INFO 2025-06-26 20:35:11,804 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 20:35:11,804 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON-ECOHAB September 2014 with rhodamine sensor on ctdDriver2, channel 1 - ctdToUse = ctd1 INFO 2025-06-26 20:35:11,804 process.py process_mission():449 [1] Processing CANON September 2014 mission 2014.268.05 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:35:11,804 process.py download_process():165 [1] Download and processing steps for 2014.268.05 INFO 2025-06-26 20:35:11,804 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014268/2014.268.05 INFO 2025-06-26 20:35:11,804 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014268/2014.268.05 to /data/auv_data/dorado/missionlogs/2014.268.05 INFO 2025-06-26 20:35:15,457 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.268.05 INFO 2025-06-26 20:35:15,457 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.268.05/ctdDriver.log (3626214 bytes) INFO 2025-06-26 20:35:15,721 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.268.05/ctdDriver2.log (3626691 bytes) INFO 2025-06-26 20:35:15,985 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.268.05/gps.log (88628 bytes) INFO 2025-06-26 20:35:16,003 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.268.05/hydroscatlog.log (3177910 bytes) INFO 2025-06-26 20:35:16,332 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.268.05/navigation.log (13558050 bytes) INFO 2025-06-26 20:35:17,301 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.268.05/isuslog.log (234677 bytes) INFO 2025-06-26 20:35:17,327 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2014.268.05/isuslog.log: [ 2 3 4 5 6 7 8 9 11] INFO 2025-06-26 20:35:17,329 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.268.05/parosci.log (4453142 bytes) INFO 2025-06-26 20:35:17,728 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.268.05/tailCone.log (2271163 bytes) INFO 2025-06-26 20:35:18,017 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.268.05/biolume.log (2645314 bytes) INFO 2025-06-26 20:35:18,279 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:35:18,415 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.96 seconds INFO 2025-06-26 20:35:18,416 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.268.05/lopc.bin (11763658 bytes) INFO 2025-06-26 20:35:18,416 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:35:18 2025 INFO 2025-06-26 20:35:18,416 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.268.05/parosci.nc INFO 2025-06-26 20:35:18,416 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:35:18,416 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.268.05/parosci.nc INFO 2025-06-26 20:35:18,419 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1411670288.6, sensor_off_time = 1411679749.2 INFO 2025-06-26 20:35:18,420 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 9460 seconds. Expecting to read 18920 L frames from the lopc.bin file. INFO 2025-06-26 20:35:18,420 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 18920 records from the lopc.bin file. INFO 2025-06-26 20:35:18,544 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-09-25 18:38:08 Z and endTime = 2014-09-25 21:15:49 Z with 18920 records expected to be read from lopc.bin INFO 2025-06-26 20:35:18,544 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.268.05/lopc.bin INFO 2025-06-26 20:35:18,544 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.268.05/lopc.nc INFO 2025-06-26 20:35:18,545 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.268.05/lopc.nc INFO 2025-06-26 20:35:18,545 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.268.05 INFO 2025-06-26 20:35:18,545 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 ERROR 2025-06-26 20:35:18,548 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:35:18,549 process.py calibrate():227 [1] Calibration steps for 2014.268.05 INFO 2025-06-26 20:35:18,678 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 20:35:18,680 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:35:19,309 calibrate.py _nudge_pos():1806 [1] 104: 0.200 -0.0009404 0.0006857 1999 6.66 -20.962 19.079 2014-09-25T18:46:30.338615040 INFO 2025-06-26 20:35:19,721 calibrate.py _nudge_pos():1806 [1] 147: 0.200 -0.0035519 0.0000496 4214 14.04 -37.541 0.655 2014-09-25T19:01:15.337988352 INFO 2025-06-26 20:35:20,360 calibrate.py _nudge_pos():1806 [1] 215: 0.010 -0.0028865 0.0004409 5095 16.98 -25.235 4.812 2014-09-25T19:19:21.533578752 INFO 2025-06-26 20:35:20,940 calibrate.py _nudge_pos():1806 [1] 277: 0.010 -0.0033698 -0.0009571 4615 15.38 -32.522 -11.531 2014-09-25T19:35:45.536169984 INFO 2025-06-26 20:35:21,026 calibrate.py _nudge_pos():1806 [1] 286: 0.010 -0.0030120 0.0007019 5270 17.56 -25.458 7.406 2014-09-25T19:53:27.533418240 INFO 2025-06-26 20:35:21,362 calibrate.py _nudge_pos():1806 [1] 322: 0.020 -0.0037074 -0.0006658 4805 16.01 -34.365 -7.704 2014-09-25T20:10:03.535187456 INFO 2025-06-26 20:35:21,545 calibrate.py _nudge_pos():1806 [1] 341: 0.020 -0.0031496 0.0006491 5190 17.30 -27.032 6.954 2014-09-25T20:27:39.532846592 INFO 2025-06-26 20:35:21,965 calibrate.py _nudge_pos():1806 [1] 385: 0.020 -0.0038137 -0.0005182 4915 16.38 -34.559 -5.862 2014-09-25T20:44:45.532560896 INFO 2025-06-26 20:35:22,308 calibrate.py _nudge_pos():1806 [1] 420: 0.030 -0.0030319 0.0006560 5140 17.13 -26.275 7.096 2014-09-25T21:02:27.529808896 INFO 2025-06-26 20:35:24,279 calibrate.py _nudge_pos():1806 [1] 631: 0.020 -0.0000065 0.0000020 15 0.05 -20.705 8.126 2014-09-25T21:06:00.535217408 INFO 2025-06-26 20:35:29,802 calibrate.py _nudge_pos():1862 [1] 1171: - - - 3 0.01 - - INFO 2025-06-26 20:35:29,802 calibrate.py _nudge_pos():1868 [1] Points in final series = 46906 INFO 2025-06-26 20:35:29,949 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 5 of 37820 INFO 2025-06-26 20:35:30,252 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:35:30,618 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 18 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:35:30,901 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 18 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:35:30,903 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.268.05/ctd1.nc INFO 2025-06-26 20:35:30,904 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:35:30,904 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 20:35:30,904 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:35:31,276 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:35:31,768 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:35:31,771 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.268.05/ctd2.nc INFO 2025-06-26 20:35:31,772 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:35:31,773 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 20:35:31,773 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:35:32,188 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:35:32,688 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:35:32,717 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2014.268.05 ERROR 2025-06-26 20:35:32,717 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.268.05 INFO 2025-06-26 20:35:32,793 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.268.05/dorado_2014.268.05_cal.nc INFO 2025-06-26 20:35:32,934 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 20:35:32,943 process.py align():251 [1] Alignment steps for 2014.268.05 INFO 2025-06-26 20:35:32,993 align.py process_cal():139 [1] Processing dorado_2014.268.05_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.268.05 INFO 2025-06-26 20:35:33,023 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:35:33,027 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:35:33,090 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:35:33,096 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:35:33,161 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:35:33,166 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:35:33,201 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:35:33,202 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:35:33,226 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:35:33,232 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:35:33,293 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:33,298 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:33,356 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:33,361 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:33,411 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:33,416 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:33,471 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:33,476 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:33,512 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:33,516 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:33,560 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:33,565 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:33,600 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:33,603 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:33,637 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:33,640 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:33,675 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:33,679 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:33,713 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:33,717 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:33,752 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:33,756 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:33,791 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:33,795 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:33,831 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:33,835 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:33,871 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:33,874 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:33,910 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:33,914 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:33,950 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:33,953 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:33,990 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:33,993 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:34,030 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:34,033 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:34,070 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:34,074 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:34,110 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:34,114 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:34,150 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:34,154 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:34,188 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.268.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:35:34,192 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:35:34,237 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:35:34,272 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:35:34,308 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:35:34,360 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:35:34,417 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:35:34,498 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 20:35:34,871 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:35:34,912 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.268.05/dorado_2014.268.05_align.nc INFO 2025-06-26 20:35:35,025 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 20:35:35,027 process.py resample():273 [1] Resampling steps for 2014.268.05 INFO 2025-06-26 20:35:35,028 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:35:35,058 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.268.05/dorado_2014.268.05_align.nc mission netCDF file INFO 2025-06-26 20:35:35,063 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.268.05/dorado_2014.268.05_align.nc mission netCDF file INFO 2025-06-26 20:35:35,065 resample.py get_mission_start_end():1145 [1] navigation: 2014-09-25T18:38:55.749756416 to 2014-09-25T21:15:49.134895360 (0 days 00:00:00.139990528 before mission_end) INFO 2025-06-26 20:35:35,066 resample.py get_mission_start_end():1145 [1] hs2 : 2014-09-25T18:38:12.902691584 to 2014-09-25T21:15:49.194891264 (0 days 00:00:00.079994624 before mission_end) INFO 2025-06-26 20:35:35,067 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-09-25T18:38:27.171714048 to 2014-09-25T21:15:49.214889984 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 20:35:35,069 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-09-25T18:38:26.961728512 to 2014-09-25T21:15:49.254887168 (0 days 00:00:00.019998720 before mission_end) INFO 2025-06-26 20:35:35,070 resample.py get_mission_start_end():1145 [1] isus : 2014-09-25T18:39:07.368960256 to 2014-09-25T21:15:48.734923008 (0 days 00:00:00.539962880 before mission_end) INFO 2025-06-26 20:35:35,071 resample.py get_mission_start_end():1145 [1] biolume : 2014-09-25T18:38:06.783076608 to 2014-09-25T21:15:48.474906368 (0 days 00:00:00.799979520 before mission_end) INFO 2025-06-26 20:35:35,073 resample.py get_mission_start_end():1145 [1] tailcone : 2014-09-25T18:38:08.472995072 to 2014-09-25T21:15:49.274885888 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:35:35,073 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.268.05/dorado_2014.268.05_align.nc mission netCDF file INFO 2025-06-26 20:35:35,074 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,196 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,220 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,244 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,270 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,296 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,318 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,341 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,361 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,382 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,403 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,423 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,443 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,463 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,482 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,502 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,522 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,541 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,568 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,595 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,622 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,643 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,664 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,684 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,705 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,718 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,730 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,742 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,753 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,764 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:35,768 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:35:35,768 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:35:36,102 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:35:36,167 resample.py add_biolume_proxies():633 [1] Zero flow values found: 5563 of 9463 - replaced with 350 ml/s INFO 2025-06-26 20:35:36,168 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:35:36,204 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:35:36,223 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:35:36,248 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:35:36,248 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:35:36,276 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:35:36,443 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.268.05/dorado_2014.268.05_1S.nc INFO 2025-06-26 20:35:38,321 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:36:00,859 create_products.py gulper_odv():522 [1] Wrote 20 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.268.05/dorado_2014.268.05_1S_Gulper.txt INFO 2025-06-26 20:36:00,859 process.py archive():337 [1] Archiving steps for 2014.268.05 INFO 2025-06-26 20:36:00,859 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.268.05/dorado_2014.268.05, BASE_PATH = /data/auv_data INFO 2025-06-26 20:36:00,860 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.268.05/dorado_2014.268.05 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:36:00,861 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.268.05_1S.nc INFO 2025-06-26 20:36:00,876 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.268.05/dorado_2014.268.05_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:36:00,877 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.268.05_cal.nc INFO 2025-06-26 20:36:00,949 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.268.05/dorado_2014.268.05_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:36:00,950 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.268.05_align.nc INFO 2025-06-26 20:36:01,051 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.268.05/dorado_2014.268.05_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:36:01,068 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.268.05/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014268/2014.268.05 done. INFO 2025-06-26 20:36:01,083 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.268.05/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014268/2014.268.05 done. INFO 2025-06-26 20:36:01,088 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.268.05/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014268/2014.268.05 done. INFO 2025-06-26 20:36:01,100 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.268.05/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014268/2014.268.05 done. INFO 2025-06-26 20:36:01,137 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.268.05/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014268/2014.268.05 done. INFO 2025-06-26 20:36:01,144 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.268.05/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014268/2014.268.05 done. INFO 2025-06-26 20:36:01,161 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.268.05/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014268/2014.268.05 done. INFO 2025-06-26 20:36:01,174 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.268.05/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014268/2014.268.05 done. INFO 2025-06-26 20:36:01,202 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.268.05/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014268/2014.268.05 done. INFO 2025-06-26 20:36:01,207 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.268.05/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014268/2014.268.05 done. INFO 2025-06-26 20:36:01,207 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:36:01,208 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.268.05_1S_Gulper.txt INFO 2025-06-26 20:36:01,213 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.268.05/dorado_2014.268.05_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:36:01,213 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.268.05/dorado_2014.268.05_processing.log /Volumes/AUVCTD/surveys/2014/netcdf