INFO 2025-06-26 20:21:30,750 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 20:21:30,750 process.py process_mission():434 [1] dorado_info[mission]["comment"] = San Pedro Bay CANON-ECOHAB - ctdToUse = ctd1 INFO 2025-06-26 20:21:30,750 process.py process_mission():449 [1] Processing CANON April 2014 mission 2014.108.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:21:30,750 process.py download_process():165 [1] Download and processing steps for 2014.108.02 INFO 2025-06-26 20:21:30,750 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014108/2014.108.02 INFO 2025-06-26 20:21:30,750 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014108/2014.108.02 to /data/auv_data/dorado/missionlogs/2014.108.02 INFO 2025-06-26 20:21:34,061 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.108.02 INFO 2025-06-26 20:21:34,061 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.108.02/ctdDriver.log (4280454 bytes) INFO 2025-06-26 20:21:34,364 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.108.02/ctdDriver2.log (4280255 bytes) INFO 2025-06-26 20:21:34,676 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.108.02/gps.log (39164 bytes) INFO 2025-06-26 20:21:34,688 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.108.02/hydroscatlog.log (3751546 bytes) INFO 2025-06-26 20:21:35,073 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.108.02/navigation.log (16033698 bytes) INFO 2025-06-26 20:21:36,214 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.108.02/isuslog.log (277141 bytes) INFO 2025-06-26 20:21:36,245 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.108.02/parosci.log (5266694 bytes) INFO 2025-06-26 20:21:36,678 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2014.108.02/parosci.log: [1] INFO 2025-06-26 20:21:36,692 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.108.02/tailCone.log (2683051 bytes) INFO 2025-06-26 20:21:37,024 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.108.02/biolume.log (3124422 bytes) INFO 2025-06-26 20:21:37,326 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:21:37,484 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.42 seconds INFO 2025-06-26 20:21:37,485 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.108.02/lopc.bin (32212336 bytes) INFO 2025-06-26 20:21:37,485 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:21:37 2025 INFO 2025-06-26 20:21:37,485 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.108.02/parosci.nc INFO 2025-06-26 20:21:37,485 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:21:37,485 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.108.02/parosci.nc INFO 2025-06-26 20:21:37,488 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1397846682.8, sensor_off_time = 1397857855.8 INFO 2025-06-26 20:21:37,489 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 11172 seconds. Expecting to read 22344 L frames from the lopc.bin file. INFO 2025-06-26 20:21:37,489 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 22344 records from the lopc.bin file. INFO 2025-06-26 20:21:37,621 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-04-18 18:44:42 Z and endTime = 2014-04-18 21:50:55 Z with 22344 records expected to be read from lopc.bin INFO 2025-06-26 20:21:37,621 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.108.02/lopc.bin INFO 2025-06-26 20:21:37,621 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.108.02/lopc.nc INFO 2025-06-26 20:21:37,622 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.108.02/lopc.nc INFO 2025-06-26 20:21:37,622 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.108.02 INFO 2025-06-26 20:21:37,622 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 20:21:37,626 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 20:21:37,719 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:21:37,719 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:21:37,719 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:21:37,831 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:21:37,832 process.py calibrate():227 [1] Calibration steps for 2014.108.02 INFO 2025-06-26 20:21:37,964 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 20:21:37,966 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:21:38,588 calibrate.py _nudge_pos():1806 [1] 104: 0.020 0.0000986 0.0003715 1300 4.33 3.512 15.898 2014-04-18T18:50:40.121007616 INFO 2025-06-26 20:21:39,050 calibrate.py _nudge_pos():1806 [1] 154: 0.020 0.0009010 -0.0005144 7975 26.58 5.232 -3.586 2014-04-18T19:18:04.118385920 INFO 2025-06-26 20:21:39,582 calibrate.py _nudge_pos():1806 [1] 211: 0.030 0.0008288 -0.0005770 10255 34.18 3.743 -3.128 2014-04-18T19:53:11.114046976 INFO 2025-06-26 20:21:40,130 calibrate.py _nudge_pos():1806 [1] 269: 0.030 0.0000320 -0.0001504 8290 27.63 0.179 -1.009 2014-04-18T20:21:46.116561152 INFO 2025-06-26 20:21:40,698 calibrate.py _nudge_pos():1806 [1] 325: 0.040 -0.0013490 -0.0000165 8395 27.98 -7.446 -0.110 2014-04-18T20:50:40.117774080 INFO 2025-06-26 20:21:41,271 calibrate.py _nudge_pos():1806 [1] 384: 0.040 -0.0001811 -0.0000284 8230 27.43 -1.020 -0.192 2014-04-18T21:19:04.121041664 INFO 2025-06-26 20:21:41,838 calibrate.py _nudge_pos():1806 [1] 444: 0.050 0.0004851 -0.0001446 8825 29.41 2.548 -0.911 2014-04-18T21:49:28.116089600 INFO 2025-06-26 20:21:42,660 calibrate.py _nudge_pos():1862 [1] 486: - - - 3 0.01 - - INFO 2025-06-26 20:21:42,661 calibrate.py _nudge_pos():1868 [1] Points in final series = 55663 INFO 2025-06-26 20:21:44,500 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 1 of 44649 INFO 2025-06-26 20:21:44,840 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:21:45,273 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:21:45,618 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:21:45,620 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.108.02/ctd1.nc INFO 2025-06-26 20:21:45,621 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:21:45,622 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 20:21:45,622 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:21:46,027 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:21:46,378 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:21:46,380 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.108.02/ctd2.nc INFO 2025-06-26 20:21:46,382 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:21:46,382 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 20:21:46,382 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:21:46,404 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:21:46,870 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 101400 101401 101402 101403 101404 101405 101406 101407 101408 101409 101410 101411 101412 101413 101414 101415 101416 101417 101418 101419 101420 101421 101422 101423 101424 101425 101426 101427 101428] INFO 2025-06-26 20:21:46,969 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -3 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:21:57,058 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.108.02 ERROR 2025-06-26 20:21:57,058 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.108.02 INFO 2025-06-26 20:21:57,104 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.108.02/dorado_2014.108.02_cal.nc INFO 2025-06-26 20:21:57,204 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 20:21:57,210 process.py align():251 [1] Alignment steps for 2014.108.02 INFO 2025-06-26 20:21:57,242 align.py process_cal():139 [1] Processing dorado_2014.108.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.108.02 INFO 2025-06-26 20:21:57,261 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:21:57,264 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:21:57,305 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:21:57,309 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:21:57,352 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:21:57,356 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:21:57,380 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:21:57,380 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:21:57,396 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:21:57,399 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:21:57,441 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:57,444 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:57,480 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:57,484 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:57,521 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:57,524 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:57,561 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:57,564 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:57,601 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:57,604 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:57,640 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:57,644 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:57,682 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:57,685 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:57,722 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:57,725 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:57,762 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:57,765 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:57,802 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:57,805 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:57,842 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:57,845 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:57,881 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:57,884 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:57,922 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:57,925 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:57,962 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:57,964 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:58,004 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:58,007 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:58,045 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:58,048 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:58,086 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:58,089 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:58,126 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:58,129 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:58,167 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:58,170 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:58,206 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:58,210 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:58,247 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:58,251 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:58,287 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.108.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:21:58,290 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:21:58,337 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:21:58,372 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:21:58,406 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:21:58,444 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:21:58,481 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:21:58,539 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:21:58,829 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:21:58,860 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.108.02/dorado_2014.108.02_align.nc INFO 2025-06-26 20:21:58,964 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 20:21:58,967 process.py resample():273 [1] Resampling steps for 2014.108.02 INFO 2025-06-26 20:21:58,967 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:21:58,998 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.108.02/dorado_2014.108.02_align.nc mission netCDF file INFO 2025-06-26 20:21:59,004 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.108.02/dorado_2014.108.02_align.nc mission netCDF file INFO 2025-06-26 20:21:59,005 resample.py get_mission_start_end():1145 [1] navigation: 2014-04-18T18:45:23.132722944 to 2014-04-18T21:50:55.720088320 (0 days 00:00:00.009999104 before mission_end) INFO 2025-06-26 20:21:59,007 resample.py get_mission_start_end():1145 [1] hs2 : 2014-04-18T18:44:49.215046400 to 2014-04-18T21:50:55.560099328 (0 days 00:00:00.169988096 before mission_end) INFO 2025-06-26 20:21:59,008 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-04-18T18:45:10.963556608 to 2014-04-18T21:50:55.730087424 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:21:59,010 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-04-18T18:45:11.263535872 to 2014-04-18T21:50:55.510102784 (0 days 00:00:00.219984640 before mission_end) INFO 2025-06-26 20:21:59,011 resample.py get_mission_start_end():1145 [1] isus : 2014-04-18T18:45:54.300587776 to 2014-04-18T21:50:55.590097152 (0 days 00:00:00.139990272 before mission_end) INFO 2025-06-26 20:21:59,012 resample.py get_mission_start_end():1145 [1] biolume : 2014-04-18T18:44:39.345688064 to 2014-04-18T21:50:55.120095232 (0 days 00:00:00.609992192 before mission_end) INFO 2025-06-26 20:21:59,014 resample.py get_mission_start_end():1145 [1] tailcone : 2014-04-18T18:44:38.615772416 to 2014-04-18T21:50:55.560099328 (0 days 00:00:00.169988096 before mission_end) INFO 2025-06-26 20:21:59,014 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.108.02/dorado_2014.108.02_align.nc mission netCDF file INFO 2025-06-26 20:21:59,015 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,149 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,173 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,196 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,219 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,241 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,262 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,283 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,304 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,323 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,342 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,362 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,381 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,400 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,419 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,438 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,457 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,475 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,496 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,516 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,537 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,557 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,577 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,597 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,617 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,629 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,641 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,652 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,662 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,673 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:21:59,677 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:21:59,677 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:22:00,082 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:22:00,152 resample.py add_biolume_proxies():633 [1] Zero flow values found: 11177 of 11177 - replaced with 350 ml/s INFO 2025-06-26 20:22:00,153 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:22:00,193 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:22:00,211 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:22:00,227 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:22:00,227 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:22:00,255 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:22:00,428 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.108.02/dorado_2014.108.02_1S.nc INFO 2025-06-26 20:22:02,102 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:22:13,286 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.108.02/dorado_2014.108.02_1S_Gulper.txt INFO 2025-06-26 20:22:13,286 process.py archive():337 [1] Archiving steps for 2014.108.02 INFO 2025-06-26 20:22:13,287 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.108.02/dorado_2014.108.02, BASE_PATH = /data/auv_data INFO 2025-06-26 20:22:13,288 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.108.02/dorado_2014.108.02 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:22:13,288 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.108.02_1S.nc INFO 2025-06-26 20:22:13,303 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.02/dorado_2014.108.02_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:22:13,304 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.108.02_cal.nc INFO 2025-06-26 20:22:13,383 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.02/dorado_2014.108.02_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:22:13,384 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.108.02_align.nc INFO 2025-06-26 20:22:13,491 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.02/dorado_2014.108.02_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:22:13,508 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014108/2014.108.02 done. INFO 2025-06-26 20:22:13,524 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014108/2014.108.02 done. INFO 2025-06-26 20:22:13,528 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014108/2014.108.02 done. INFO 2025-06-26 20:22:13,542 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014108/2014.108.02 done. INFO 2025-06-26 20:22:13,590 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014108/2014.108.02 done. INFO 2025-06-26 20:22:13,597 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.02/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014108/2014.108.02 done. INFO 2025-06-26 20:22:13,615 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014108/2014.108.02 done. INFO 2025-06-26 20:22:13,628 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014108/2014.108.02 done. INFO 2025-06-26 20:22:13,662 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014108/2014.108.02 done. INFO 2025-06-26 20:22:13,667 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.02/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014108/2014.108.02 done. INFO 2025-06-26 20:22:13,667 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:22:13,669 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.108.02_1S_Gulper.txt INFO 2025-06-26 20:22:13,673 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.108.02/dorado_2014.108.02_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:22:13,673 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.108.02/dorado_2014.108.02_processing.log /Volumes/AUVCTD/surveys/2014/netcdf