INFO 2025-06-26 20:09:12,300 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 20:09:12,300 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ October 2013 in Soquel Bight - ctdToUse = ctd1 INFO 2025-06-26 20:09:12,300 process.py process_mission():449 [1] Processing SIMZ October 2013 mission 2013.298.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:09:12,300 process.py download_process():165 [1] Download and processing steps for 2013.298.00 INFO 2025-06-26 20:09:12,300 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013298/2013.298.00 INFO 2025-06-26 20:09:12,301 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013298/2013.298.00 to /data/auv_data/dorado/missionlogs/2013.298.00 INFO 2025-06-26 20:09:15,415 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.298.00 INFO 2025-06-26 20:09:15,416 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.298.00/ctdDriver.log (4230054 bytes) INFO 2025-06-26 20:09:15,709 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.298.00/ctdDriver2.log (4229855 bytes) INFO 2025-06-26 20:09:16,011 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.298.00/gps.log (351932 bytes) INFO 2025-06-26 20:09:16,055 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.298.00/hydroscatlog.log (3705766 bytes) INFO 2025-06-26 20:09:16,442 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.298.00/navigation.log (14968838 bytes) INFO 2025-06-26 20:09:17,497 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.298.00/parosci.log (5213366 bytes) INFO 2025-06-26 20:09:17,928 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.298.00/tailCone.log (2650171 bytes) INFO 2025-06-26 20:09:18,253 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.298.00/biolume.log (3085798 bytes) INFO 2025-06-26 20:09:18,555 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:09:18,709 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.29 seconds INFO 2025-06-26 20:09:18,709 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.298.00/lopc.bin (22025702 bytes) INFO 2025-06-26 20:09:18,710 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:09:18 2025 INFO 2025-06-26 20:09:18,710 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.298.00/parosci.nc INFO 2025-06-26 20:09:18,710 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:09:18,710 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.298.00/parosci.nc INFO 2025-06-26 20:09:18,713 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1382711419.7, sensor_off_time = 1382722458.6 INFO 2025-06-26 20:09:18,713 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 11038 seconds. Expecting to read 22076 L frames from the lopc.bin file. INFO 2025-06-26 20:09:18,713 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 22076 records from the lopc.bin file. INFO 2025-06-26 20:09:18,842 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-10-25 14:30:19 Z and endTime = 2013-10-25 17:34:18 Z with 22076 records expected to be read from lopc.bin INFO 2025-06-26 20:09:18,842 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.298.00/lopc.bin INFO 2025-06-26 20:09:18,843 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.298.00/lopc.nc INFO 2025-06-26 20:09:18,843 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.298.00/lopc.nc INFO 2025-06-26 20:09:18,843 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.298.00 INFO 2025-06-26 20:09:18,843 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 20:09:18,846 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 20:09:18,883 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:09:18,883 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:09:18,884 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:09:25,806 process.py download_process():223 [1] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-06-26 20:09:25,807 process.py calibrate():227 [1] Calibration steps for 2013.298.00 INFO 2025-06-26 20:09:25,936 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 20:09:25,938 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:09:26,384 calibrate.py _nudge_pos():1806 [1] 78: 0.160 0.0000650 0.0000623 395 1.31 7.331 8.789 2013-10-25T14:32:51.953990656 INFO 2025-06-26 20:09:26,394 calibrate.py _nudge_pos():1806 [1] 79: 0.160 0.0000324 -0.0000263 45 0.15 32.723 -33.231 2013-10-25T14:33:00.953374208 INFO 2025-06-26 20:09:26,906 calibrate.py _nudge_pos():1806 [1] 134: 0.160 0.0000571 0.0012811 9075 30.25 0.280 7.849 2013-10-25T15:04:09.955338752 INFO 2025-06-26 20:09:27,453 calibrate.py _nudge_pos():1806 [1] 192: 0.170 0.0000589 0.0010764 9135 30.45 0.286 6.551 2013-10-25T15:35:33.956275968 INFO 2025-06-26 20:09:27,868 calibrate.py _nudge_pos():1806 [1] 236: 0.170 0.0001583 0.0009200 7495 24.98 0.939 6.825 2013-10-25T16:01:15.960641280 INFO 2025-06-26 20:09:28,365 calibrate.py _nudge_pos():1806 [1] 289: 0.170 0.0003064 0.0002788 4660 15.53 2.924 3.326 2013-10-25T16:17:39.953233152 INFO 2025-06-26 20:09:28,385 calibrate.py _nudge_pos():1806 [1] 291: 0.180 0.0000112 0.0000100 65 0.21 7.795 8.669 2013-10-25T16:17:53.952274176 INFO 2025-06-26 20:10:11,780 calibrate.py _nudge_pos():1862 [1] 4838: - - - 3 0.01 - - INFO 2025-06-26 20:10:11,781 calibrate.py _nudge_pos():1868 [1] Points in final series = 55023 INFO 2025-06-26 20:10:12,351 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 7 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:10:12,771 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:10:13,118 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:10:13,120 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.298.00/ctd1.nc INFO 2025-06-26 20:10:13,121 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:10:13,122 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 20:10:13,122 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:10:13,518 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:10:13,847 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:10:13,849 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.298.00/ctd2.nc INFO 2025-06-26 20:10:13,851 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:10:13,851 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 20:10:13,851 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 20:10:13,852 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.298.00 INFO 2025-06-26 20:10:13,861 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:10:14,326 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 647520] INFO 2025-06-26 20:10:14,424 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:10:24,341 calibrate.py process_logs():3542 [1] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2013.298.00 ERROR 2025-06-26 20:10:24,341 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.298.00 INFO 2025-06-26 20:10:24,387 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.298.00/dorado_2013.298.00_cal.nc INFO 2025-06-26 20:10:24,481 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, 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 20:10:24,487 process.py align():251 [1] Alignment steps for 2013.298.00 INFO 2025-06-26 20:10:24,519 align.py process_cal():139 [1] Processing dorado_2013.298.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.298.00 INFO 2025-06-26 20:10:24,539 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:10:24,542 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:10:24,584 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:10:24,588 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:10:24,631 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:10:24,635 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:10:24,660 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:10:24,660 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:10:24,677 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:10:24,681 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:10:24,723 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:24,727 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:24,764 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:24,768 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:24,806 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:24,809 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:24,845 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:24,848 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:24,888 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:24,891 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:24,928 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:24,931 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:24,968 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:24,972 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:25,008 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:25,012 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:25,051 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:25,054 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:25,090 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:25,094 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:25,132 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:25,136 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:25,181 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:25,185 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:25,221 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:25,225 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:25,261 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:25,263 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:25,300 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:25,304 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:25,340 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:25,344 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:25,381 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:25,384 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:25,420 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:25,424 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:25,461 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:25,464 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:25,501 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:25,504 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:25,541 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:25,545 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:25,581 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.298.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:10:25,584 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:10:25,631 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:10:25,669 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:10:25,725 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 20:10:26,014 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:10:26,045 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.298.00/dorado_2013.298.00_align.nc INFO 2025-06-26 20:10:26,139 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, 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 20:10:26,141 process.py resample():273 [1] Resampling steps for 2013.298.00 INFO 2025-06-26 20:10:26,142 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:10:26,171 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.298.00/dorado_2013.298.00_align.nc mission netCDF file INFO 2025-06-26 20:10:26,175 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.298.00/dorado_2013.298.00_align.nc mission netCDF file INFO 2025-06-26 20:10:26,176 resample.py get_mission_start_end():1145 [1] navigation: 2013-10-25T14:30:53.962073600 to 2013-10-25T17:34:18.558207232 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:10:26,178 resample.py get_mission_start_end():1145 [1] hs2 : 2013-10-25T14:30:26.783935488 to 2013-10-25T17:34:18.378219520 (0 days 00:00:00.179987712 before mission_end) INFO 2025-06-26 20:10:26,179 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-10-25T14:30:44.792701696 to 2013-10-25T17:34:18.548207872 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 20:10:26,181 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-10-25T14:30:44.992688128 to 2013-10-25T17:34:18.498211328 (0 days 00:00:00.059995904 before mission_end) INFO 2025-06-26 20:10:26,182 resample.py get_mission_start_end():1145 [1] biolume : 2013-10-25T14:30:18.234486784 to 2013-10-25T17:34:17.168268288 (0 days 00:00:01.389938944 before mission_end) INFO 2025-06-26 20:10:26,184 resample.py get_mission_start_end():1145 [1] tailcone : 2013-10-25T14:30:18.174525184 to 2013-10-25T17:34:18.408217344 (0 days 00:00:00.149989888 before mission_end) INFO 2025-06-26 20:10:26,185 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.298.00/dorado_2013.298.00_align.nc mission netCDF file INFO 2025-06-26 20:10:26,185 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,316 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,340 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,364 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,387 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,409 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,429 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,450 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,470 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,489 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,508 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,526 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,545 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,564 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,583 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,602 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,621 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,639 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,660 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,681 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,701 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,721 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,742 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,762 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,783 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,795 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,805 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:26,809 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:10:26,809 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:10:27,227 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:10:27,296 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:10:27,337 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:10:27,355 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:10:27,371 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:10:27,371 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:10:27,400 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:10:27,565 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.298.00/dorado_2013.298.00_1S.nc INFO 2025-06-26 20:10:32,566 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:10:44,819 create_products.py gulper_odv():522 [1] Wrote 9 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.298.00/dorado_2013.298.00_1S_Gulper.txt INFO 2025-06-26 20:10:44,820 process.py archive():337 [1] Archiving steps for 2013.298.00 INFO 2025-06-26 20:10:44,820 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.298.00/dorado_2013.298.00, BASE_PATH = /data/auv_data INFO 2025-06-26 20:10:44,821 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.298.00/dorado_2013.298.00 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 20:10:44,822 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.298.00_1S.nc INFO 2025-06-26 20:10:44,835 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.00/dorado_2013.298.00_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:10:44,837 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.298.00_cal.nc INFO 2025-06-26 20:10:44,918 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.00/dorado_2013.298.00_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:10:44,920 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.298.00_align.nc INFO 2025-06-26 20:10:45,032 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.00/dorado_2013.298.00_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:10:45,050 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013298/2013.298.00 done. INFO 2025-06-26 20:10:45,066 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013298/2013.298.00 done. INFO 2025-06-26 20:10:45,072 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013298/2013.298.00 done. INFO 2025-06-26 20:10:45,087 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013298/2013.298.00 done. INFO 2025-06-26 20:10:45,130 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013298/2013.298.00 done. INFO 2025-06-26 20:10:45,149 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013298/2013.298.00 done. INFO 2025-06-26 20:10:45,164 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013298/2013.298.00 done. INFO 2025-06-26 20:10:45,197 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013298/2013.298.00 done. INFO 2025-06-26 20:10:45,212 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013298/2013.298.00 done. INFO 2025-06-26 20:10:45,212 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:10:45,214 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.298.00_1S_Gulper.txt INFO 2025-06-26 20:10:45,219 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.298.00/dorado_2013.298.00_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 20:10:45,219 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.00/dorado_2013.298.00_processing.log /Volumes/AUVCTD/surveys/2013/netcdf