INFO 2023-08-28 11:49:57,123 logs2netcdfs.py download_process_logs():664 [71853] src_dir = '/Volumes/AUVCTD/missionlogs/2007/2007171/2007.171.04' INFO 2023-08-28 11:49:57,124 logs2netcdfs.py download_process_logs():677 [71853] /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2007.171.04 exists INFO 2023-08-28 11:49:57,124 logs2netcdfs.py download_process_logs():700 [71853] Processing mission: dorado 2007.171.04 INFO 2023-08-28 11:49:57,125 logs2netcdfs.py download_process_logs():709 [71853] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2007.171.04/ctdDriver.log (19886195 bytes) INFO 2023-08-28 11:50:12,129 logs2netcdfs.py _process_log_file():644 [71853] Non-monotonic increasing time indices in /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2007.171.04/ctdDriver.log: [ 143 226 235 380 437 459 552 623 650 722 738 807 965 1001 1233 1364 1490 1526 1582 1707 2234 2409 2425 2728 3026 3219 3605 4157 4577 4817 4837 4869 4870 5292 5397 5781 5805 6251 6335 6913 7213 7311 7369 9582 9996 10547 10800 11065 11308 11707 12038 13122 13495 15286 16785 17066 18064 19228 20059 21776 22331 22486 23218 24016 24671 24770 26342 27047 27345 29642 29937 30713 32746 33086 33455 35438 36651 36822 36973 40572 40597 42674 46905 47683 48513 50083 54797 56798 58867 59830 61912 62365 66212 66818 67687 67688 69997 70236 76143 78119 79540 82809 83664 86855 88767 93122 93829 97090 100627 100749 103790 103805 104594 107492 110524 111711 113553 113962 115634 116895 117239 118824 121890 123953 125935 127049 128645 128795 130637 131336 137382 138138 140164 143813 144098 144795 147275 147864 148569 149533 150813 151005 152143 155167 157527 160097 160464 163733 163760 167092 168145 168509 168618 175647 177674 188890 191102 193242 197815 198722 202823 204526 208393 209434 211240 220578 224665 225509] INFO 2023-08-28 11:50:12,219 logs2netcdfs.py download_process_logs():709 [71853] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2007.171.04/ctdDriver2.log (19887069 bytes) INFO 2023-08-28 11:50:26,775 logs2netcdfs.py _process_log_file():644 [71853] Non-monotonic increasing time indices in /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2007.171.04/ctdDriver2.log: [ 6 226 235 380 437 459 552 623 722 738 808 966 1002 1234 1365 1528 1584 1599 1709 2236 2258 2430 2733 3031 3225 3611 4584 4824 4876 5298 5403 6257 6341 6919 7219 7318 7376 9589 10553 10806 11071 11314 11713 12044 13129 13502 16793 17074 18072 19236 20067 21264 22340 23228 24025 24680 26351 27056 27353 27354 29649 29945 30721 32754 33094 33464 35447 36660 36831 36982 40606 42684 46915 47694 48524 50094 51203 53364 54809 55615 56810 58879 62376 66221 66827 70005 75032 76152 78127 79548 82818 83673 86864 88776 93130 93837 97099 100636 100758 103800 103815 104604 110532 111717 113559 115640 116899 117244 118828 122690 123959 125941 127055 128650 128800 130642 137385 138140 140165 143814 144100 144797 145642 146516 147279 147868 148574 149538 150817 151009 157530 160100 163736 163764 168151 168515 168624 171496 175653 177679 188894 190654 191107 193870 204533 205454 206460 208401 209441 211248 220587 224675 225520] INFO 2023-08-28 11:50:26,992 logs2netcdfs.py download_process_logs():709 [71853] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2007.171.04/gps.log (1462028 bytes) INFO 2023-08-28 11:50:28,606 logs2netcdfs.py download_process_logs():709 [71853] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2007.171.04/hydroscatlog.log (13562114 bytes) INFO 2023-08-28 11:50:44,825 logs2netcdfs.py _process_log_file():644 [71853] Non-monotonic increasing time indices in /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2007.171.04/hydroscatlog.log: [ 3 4 27 105 109 228 315 325 471 527 640 714 814 968 1059 1081 1096 1459 1586 1678 1693 1708 2331 2345 2354 2417 2526 3632 3796 4070 4680 4803 4920 4939 4972 5330 5432 5884 5907 6439 7018 7318 7418 7474 8118 8186 9688 9890 10103 11088 11811 12212 13227 13419 13860 14279 14565 15978 16595 16596 16605 16616 16890 17171 17720 21881 22435 23965 24775 26077 26447 27162 27451 27771 29745 30040 30041 30817 32015 32849 33189 33558 33559 35539 36925 37075 38403 40674 40700 43471 47008 47784 48615 50185 51294 53151 56216 56900 56950 58969 59930 62062 62465 66310 66916 67785 69128 70717 75120 76238 77045 80948 82905 83226 83767 86777 86951 88861 90463 93213 93214 93921 97180 97181 97571 98121 98943 99060 100716 103878 106397 108217 110610 114046 116370 118907 122767 123216 124034 126016 127130 128724 128874 130363 130716 137457 137674 140236 144866 148641 149605 150489 151077 152214 154459 155238 157596 160164 160531 160714 161571 163798 163826 164312 168417 168575 171026 175710 175793 175994 177737 178672 178673 184447 188508 188947 190012 194229 197870 198207 198756 198779 205711 206508 208446 209486 209487 213208 218003 220627 220706 225557] INFO 2023-08-28 11:50:44,992 logs2netcdfs.py download_process_logs():709 [71853] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2007.171.04/navigation.log (66607114 bytes) INFO 2023-08-28 11:51:37,917 logs2netcdfs.py download_process_logs():709 [71853] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2007.171.04/isuslog.log (1337365 bytes) INFO 2023-08-28 11:51:40,144 logs2netcdfs.py download_process_logs():709 [71853] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2007.171.04/parosci.log (23767766 bytes) INFO 2023-08-28 11:52:02,268 logs2netcdfs.py download_process_logs():709 [71853] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2007.171.04/tailCone.log (2963467 bytes) INFO 2023-08-28 11:52:06,960 logs2netcdfs.py download_process_logs():709 [71853] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2007.171.04/biolume.log (15384188 bytes) INFO 2023-08-28 11:52:23,326 logs2netcdfs.py write_variables():523 [71853] Expanding original timeTag to time60Hz variable for raw data INFO 2023-08-28 11:52:25,740 logs2netcdfs.py download_process_logs():726 [71853] Time to process: 148.62 seconds WARNING 2023-08-28 11:52:25,741 process.py download_process():169 [71853] No lopc.bin file for 2007.171.04 INFO 2023-08-28 11:52:27,988 calibrate.py _nudge_pos():884 [71853] 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 2023-08-28 11:52:27,993 calibrate.py _nudge_pos():908 [71853] - - - 0 0.00 - - - INFO 2023-08-28 11:52:32,442 calibrate.py _nudge_pos():1003 [71853] 119: 0.190 -0.0001195 0.0004234 2432 8.20 -2.162 9.572 2007-06-20T23:45:59.984055296 INFO 2023-08-28 11:52:37,921 calibrate.py _nudge_pos():1003 [71853] 227: 0.180 -0.0000351 0.0000682 3526 11.81 -0.441 1.069 2007-06-20T23:59:35.988155136 INFO 2023-08-28 11:52:41,761 calibrate.py _nudge_pos():1003 [71853] 314: 0.190 -0.0002107 0.0000476 8006 26.76 -1.167 0.329 2007-06-21T00:27:47.992244992 INFO 2023-08-28 11:52:45,406 calibrate.py _nudge_pos():1003 [71853] 395: 0.190 -0.0001774 0.0000065 6903 23.06 -1.140 0.052 2007-06-21T00:52:11.991954176 INFO 2023-08-28 11:52:49,513 calibrate.py _nudge_pos():1003 [71853] 469: 0.190 -0.0001704 -0.0001000 9585 31.98 -0.790 -0.580 2007-06-21T01:25:23.985493248 INFO 2023-08-28 11:52:53,072 calibrate.py _nudge_pos():1003 [71853] 543: 0.180 -0.0001191 -0.0001759 9256 30.88 -0.571 -1.056 2007-06-21T01:57:29.993552640 INFO 2023-08-28 11:52:53,541 calibrate.py _nudge_pos():1003 [71853] 551: 0.180 -0.0000012 -0.0000606 20 0.06 -2.915 -177.212 2007-06-21T01:57:41.992730624 INFO 2023-08-28 11:52:56,183 calibrate.py _nudge_pos():1003 [71853] 625: 0.200 -0.0001700 -0.0001236 10353 34.56 -0.729 -0.663 2007-06-21T02:33:29.985583104 INFO 2023-08-28 11:52:59,026 calibrate.py _nudge_pos():1003 [71853] 692: 0.200 -0.0000702 -0.0000437 11300 37.69 -0.276 -0.215 2007-06-21T03:12:17.986104064 INFO 2023-08-28 11:53:03,884 calibrate.py _nudge_pos():1003 [71853] 771: 0.190 0.0000630 -0.0000018 8062 26.89 0.347 -0.012 2007-06-21T03:40:29.990193920 INFO 2023-08-28 11:53:06,557 calibrate.py _nudge_pos():1003 [71853] 843: 0.200 0.0000497 -0.0000152 6834 22.81 0.323 -0.123 2007-06-21T04:04:29.991546880 INFO 2023-08-28 11:53:11,052 calibrate.py _nudge_pos():1003 [71853] 926: 0.200 0.0000402 -0.0000843 5610 18.73 0.317 -0.834 2007-06-21T04:24:35.988930560 INFO 2023-08-28 11:53:13,647 calibrate.py _nudge_pos():1003 [71853] 994: 0.200 0.0001199 -0.0002177 4521 15.08 1.178 -2.676 2007-06-21T04:40:47.992343552 INFO 2023-08-28 11:53:17,610 calibrate.py _nudge_pos():1003 [71853] 1085: 0.200 0.0000485 -0.0000732 2098 6.99 1.027 -1.940 2007-06-21T04:49:17.987406848 INFO 2023-08-28 11:53:59,677 calibrate.py _nudge_pos():1003 [71853] 2056: 0.010 0.0005454 0.0007388 6812 22.73 3.554 6.023 2007-06-21T05:28:12.187503104 INFO 2023-08-28 11:54:09,262 calibrate.py _nudge_pos():1003 [71853] 2287: 0.010 0.0007864 0.0009863 8054 26.86 4.336 6.803 2007-06-21T05:58:54.191316992 INFO 2023-08-28 11:54:12,086 calibrate.py _nudge_pos():1003 [71853] 2361: 0.010 0.0003788 0.0002636 2034 6.78 8.276 7.205 2007-06-21T06:06:54.188435200 INFO 2023-08-28 11:54:15,300 calibrate.py _nudge_pos():1003 [71853] 2436: 0.010 0.0051325 -0.0016682 11203 37.36 20.355 -8.273 2007-06-21T06:45:30.189778176 INFO 2023-08-28 11:54:19,300 calibrate.py _nudge_pos():1003 [71853] 2513: 0.020 0.0046757 -0.0022018 11697 39.03 17.759 -10.454 2007-06-21T07:25:48.184133888 INFO 2023-08-28 11:54:23,394 calibrate.py _nudge_pos():1003 [71853] 2596: 0.020 0.0027622 -0.0015698 7953 26.53 15.438 -10.964 2007-06-21T07:53:42.189456896 INFO 2023-08-28 11:54:29,341 calibrate.py _nudge_pos():1003 [71853] 2696: 0.030 0.0023397 -0.0011556 10748 35.85 9.680 -5.974 2007-06-21T08:31:12.185321472 INFO 2023-08-28 11:54:33,157 calibrate.py _nudge_pos():1003 [71853] 2767: 0.020 0.0015289 -0.0011181 7833 26.13 8.680 -7.929 2007-06-21T08:58:30.193110528 INFO 2023-08-28 11:54:36,054 calibrate.py _nudge_pos():1003 [71853] 2830: 0.020 0.0025645 -0.0024472 10934 36.46 10.437 -12.436 2007-06-21T09:36:00.188975104 INFO 2023-08-28 11:54:38,797 calibrate.py _nudge_pos():1003 [71853] 2895: 0.020 -0.0015534 -0.0026057 15266 50.93 -4.528 -9.480 2007-06-21T10:28:00.185240832 INFO 2023-08-28 11:54:50,714 calibrate.py _nudge_pos():1003 [71853] 3099: 0.020 -0.0000004 0.0000590 25 0.08 -0.804 136.715 2007-06-21T10:31:28.190991360 INFO 2023-08-28 11:55:01,129 calibrate.py _nudge_pos():1003 [71853] 3296: 0.030 -0.0000163 0.0000064 40 0.13 -18.621 9.064 2007-06-21T10:34:52.187016704 INFO 2023-08-28 12:07:32,415 calibrate.py _nudge_pos():1060 [71853] 20262: - - - 5 0.01 - - INFO 2023-08-28 12:07:32,415 calibrate.py _nudge_pos():1066 [71853] Points in final series = 281765 WARNING 2023-08-28 12:07:33,906 calibrate.py _depth_process():1368 [71853] Expected sample_rate to be 10 Hz, instead it's 9.090909090909092 Hz INFO 2023-08-28 12:09:22,051 calibrate.py _geometric_depth_correction():2497 [71853] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: 0 seconds, INFO 2023-08-28 12:10:44,797 calibrate.py _geometric_depth_correction():2497 [71853] ctd1: d_beg_time_diff: 23 seconds, d_end_time_diff: 0 seconds, INFO 2023-08-28 12:10:49,366 calibrate.py _geometric_depth_correction():2497 [71853] ctd1: d_beg_time_diff: 23 seconds, d_end_time_diff: 0 seconds, INFO 2023-08-28 12:10:49,402 calibrate.py _ctd_process():2047 [71853] Performing range checking of ['ctd1_salinity'] in 2007.171.04/ctd1.nc INFO 2023-08-28 12:10:49,409 calibrate.py _range_qc_combined_nc():400 [71853] Setting 0 ctd1_salinity values to NaN INFO 2023-08-28 12:10:49,410 calibrate.py _range_qc_combined_nc():414 [71853] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2023-08-28 12:10:49,411 calibrate.py _range_qc_combined_nc():440 [71853] Done range checking ctd1 INFO 2023-08-28 12:11:56,332 calibrate.py _geometric_depth_correction():2497 [71853] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds, INFO 2023-08-28 12:12:01,037 calibrate.py _geometric_depth_correction():2497 [71853] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds, INFO 2023-08-28 12:12:01,062 calibrate.py _ctd_process():2047 [71853] Performing range checking of ['ctd2_salinity'] in 2007.171.04/ctd2.nc INFO 2023-08-28 12:12:01,069 calibrate.py _range_qc_combined_nc():400 [71853] Setting 18 ctd2_salinity values to NaN INFO 2023-08-28 12:12:01,070 calibrate.py _range_qc_combined_nc():414 [71853] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2023-08-28 12:12:01,071 calibrate.py _range_qc_combined_nc():440 [71853] Done range checking ctd2 INFO 2023-08-28 12:12:01,338 calibrate.py _biolume_process():2223 [71853] Checking for non-monotonic increasing time60hz INFO 2023-08-28 12:12:14,516 calibrate.py _biolume_process():2226 [71853] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 3386047 3386048 3386049] INFO 2023-08-28 12:12:15,998 calibrate.py _geometric_depth_correction():2497 [71853] biolume: d_beg_time_diff: -5 seconds, d_end_time_diff: -1 seconds, ERROR 2023-08-28 12:12:16,029 calibrate.py process_logs():2615 [71853] Error processing biolume: missing variable 'avg_biolume' ERROR 2023-08-28 12:12:16,035 calibrate.py process_logs():2613 [71853] Error processing lopc: lopc has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.171.04 ERROR 2023-08-28 12:12:16,035 calibrate.py process_logs():2613 [71853] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2007.171.04 INFO 2023-08-28 12:12:16,222 calibrate.py write_netcdf():2584 [71853] Writing calibrated instrument data to /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04/dorado_2007.171.04_cal.nc INFO 2023-08-28 12:12:16,608 calibrate.py write_netcdf():2588 [71853] 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_bb470, hs2_bb676, hs2_depth, hs2_fl676, hs2_time, isus_nitrate, isus_temp, isus_time, 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 2023-08-28 12:12:17,213 align.py process_cal():145 [71853] Processing dorado_2007.171.04_cal.nc from /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04 INFO 2023-08-28 12:12:17,538 align.py process_cal():221 [71853] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2023-08-28 12:12:17,593 align.py process_cal():282 [71853] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2023-08-28 12:12:18,127 align.py process_cal():221 [71853] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2023-08-28 12:12:18,145 align.py process_cal():282 [71853] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2023-08-28 12:12:18,471 align.py process_cal():221 [71853] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2023-08-28 12:12:18,535 align.py process_cal():282 [71853] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2023-08-28 12:12:19,033 align.py process_cal():168 [71853] Skipping navigation_posx INFO 2023-08-28 12:12:19,036 align.py process_cal():168 [71853] Skipping navigation_posy INFO 2023-08-28 12:12:19,373 align.py process_cal():221 [71853] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2023-08-28 12:12:19,395 align.py process_cal():282 [71853] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2023-08-28 12:12:19,804 align.py process_cal():221 [71853] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:19,820 align.py process_cal():282 [71853] hs2_bb470: instrument_sample_rate_hz = 3.99 INFO 2023-08-28 12:12:20,373 align.py process_cal():221 [71853] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:20,412 align.py process_cal():282 [71853] hs2_bb676: instrument_sample_rate_hz = 3.99 INFO 2023-08-28 12:12:20,740 align.py process_cal():221 [71853] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:20,755 align.py process_cal():282 [71853] hs2_fl676: instrument_sample_rate_hz = 3.99 INFO 2023-08-28 12:12:21,158 align.py process_cal():221 [71853] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:21,219 align.py process_cal():282 [71853] hs2_depth: instrument_sample_rate_hz = 3.99 INFO 2023-08-28 12:12:21,919 align.py process_cal():221 [71853] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:21,937 align.py process_cal():282 [71853] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2023-08-28 12:12:22,240 align.py process_cal():221 [71853] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:22,272 align.py process_cal():282 [71853] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2023-08-28 12:12:22,764 align.py process_cal():221 [71853] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:22,820 align.py process_cal():282 [71853] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2023-08-28 12:12:23,505 align.py process_cal():221 [71853] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:23,527 align.py process_cal():282 [71853] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2023-08-28 12:12:23,855 align.py process_cal():221 [71853] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:23,871 align.py process_cal():282 [71853] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2023-08-28 12:12:24,538 align.py process_cal():221 [71853] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:24,556 align.py process_cal():282 [71853] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2023-08-28 12:12:24,891 align.py process_cal():221 [71853] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:24,906 align.py process_cal():282 [71853] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2023-08-28 12:12:25,511 align.py process_cal():221 [71853] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:25,584 align.py process_cal():282 [71853] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2023-08-28 12:12:26,286 align.py process_cal():221 [71853] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:26,337 align.py process_cal():282 [71853] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2023-08-28 12:12:26,631 align.py process_cal():221 [71853] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:26,650 align.py process_cal():282 [71853] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2023-08-28 12:12:26,957 align.py process_cal():221 [71853] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:26,975 align.py process_cal():282 [71853] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2023-08-28 12:12:27,582 align.py process_cal():221 [71853] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:27,666 align.py process_cal():282 [71853] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2023-08-28 12:12:28,232 align.py process_cal():221 [71853] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:28,250 align.py process_cal():282 [71853] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2023-08-28 12:12:28,526 align.py process_cal():221 [71853] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:28,543 align.py process_cal():282 [71853] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2023-08-28 12:12:29,263 align.py process_cal():221 [71853] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:29,326 align.py process_cal():282 [71853] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2023-08-28 12:12:29,904 align.py process_cal():221 [71853] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:29,926 align.py process_cal():282 [71853] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2023-08-28 12:12:30,276 align.py process_cal():221 [71853] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2007.171.04_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2023-08-28 12:12:30,291 align.py process_cal():282 [71853] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2023-08-28 12:12:31,005 align.py process_cal():282 [71853] isus_nitrate: instrument_sample_rate_hz = 0.74 INFO 2023-08-28 12:12:31,618 align.py process_cal():282 [71853] isus_temp: instrument_sample_rate_hz = 0.74 INFO 2023-08-28 12:12:31,917 align.py process_cal():282 [71853] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2023-08-28 12:12:32,487 align.py process_cal():282 [71853] tailcone_propRpm: instrument_sample_rate_hz = 1.09 INFO 2023-08-28 12:12:32,626 align.py write_netcdf():367 [71853] Writing aligned data to /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04/dorado_2007.171.04_align.nc INFO 2023-08-28 12:12:32,958 align.py write_netcdf():372 [71853] 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_bb470, hs2_bb676, hs2_depth, hs2_fl676, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_temp, isus_time, 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 2023-08-28 12:12:33,473 resample.py instruments_variables():233 [71853] Reading variables from /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04/dorado_2007.171.04_align.nc mission netCDF file INFO 2023-08-28 12:12:33,595 resample.py instruments_variables():233 [71853] Reading variables from /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04/dorado_2007.171.04_align.nc mission netCDF file INFO 2023-08-28 12:12:33,620 resample.py get_mission_start_end():815 [71853] navigation: 2007-06-20T23:36:22.453618688 to 2007-06-21T15:18:10.192573440 (0 days 00:00:00 before mission_end) INFO 2023-08-28 12:12:33,653 resample.py get_mission_start_end():815 [71853] hs2 : 2007-06-20T23:35:56.725381376 to 2007-06-21T15:18:10.182574336 (0 days 00:00:00.009999104 before mission_end) INFO 2023-08-28 12:12:33,674 resample.py get_mission_start_end():815 [71853] ctd1 : 2007-06-20T23:36:16.624018176 to 2007-06-21T15:18:10.182574336 (0 days 00:00:00.009999104 before mission_end) INFO 2023-08-28 12:12:33,700 resample.py get_mission_start_end():815 [71853] ctd2 : 2007-06-20T23:36:18.853865472 to 2007-06-21T15:18:10.042583808 (0 days 00:00:00.149989632 before mission_end) INFO 2023-08-28 12:12:33,712 resample.py get_mission_start_end():815 [71853] isus : 2007-06-20T23:37:07.670521344 to 2007-06-21T15:18:08.772670720 (0 days 00:00:01.419902720 before mission_end) INFO 2023-08-28 12:12:33,732 resample.py get_mission_start_end():815 [71853] biolume : 2007-06-20T23:35:47.725963520 to 2007-06-21T15:18:09.232604928 (0 days 00:00:00.959968512 before mission_end) INFO 2023-08-28 12:12:33,750 resample.py get_mission_start_end():815 [71853] tailcone : 2007-06-20T23:35:53.795581952 to 2007-06-21T15:18:09.422626304 (0 days 00:00:00.769947136 before mission_end) INFO 2023-08-28 12:12:33,767 resample.py instruments_variables():233 [71853] Reading variables from /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04/dorado_2007.171.04_align.nc mission netCDF file INFO 2023-08-28 12:12:33,776 resample.py resample_coordinates():247 [71853] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:34,358 resample.py resample_variable():710 [71853] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:34,620 resample.py resample_variable():710 [71853] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:34,997 resample.py resample_variable():710 [71853] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:35,478 resample.py resample_variable():710 [71853] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:35,656 resample.py resample_variable():710 [71853] Resampling hs2_bb470 with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:35,803 resample.py resample_variable():710 [71853] Resampling hs2_bb676 with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:35,932 resample.py resample_variable():710 [71853] Resampling hs2_fl676 with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:36,275 resample.py resample_variable():710 [71853] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:36,553 resample.py resample_variable():710 [71853] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:36,635 resample.py resample_variable():710 [71853] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:36,756 resample.py resample_variable():710 [71853] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:36,869 resample.py resample_variable():710 [71853] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:37,001 resample.py resample_variable():710 [71853] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:37,311 resample.py resample_variable():710 [71853] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:37,649 resample.py resample_variable():710 [71853] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:37,909 resample.py resample_variable():710 [71853] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:38,252 resample.py resample_variable():710 [71853] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:38,436 resample.py resample_variable():710 [71853] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:38,532 resample.py resample_variable():710 [71853] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:38,623 resample.py resample_variable():710 [71853] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:38,758 resample.py resample_variable():710 [71853] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:38,874 resample.py resample_variable():710 [71853] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:38,930 resample.py resample_variable():710 [71853] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:39,054 resample.py resample_variable():710 [71853] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:39,203 resample.py resample_variable():710 [71853] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:39,295 resample.py resample_mission():903 [71853] Not saving instrument coordinate variable biolume_latitude to resampled file INFO 2023-08-28 12:12:39,298 resample.py resample_mission():903 [71853] Not saving instrument coordinate variable biolume_longitude to resampled file INFO 2023-08-28 12:12:39,404 resample.py resample_variable():710 [71853] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2023-08-28 12:12:43,257 resample.py resample_mission():946 [71853] Saved resampled mission to /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04/dorado_2007.171.04_1S.nc INFO 2023-08-28 12:12:54,203 create_products.py _get_best_ctd():112 [71853] ctdToUse = ctd1 INFO 2023-08-28 12:13:02,779 create_products.py gulper_odv():239 [71853] Wrote 5 Gulper data lines to /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionodvs/2007.171.04/dorado_2007.171.04_1S_Gulper.txt INFO 2023-08-28 12:13:02,780 archive.py copy_to_AUVTCD():50 [71853] Archiving /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04/dorado_2007.171.04 files to /Volumes/AUVCTD/surveys/2007/netcdf INFO 2023-08-28 12:13:03,177 archive.py copy_to_AUVTCD():60 [71853] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04/dorado_2007.171.04_1S.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2023-08-28 12:13:05,620 archive.py copy_to_AUVTCD():60 [71853] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04/dorado_2007.171.04_cal.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2023-08-28 12:13:07,607 archive.py copy_to_AUVTCD():60 [71853] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04/dorado_2007.171.04_align.nc /Volumes/AUVCTD/surveys/2007/netcdf done. INFO 2023-08-28 12:13:08,094 archive.py copy_to_AUVTCD():75 [71853] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007171/2007.171.04 done. INFO 2023-08-28 12:13:08,783 archive.py copy_to_AUVTCD():75 [71853] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007171/2007.171.04 done. INFO 2023-08-28 12:13:08,848 archive.py copy_to_AUVTCD():75 [71853] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04/gps.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007171/2007.171.04 done. INFO 2023-08-28 12:13:09,281 archive.py copy_to_AUVTCD():75 [71853] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007171/2007.171.04 done. INFO 2023-08-28 12:13:11,240 archive.py copy_to_AUVTCD():75 [71853] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007171/2007.171.04 done. INFO 2023-08-28 12:13:11,364 archive.py copy_to_AUVTCD():75 [71853] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007171/2007.171.04 done. INFO 2023-08-28 12:13:11,900 archive.py copy_to_AUVTCD():75 [71853] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007171/2007.171.04 done. INFO 2023-08-28 12:13:12,029 archive.py copy_to_AUVTCD():75 [71853] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007171/2007.171.04 done. INFO 2023-08-28 12:13:13,731 archive.py copy_to_AUVTCD():75 [71853] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2007/2007171/2007.171.04 done. INFO 2023-08-28 12:13:13,732 archive.py copy_to_AUVTCD():80 [71853] Archiving product files INFO 2023-08-28 12:13:54,898 archive.py copy_to_AUVTCD():89 [71853] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionodvs/2007.171.04/* /Volumes/AUVCTD/surveys/2007/odv done. INFO 2023-08-28 12:14:03,340 archive.py copy_to_AUVTCD():97 [71853] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2007.171.04/dorado_2007.171.04_processing.log /Volumes/AUVCTD/surveys/2007/netcdf