066 1068067 1068068 1068069 1068070 1068071 1096140 1096141 1096142 1113300 1113301 1113302 1113303 1113304 1113305 1113306 1113307 1113308 1113309 1113310 1113311 1113312 1113313 1113314 1113315 1113316 1113317 1113318 1131660 1131661 1131662 1131663 1131664 1131665 1131666 1131667 1131668 1131669 1131670 1134600 1144980 1144981 1144982 1144983 1144984 1144985 1144986 1154280 1154281 1154282 1154283 1154284 1154285 1154286] INFO 2025-06-26 15:29:11,534 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 15:29:11,540 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 15:29:11,550 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2009.313.02 INFO 2025-06-26 15:29:11,568 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2009.313.02/dorado_2009.313.02_cal.nc INFO 2025-06-26 15:29:17,570 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 15:29:17,577 process.py align():251 [1] Alignment steps for 2009.313.02 INFO 2025-06-26 15:29:17,607 align.py process_cal():139 [1] Processing dorado_2009.313.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2009.313.02 INFO 2025-06-26 15:29:17,636 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:29:17,639 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:29:17,706 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:29:17,710 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:29:17,775 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:29:17,780 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:29:17,820 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 15:29:17,820 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 15:29:17,845 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:29:17,849 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:29:17,912 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.313.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:29:17,916 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:29:17,973 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.313.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:29:17,978 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:29:18,038 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.313.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:29:18,042 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:29:18,098 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.313.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:29:18,102 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:29:18,161 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.313.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:29:18,165 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:29:18,222 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.313.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:29:18,227 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:29:18,285 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.313.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:29:18,290 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:29:18,347 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.313.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:29:18,351 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:29:18,409 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.313.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:29:18,413 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:29:18,470 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.313.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:29:18,475 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:29:18,533 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.313.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:29:18,537 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:29:18,593 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.313.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:29:18,598 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:29:18,655 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.313.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:29:18,658 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:29:18,715 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.313.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:29:18,720 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:29:18,778 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.313.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:29:18,783 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:29:18,839 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.313.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:29:18,843 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:29:18,901 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.313.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:29:18,906 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:29:18,962 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.313.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:29:18,967 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:29:19,026 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.313.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:29:19,031 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:29:19,087 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.313.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:29:19,092 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:29:19,160 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:29:19,206 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:29:19,255 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:29:19,306 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 15:29:19,354 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 15:29:19,397 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 15:29:19,439 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 15:29:19,482 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 15:29:19,525 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 15:29:19,570 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.03 INFO 2025-06-26 15:29:19,591 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2009.313.02/dorado_2009.313.02_align.nc INFO 2025-06-26 15:29:19,675 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 15:29:19,678 process.py resample():273 [1] Resampling steps for 2009.313.02 INFO 2025-06-26 15:29:19,679 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 15:29:19,704 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.313.02/dorado_2009.313.02_align.nc mission netCDF file INFO 2025-06-26 15:29:19,711 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.313.02/dorado_2009.313.02_align.nc mission netCDF file INFO 2025-06-26 15:29:19,712 resample.py get_mission_start_end():1145 [1] navigation: 2009-11-09T16:11:26.908110848 to 2009-11-09T21:31:41.501820928 (0 days 00:21:48.138534656 before mission_end) WARNING 2025-06-26 15:29:19,713 resample.py get_mission_start_end():1156 [1] Instrument navigation has a gap > 5 minutes at the end of the mission: 0 days 00:21:48.138534656 INFO 2025-06-26 15:29:19,714 resample.py get_mission_start_end():1145 [1] hs2 : 2009-11-09T16:10:59.619980288 to 2009-11-09T21:31:41.541818368 (0 days 00:21:48.098537216 before mission_end) WARNING 2025-06-26 15:29:19,715 resample.py get_mission_start_end():1156 [1] Instrument hs2 has a gap > 5 minutes at the end of the mission: 0 days 00:21:48.098537216 INFO 2025-06-26 15:29:19,716 resample.py get_mission_start_end():1145 [1] ctd1 : 2009-11-09T16:11:21.238499072 to 2009-11-09T21:31:41.341831936 (0 days 00:21:48.298523648 before mission_end) WARNING 2025-06-26 15:29:19,717 resample.py get_mission_start_end():1156 [1] Instrument ctd1 has a gap > 5 minutes at the end of the mission: 0 days 00:21:48.298523648 INFO 2025-06-26 15:29:19,718 resample.py get_mission_start_end():1145 [1] ctd2 : 2009-11-09T16:11:21.758463744 to 2009-11-09T21:31:41.331832576 (0 days 00:21:48.308523008 before mission_end) WARNING 2025-06-26 15:29:19,719 resample.py get_mission_start_end():1156 [1] Instrument ctd2 has a gap > 5 minutes at the end of the mission: 0 days 00:21:48.308523008 INFO 2025-06-26 15:29:19,720 resample.py get_mission_start_end():1145 [1] isus : 2009-11-09T16:12:08.985228288 to 2009-11-09T21:31:40.991856128 (0 days 00:21:48.648499456 before mission_end) WARNING 2025-06-26 15:29:19,721 resample.py get_mission_start_end():1156 [1] Instrument isus has a gap > 5 minutes at the end of the mission: 0 days 00:21:48.648499456 INFO 2025-06-26 15:29:19,722 resample.py get_mission_start_end():1145 [1] biolume : 2009-11-09T16:10:53.000399360 to 2009-11-09T21:31:40.831832576 (0 days 00:21:48.808523008 before mission_end) WARNING 2025-06-26 15:29:19,723 resample.py get_mission_start_end():1156 [1] Instrument biolume has a gap > 5 minutes at the end of the mission: 0 days 00:21:48.808523008 INFO 2025-06-26 15:29:19,724 resample.py get_mission_start_end():1145 [1] lopc : 2009-11-09T16:35:31.140355584 to 2009-11-09T21:53:29.640355584 (0 days 00:00:00 before mission_end) INFO 2025-06-26 15:29:19,725 resample.py get_mission_start_end():1145 [1] tailcone : 2009-11-09T16:10:58.630048000 to 2009-11-09T21:31:41.331832576 (0 days 00:21:48.308523008 before mission_end) WARNING 2025-06-26 15:29:19,726 resample.py get_mission_start_end():1156 [1] Instrument tailcone has a gap > 5 minutes at the end of the mission: 0 days 00:21:48.308523008 INFO 2025-06-26 15:29:19,726 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.313.02/dorado_2009.313.02_align.nc mission netCDF file INFO 2025-06-26 15:29:19,727 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:19,940 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:19,940 resample.py resample_variable():1038 [1] Padding navigation_roll with 0 days 00:21:48.138534656 of NaNs to the end of mission INFO 2025-06-26 15:29:19,978 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:19,979 resample.py resample_variable():1038 [1] Padding navigation_pitch with 0 days 00:21:48.138534656 of NaNs to the end of mission INFO 2025-06-26 15:29:20,018 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,019 resample.py resample_variable():1038 [1] Padding navigation_yaw with 0 days 00:21:48.138534656 of NaNs to the end of mission INFO 2025-06-26 15:29:20,059 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,060 resample.py resample_variable():1038 [1] Padding navigation_mWaterSpeed with 0 days 00:21:48.138534656 of NaNs to the end of mission INFO 2025-06-26 15:29:20,097 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,098 resample.py resample_variable():1038 [1] Padding hs2_bbp420 with 0 days 00:21:48.098537216 of NaNs to the end of mission INFO 2025-06-26 15:29:20,132 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,133 resample.py resample_variable():1038 [1] Padding hs2_bbp700 with 0 days 00:21:48.098537216 of NaNs to the end of mission INFO 2025-06-26 15:29:20,165 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,166 resample.py resample_variable():1038 [1] Padding hs2_fl700 with 0 days 00:21:48.098537216 of NaNs to the end of mission INFO 2025-06-26 15:29:20,198 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,198 resample.py resample_variable():1038 [1] Padding ctd1_temperature with 0 days 00:21:48.298523648 of NaNs to the end of mission INFO 2025-06-26 15:29:20,230 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,230 resample.py resample_variable():1038 [1] Padding ctd1_conductivity with 0 days 00:21:48.298523648 of NaNs to the end of mission INFO 2025-06-26 15:29:20,271 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,272 resample.py resample_variable():1038 [1] Padding ctd1_salinity with 0 days 00:21:48.298523648 of NaNs to the end of mission INFO 2025-06-26 15:29:20,304 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,304 resample.py resample_variable():1038 [1] Padding ctd1_temperature_onboard with 0 days 00:21:48.298523648 of NaNs to the end of mission INFO 2025-06-26 15:29:20,336 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,336 resample.py resample_variable():1038 [1] Padding ctd1_conductivity_onboard with 0 days 00:21:48.298523648 of NaNs to the end of mission INFO 2025-06-26 15:29:20,368 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,368 resample.py resample_variable():1038 [1] Padding ctd1_dissolvedO2 with 0 days 00:21:48.298523648 of NaNs to the end of mission INFO 2025-06-26 15:29:20,400 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,400 resample.py resample_variable():1038 [1] Padding ctd1_oxygen_mll with 0 days 00:21:48.298523648 of NaNs to the end of mission INFO 2025-06-26 15:29:20,431 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,431 resample.py resample_variable():1038 [1] Padding ctd1_oxygen_umolkg with 0 days 00:21:48.298523648 of NaNs to the end of mission INFO 2025-06-26 15:29:20,463 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,463 resample.py resample_variable():1038 [1] Padding ctd1_flow1 with 0 days 00:21:48.298523648 of NaNs to the end of mission INFO 2025-06-26 15:29:20,497 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,497 resample.py resample_variable():1038 [1] Padding ctd2_temperature with 0 days 00:21:48.308523008 of NaNs to the end of mission INFO 2025-06-26 15:29:20,531 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,531 resample.py resample_variable():1038 [1] Padding ctd2_conductivity with 0 days 00:21:48.308523008 of NaNs to the end of mission INFO 2025-06-26 15:29:20,565 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,566 resample.py resample_variable():1038 [1] Padding ctd2_salinity with 0 days 00:21:48.308523008 of NaNs to the end of mission INFO 2025-06-26 15:29:20,598 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,598 resample.py resample_variable():1038 [1] Padding ctd2_temperature_onboard with 0 days 00:21:48.308523008 of NaNs to the end of mission INFO 2025-06-26 15:29:20,630 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,630 resample.py resample_variable():1038 [1] Padding ctd2_conductivity_onboard with 0 days 00:21:48.308523008 of NaNs to the end of mission INFO 2025-06-26 15:29:20,662 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,663 resample.py resample_variable():1038 [1] Padding ctd2_flow2 with 0 days 00:21:48.308523008 of NaNs to the end of mission INFO 2025-06-26 15:29:20,680 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,680 resample.py resample_variable():1038 [1] Padding isus_nitrate with 0 days 00:21:48.648499456 of NaNs to the end of mission INFO 2025-06-26 15:29:20,696 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,696 resample.py resample_variable():1038 [1] Padding isus_temp with 0 days 00:21:48.648499456 of NaNs to the end of mission INFO 2025-06-26 15:29:20,710 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,710 resample.py resample_variable():1038 [1] Padding isus_quality with 0 days 00:21:48.648499456 of NaNs to the end of mission INFO 2025-06-26 15:29:20,727 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,727 resample.py resample_variable():1038 [1] Padding biolume_flow with 0 days 00:21:48.808523008 of NaNs to the end of mission INFO 2025-06-26 15:29:20,739 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,749 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,758 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,767 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,777 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,791 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 15:29:20,791 resample.py resample_variable():1038 [1] Padding tailcone_propRpm with 0 days 00:21:48.308523008 of NaNs to the end of mission INFO 2025-06-26 15:29:21,006 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2009.313.02/dorado_2009.313.02_1S.nc INFO 2025-06-26 15:29:24,259 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 15:29:38,625 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2009.313.02/dorado_2009.313.02_1S_Gulper.txt INFO 2025-06-26 15:29:38,626 process.py archive():337 [1] Archiving steps for 2009.313.02 INFO 2025-06-26 15:29:38,626 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2009.313.02/dorado_2009.313.02, BASE_PATH = /data/auv_data INFO 2025-06-26 15:29:38,627 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2009.313.02/dorado_2009.313.02 files to /Volumes/AUVCTD/surveys/2009/netcdf INFO 2025-06-26 15:29:38,628 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.313.02_1S.nc INFO 2025-06-26 15:29:38,646 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.313.02/dorado_2009.313.02_1S.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:29:38,647 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.313.02_cal.nc INFO 2025-06-26 15:29:38,718 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.313.02/dorado_2009.313.02_cal.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:29:38,719 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.313.02_align.nc INFO 2025-06-26 15:29:38,785 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.313.02/dorado_2009.313.02_align.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:29:38,808 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.313.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009313/2009.313.02 done. INFO 2025-06-26 15:29:38,830 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.313.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009313/2009.313.02 done. INFO 2025-06-26 15:29:38,834 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.313.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009313/2009.313.02 done. INFO 2025-06-26 15:29:38,856 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.313.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009313/2009.313.02 done. INFO 2025-06-26 15:29:38,921 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.313.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009313/2009.313.02 done. INFO 2025-06-26 15:29:38,927 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.313.02/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009313/2009.313.02 done. INFO 2025-06-26 15:29:38,950 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.313.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009313/2009.313.02 done. INFO 2025-06-26 15:29:38,957 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.313.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009313/2009.313.02 done. INFO 2025-06-26 15:29:39,007 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.313.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009313/2009.313.02 done. INFO 2025-06-26 15:29:39,070 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.313.02/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009313/2009.313.02 done. INFO 2025-06-26 15:29:39,070 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 15:29:39,071 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2009/odv/dorado_2009.313.02_1S_Gulper.txt INFO 2025-06-26 15:29:39,076 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2009.313.02/dorado_2009.313.02_1S_Gulper.txt /Volumes/AUVCTD/surveys/2009/odv done. INFO 2025-06-26 15:29:39,077 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.313.02/dorado_2009.313.02_processing.log /Volumes/AUVCTD/surveys/2009/netcdf