INFO 2025-06-26 19:59:50,363 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 19:59:50,363 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Autonomy group's short missions in Soquel Bight - ctdToUse = ctd1 INFO 2025-06-26 19:59:50,363 process.py process_mission():449 [1] Processing AUVCTD mission 2013.287.00 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:59:50,363 process.py download_process():165 [1] Download and processing steps for 2013.287.00 INFO 2025-06-26 19:59:50,363 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013287/2013.287.00 INFO 2025-06-26 19:59:50,364 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013287/2013.287.00 to /data/auv_data/dorado/missionlogs/2013.287.00 INFO 2025-06-26 19:59:51,620 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.287.00 INFO 2025-06-26 19:59:51,621 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.00/ctdDriver.log (1468518 bytes) INFO 2025-06-26 19:59:51,727 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.00/ctdDriver2.log (1474943 bytes) INFO 2025-06-26 19:59:51,834 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.00/gps.log (279500 bytes) INFO 2025-06-26 19:59:51,870 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.00/hydroscatlog.log (1297150 bytes) INFO 2025-06-26 19:59:52,012 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.00/navigation.log (5215190 bytes) INFO 2025-06-26 19:59:52,396 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.00/parosci.log (1826102 bytes) INFO 2025-06-26 19:59:52,552 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.00/tailCone.log (928267 bytes) INFO 2025-06-26 19:59:52,672 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.00/biolume.log (1083030 bytes) INFO 2025-06-26 19:59:52,784 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:59:52,844 logs2netcdfs.py download_process_logs():807 [1] Time to process: 1.22 seconds INFO 2025-06-26 19:59:52,844 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.287.00/lopc.bin (3560300 bytes) INFO 2025-06-26 19:59:52,844 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:59:52 2025 INFO 2025-06-26 19:59:52,844 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.287.00/parosci.nc INFO 2025-06-26 19:59:52,844 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:59:52,845 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.287.00/parosci.nc INFO 2025-06-26 19:59:52,847 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1381764788.8, sensor_off_time = 1381768654.2 INFO 2025-06-26 19:59:52,847 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 3865 seconds. Expecting to read 7730 L frames from the lopc.bin file. INFO 2025-06-26 19:59:52,847 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 7730 records from the lopc.bin file. INFO 2025-06-26 19:59:52,894 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-10-14 15:33:08 Z and endTime = 2013-10-14 16:37:34 Z with 7730 records expected to be read from lopc.bin INFO 2025-06-26 19:59:52,894 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.287.00/lopc.bin INFO 2025-06-26 19:59:52,894 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.287.00/lopc.nc INFO 2025-06-26 19:59:52,894 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.287.00/lopc.nc INFO 2025-06-26 19:59:52,895 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.287.00 INFO 2025-06-26 19:59:52,895 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 19:59:52,942 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:59:52,942 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:59:52,942 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-26 19:59:57,340 lopcToNetCDF.py main():2345 [1] >>> Done reading file. INFO 2025-06-26 19:59:57,340 lopcToNetCDF.py main():2346 [1] lFrameCount = 7730, mFrameCount = 10779 INFO 2025-06-26 19:59:57,341 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.287.00/parosci.nc INFO 2025-06-26 19:59:57,341 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:59:57,341 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.287.00/parosci.nc INFO 2025-06-26 19:59:57,343 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1381764788.8, sensor_off_time = 1381768654.2 INFO 2025-06-26 19:59:57,343 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 3865 seconds. Expecting to read 7730 L frames from the lopc.bin file. INFO 2025-06-26 19:59:57,343 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 7730 records from the lopc.bin file. INFO 2025-06-26 19:59:57,343 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 1 and len(sampleCountList) = 7730 INFO 2025-06-26 19:59:57,344 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [] INFO 2025-06-26 19:59:57,344 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [ 1 2 3 ... 7728 7729 7730] INFO 2025-06-26 19:59:57,345 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 19:59:57,345 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-26 19:59:57,345 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [1 1 1 ... 1 1 1] INFO 2025-06-26 19:59:57,345 lopcToNetCDF.py deSpike():1590 [1] Found 0 spike indicators at indices: [] INFO 2025-06-26 19:59:57,345 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [ 1 2 3 ... 7728 7729 7730] INFO 2025-06-26 19:59:57,345 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [ 1 2 3 ... 7728 7729 7730] with len(correctedSampleCountList) = 7730 INFO 2025-06-26 19:59:57,345 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 1 from all values of correctedSampleCountList INFO 2025-06-26 19:59:57,345 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 19:59:57,346 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [0.0000e+00 5.0000e-01 1.0000e+00 ... 3.8635e+03 3.8640e+03 3.8645e+03] INFO 2025-06-26 19:59:57,346 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.38176479e+09 1.38176479e+09 1.38176479e+09 ... 1.38176865e+09 1.38176865e+09 1.38176865e+09] INFO 2025-06-26 19:59:57,346 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1381764788.8 1381764789.3, ..., timestampArray[-2:] = 1381768652.8 1381768653.3] INFO 2025-06-26 19:59:57,354 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1381764788.845326), np.float64(1381764789.345326)], ..., timestampList[-2:] = [np.float64(1381768652.845326), np.float64(1381768653.345326)]] INFO 2025-06-26 19:59:57,354 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 7730) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 19:59:57,354 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [7706, 7727] INFO 2025-06-26 19:59:57,354 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 368 INFO 2025-06-26 19:59:57,354 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 7730 INFO 2025-06-26 19:59:57,354 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1381764788.845326), np.float64(1381764789.345326)], ..., timestampList[-2:] = [np.float64(1381768652.845326), np.float64(1381768653.345326)]] INFO 2025-06-26 19:59:57,354 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 7730) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 19:59:57,355 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(7705), np.int32(7726)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 19:59:57,355 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 368 INFO 2025-06-26 19:59:57,355 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 INFO 2025-06-26 19:59:57,362 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 368 INFO 2025-06-26 19:59:57,362 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1381764798.345326)], ..., tsList[-2:] = [np.float64(1381768641.345326), np.float64(1381768651.845326)] INFO 2025-06-26 19:59:57,362 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2013-10-14 15:33:18 Z INFO 2025-06-26 19:59:57,362 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2013-10-14 16:37:31 Z INFO 2025-06-26 19:59:57,362 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 368 INFO 2025-06-26 19:59:57,362 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [1.38176537e+09], ..., cFrameEsecsList[-2:] = [1.38176537e+09 1.38176537e+09] INFO 2025-06-26 19:59:57,363 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 2013-10-14 15:42:48 Z INFO 2025-06-26 19:59:57,363 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 2013-10-14 15:42:48 Z INFO 2025-06-26 19:59:57,366 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2013.287.00/lopc.nc INFO 2025-06-26 19:59:57,367 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 19:59:57 2025 Elapsed processing time from start of processing = 4 seconds INFO 2025-06-26 19:59:57,367 process.py calibrate():227 [1] Calibration steps for 2013.287.00 WARNING 2025-06-26 19:59:57,453 calibrate.py _navigation_process():1588 [1] No positive depths found in 2013.287.00/navigation.nc INFO 2025-06-26 19:59:57,457 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 19:59:57,458 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:00:33,132 calibrate.py _nudge_pos():1862 [1] 3834: - - - 0 0.00 - - INFO 2025-06-26 20:00:33,133 calibrate.py _nudge_pos():1868 [1] Points in final series = 19165 INFO 2025-06-26 20:00:33,392 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:00:33,555 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 43 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:00:33,675 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 43 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:00:33,677 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.287.00/ctd1.nc INFO 2025-06-26 20:00:33,678 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:00:33,678 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 20:00:33,678 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:00:33,829 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:00:33,947 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:00:33,948 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.287.00/ctd2.nc INFO 2025-06-26 20:00:33,949 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:00:33,950 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 20:00:33,950 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 20:00:33,950 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.287.00 INFO 2025-06-26 20:00:33,954 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:00:34,120 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90] INFO 2025-06-26 20:00:34,156 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:00:37,696 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.287.00 INFO 2025-06-26 20:00:37,714 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.287.00/dorado_2013.287.00_cal.nc INFO 2025-06-26 20:00:37,776 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, lopc_LCcount, lopc_countListSum, lopc_flowSpeed, lopc_nonTransCount, lopc_time, lopc_transCount, 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 20:00:37,781 process.py align():251 [1] Alignment steps for 2013.287.00 INFO 2025-06-26 20:00:37,809 align.py process_cal():139 [1] Processing dorado_2013.287.00_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.287.00 INFO 2025-06-26 20:00:37,818 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:00:37,820 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:00:37,841 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:00:37,843 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:00:37,861 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:00:37,864 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:00:37,875 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:00:37,875 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:00:37,883 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:00:37,885 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:00:37,904 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:37,906 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:37,924 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:37,926 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:37,944 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:37,946 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:37,964 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:37,966 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:37,985 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:37,987 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:38,005 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:38,007 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:38,025 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:38,027 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:38,045 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:38,047 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:38,065 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:38,067 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:38,086 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:38,089 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:38,107 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:38,109 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:38,127 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:38,129 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:38,147 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:38,149 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:38,167 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:38,169 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:38,188 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:38,190 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:38,209 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:38,211 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:38,230 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:38,232 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:38,251 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:38,253 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:38,272 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:38,274 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:38,292 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:38,295 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:38,314 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:38,316 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:38,334 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.287.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:00:38,336 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:00:38,361 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:00:38,381 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:00:38,406 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:00:38,516 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:00:38,536 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:00:38,555 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:00:38,574 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:00:38,593 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:00:38,613 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:00:38,630 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.287.00/dorado_2013.287.00_align.nc INFO 2025-06-26 20:00:38,701 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, lopc_LCcount, lopc_countListSum, lopc_depth, lopc_flowSpeed, lopc_latitude, lopc_longitude, lopc_nonTransCount, lopc_time, lopc_transCount, 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 20:00:38,703 process.py resample():273 [1] Resampling steps for 2013.287.00 INFO 2025-06-26 20:00:38,704 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:00:38,730 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.287.00/dorado_2013.287.00_align.nc mission netCDF file INFO 2025-06-26 20:00:38,734 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.287.00/dorado_2013.287.00_align.nc mission netCDF file INFO 2025-06-26 20:00:38,735 resample.py get_mission_start_end():1145 [1] navigation: 2013-10-14T15:33:41.323100928 to 2013-10-14T16:37:34.110536960 (0 days 00:00:00.099993344 before mission_end) INFO 2025-06-26 20:00:38,737 resample.py get_mission_start_end():1145 [1] hs2 : 2013-10-14T15:33:15.064899840 to 2013-10-14T16:37:34.170532864 (0 days 00:00:00.039997440 before mission_end) INFO 2025-06-26 20:00:38,738 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-10-14T15:33:52.052366080 to 2013-10-14T16:37:34.200530944 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-26 20:00:38,739 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-10-14T15:33:35.263516160 to 2013-10-14T16:37:34.160533760 (0 days 00:00:00.049996544 before mission_end) INFO 2025-06-26 20:00:38,740 resample.py get_mission_start_end():1145 [1] biolume : 2013-10-14T15:33:06.965420544 to 2013-10-14T16:37:33.220563968 (0 days 00:00:00.989966336 before mission_end) INFO 2025-06-26 20:00:38,742 resample.py get_mission_start_end():1145 [1] lopc : 2013-10-14T15:33:18.345325824 to 2013-10-14T16:37:31.845325824 (0 days 00:00:02.365204480 before mission_end) INFO 2025-06-26 20:00:38,743 resample.py get_mission_start_end():1145 [1] tailcone : 2013-10-14T15:33:08.815328000 to 2013-10-14T16:37:34.210530304 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:00:38,744 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.287.00/dorado_2013.287.00_align.nc mission netCDF file INFO 2025-06-26 20:00:38,744 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:38,806 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:38,819 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:38,832 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:38,845 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:38,857 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:38,869 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:38,881 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:38,893 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:38,904 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:38,914 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:38,925 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:38,935 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:38,946 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:38,956 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:38,967 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:38,977 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:38,988 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:39,000 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:39,013 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:39,025 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:39,037 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:39,049 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:39,060 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:39,072 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:39,080 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:39,088 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:39,091 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:00:39,091 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:00:39,239 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:00:39,266 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:00:39,282 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:00:39,289 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:00:39,296 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:00:39,296 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:00:39,309 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:39,317 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:39,325 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:39,333 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:39,342 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:39,355 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:00:39,491 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.287.00/dorado_2013.287.00_1S.nc INFO 2025-06-26 20:00:40,708 create_products.py gulper_odv():401 [1] No gulper times found for 2013.287.00 INFO 2025-06-26 20:00:40,708 process.py archive():337 [1] Archiving steps for 2013.287.00 INFO 2025-06-26 20:00:40,708 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.287.00/dorado_2013.287.00, BASE_PATH = /data/auv_data INFO 2025-06-26 20:00:40,708 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.287.00/dorado_2013.287.00 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 20:00:40,709 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.287.00_1S.nc INFO 2025-06-26 20:00:40,720 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.00/dorado_2013.287.00_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:00:40,721 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.287.00_cal.nc INFO 2025-06-26 20:00:40,751 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.00/dorado_2013.287.00_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:00:40,752 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.287.00_align.nc INFO 2025-06-26 20:00:40,793 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.00/dorado_2013.287.00_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:00:40,803 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.00 done. INFO 2025-06-26 20:00:40,812 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.00 done. INFO 2025-06-26 20:00:40,817 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.00 done. INFO 2025-06-26 20:00:40,825 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.00 done. INFO 2025-06-26 20:00:40,843 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.00 done. INFO 2025-06-26 20:00:40,853 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.00 done. INFO 2025-06-26 20:00:40,862 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.00 done. INFO 2025-06-26 20:00:40,877 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.00 done. INFO 2025-06-26 20:00:40,893 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.00/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013287/2013.287.00 done. INFO 2025-06-26 20:00:40,893 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:00:40,894 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.287.00/dorado_2013.287.00_processing.log /Volumes/AUVCTD/surveys/2013/netcdf