INFO 2025-03-02 18:16:57,609 process.py process_mission():387 [86521] self.commandline = 'src/data/process_dorado.py --mission 2011.256.02 -v --no_cleanup --noinput' INFO 2025-03-02 18:16:57,609 process.py process_mission():392 [86521] dorado_info[mission]["comment"] = 'TREX mission - Following SIO_WWL_1 for September 2011 CANON - ctdToUse = ctd1 ' INFO 2025-03-02 18:16:57,609 process.py process_mission():404 [86521] Processing CANON September 2011 mission 2011.256.02 by user mccann on host MBARI2597.local INFO 2025-03-02 18:16:57,609 process.py download_process():155 [86521] Download and processing steps for 2011.256.02 INFO 2025-03-02 18:16:57,609 logs2netcdfs.py download_process_logs():664 [86521] src_dir = '/Volumes/AUVCTD/missionlogs/2011/2011256/2011.256.02' INFO 2025-03-02 18:16:57,609 logs2netcdfs.py download_process_logs():677 [86521] /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2011.256.02 exists INFO 2025-03-02 18:16:57,609 logs2netcdfs.py download_process_logs():700 [86521] Processing mission: dorado 2011.256.02 INFO 2025-03-02 18:16:57,609 logs2netcdfs.py download_process_logs():709 [86521] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2011.256.02/ctdDriver.log (697830 bytes) INFO 2025-03-02 18:16:57,659 logs2netcdfs.py download_process_logs():709 [86521] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2011.256.02/ctdDriver2.log (697823 bytes) INFO 2025-03-02 18:16:57,708 logs2netcdfs.py download_process_logs():709 [86521] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2011.256.02/gps.log (28220 bytes) INFO 2025-03-02 18:16:57,714 logs2netcdfs.py download_process_logs():709 [86521] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2011.256.02/hydroscatlog.log (617506 bytes) INFO 2025-03-02 18:16:57,773 logs2netcdfs.py download_process_logs():709 [86521] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2011.256.02/navigation.log (2463366 bytes) INFO 2025-03-02 18:16:57,969 logs2netcdfs.py download_process_logs():709 [86521] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2011.256.02/isuslog.log (56309 bytes) INFO 2025-03-02 18:16:57,975 logs2netcdfs.py download_process_logs():709 [86521] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2011.256.02/parosci.log (749750 bytes) INFO 2025-03-02 18:16:58,030 logs2netcdfs.py download_process_logs():709 [86521] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2011.256.02/tailCone.log (442843 bytes) INFO 2025-03-02 18:16:58,079 logs2netcdfs.py download_process_logs():709 [86521] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2011.256.02/biolume.log (518154 bytes) INFO 2025-03-02 18:16:58,128 logs2netcdfs.py write_variables():523 [86521] Expanding original timeTag to time60Hz variable for raw data INFO 2025-03-02 18:16:58,143 logs2netcdfs.py download_process_logs():726 [86521] Time to process: 0.53 seconds INFO 2025-03-02 18:16:58,143 process.py download_process():184 [86521] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2011.256.02/lopc.bin (10356000 bytes) INFO 2025-03-02 18:16:58,143 lopcToNetCDF.py main():2274 [86521] Processing begun: Sun Mar 2 18:16:58 2025 INFO 2025-03-02 18:16:58,143 lopcToNetCDF.py constructTimestampList():1293 [86521] parosci_nc = /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/parosci.nc INFO 2025-03-02 18:16:58,143 lopcToNetCDF.py constructTimestampList():1294 [86521] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-03-02 18:16:58,143 lopcToNetCDF.py constructTimestampList():1297 [86521] /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/parosci.nc INFO 2025-03-02 18:16:58,144 lopcToNetCDF.py constructTimestampList():1314 [86521] From associated parosci.nc file: sensor_on_time = 1315951939.7, sensor_off_time = 1315953783.5 INFO 2025-03-02 18:16:58,144 lopcToNetCDF.py constructTimestampList():1318 [86521] Duration is 1843 seconds. Expecting to read 3686 L frames from the lopc.bin file. INFO 2025-03-02 18:16:58,144 lopcToNetCDF.py constructTimestampList():1328 [86521] recCount not passed in, assuming we'll have 3686 records from the lopc.bin file. INFO 2025-03-02 18:16:58,160 lopcToNetCDF.py main():2296 [86521] Examined sibling parosci.nc file to find startTime = 2011-09-13 22:12:19 Z and endTime = 2011-09-13 22:43:03 Z with 3686 records expected to be read from lopc.bin INFO 2025-03-02 18:16:58,160 lopcToNetCDF.py unpackLOPCbin():723 [86521] >>> Unpacking LOPC data from /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2011.256.02/lopc.bin INFO 2025-03-02 18:16:58,160 lopcToNetCDF.py unpackLOPCbin():724 [86521] >>> Will write to NetCDF file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/lopc.nc INFO 2025-03-02 18:16:58,160 lopcToNetCDF.py openNetCDFFile():1850 [86521] Will output NetCDF file to /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/lopc.nc INFO 2025-03-02 18:16:58,160 lopcToNetCDF.py openNetCDFFile():1880 [86521] missionName = 2011.256.02 INFO 2025-03-02 18:16:58,160 lopcToNetCDF.py openNetCDFFile():1899 [86521] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 ERROR 2025-03-02 18:16:58,168 process.py download_process():205 [86521] UnexpectedAreaOfCode: Encountered unexpected area of code - lopc.nc file is probably corrupt INFO 2025-03-02 18:16:58,168 process.py calibrate():209 [86521] Calibration steps for 2011.256.02 INFO 2025-03-02 18:16:58,229 calibrate.py _nudge_pos():1570 [86521] 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 2025-03-02 18:16:58,230 calibrate.py _nudge_pos():1594 [86521] - - - 0 0.00 - - - INFO 2025-03-02 18:16:58,368 calibrate.py _nudge_pos():1691 [86521] 56: 0.200 0.0000033 0.0000307 34 0.11 4.469 51.695 2011-09-13T22:13:19.326705920 INFO 2025-03-02 18:16:59,640 calibrate.py _nudge_pos():1691 [86521] 325: 0.210 0.0036709 -0.0028250 7289 24.29 22.413 -21.548 2011-09-13T22:42:05.318467584 INFO 2025-03-02 18:16:59,703 calibrate.py _nudge_pos():1691 [86521] 338: 0.200 0.0000072 0.0000039 19 0.06 17.879 12.108 2011-09-13T22:42:21.327371008 INFO 2025-03-02 18:16:59,899 calibrate.py _nudge_pos():1748 [86521] 344: - - - 4 0.01 - - INFO 2025-03-02 18:16:59,899 calibrate.py _nudge_pos():1754 [86521] Points in final series = 8922 WARNING 2025-03-02 18:16:59,906 calibrate.py _depth_process():2058 [86521] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-03-02 18:16:59,966 calibrate.py _geometric_depth_correction():3245 [86521] hs2: d_beg_time_diff: 8 seconds, d_end_time_diff: -1 seconds, INFO 2025-03-02 18:17:00,015 calibrate.py _geometric_depth_correction():3245 [86521] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds, INFO 2025-03-02 18:17:00,047 calibrate.py _geometric_depth_correction():3245 [86521] ctd1: d_beg_time_diff: 28 seconds, d_end_time_diff: -1 seconds, INFO 2025-03-02 18:17:00,048 calibrate.py _ctd_process():2767 [86521] Performing range checking of ['ctd1_salinity'] in 2011.256.02/ctd1.nc INFO 2025-03-02 18:17:00,049 calibrate.py _range_qc_combined_nc():880 [86521] Setting 0 ctd1_salinity values to NaN INFO 2025-03-02 18:17:00,049 calibrate.py _range_qc_combined_nc():894 [86521] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-03-02 18:17:00,049 calibrate.py _range_qc_combined_nc():920 [86521] Done range checking ctd1 INFO 2025-03-02 18:17:00,116 calibrate.py _geometric_depth_correction():3245 [86521] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds, INFO 2025-03-02 18:17:00,151 calibrate.py _geometric_depth_correction():3245 [86521] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds, INFO 2025-03-02 18:17:00,152 calibrate.py _ctd_process():2767 [86521] Performing range checking of ['ctd2_salinity'] in 2011.256.02/ctd2.nc INFO 2025-03-02 18:17:00,153 calibrate.py _range_qc_combined_nc():880 [86521] Setting 95 ctd2_salinity values to NaN INFO 2025-03-02 18:17:00,153 calibrate.py _range_qc_combined_nc():894 [86521] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-03-02 18:17:00,153 calibrate.py _range_qc_combined_nc():920 [86521] Done range checking ctd2 INFO 2025-03-02 18:17:00,158 calibrate.py _biolume_process():2959 [86521] Checking for non-monotonic increasing time60hz INFO 2025-03-02 18:17:00,214 calibrate.py _biolume_process():2962 [86521] 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152] INFO 2025-03-02 18:17:00,225 calibrate.py _geometric_depth_correction():3245 [86521] biolume: d_beg_time_diff: 1 seconds, d_end_time_diff: 0 seconds, ERROR 2025-03-02 18:17:01,331 calibrate.py process_logs():3366 [86521] Error processing lopc: lopc has no time coordinate - likely an incomplete lopc.nc file in missionlogs/2011.256.02 ERROR 2025-03-02 18:17:01,331 calibrate.py process_logs():3366 [86521] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2011.256.02 INFO 2025-03-02 18:17:01,336 calibrate.py write_netcdf():3332 [86521] Writing calibrated instrument data to /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/dorado_2011.256.02_cal.nc INFO 2025-03-02 18:17:01,364 calibrate.py write_netcdf():3336 [86521] 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 2025-03-02 18:17:01,366 process.py align():233 [86521] Alignment steps for 2011.256.02 INFO 2025-03-02 18:17:01,384 align.py process_cal():139 [86521] Processing dorado_2011.256.02_cal.nc from /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02 INFO 2025-03-02 18:17:01,386 align.py process_cal():215 [86521] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-03-02 18:17:01,387 align.py process_cal():279 [86521] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-03-02 18:17:01,394 align.py process_cal():215 [86521] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-03-02 18:17:01,395 align.py process_cal():279 [86521] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-03-02 18:17:01,402 align.py process_cal():215 [86521] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-03-02 18:17:01,403 align.py process_cal():279 [86521] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-03-02 18:17:01,407 align.py process_cal():161 [86521] Skipping navigation_posx INFO 2025-03-02 18:17:01,407 align.py process_cal():161 [86521] Skipping navigation_posy INFO 2025-03-02 18:17:01,410 align.py process_cal():215 [86521] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-03-02 18:17:01,411 align.py process_cal():279 [86521] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-03-02 18:17:01,418 align.py process_cal():215 [86521] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,418 align.py process_cal():279 [86521] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,438 align.py process_cal():215 [86521] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,439 align.py process_cal():279 [86521] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,446 align.py process_cal():215 [86521] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,447 align.py process_cal():279 [86521] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,454 align.py process_cal():215 [86521] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,455 align.py process_cal():279 [86521] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,462 align.py process_cal():215 [86521] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,462 align.py process_cal():279 [86521] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,469 align.py process_cal():215 [86521] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,470 align.py process_cal():279 [86521] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,477 align.py process_cal():215 [86521] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,477 align.py process_cal():279 [86521] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,483 align.py process_cal():215 [86521] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,484 align.py process_cal():279 [86521] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,491 align.py process_cal():215 [86521] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,492 align.py process_cal():279 [86521] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,498 align.py process_cal():215 [86521] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,499 align.py process_cal():279 [86521] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,505 align.py process_cal():215 [86521] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,508 align.py process_cal():279 [86521] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,515 align.py process_cal():215 [86521] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,515 align.py process_cal():279 [86521] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,522 align.py process_cal():215 [86521] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,523 align.py process_cal():279 [86521] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,529 align.py process_cal():215 [86521] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,530 align.py process_cal():279 [86521] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,537 align.py process_cal():215 [86521] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,538 align.py process_cal():279 [86521] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,545 align.py process_cal():215 [86521] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,546 align.py process_cal():279 [86521] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,553 align.py process_cal():215 [86521] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,554 align.py process_cal():279 [86521] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,561 align.py process_cal():215 [86521] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,562 align.py process_cal():279 [86521] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,568 align.py process_cal():215 [86521] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,569 align.py process_cal():279 [86521] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,576 align.py process_cal():215 [86521] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,577 align.py process_cal():279 [86521] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,584 align.py process_cal():215 [86521] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,584 align.py process_cal():279 [86521] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,591 align.py process_cal():215 [86521] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2011.256.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-03-02 18:17:01,592 align.py process_cal():279 [86521] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-03-02 18:17:01,601 align.py process_cal():279 [86521] isus_nitrate: instrument_sample_rate_hz = 0.99 INFO 2025-03-02 18:17:01,607 align.py process_cal():279 [86521] isus_temp: instrument_sample_rate_hz = 0.99 INFO 2025-03-02 18:17:01,614 align.py process_cal():279 [86521] isus_quality: instrument_sample_rate_hz = 0.99 INFO 2025-03-02 18:17:01,622 align.py process_cal():279 [86521] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-03-02 18:17:01,630 align.py process_cal():279 [86521] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-03-02 18:17:01,639 align.py process_cal():279 [86521] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-03-02 18:17:01,670 align.py process_cal():279 [86521] tailcone_propRpm: instrument_sample_rate_hz = 5.00 WARNING 2025-03-02 18:17:01,700 align.py global_metadata():76 [86521] Could not save time_coverage_duration - likely because all data are bad and min_time and max_time were not set INFO 2025-03-02 18:17:01,700 align.py write_netcdf():374 [86521] Writing aligned data to /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/dorado_2011.256.02_align.nc INFO 2025-03-02 18:17:01,734 align.py write_netcdf():379 [86521] 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 2025-03-02 18:17:01,736 process.py resample():254 [86521] Resampling steps for 2011.256.02 INFO 2025-03-02 18:17:01,753 resample.py instruments_variables():233 [86521] Reading variables from /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/dorado_2011.256.02_align.nc mission netCDF file INFO 2025-03-02 18:17:01,756 resample.py instruments_variables():233 [86521] Reading variables from /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/dorado_2011.256.02_align.nc mission netCDF file INFO 2025-03-02 18:17:01,756 resample.py get_mission_start_end():805 [86521] navigation: 2011-09-13T22:12:53.938445312 to 2011-09-13T22:43:03.324493824 (0 days 00:00:00.169988352 before mission_end) INFO 2025-03-02 18:17:01,756 resample.py get_mission_start_end():805 [86521] hs2 : 2011-09-13T22:12:27.820234496 to 2011-09-13T22:43:03.334493184 (0 days 00:00:00.159988992 before mission_end) INFO 2025-03-02 18:17:01,757 resample.py get_mission_start_end():805 [86521] ctd1 : 2011-09-13T22:12:48.368826880 to 2011-09-13T22:43:03.434486272 (0 days 00:00:00.059995904 before mission_end) INFO 2025-03-02 18:17:01,758 resample.py get_mission_start_end():805 [86521] ctd2 : 2011-09-13T22:12:48.378826240 to 2011-09-13T22:43:03.494482176 (0 days 00:00:00 before mission_end) INFO 2025-03-02 18:17:01,758 resample.py get_mission_start_end():805 [86521] isus : 2011-09-13T22:13:43.215069440 to 2011-09-13T22:43:03.264497920 (0 days 00:00:00.229984256 before mission_end) INFO 2025-03-02 18:17:01,759 resample.py get_mission_start_end():805 [86521] biolume : 2011-09-13T22:12:20.740685312 to 2011-09-13T22:43:02.984482816 (0 days 00:00:00.509999360 before mission_end) INFO 2025-03-02 18:17:01,759 resample.py get_mission_start_end():805 [86521] tailcone : 2011-09-13T22:12:19.040835840 to 2011-09-13T22:43:03.354491648 (0 days 00:00:00.139990528 before mission_end) INFO 2025-03-02 18:17:01,760 resample.py instruments_variables():233 [86521] Reading variables from /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/dorado_2011.256.02_align.nc mission netCDF file INFO 2025-03-02 18:17:01,760 resample.py resample_coordinates():247 [86521] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,778 resample.py resample_variable():700 [86521] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,782 resample.py resample_variable():700 [86521] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,788 resample.py resample_variable():700 [86521] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,792 resample.py resample_variable():700 [86521] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,797 resample.py resample_variable():700 [86521] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,803 resample.py resample_variable():700 [86521] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,807 resample.py resample_variable():700 [86521] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,812 resample.py resample_variable():700 [86521] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,815 resample.py resample_variable():700 [86521] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,819 resample.py resample_variable():700 [86521] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,824 resample.py resample_variable():700 [86521] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,828 resample.py resample_variable():700 [86521] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,832 resample.py resample_variable():700 [86521] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,837 resample.py resample_variable():700 [86521] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,840 resample.py resample_variable():700 [86521] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,844 resample.py resample_variable():700 [86521] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,848 resample.py resample_variable():700 [86521] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,853 resample.py resample_variable():700 [86521] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,858 resample.py resample_variable():700 [86521] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,863 resample.py resample_variable():700 [86521] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,868 resample.py resample_variable():700 [86521] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,872 resample.py resample_variable():700 [86521] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,876 resample.py resample_variable():700 [86521] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,880 resample.py resample_variable():700 [86521] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,884 resample.py resample_variable():700 [86521] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,889 resample.py resample_variable():700 [86521] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,893 resample.py resample_variable():700 [86521] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,896 resample.py resample_variable():700 [86521] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,899 resample.py resample_variable():700 [86521] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:01,901 resample.py add_biolume_proxies():479 [86521] Adding biolume proxy variables computed from biolume_raw INFO 2025-03-02 18:17:01,943 resample.py add_biolume_proxies():519 [86521] Using flash_threshold = 1.0000e+11 INFO 2025-03-02 18:17:01,953 resample.py add_biolume_proxies():566 [86521] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-03-02 18:17:01,959 resample.py add_biolume_proxies():594 [86521] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-03-02 18:17:01,963 resample.py add_biolume_proxies():614 [86521] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-03-02 18:17:01,966 resample.py select_nighttime_bl_raw():392 [86521] Sun is up at start, but no sunset in this mission INFO 2025-03-02 18:17:01,966 resample.py select_nighttime_bl_raw():403 [86521] No sunset during this mission. No biolume_raw data will be extracted. INFO 2025-03-02 18:17:01,967 resample.py add_biolume_proxies():624 [86521] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-03-02 18:17:01,975 resample.py resample_variable():700 [86521] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-03-02 18:17:02,076 resample.py resample_mission():939 [86521] Saved resampled mission to /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/dorado_2011.256.02_1S.nc INFO 2025-03-02 18:17:05,877 create_products.py _get_best_ctd():376 [86521] ctdToUse = ctd1 INFO 2025-03-02 18:17:06,106 create_products.py gulper_odv():514 [86521] Wrote 2 Gulper data lines to /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionodvs/2011.256.02/dorado_2011.256.02_1S_Gulper.txt INFO 2025-03-02 18:17:06,106 process.py archive():310 [86521] Archiving steps for 2011.256.02 INFO 2025-03-02 18:17:06,168 archive.py copy_to_AUVTCD():53 [86521] Archiving /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/dorado_2011.256.02 files to /Volumes/AUVCTD/surveys/2011/netcdf INFO 2025-03-02 18:17:11,262 archive.py copy_to_AUVTCD():98 [86521] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.02 done. INFO 2025-03-02 18:17:16,139 archive.py copy_to_AUVTCD():98 [86521] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.02 done. INFO 2025-03-02 18:17:17,962 archive.py copy_to_AUVTCD():98 [86521] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.02 done. INFO 2025-03-02 18:17:22,439 archive.py copy_to_AUVTCD():98 [86521] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.02 done. INFO 2025-03-02 18:17:35,140 archive.py copy_to_AUVTCD():98 [86521] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.02 done. INFO 2025-03-02 18:17:37,059 archive.py copy_to_AUVTCD():98 [86521] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.02 done. INFO 2025-03-02 18:17:42,242 archive.py copy_to_AUVTCD():98 [86521] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.02 done. INFO 2025-03-02 18:17:46,499 archive.py copy_to_AUVTCD():98 [86521] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.02 done. INFO 2025-03-02 18:17:56,481 archive.py copy_to_AUVTCD():98 [86521] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2011/2011256/2011.256.02 done. INFO 2025-03-02 18:17:56,482 archive.py copy_to_AUVTCD():103 [86521] Archiving product files INFO 2025-03-02 18:17:58,157 archive.py copy_to_AUVTCD():112 [86521] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionodvs/2011.256.02/* /Volumes/AUVCTD/surveys/2011/odv done. INFO 2025-03-02 18:17:58,158 archive.py copy_to_AUVTCD():125 [86521] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2011.256.02/dorado_2011.256.02_processing.log /Volumes/AUVCTD/surveys/2011/netcdf