INFO 2025-06-26 18:26:40,614 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 18:26:40,614 process.py process_mission():434 [1] dorado_info[mission]["comment"] = TREX mission - Following SIO_WWL_1 for September 2011 CANON - ctdToUse = ctd1 INFO 2025-06-26 18:26:40,614 process.py process_mission():449 [1] Processing CANON September 2011 mission 2011.256.03 by user docker_user on host eae60d30a712 INFO 2025-06-26 18:26:40,614 process.py download_process():165 [1] Download and processing steps for 2011.256.03 INFO 2025-06-26 18:26:40,615 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2011/2011256/2011.256.03 INFO 2025-06-26 18:26:40,615 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2011/2011256/2011.256.03 to /data/auv_data/dorado/missionlogs/2011.256.03 INFO 2025-06-26 18:26:44,105 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2011.256.03 INFO 2025-06-26 18:26:44,105 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.256.03/ctdDriver.log (6443142 bytes) INFO 2025-06-26 18:26:44,604 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.256.03/ctdDriver2.log (6443327 bytes) INFO 2025-06-26 18:26:45,140 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.256.03/gps.log (296276 bytes) INFO 2025-06-26 18:26:45,181 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.256.03/hydroscatlog.log (5642890 bytes) INFO 2025-06-26 18:26:45,834 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.256.03/navigation.log (22807878 bytes) INFO 2025-06-26 18:26:47,666 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.256.03/isuslog.log (533301 bytes) INFO 2025-06-26 18:26:47,723 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.256.03/parosci.log (6835334 bytes) INFO 2025-06-26 18:26:48,402 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.256.03/tailCone.log (4033435 bytes) INFO 2025-06-26 18:26:48,971 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2011.256.03/biolume.log (4695794 bytes) INFO 2025-06-26 18:26:49,455 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 18:26:49,722 logs2netcdfs.py download_process_logs():807 [1] Time to process: 5.62 seconds INFO 2025-06-26 18:26:49,722 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2011.256.03/lopc.bin (90985349 bytes) INFO 2025-06-26 18:26:49,723 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 18:26:49 2025 INFO 2025-06-26 18:26:49,723 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2011.256.03/parosci.nc INFO 2025-06-26 18:26:49,723 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 18:26:49,723 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2011.256.03/parosci.nc INFO 2025-06-26 18:26:49,727 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1315954775.3, sensor_off_time = 1315971579.9 INFO 2025-06-26 18:26:49,727 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 16804 seconds. Expecting to read 33608 L frames from the lopc.bin file. INFO 2025-06-26 18:26:49,727 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 33608 records from the lopc.bin file. INFO 2025-06-26 18:26:49,929 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2011-09-13 22:59:35 Z and endTime = 2011-09-14 03:39:39 Z with 33608 records expected to be read from lopc.bin INFO 2025-06-26 18:26:49,929 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2011.256.03/lopc.bin INFO 2025-06-26 18:26:49,929 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2011.256.03/lopc.nc INFO 2025-06-26 18:26:49,930 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2011.256.03/lopc.nc INFO 2025-06-26 18:26:49,930 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2011.256.03 INFO 2025-06-26 18:26:49,931 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 ERROR 2025-06-26 18:26:49,939 lopcToNetCDF.py main():2340 [1] UnicodeDecodeError: 'utf-8' codec can't decode byte 0x89 in position 0: invalid start byte INFO 2025-06-26 18:26:49,939 lopcToNetCDF.py main():2341 [1] Failed to decode all of lopc.bin - resulting lopc.nc file likely incomplete INFO 2025-06-26 18:26:49,939 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2011.256.03/parosci.nc INFO 2025-06-26 18:26:49,939 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 18:26:49,939 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2011.256.03/parosci.nc INFO 2025-06-26 18:26:49,943 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1315954775.3, sensor_off_time = 1315971579.9 INFO 2025-06-26 18:26:49,943 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 16804 seconds. Expecting to read 33608 L frames from the lopc.bin file. INFO 2025-06-26 18:26:49,943 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 33608 records from the lopc.bin file. INFO 2025-06-26 18:26:49,944 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 1 and len(sampleCountList) = 3 INFO 2025-06-26 18:26:49,944 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [] INFO 2025-06-26 18:26:49,944 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [1 2 3] INFO 2025-06-26 18:26:49,945 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 18:26:49,945 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-26 18:26:49,946 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [1 1] INFO 2025-06-26 18:26:49,946 lopcToNetCDF.py deSpike():1590 [1] Found 0 spike indicators at indices: [] INFO 2025-06-26 18:26:49,946 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [1 2 3] INFO 2025-06-26 18:26:49,946 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [1 2 3] with len(correctedSampleCountList) = 3 INFO 2025-06-26 18:26:49,946 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 1 from all values of correctedSampleCountList INFO 2025-06-26 18:26:49,946 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 18:26:49,946 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [0. 0.5 1. ] INFO 2025-06-26 18:26:49,947 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.31595478e+09 1.31595478e+09 1.31595478e+09] INFO 2025-06-26 18:26:49,947 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1315954775.3 1315954775.8, ..., timestampArray[-2:] = 1315954775.8 1315954776.3] INFO 2025-06-26 18:26:49,947 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1315954775.2765405), np.float64(1315954775.7765405)], ..., timestampList[-2:] = [np.float64(1315954775.7765405), np.float64(1315954776.2765405)]] INFO 2025-06-26 18:26:49,947 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 3) according to what got written to the netCDF file by the binning interval ERROR 2025-06-26 18:26:49,947 lopcToNetCDF.py main():2376 [1] KeyError: sampleCountList or cFrameEsecsList not found in self.dataStructure INFO 2025-06-26 18:26:49,947 lopcToNetCDF.py main():2379 [1] No lopc.nc file created INFO 2025-06-26 18:26:49,948 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 18:26:49 2025 Elapsed processing time from start of processing = 0 seconds INFO 2025-06-26 18:26:49,948 process.py calibrate():227 [1] Calibration steps for 2011.256.03 INFO 2025-06-26 18:26:50,151 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 18:26:50,153 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 18:26:55,157 calibrate.py _nudge_pos():1806 [1] 546: 0.180 -0.0025376 -0.0019375 6125 20.41 -18.435 -17.587 2011-09-13T23:29:04.365349632 INFO 2025-06-26 18:26:57,163 calibrate.py _nudge_pos():1806 [1] 758: 0.170 0.0000033 -0.0000034 15 0.05 10.476 -13.314 2011-09-13T23:32:38.370689280 INFO 2025-06-26 18:26:57,473 calibrate.py _nudge_pos():1806 [1] 791: 0.170 0.0020155 -0.0016126 7020 23.40 12.778 -12.772 2011-09-13T23:56:34.372316416 INFO 2025-06-26 18:26:59,531 calibrate.py _nudge_pos():1806 [1] 1010: 0.170 0.0015580 -0.0013174 4040 13.46 17.164 -18.132 2011-09-14T00:13:40.372030464 INFO 2025-06-26 18:27:00,260 calibrate.py _nudge_pos():1806 [1] 1086: 0.180 0.0000580 0.0000052 25 0.08 107.459 12.007 2011-09-14T00:15:00.366550528 INFO 2025-06-26 18:27:03,787 calibrate.py _nudge_pos():1806 [1] 1455: 0.180 0.0000132 -0.0000138 30 0.10 20.243 -26.386 2011-09-14T00:21:14.370929408 INFO 2025-06-26 18:27:06,052 calibrate.py _nudge_pos():1806 [1] 1693: 0.170 -0.0009379 -0.0018332 6625 22.08 -6.299 -15.385 2011-09-14T00:47:16.373924864 INFO 2025-06-26 18:27:07,406 calibrate.py _nudge_pos():1806 [1] 1835: 0.180 0.0026645 -0.0027250 8950 29.83 13.248 -16.927 2011-09-14T01:19:28.371574272 INFO 2025-06-26 18:27:10,294 calibrate.py _nudge_pos():1806 [1] 2136: 0.190 0.0012714 -0.0006017 4500 15.00 12.573 -7.434 2011-09-14T01:39:28.369368576 INFO 2025-06-26 18:27:17,198 calibrate.py _nudge_pos():1806 [1] 2859: 0.180 0.0000032 0.0000412 25 0.08 5.845 95.496 2011-09-14T01:51:35.369565696 INFO 2025-06-26 18:27:17,562 calibrate.py _nudge_pos():1806 [1] 2897: 0.190 -0.0000224 0.0000153 15 0.05 -71.230 60.594 2011-09-14T01:52:15.366825472 INFO 2025-06-26 18:27:18,486 calibrate.py _nudge_pos():1806 [1] 2994: 0.200 -0.0007328 -0.0029151 6995 23.31 -4.661 -23.170 2011-09-14T02:17:10.364411392 INFO 2025-06-26 18:27:20,767 calibrate.py _nudge_pos():1806 [1] 3230: 0.190 0.0003827 -0.0021101 6985 23.28 2.438 -16.796 2011-09-14T02:44:22.372611072 INFO 2025-06-26 18:27:23,605 calibrate.py _nudge_pos():1806 [1] 3525: 0.200 0.0009310 -0.0002275 4679 15.59 8.854 -2.703 2011-09-14T03:04:52.368350464 INFO 2025-06-26 18:27:28,572 calibrate.py _nudge_pos():1806 [1] 4037: 0.200 0.0006987 -0.0037456 7555 25.18 4.115 -27.564 2011-09-14T03:38:34.369833984 INFO 2025-06-26 18:27:29,217 calibrate.py _nudge_pos():1862 [1] 4066: - - - 1 0.00 - - INFO 2025-06-26 18:27:29,217 calibrate.py _nudge_pos():1868 [1] Points in final series = 83022 WARNING 2025-06-26 18:27:29,328 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 18:27:29,447 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 2 of 67165 INFO 2025-06-26 18:27:29,961 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:27:30,591 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:27:31,091 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:27:31,093 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2011.256.03/ctd1.nc INFO 2025-06-26 18:27:31,094 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 18:27:31,095 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 18:27:31,095 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 18:27:31,699 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:27:32,210 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 18:27:32,212 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2011.256.03/ctd2.nc INFO 2025-06-26 18:27:32,213 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd2_salinity values to NaN INFO 2025-06-26 18:27:32,214 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 18:27:32,214 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 18:27:32,246 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 18:27:33,035 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60] INFO 2025-06-26 18:27:33,180 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 18:27:48,322 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2011.256.03 ERROR 2025-06-26 18:27:48,322 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2011.256.03 INFO 2025-06-26 18:27:48,389 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2011.256.03/dorado_2011.256.03_cal.nc INFO 2025-06-26 18:27:48,514 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, isus_nitrate, isus_quality, 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 2025-06-26 18:27:48,520 process.py align():251 [1] Alignment steps for 2011.256.03 INFO 2025-06-26 18:27:48,559 align.py process_cal():139 [1] Processing dorado_2011.256.03_cal.nc from /data/auv_data/dorado/missionnetcdfs/2011.256.03 INFO 2025-06-26 18:27:48,584 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:27:48,588 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:27:48,659 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:27:48,664 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:27:48,744 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:27:48,748 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:27:48,783 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 18:27:48,783 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 18:27:48,806 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 18:27:48,810 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:27:48,867 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:48,871 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:48,922 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:48,926 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:48,978 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:48,982 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:49,034 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:49,038 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:49,090 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:49,094 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:49,144 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:49,148 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:49,200 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:49,204 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:49,254 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:49,258 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:49,310 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:49,314 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:49,364 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:49,369 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:49,421 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:49,425 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:49,476 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:49,480 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:49,532 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:49,536 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:49,587 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:49,590 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:49,644 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:49,648 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:49,700 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:49,704 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:49,759 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:49,763 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:49,815 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:49,820 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:49,873 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:49,878 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:49,929 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:49,934 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:49,987 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:49,991 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:50,044 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 18:27:50,048 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 18:27:50,110 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 18:27:50,153 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 18:27:50,198 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 18:27:50,245 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 18:27:50,291 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 18:27:50,363 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 18:27:50,786 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 18:27:50,829 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2011.256.03/dorado_2011.256.03_align.nc INFO 2025-06-26 18:27:50,957 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, 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 2025-06-26 18:27:50,960 process.py resample():273 [1] Resampling steps for 2011.256.03 INFO 2025-06-26 18:27:50,961 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 18:27:50,996 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.256.03/dorado_2011.256.03_align.nc mission netCDF file INFO 2025-06-26 18:27:51,002 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.256.03/dorado_2011.256.03_align.nc mission netCDF file INFO 2025-06-26 18:27:51,004 resample.py get_mission_start_end():1145 [1] navigation: 2011-09-13T23:00:11.184080640 to 2011-09-14T03:39:39.765354240 (0 days 00:00:00.049996544 before mission_end) INFO 2025-06-26 18:27:51,005 resample.py get_mission_start_end():1145 [1] hs2 : 2011-09-13T22:59:40.946151936 to 2011-09-14T03:39:39.705358336 (0 days 00:00:00.109992448 before mission_end) INFO 2025-06-26 18:27:51,007 resample.py get_mission_start_end():1145 [1] ctd1 : 2011-09-13T23:00:03.194628096 to 2011-09-14T03:39:39.815350784 (0 days 00:00:00 before mission_end) INFO 2025-06-26 18:27:51,009 resample.py get_mission_start_end():1145 [1] ctd2 : 2011-09-13T23:00:02.664664320 to 2011-09-14T03:39:39.775353344 (0 days 00:00:00.039997440 before mission_end) INFO 2025-06-26 18:27:51,010 resample.py get_mission_start_end():1145 [1] isus : 2011-09-13T23:00:58.140864000 to 2011-09-14T03:39:39.625363712 (0 days 00:00:00.189987072 before mission_end) INFO 2025-06-26 18:27:51,012 resample.py get_mission_start_end():1145 [1] biolume : 2011-09-13T22:59:34.016592384 to 2011-09-14T03:39:38.695393024 (0 days 00:00:01.119957760 before mission_end) INFO 2025-06-26 18:27:51,014 resample.py get_mission_start_end():1145 [1] tailcone : 2011-09-13T22:59:36.206476800 to 2011-09-14T03:39:39.805351168 (0 days 00:00:00.009999616 before mission_end) INFO 2025-06-26 18:27:51,014 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2011.256.03/dorado_2011.256.03_align.nc mission netCDF file INFO 2025-06-26 18:27:51,015 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,206 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,239 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,272 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,305 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,334 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,363 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,391 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,418 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,445 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,470 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,496 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,522 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,548 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,574 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,599 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,625 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,651 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,680 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,708 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,735 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,761 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,788 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,815 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,843 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,859 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,873 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,887 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,899 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,911 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:51,916 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 18:27:51,916 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 18:27:52,539 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 18:27:52,650 resample.py add_biolume_proxies():633 [1] Zero flow values found: 3 of 16805 - replaced with 350 ml/s INFO 2025-06-26 18:27:52,651 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 18:27:52,712 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 18:27:52,739 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 18:27:52,760 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 18:27:52,760 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 18:27:52,796 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 18:27:53,002 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2011.256.03/dorado_2011.256.03_1S.nc INFO 2025-06-26 18:27:56,506 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 18:28:05,158 create_products.py gulper_odv():522 [1] Wrote 6 Gulper data lines to /data/auv_data/dorado/missionodvs/2011.256.03/dorado_2011.256.03_1S_Gulper.txt INFO 2025-06-26 18:28:05,158 process.py archive():337 [1] Archiving steps for 2011.256.03 INFO 2025-06-26 18:28:05,158 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2011.256.03/dorado_2011.256.03, BASE_PATH = /data/auv_data INFO 2025-06-26 18:28:05,160 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2011.256.03/dorado_2011.256.03 files to /Volumes/AUVCTD/surveys/2011/netcdf INFO 2025-06-26 18:28:05,161 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.256.03_1S.nc INFO 2025-06-26 18:28:05,179 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.03/dorado_2011.256.03_1S.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 18:28:05,180 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.256.03_cal.nc INFO 2025-06-26 18:28:05,294 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.03/dorado_2011.256.03_cal.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 18:28:05,295 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2011/netcdf/dorado_2011.256.03_align.nc INFO 2025-06-26 18:28:05,453 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.03/dorado_2011.256.03_align.nc /Volumes/AUVCTD/surveys/2011/netcdf done. INFO 2025-06-26 18:28:05,476 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.03/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.03 done. INFO 2025-06-26 18:28:05,498 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.03/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.03 done. INFO 2025-06-26 18:28:05,503 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.03/gps.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.03 done. INFO 2025-06-26 18:28:05,522 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.03/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.03 done. INFO 2025-06-26 18:28:05,580 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.03/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.03 done. INFO 2025-06-26 18:28:05,586 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.03/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.03 done. INFO 2025-06-26 18:28:05,607 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.03/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.03 done. INFO 2025-06-26 18:28:05,624 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.03/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.03 done. INFO 2025-06-26 18:28:05,668 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.03/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.03 done. INFO 2025-06-26 18:28:05,673 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.03/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.03 done. INFO 2025-06-26 18:28:05,673 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 18:28:05,674 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2011/odv/dorado_2011.256.03_1S_Gulper.txt INFO 2025-06-26 18:28:05,679 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2011.256.03/dorado_2011.256.03_1S_Gulper.txt /Volumes/AUVCTD/surveys/2011/odv done. INFO 2025-06-26 18:28:05,679 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2011.256.03/dorado_2011.256.03_processing.log /Volumes/AUVCTD/surveys/2011/netcdf