INFO 2025-06-26 15:12:39,793 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 15:12:39,793 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Short missions, The .01 mission was very short but two gulpers fired - ctdToUse = ctd1 INFO 2025-06-26 15:12:39,794 process.py process_mission():449 [1] Processing AUVCTD mission 2009.278.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 15:12:39,794 process.py download_process():165 [1] Download and processing steps for 2009.278.02 INFO 2025-06-26 15:12:39,794 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2009/2009278/2009.278.02 INFO 2025-06-26 15:12:39,794 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2009/2009278/2009.278.02 to /data/auv_data/dorado/missionlogs/2009.278.02 INFO 2025-06-26 15:12:46,935 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2009.278.02 INFO 2025-06-26 15:12:46,935 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.278.02/ctdDriver.log (25772934 bytes) INFO 2025-06-26 15:12:48,801 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.278.02/ctdDriver.log: [119705 152255 180695 205232 213215 216242] INFO 2025-06-26 15:12:48,883 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.278.02/ctdDriver2.log (25772159 bytes) INFO 2025-06-26 15:12:50,714 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.278.02/ctdDriver2.log: [163855 194908] INFO 2025-06-26 15:12:50,797 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.278.02/gps.log (352652 bytes) INFO 2025-06-26 15:12:50,842 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.278.02/hydroscatlog.log (22547722 bytes) INFO 2025-06-26 15:12:53,097 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2009.278.02/hydroscatlog.log: [ 69146 196546 221410] INFO 2025-06-26 15:12:53,167 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.278.02/navigation.log (79186150 bytes) INFO 2025-06-26 15:12:58,839 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.278.02/isuslog.log (1561429 bytes) INFO 2025-06-26 15:12:58,991 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.278.02/parosci.log (27497798 bytes) INFO 2025-06-26 15:13:01,332 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.278.02/tailCone.log (16110379 bytes) INFO 2025-06-26 15:13:03,293 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.278.02/biolume.log (18268748 bytes) INFO 2025-06-26 15:13:05,031 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 15:13:05,948 logs2netcdfs.py download_process_logs():807 [1] Time to process: 19.01 seconds INFO 2025-06-26 15:13:05,948 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2009.278.02/lopc.bin (66847489 bytes) INFO 2025-06-26 15:13:05,948 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 15:13:05 2025 INFO 2025-06-26 15:13:05,948 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2009.278.02/parosci.nc INFO 2025-06-26 15:13:05,948 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 15:13:05,949 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2009.278.02/parosci.nc INFO 2025-06-26 15:13:05,952 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1254775876.1, sensor_off_time = 1254843020.8 INFO 2025-06-26 15:13:05,952 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 67144 seconds. Expecting to read 134288 L frames from the lopc.bin file. INFO 2025-06-26 15:13:05,952 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 134288 records from the lopc.bin file. INFO 2025-06-26 15:13:06,754 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2009-10-05 20:51:16 Z and endTime = 2009-10-06 15:30:20 Z with 134288 records expected to be read from lopc.bin INFO 2025-06-26 15:13:06,754 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2009.278.02/lopc.bin INFO 2025-06-26 15:13:06,754 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2009.278.02/lopc.nc INFO 2025-06-26 15:13:06,754 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2009.278.02/lopc.nc INFO 2025-06-26 15:13:06,755 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2009.278.02 INFO 2025-06-26 15:13:06,755 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 15:13:06,879 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 15:13:06,879 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 15:13:06,879 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-26 15:13:14,363 lopcToNetCDF.py unpackLOPCbin():1013 [1] 10000 18856 18581 0 0 0 0 89 7.6 seconds, last L Frame: 134288 INFO 2025-06-26 15:13:21,653 lopcToNetCDF.py unpackLOPCbin():1013 [1] 20000 28962 36234 0 0 0 0 195 7.3 seconds, last L Frame: 134288 INFO 2025-06-26 15:13:27,453 lopcToNetCDF.py unpackLOPCbin():1013 [1] 30000 39039 49527 0 0 0 0 272 5.8 seconds, last L Frame: 134288 INFO 2025-06-26 15:13:35,947 lopcToNetCDF.py unpackLOPCbin():1013 [1] 40000 49136 71293 0 0 0 0 369 8.5 seconds, last L Frame: 134288 INFO 2025-06-26 15:13:43,044 lopcToNetCDF.py unpackLOPCbin():1013 [1] 50000 59213 88743 0 0 0 0 446 7.1 seconds, last L Frame: 134288 INFO 2025-06-26 15:13:49,189 lopcToNetCDF.py unpackLOPCbin():1013 [1] 60000 4023 103435 0 0 0 0 792 6.1 seconds, last L Frame: 134288 INFO 2025-06-26 15:13:54,296 lopcToNetCDF.py unpackLOPCbin():1013 [1] 70000 14099 115123 0 0 0 0 868 5.1 seconds, last L Frame: 134288 INFO 2025-06-26 15:13:59,825 lopcToNetCDF.py unpackLOPCbin():1013 [1] 80000 24190 128458 0 0 0 0 959 5.5 seconds, last L Frame: 134288 INFO 2025-06-26 15:14:06,322 lopcToNetCDF.py unpackLOPCbin():1013 [1] 90000 34282 143926 0 0 0 0 1051 6.5 seconds, last L Frame: 134288 INFO 2025-06-26 15:14:12,821 lopcToNetCDF.py unpackLOPCbin():1013 [1] 100000 44373 159744 0 0 0 0 1142 6.5 seconds, last L Frame: 134288 INFO 2025-06-26 15:14:20,966 lopcToNetCDF.py unpackLOPCbin():1013 [1] 110000 54468 180236 0 0 0 0 1237 8.1 seconds, last L Frame: 134288 INFO 2025-06-26 15:14:27,536 lopcToNetCDF.py unpackLOPCbin():1013 [1] 120000 64551 195948 0 0 0 0 1320 6.6 seconds, last L Frame: 134288 INFO 2025-06-26 15:14:34,161 lopcToNetCDF.py unpackLOPCbin():1013 [1] 130000 9366 212113 2 1 0 0 1667 6.6 seconds, last L Frame: 134288 INFO 2025-06-26 15:14:35,535 lopcToNetCDF.py main():2345 [1] >>> Done reading file. INFO 2025-06-26 15:14:35,535 lopcToNetCDF.py main():2346 [1] lFrameCount = 132600, mFrameCount = 215280 INFO 2025-06-26 15:14:35,535 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2009.278.02/parosci.nc INFO 2025-06-26 15:14:35,535 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 15:14:35,535 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2009.278.02/parosci.nc INFO 2025-06-26 15:14:35,539 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1254775876.1, sensor_off_time = 1254843020.8 INFO 2025-06-26 15:14:35,539 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 67144 seconds. Expecting to read 134288 L frames from the lopc.bin file. INFO 2025-06-26 15:14:35,539 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 134288 records from the lopc.bin file. INFO 2025-06-26 15:14:35,539 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 8139 and len(sampleCountList) = 134278 INFO 2025-06-26 15:14:35,551 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [ 56762 122294] INFO 2025-06-26 15:14:35,551 lopcToNetCDF.py correctSampleCountList():1740 [1] Assigning values from slice starting at index 56762, i = 1 INFO 2025-06-26 15:14:35,554 lopcToNetCDF.py correctSampleCountList():1740 [1] Assigning values from slice starting at index 122294, i = 2 INFO 2025-06-26 15:14:35,555 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [ 8139 8140 8770 ... 143059 143060 143061] INFO 2025-06-26 15:14:35,555 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 15:14:35,555 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 510 stuck values at indices: [ 56507 56508 56509 56510 56511 56512 56513 56514 56515 56516 56517 56518 56519 56520 56521 56522 56523 56524 56525 56526 56527 56528 56529 56530 56531 56532 56533 56534 56535 56536 56537 56538 56539 56540 56541 56542 56543 56544 56545 56546 56547 56548 56549 56550 56551 56552 56553 56554 56555 56556 56557 56558 56559 56560 56561 56562 56563 56564 56565 56566 56567 56568 56569 56570 56571 56572 56573 56574 56575 56576 56577 56578 56579 56580 56581 56582 56583 56584 56585 56586 56587 56588 56589 56590 56591 56592 56593 56594 56595 56596 56597 56598 56599 56600 56601 56602 56603 56604 56605 56606 56607 56608 56609 56610 56611 56612 56613 56614 56615 56616 56617 56618 56619 56620 56621 56622 56623 56624 56625 56626 56627 56628 56629 56630 56631 56632 56633 56634 56635 56636 56637 56638 56639 56640 56641 56642 56643 56644 56645 56646 56647 56648 56649 56650 56651 56652 56653 56654 56655 56656 56657 56658 56659 56660 56661 56662 56663 56664 56665 56666 56667 56668 56669 56670 56671 56672 56673 56674 56675 56676 56677 56678 56679 56680 56681 56682 56683 56684 56685 56686 56687 56688 56689 56690 56691 56692 56693 56694 56695 56696 56697 56698 56699 56700 56701 56702 56703 56704 56705 56706 56707 56708 56709 56710 56711 56712 56713 56714 56715 56716 56717 56718 56719 56720 56721 56722 56723 56724 56725 56726 56727 56728 56729 56730 56731 56732 56733 56734 56735 56736 56737 56738 56739 56740 56741 56742 56743 56744 56745 56746 56747 56748 56749 56750 56751 56752 56753 56754 56755 56756 56757 56758 56759 56760 56761 122039 122040 122041 122042 122043 122044 122045 122046 122047 122048 122049 122050 122051 122052 122053 122054 122055 122056 122057 122058 122059 122060 122061 122062 122063 122064 122065 122066 122067 122068 122069 122070 122071 122072 122073 122074 122075 122076 122077 122078 122079 122080 122081 122082 122083 122084 122085 122086 122087 122088 122089 122090 122091 122092 122093 122094 122095 122096 122097 122098 122099 122100 122101 122102 122103 122104 122105 122106 122107 122108 122109 122110 122111 122112 122113 122114 122115 122116 122117 122118 122119 122120 122121 122122 122123 122124 122125 122126 122127 122128 122129 122130 122131 122132 122133 122134 122135 122136 122137 122138 122139 122140 122141 122142 122143 122144 122145 122146 122147 122148 122149 122150 122151 122152 122153 122154 122155 122156 122157 122158 122159 122160 122161 122162 122163 122164 122165 122166 122167 122168 122169 122170 122171 122172 122173 122174 122175 122176 122177 122178 122179 122180 122181 122182 122183 122184 122185 122186 122187 122188 122189 122190 122191 122192 122193 122194 122195 122196 122197 122198 122199 122200 122201 122202 122203 122204 122205 122206 122207 122208 122209 122210 122211 122212 122213 122214 122215 122216 122217 122218 122219 122220 122221 122222 122223 122224 122225 122226 122227 122228 122229 122230 122231 122232 122233 122234 122235 122236 122237 122238 122239 122240 122241 122242 122243 122244 122245 122246 122247 122248 122249 122250 122251 122252 122253 122254 122255 122256 122257 122258 122259 122260 122261 122262 122263 122264 122265 122266 122267 122268 122269 122270 122271 122272 122273 122274 122275 122276 122277 122278 122279 122280 122281 122282 122283 122284 122285 122286 122287 122288 122289 122290 122291 122292 122293] INFO 2025-06-26 15:14:35,558 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [ 1 630 1 ... 1 1 1] INFO 2025-06-26 15:14:35,559 lopcToNetCDF.py deSpike():1590 [1] Found 1 spike indicators at indices: [2] INFO 2025-06-26 15:14:35,559 lopcToNetCDF.py deSpike():1595 [1] Identifying nature of spike value = 8770 at index = 2 INFO 2025-06-26 15:14:35,559 lopcToNetCDF.py deSpike():1714 [1] This is the last element in spike_indx. No need to deSpike(). INFO 2025-06-26 15:14:35,559 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [ 8139 8140 8770 ... 143059 143060 143061] INFO 2025-06-26 15:14:35,559 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [ 8139 8140 8770 ... 143059 143060 143061] with len(correctedSampleCountList) = 134278 INFO 2025-06-26 15:14:35,559 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 8139 from all values of correctedSampleCountList INFO 2025-06-26 15:14:35,559 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 15:14:35,560 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [0.00000e+00 5.00000e-01 3.15500e+02 ... 6.74600e+04 6.74605e+04 6.74610e+04] INFO 2025-06-26 15:14:35,561 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.25477588e+09 1.25477588e+09 1.25477619e+09 ... 1.25484334e+09 1.25484334e+09 1.25484334e+09] INFO 2025-06-26 15:14:35,561 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1254775876.1 1254775876.6, ..., timestampArray[-2:] = 1254843336.6 1254843337.1] INFO 2025-06-26 15:14:35,697 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1254775876.0606723), np.float64(1254775876.5606723)], ..., timestampList[-2:] = [np.float64(1254843336.5606723), np.float64(1254843337.0606723)]] INFO 2025-06-26 15:14:35,697 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 134278) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 15:14:35,697 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [132572, 132593] INFO 2025-06-26 15:14:35,698 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 6314 INFO 2025-06-26 15:14:35,698 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 134278 INFO 2025-06-26 15:14:35,698 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1254775876.0606723), np.float64(1254775876.5606723)], ..., timestampList[-2:] = [np.float64(1254843336.5606723), np.float64(1254843337.0606723)]] INFO 2025-06-26 15:14:35,698 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 134278) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 15:14:35,699 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(132571), np.int32(132592)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 15:14:35,705 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 6314 INFO 2025-06-26 15:14:35,707 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 ERROR 2025-06-26 15:14:35,718 lopcToNetCDF.py constructTimestampList():1501 [1] Cannot interpolate to cFrameEsecsListInterpolated: array of sample points is empty INFO 2025-06-26 15:14:35,734 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 6314 INFO 2025-06-26 15:14:35,735 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1254776200.0606723)], ..., tsList[-2:] = [np.float64(1254842484.0606723), np.float64(1254842494.5606723)] INFO 2025-06-26 15:14:35,735 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2009-10-05 20:56:40 Z INFO 2025-06-26 15:14:35,735 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2009-10-06 15:21:34 Z INFO 2025-06-26 15:14:35,735 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 132600 INFO 2025-06-26 15:14:35,735 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [-9999], ..., cFrameEsecsList[-2:] = [-9999, -9999] INFO 2025-06-26 15:14:35,735 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 1969-12-31 21:13:21 Z INFO 2025-06-26 15:14:35,735 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 1969-12-31 21:13:21 Z INFO 2025-06-26 15:14:35,739 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2009.278.02/lopc.nc INFO 2025-06-26 15:14:35,739 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 15:14:35 2025 Elapsed processing time from start of processing = 89 seconds INFO 2025-06-26 15:14:35,743 process.py calibrate():227 [1] Calibration steps for 2009.278.02 INFO 2025-06-26 15:14:36,368 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 15:14:36,370 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 15:14:37,180 calibrate.py _nudge_pos():1806 [1] 106: 0.170 -0.0000335 -0.0000303 425 1.41 -3.512 -3.970 2009-10-05T20:54:22.977867520 INFO 2025-06-26 15:14:37,895 calibrate.py _nudge_pos():1806 [1] 178: 0.180 0.0005035 -0.0000441 12065 40.21 1.856 -0.203 2009-10-05T21:35:46.977702144 INFO 2025-06-26 15:14:38,538 calibrate.py _nudge_pos():1806 [1] 242: 0.200 0.0002246 -0.0000870 10120 33.73 0.987 -0.478 2009-10-05T22:10:34.974664448 INFO 2025-06-26 15:14:39,193 calibrate.py _nudge_pos():1806 [1] 307: 0.200 -0.0002601 -0.0010423 11770 39.23 -0.982 -4.923 2009-10-05T22:50:52.969020672 INFO 2025-06-26 15:14:39,907 calibrate.py _nudge_pos():1806 [1] 378: 0.010 -0.0003265 -0.0010518 11980 39.93 -1.211 -4.881 2009-10-05T23:31:59.170074112 INFO 2025-06-26 15:14:40,368 calibrate.py _nudge_pos():1806 [1] 422: 0.200 -0.0000099 0.0000370 24 0.08 -19.087 89.528 2009-10-05T23:32:46.976799232 INFO 2025-06-26 15:14:40,422 calibrate.py _nudge_pos():1806 [1] 427: 0.200 0.0000213 0.0000088 14 0.04 72.715 37.726 2009-10-05T23:32:53.976319488 INFO 2025-06-26 15:14:40,597 calibrate.py _nudge_pos():1806 [1] 444: 0.020 -0.0002675 -0.0006914 9150 30.50 -1.299 -4.201 2009-10-06T00:03:41.169778432 INFO 2025-06-26 15:14:41,141 calibrate.py _nudge_pos():1806 [1] 496: 0.020 0.0033672 0.0019439 13485 44.95 11.101 8.014 2009-10-06T00:49:29.171527168 INFO 2025-06-26 15:14:41,742 calibrate.py _nudge_pos():1806 [1] 552: 0.010 0.0000118 0.0000052 20 0.06 27.521 15.293 2009-10-06T00:50:28.177485056 INFO 2025-06-26 15:14:41,881 calibrate.py _nudge_pos():1806 [1] 565: 0.030 0.0034642 0.0018314 13625 45.41 11.307 7.473 2009-10-06T01:36:05.169988096 INFO 2025-06-26 15:14:42,597 calibrate.py _nudge_pos():1806 [1] 633: 0.030 0.0025639 0.0007054 13044 43.48 8.743 3.006 2009-10-06T02:20:41.176669184 INFO 2025-06-26 15:14:43,016 calibrate.py _nudge_pos():1806 [1] 672: 0.030 0.0000126 0.0000061 35 0.11 16.452 9.981 2009-10-06T02:21:26.173586688 INFO 2025-06-26 15:14:43,322 calibrate.py _nudge_pos():1806 [1] 701: 0.040 0.0028269 0.0003991 14094 46.98 8.923 1.574 2009-10-06T03:08:53.178553600 INFO 2025-06-26 15:14:43,911 calibrate.py _nudge_pos():1806 [1] 757: 0.040 0.0000033 -0.0000057 15 0.05 10.404 -22.807 2009-10-06T03:09:51.174580480 INFO 2025-06-26 15:14:44,033 calibrate.py _nudge_pos():1806 [1] 768: 0.050 0.0001036 -0.0000920 2900 9.66 1.589 -1.763 2009-10-06T03:19:41.174162944 INFO 2025-06-26 15:14:46,412 calibrate.py _nudge_pos():1806 [1] 991: 0.040 0.0000781 -0.0000552 1765 5.88 1.969 -1.740 2009-10-06T03:29:17.174704128 INFO 2025-06-26 15:14:46,922 calibrate.py _nudge_pos():1806 [1] 1039: 0.050 0.0001081 -0.0001342 3755 12.51 1.281 -1.988 2009-10-06T03:42:35.170037504 INFO 2025-06-26 15:14:47,712 calibrate.py _nudge_pos():1806 [1] 1113: 0.040 0.0000473 -0.0000472 1975 6.58 1.065 -1.330 2009-10-06T03:50:23.177976832 INFO 2025-06-26 15:14:47,745 calibrate.py _nudge_pos():1806 [1] 1116: 0.050 0.0000181 -0.0000098 160 0.53 5.074 -3.442 2009-10-06T03:50:57.175647744 INFO 2025-06-26 15:14:48,452 calibrate.py _nudge_pos():1806 [1] 1182: 0.050 0.0006522 -0.0001194 12074 40.25 2.402 -0.550 2009-10-06T04:32:17.175756288 INFO 2025-06-26 15:14:49,068 calibrate.py _nudge_pos():1806 [1] 1240: 0.060 -0.0000056 0.0000043 20 0.06 -13.131 12.641 2009-10-06T04:33:18.171577600 INFO 2025-06-26 15:14:49,185 calibrate.py _nudge_pos():1806 [1] 1251: 0.060 0.0003585 -0.0000984 8434 28.11 1.890 -0.648 2009-10-06T05:01:35.175324928 INFO 2025-06-26 15:14:49,767 calibrate.py _nudge_pos():1806 [1] 1306: 0.060 -0.0003847 -0.0010386 11939 39.80 -1.432 -4.836 2009-10-06T05:42:17.178036480 INFO 2025-06-26 15:14:50,409 calibrate.py _nudge_pos():1806 [1] 1365: 0.080 -0.0004227 -0.0010526 11679 38.93 -1.608 -5.010 2009-10-06T06:22:11.174036224 INFO 2025-06-26 15:14:51,131 calibrate.py _nudge_pos():1806 [1] 1432: 0.080 -0.0001342 -0.0006503 7617 25.40 -0.783 -4.745 2009-10-06T06:48:41.175113984 INFO 2025-06-26 15:14:51,683 calibrate.py _nudge_pos():1806 [1] 1483: 0.090 0.0031120 0.0018124 13547 45.16 10.210 7.436 2009-10-06T07:34:41.176040960 INFO 2025-06-26 15:14:52,390 calibrate.py _nudge_pos():1806 [1] 1548: 0.090 0.0031435 0.0017464 13627 45.43 10.257 7.123 2009-10-06T08:21:11.174913024 INFO 2025-06-26 15:14:53,177 calibrate.py _nudge_pos():1806 [1] 1620: 0.100 0.0018122 0.0005342 13441 44.81 5.995 2.209 2009-10-06T09:07:11.175840000 INFO 2025-06-26 15:14:53,983 calibrate.py _nudge_pos():1806 [1] 1694: 0.110 0.0038505 0.0015674 13823 46.08 12.392 6.303 2009-10-06T09:54:29.171423744 INFO 2025-06-26 15:14:54,876 calibrate.py _nudge_pos():1806 [1] 1775: 0.120 0.0005199 -0.0000702 12167 40.56 1.900 -0.321 2009-10-06T10:36:23.169202944 INFO 2025-06-26 15:14:55,675 calibrate.py _nudge_pos():1806 [1] 1847: 0.120 0.0005380 -0.0000971 11973 39.91 1.998 -0.451 2009-10-06T11:17:29.170270464 INFO 2025-06-26 15:14:56,452 calibrate.py _nudge_pos():1806 [1] 1918: 0.120 0.0000495 -0.0000533 2979 9.93 0.738 -0.994 2009-10-06T11:28:35.174646016 INFO 2025-06-26 15:14:57,029 calibrate.py _nudge_pos():1806 [1] 1970: 0.130 -0.0003407 -0.0010256 11914 39.71 -1.271 -4.785 2009-10-06T12:09:09.177905408 INFO 2025-06-26 15:14:57,866 calibrate.py _nudge_pos():1806 [1] 2045: 0.140 -0.0006225 -0.0009715 12298 41.00 -2.249 -4.391 2009-10-06T12:51:23.174314752 INFO 2025-06-26 15:14:58,595 calibrate.py _nudge_pos():1806 [1] 2108: 0.150 -0.0001267 -0.0006074 8029 26.76 -0.701 -4.206 2009-10-06T13:19:11.170049280 INFO 2025-06-26 15:14:59,167 calibrate.py _nudge_pos():1806 [1] 2159: 0.140 0.0030381 0.0018669 13337 44.46 10.125 7.780 2009-10-06T14:04:29.173853184 INFO 2025-06-26 15:14:59,940 calibrate.py _nudge_pos():1806 [1] 2230: 0.150 0.0027570 0.0015659 12127 40.43 10.107 7.177 2009-10-06T14:46:05.172865536 INFO 2025-06-26 15:15:29,684 calibrate.py _nudge_pos():1862 [1] 4852: - - - 3 0.01 - - INFO 2025-06-26 15:15:29,684 calibrate.py _nudge_pos():1868 [1] Points in final series = 335395 WARNING 2025-06-26 15:15:30,129 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 15:16:03,832 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 57 of 268410 INFO 2025-06-26 15:16:05,901 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:16:25,221 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:16:27,225 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:16:27,229 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2009.278.02/ctd1.nc WARNING 2025-06-26 15:16:27,231 calibrate.py _range_qc_combined_nc():890 [1] More than 500 (3596) ctd1_salinity values found outside of range. This may indicate a problem with the ctd1 data. INFO 2025-06-26 15:16:27,231 calibrate.py _range_qc_combined_nc():898 [1] Setting 3596 ctd1_salinity values to NaN INFO 2025-06-26 15:16:27,231 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 15:16:27,231 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 15:16:42,191 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 15:16:44,236 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 15:16:44,240 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2009.278.02/ctd2.nc INFO 2025-06-26 15:16:44,242 calibrate.py _range_qc_combined_nc():898 [1] Setting 302 ctd2_salinity values to NaN INFO 2025-06-26 15:16:44,243 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 15:16:44,243 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 15:16:44,341 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 15:16:47,478 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 65 66 67 68 360 480 481 482 483 19440 19441 19442 20340 21420 21421 21422 21423 43500 43501 43502 52620 52621 52622 70980 70981 70982 70983 89400 89401 89402 89403 173940 173941 173942 400680 400681 400682 400683 1106880 1106881 1106882 1276800 1276801 1276802 1276803 1276804 1276805 1278840 1358220 1358221 1358222 1358223 1358224 1358225 1358226 1358227 1358228 1359780 1359781 1359782 1359783 1359784 1359785 1359786 1359787 1359788 1359789 1359790 1389180 1389181 1389182 1389183 1389184 1407300 1415700 1415701 1415702 1415703 1415704 1462200 1462201 1462202 1462203 1462204 1462205 1617060 1617061 1617062 1695840 1695841 1695842 1695843 1695844 1695845 1695846 1695847 1695848 1695849 1721340 1721341 1721342 1721343 1721344 1721345 1721346 1726320 1726321 1726322 1726323 1726324 1726325 1726326 1726327 1726328 1968840 2028660 2028661 2028662 2028663 2028664 2028665 2028666 2028667 2028668 2028669 2028670 2028671 2028672 2028673 2180400 2180401 2180402 2180403 2180404 2180405 2180406 2191200 2191201 2191202 2191203 2191204 2191205 2191206 2191207 2285880 2285881 2285882 2285883 2335980 2335981 2335982 2335983 2335984 2335985 2335986 2335987 2335988 2335989 2335990 2400780 2472780 2472781 2472782 2643300 2643301 2643302 2643303 2643304 2643305 2643306 2643307 2643308 2683560 2683561 2683562 2683563 2683564 2683565 2683566 2683567 2683568 2777280 2777281 2777282 2908140 2908141 2908142 2908143 2908144 2908145 2908146 2908147 2908148 2911980 2911981 2911982 2911983 2911984 2911985 2911986 2911987 2911988 2911989 2911990 2911991 2911992 2962740 2962741 2962742 2962743 2962744 2962745 2962746 2962747 2962748 2962749 2962750 2962751 2962752 3052800 3052801 3052802 3052803 3052804 3117660 3117661 3117662 3117663 3117664 3198660 3198661 3198662 3198663 3198664 3198665 3198666 3210240 3210241 3210242 3245880 3245881 3245882 3245883 3245884 3245885 3245886 3245887 3257880 3299940 3299941 3299942 3299943 3310920 3310921 3310922 3375120 3375121 3375122 3565200 3644880 3644881 3644882 3644883 3644884 3644885 3644886 3713700 3713701 3713702 3713703 3713704 3713705 3713706 3779220 3779221 3779222 3867180 3885900 3885901 3885902 3885903 3885904 3885905 3885906 3885907 3885908 3885909 3885910 3885911 3885912 3885913 3979260 3979261 3979262 3979263 3979264 3979265 3979266 3979267 3979268 3979269 3979270 3979271 3979272 3979273 3979274 3992580 3992581 4015800 4015801 4015802 4015803] INFO 2025-06-26 15:16:48,101 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 15:16:48,108 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 15:16:48,118 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2009.278.02 INFO 2025-06-26 15:16:48,377 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2009.278.02/dorado_2009.278.02_cal.nc INFO 2025-06-26 15:17:18,082 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_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, 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 15:17:18,093 process.py align():251 [1] Alignment steps for 2009.278.02 INFO 2025-06-26 15:17:18,140 align.py process_cal():139 [1] Processing dorado_2009.278.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2009.278.02 INFO 2025-06-26 15:17:18,231 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:17:18,240 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:17:18,474 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:17:18,490 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:17:18,694 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:17:18,709 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:17:18,833 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 15:17:18,833 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 15:17:18,920 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:17:18,933 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:17:19,135 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:19,145 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:19,322 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:19,332 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:19,508 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:19,518 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:19,698 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:19,707 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:19,890 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:19,899 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:20,080 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:20,091 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:20,271 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:20,281 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:20,458 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:20,468 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:20,650 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:20,664 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:20,845 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:20,857 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:21,036 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:21,046 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:21,228 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:21,238 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:21,418 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:21,428 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:21,606 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:21,615 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:21,795 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:21,805 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:21,983 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:21,993 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:22,177 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:22,188 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:22,365 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:22,378 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:22,558 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:22,568 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:22,745 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:22,754 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:22,935 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:22,945 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:23,124 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.278.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:17:23,133 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:17:23,348 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:17:23,480 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:17:23,617 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:17:23,757 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 15:17:23,899 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 15:17:24,018 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 15:17:24,138 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 15:17:24,257 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 15:17:24,376 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 15:17:24,502 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:17:24,636 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2009.278.02/dorado_2009.278.02_align.nc INFO 2025-06-26 15:17:24,803 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_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, 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 15:17:24,806 process.py resample():273 [1] Resampling steps for 2009.278.02 INFO 2025-06-26 15:17:24,807 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 15:17:24,845 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.278.02/dorado_2009.278.02_align.nc mission netCDF file INFO 2025-06-26 15:17:24,855 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.278.02/dorado_2009.278.02_align.nc mission netCDF file INFO 2025-06-26 15:17:24,857 resample.py get_mission_start_end():1145 [1] navigation: 2009-10-05T20:51:47.258535168 to 2009-10-06T15:30:20.770944512 (0 days 00:00:00.019998976 before mission_end) INFO 2025-06-26 15:17:24,860 resample.py get_mission_start_end():1145 [1] hs2 : 2009-10-05T20:51:22.680218880 to 2009-10-06T15:30:20.670951680 (0 days 00:00:00.119991808 before mission_end) INFO 2025-06-26 15:17:24,863 resample.py get_mission_start_end():1145 [1] ctd1 : 2009-10-05T20:51:42.338872320 to 2009-10-06T15:30:20.740946688 (0 days 00:00:00.049996800 before mission_end) INFO 2025-06-26 15:17:24,865 resample.py get_mission_start_end():1145 [1] ctd2 : 2009-10-05T20:51:43.228811264 to 2009-10-06T15:30:20.790943488 (0 days 00:00:00 before mission_end) INFO 2025-06-26 15:17:24,867 resample.py get_mission_start_end():1145 [1] isus : 2009-10-05T20:52:32.185457408 to 2009-10-06T15:30:20.310976256 (0 days 00:00:00.479967232 before mission_end) INFO 2025-06-26 15:17:24,868 resample.py get_mission_start_end():1145 [1] biolume : 2009-10-05T20:51:14.390752512 to 2009-10-06T15:30:20.230947584 (0 days 00:00:00.559995904 before mission_end) INFO 2025-06-26 15:17:24,870 resample.py get_mission_start_end():1145 [1] lopc : 2009-10-05T20:56:40.060672256 to 2009-10-06T15:21:34.560672256 (0 days 00:08:46.230271232 before mission_end) WARNING 2025-06-26 15:17:24,871 resample.py get_mission_start_end():1156 [1] Instrument lopc has a gap > 5 minutes at the end of the mission: 0 days 00:08:46.230271232 INFO 2025-06-26 15:17:24,872 resample.py get_mission_start_end():1145 [1] tailcone : 2009-10-05T20:51:16.640632576 to 2009-10-06T15:30:20.790943488 (0 days 00:00:00 before mission_end) INFO 2025-06-26 15:17:24,873 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.278.02/dorado_2009.278.02_align.nc mission netCDF file INFO 2025-06-26 15:17:24,874 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:25,551 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:25,661 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:25,765 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:25,870 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:25,960 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:26,054 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:26,142 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:26,230 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:26,312 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:26,408 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:26,490 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:26,573 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:26,656 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:26,738 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:26,820 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:26,903 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:26,987 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:27,074 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:27,164 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:27,258 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:27,344 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:27,430 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:27,519 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:27,609 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:27,644 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:27,672 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:27,698 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:27,729 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:27,746 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:27,746 resample.py resample_variable():1038 [1] Padding lopc_countListSum with 0 days 00:08:46.230271232 of NaNs to the end of mission INFO 2025-06-26 15:17:27,764 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:27,764 resample.py resample_variable():1038 [1] Padding lopc_transCount with 0 days 00:08:46.230271232 of NaNs to the end of mission INFO 2025-06-26 15:17:27,781 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:27,782 resample.py resample_variable():1038 [1] Padding lopc_nonTransCount with 0 days 00:08:46.230271232 of NaNs to the end of mission INFO 2025-06-26 15:17:27,798 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:27,798 resample.py resample_variable():1038 [1] Padding lopc_LCcount with 0 days 00:08:46.230271232 of NaNs to the end of mission INFO 2025-06-26 15:17:27,815 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:27,816 resample.py resample_variable():1038 [1] Padding lopc_flowSpeed with 0 days 00:08:46.230271232 of NaNs to the end of mission INFO 2025-06-26 15:17:27,914 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 15:17:28,420 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2009.278.02/dorado_2009.278.02_1S.nc INFO 2025-06-26 15:17:31,790 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 15:17:35,364 create_products.py gulper_odv():522 [1] Wrote 3 Gulper data lines to /data/auv_data/dorado/missionodvs/2009.278.02/dorado_2009.278.02_1S_Gulper.txt INFO 2025-06-26 15:17:35,365 process.py archive():337 [1] Archiving steps for 2009.278.02 INFO 2025-06-26 15:17:35,365 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2009.278.02/dorado_2009.278.02, BASE_PATH = /data/auv_data INFO 2025-06-26 15:17:35,366 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2009.278.02/dorado_2009.278.02 files to /Volumes/AUVCTD/surveys/2009/netcdf INFO 2025-06-26 15:17:35,367 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.278.02_1S.nc INFO 2025-06-26 15:17:35,423 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.278.02/dorado_2009.278.02_1S.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:17:35,424 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.278.02_cal.nc INFO 2025-06-26 15:17:35,669 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.278.02/dorado_2009.278.02_cal.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:17:35,670 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.278.02_align.nc INFO 2025-06-26 15:17:35,923 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.278.02/dorado_2009.278.02_align.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:17:35,990 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.278.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009278/2009.278.02 done. INFO 2025-06-26 15:17:36,067 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.278.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009278/2009.278.02 done. INFO 2025-06-26 15:17:36,073 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.278.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009278/2009.278.02 done. INFO 2025-06-26 15:17:36,141 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.278.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009278/2009.278.02 done. INFO 2025-06-26 15:17:36,335 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.278.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009278/2009.278.02 done. INFO 2025-06-26 15:17:36,344 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.278.02/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009278/2009.278.02 done. INFO 2025-06-26 15:17:36,421 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.278.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009278/2009.278.02 done. INFO 2025-06-26 15:17:36,475 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.278.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009278/2009.278.02 done. INFO 2025-06-26 15:17:36,645 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.278.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009278/2009.278.02 done. INFO 2025-06-26 15:17:36,851 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.278.02/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009278/2009.278.02 done. INFO 2025-06-26 15:17:36,851 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 15:17:36,853 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2009/odv/dorado_2009.278.02_1S_Gulper.txt INFO 2025-06-26 15:17:36,858 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2009.278.02/dorado_2009.278.02_1S_Gulper.txt /Volumes/AUVCTD/surveys/2009/odv done. INFO 2025-06-26 15:17:36,858 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.278.02/dorado_2009.278.02_processing.log /Volumes/AUVCTD/surveys/2009/netcdf