INFO 2025-06-26 19:31:48,775 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 19:31:48,775 process.py process_mission():434 [1] dorado_info[mission]["comment"] = ECOHAB - CANON March 2013 - Inbound mission, Yanwu's adaptive samping algorithm, all 9 Gulpers fired - ctdToUse = ctd1 INFO 2025-06-26 19:31:48,775 process.py process_mission():449 [1] Processing CANON March 2013 mission 2013.081.06 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:31:48,775 process.py download_process():165 [1] Download and processing steps for 2013.081.06 INFO 2025-06-26 19:31:48,776 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013081/2013.081.06 INFO 2025-06-26 19:31:48,776 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013081/2013.081.06 to /data/auv_data/dorado/missionlogs/2013.081.06 INFO 2025-06-26 19:31:50,698 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.081.06 INFO 2025-06-26 19:31:50,698 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.081.06/ctdDriver.log (2994342 bytes) INFO 2025-06-26 19:31:50,915 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.081.06/ctdDriver2.log (2994431 bytes) INFO 2025-06-26 19:31:51,126 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.081.06/gps.log (32900 bytes) INFO 2025-06-26 19:31:51,136 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.081.06/hydroscatlog.log (2625946 bytes) INFO 2025-06-26 19:31:51,411 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.081.06/navigation.log (10596438 bytes) INFO 2025-06-26 19:31:52,150 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.081.06/isuslog.log (230997 bytes) INFO 2025-06-26 19:31:52,176 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.081.06/parosci.log (3681542 bytes) INFO 2025-06-26 19:31:52,483 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.081.06/parosci.log: [2] INFO 2025-06-26 19:31:52,492 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.081.06/tailCone.log (1878187 bytes) INFO 2025-06-26 19:31:52,720 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.081.06/biolume.log (2187506 bytes) INFO 2025-06-26 19:31:52,932 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:31:53,045 logs2netcdfs.py download_process_logs():807 [1] Time to process: 2.35 seconds INFO 2025-06-26 19:31:53,045 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.081.06/lopc.bin (5913582 bytes) INFO 2025-06-26 19:31:53,046 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:31:53 2025 INFO 2025-06-26 19:31:53,046 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.081.06/parosci.nc INFO 2025-06-26 19:31:53,046 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:31:53,046 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.081.06/parosci.nc INFO 2025-06-26 19:31:53,049 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1363979627.3, sensor_off_time = 1363987449.3 INFO 2025-06-26 19:31:53,049 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 7821 seconds. Expecting to read 15642 L frames from the lopc.bin file. INFO 2025-06-26 19:31:53,049 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 15642 records from the lopc.bin file. INFO 2025-06-26 19:31:53,141 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-03-22 19:13:47 Z and endTime = 2013-03-22 21:24:09 Z with 15642 records expected to be read from lopc.bin INFO 2025-06-26 19:31:53,142 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.081.06/lopc.bin INFO 2025-06-26 19:31:53,142 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.081.06/lopc.nc INFO 2025-06-26 19:31:53,142 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.081.06/lopc.nc INFO 2025-06-26 19:31:53,142 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.081.06 INFO 2025-06-26 19:31:53,143 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 19:31:53,145 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 19:31:53,181 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:31:53,181 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:31:53,181 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-26 19:31:57,496 lopcToNetCDF.py unpackLOPCbin():1013 [1] 10000 40513 9554 0 0 1 0 0 4.4 seconds, last L Frame: 15642 INFO 2025-06-26 19:32:00,171 lopcToNetCDF.py main():2345 [1] >>> Done reading file. INFO 2025-06-26 19:32:00,171 lopcToNetCDF.py main():2346 [1] lFrameCount = 15650, mFrameCount = 15673 INFO 2025-06-26 19:32:00,171 lopcToNetCDF.py main():2352 [1] countBeginMFrameWithoutEndOfPreviousFrame = 1, countBeginLFrameWithoutEndOfPreviousFrame = 0 INFO 2025-06-26 19:32:00,172 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.081.06/parosci.nc INFO 2025-06-26 19:32:00,172 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:32:00,172 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.081.06/parosci.nc INFO 2025-06-26 19:32:00,175 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1363979627.3, sensor_off_time = 1363987449.3 INFO 2025-06-26 19:32:00,175 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 7821 seconds. Expecting to read 15642 L frames from the lopc.bin file. INFO 2025-06-26 19:32:00,176 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 15642 records from the lopc.bin file. INFO 2025-06-26 19:32:00,176 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 23672 and len(sampleCountList) = 15650 INFO 2025-06-26 19:32:00,177 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [] INFO 2025-06-26 19:32:00,177 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [23672 23673 23674 ... 46161 46162 46163] INFO 2025-06-26 19:32:00,178 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 19:32:00,178 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-26 19:32:00,178 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [1 1 1 ... 1 1 1] INFO 2025-06-26 19:32:00,178 lopcToNetCDF.py deSpike():1590 [1] Found 1 spike indicators at indices: [6] INFO 2025-06-26 19:32:00,178 lopcToNetCDF.py deSpike():1595 [1] Identifying nature of spike value = 30520 at index = 6 INFO 2025-06-26 19:32:00,178 lopcToNetCDF.py deSpike():1714 [1] This is the last element in spike_indx. No need to deSpike(). INFO 2025-06-26 19:32:00,178 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [23672 23673 23674 ... 46161 46162 46163] INFO 2025-06-26 19:32:00,179 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [23672 23673 23674 ... 46161 46162 46163] with len(correctedSampleCountList) = 15650 INFO 2025-06-26 19:32:00,179 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 23672 from all values of correctedSampleCountList INFO 2025-06-26 19:32:00,179 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 19:32:00,179 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [0.00000e+00 5.00000e-01 1.00000e+00 ... 1.12445e+04 1.12450e+04 1.12455e+04] INFO 2025-06-26 19:32:00,180 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.36397963e+09 1.36397963e+09 1.36397963e+09 ... 1.36399087e+09 1.36399087e+09 1.36399087e+09] INFO 2025-06-26 19:32:00,180 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1363979627.3 1363979627.8, ..., timestampArray[-2:] = 1363990872.3 1363990872.8] INFO 2025-06-26 19:32:00,196 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1363979627.3134923), np.float64(1363979627.8134923)], ..., timestampList[-2:] = [np.float64(1363990872.3134923), np.float64(1363990872.8134923)]] INFO 2025-06-26 19:32:00,196 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 15650) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 19:32:00,196 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [15623, 15644] INFO 2025-06-26 19:32:00,197 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 745 INFO 2025-06-26 19:32:00,197 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 15650 INFO 2025-06-26 19:32:00,197 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1363979627.3134923), np.float64(1363979627.8134923)], ..., timestampList[-2:] = [np.float64(1363990872.3134923), np.float64(1363990872.8134923)]] INFO 2025-06-26 19:32:00,197 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 15650) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 19:32:00,197 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(15622), np.int32(15643)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 19:32:00,198 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 745 INFO 2025-06-26 19:32:00,198 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 INFO 2025-06-26 19:32:00,211 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 745 INFO 2025-06-26 19:32:00,211 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1363983057.8134923)], ..., tsList[-2:] = [np.float64(1363990859.3134923), np.float64(1363990869.8134923)] INFO 2025-06-26 19:32:00,211 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2013-03-22 20:10:57 Z INFO 2025-06-26 19:32:00,211 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2013-03-22 22:21:09 Z INFO 2025-06-26 19:32:00,211 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 745 INFO 2025-06-26 19:32:00,211 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [1.36398444e+09], ..., cFrameEsecsList[-2:] = [1.36398444e+09 1.36398444e+09] INFO 2025-06-26 19:32:00,212 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 2013-03-22 20:34:04 Z INFO 2025-06-26 19:32:00,212 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 2013-03-22 20:34:04 Z INFO 2025-06-26 19:32:00,216 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2013.081.06/lopc.nc INFO 2025-06-26 19:32:00,217 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 19:32:00 2025 Elapsed processing time from start of processing = 7 seconds INFO 2025-06-26 19:32:00,217 process.py calibrate():227 [1] Calibration steps for 2013.081.06 INFO 2025-06-26 19:32:00,333 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 19:32:00,335 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:32:01,026 calibrate.py _nudge_pos():1806 [1] 102: 0.010 0.0004234 -0.0030656 4270 14.23 4.597 -39.919 2013-03-22T19:29:40.228213248 INFO 2025-06-26 19:32:01,507 calibrate.py _nudge_pos():1806 [1] 154: 0.020 0.0044390 -0.0029236 8265 27.55 24.890 -19.667 2013-03-22T19:58:04.221481728 INFO 2025-06-26 19:32:02,056 calibrate.py _nudge_pos():1806 [1] 213: 0.020 0.0038788 -0.0023700 9160 30.53 19.620 -14.384 2013-03-22T20:29:34.222007808 INFO 2025-06-26 19:32:02,626 calibrate.py _nudge_pos():1806 [1] 275: 0.020 0.0033514 -0.0018716 7675 25.58 20.229 -13.558 2013-03-22T20:56:10.222674432 INFO 2025-06-26 19:32:03,145 calibrate.py _nudge_pos():1806 [1] 331: 0.020 0.0036453 -0.0015924 7495 24.98 22.527 -11.812 2013-03-22T21:22:04.226217728 INFO 2025-06-26 19:32:03,193 calibrate.py _nudge_pos():1806 [1] 336: 0.030 0.0000079 0.0000047 60 0.20 6.213 4.422 2013-03-22T21:22:20.225121792 INFO 2025-06-26 19:32:04,203 calibrate.py _nudge_pos():1862 [1] 411: - - - 0 0.00 - - INFO 2025-06-26 19:32:04,203 calibrate.py _nudge_pos():1868 [1] Points in final series = 38944 INFO 2025-06-26 19:32:05,737 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:32:06,047 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:32:06,286 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:32:06,288 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.081.06/ctd1.nc INFO 2025-06-26 19:32:06,289 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 19:32:06,290 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 19:32:06,290 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:32:06,581 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:32:06,822 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 25 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:32:06,825 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.081.06/ctd2.nc INFO 2025-06-26 19:32:06,826 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 19:32:06,826 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 19:32:06,827 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:32:06,844 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:32:07,236 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] INFO 2025-06-26 19:32:07,307 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:32:14,470 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.081.06 INFO 2025-06-26 19:32:14,504 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.081.06/dorado_2013.081.06_cal.nc INFO 2025-06-26 19:32:14,590 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, 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 19:32:14,596 process.py align():251 [1] Alignment steps for 2013.081.06 INFO 2025-06-26 19:32:14,627 align.py process_cal():139 [1] Processing dorado_2013.081.06_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.081.06 INFO 2025-06-26 19:32:14,642 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:32:14,644 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:32:14,677 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:32:14,679 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:32:14,711 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:32:14,714 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:32:14,732 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:32:14,732 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:32:14,744 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:32:14,747 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:32:14,777 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:14,780 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:14,808 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:14,810 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:14,838 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:14,841 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:14,869 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:14,871 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:14,899 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:14,902 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:14,930 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:14,932 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:14,960 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:14,963 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:14,990 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:14,993 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:15,022 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:15,024 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:15,052 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:15,055 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:15,083 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:15,086 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:15,114 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:15,116 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:15,145 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:15,147 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:15,175 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:15,177 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:15,205 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:15,208 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:15,236 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:15,239 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:15,268 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:15,270 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:15,299 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:15,301 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:15,331 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:15,333 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:15,362 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:15,365 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:15,395 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:15,397 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:15,426 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.081.06_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:32:15,429 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:32:15,464 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:32:15,493 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:32:15,521 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:32:15,550 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:32:15,579 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:32:15,620 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:32:15,830 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 19:32:15,857 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 19:32:15,883 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 19:32:15,909 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 19:32:15,935 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 19:32:15,962 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:32:15,987 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.081.06/dorado_2013.081.06_align.nc INFO 2025-06-26 19:32:16,085 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, 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 19:32:16,088 process.py resample():273 [1] Resampling steps for 2013.081.06 INFO 2025-06-26 19:32:16,089 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:32:16,121 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.081.06/dorado_2013.081.06_align.nc mission netCDF file INFO 2025-06-26 19:32:16,127 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.081.06/dorado_2013.081.06_align.nc mission netCDF file INFO 2025-06-26 19:32:16,128 resample.py get_mission_start_end():1145 [1] navigation: 2013-03-22T19:14:19.641277696 to 2013-03-22T21:24:09.227654656 (0 days 00:57:00.585837568 before mission_end) WARNING 2025-06-26 19:32:16,129 resample.py get_mission_start_end():1156 [1] Instrument navigation has a gap > 5 minutes at the end of the mission: 0 days 00:57:00.585837568 INFO 2025-06-26 19:32:16,130 resample.py get_mission_start_end():1145 [1] hs2 : 2013-03-22T19:13:53.123094272 to 2013-03-22T21:24:09.097663488 (0 days 00:57:00.715828736 before mission_end) WARNING 2025-06-26 19:32:16,131 resample.py get_mission_start_end():1156 [1] Instrument hs2 has a gap > 5 minutes at the end of the mission: 0 days 00:57:00.715828736 INFO 2025-06-26 19:32:16,132 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-03-22T19:14:13.541695488 to 2013-03-22T21:24:09.107662848 (0 days 00:57:00.705829376 before mission_end) WARNING 2025-06-26 19:32:16,133 resample.py get_mission_start_end():1156 [1] Instrument ctd1 has a gap > 5 minutes at the end of the mission: 0 days 00:57:00.705829376 INFO 2025-06-26 19:32:16,134 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-03-22T19:14:13.281713408 to 2013-03-22T21:24:09.097663488 (0 days 00:57:00.715828736 before mission_end) WARNING 2025-06-26 19:32:16,135 resample.py get_mission_start_end():1156 [1] Instrument ctd2 has a gap > 5 minutes at the end of the mission: 0 days 00:57:00.715828736 INFO 2025-06-26 19:32:16,136 resample.py get_mission_start_end():1145 [1] isus : 2013-03-22T19:15:01.948379392 to 2013-03-22T21:24:09.277650944 (0 days 00:57:00.535841280 before mission_end) WARNING 2025-06-26 19:32:16,136 resample.py get_mission_start_end():1156 [1] Instrument isus has a gap > 5 minutes at the end of the mission: 0 days 00:57:00.535841280 INFO 2025-06-26 19:32:16,137 resample.py get_mission_start_end():1145 [1] biolume : 2013-03-22T19:13:46.193534976 to 2013-03-22T21:24:08.487671040 (0 days 00:57:01.325821184 before mission_end) WARNING 2025-06-26 19:32:16,138 resample.py get_mission_start_end():1156 [1] Instrument biolume has a gap > 5 minutes at the end of the mission: 0 days 00:57:01.325821184 INFO 2025-06-26 19:32:16,139 resample.py get_mission_start_end():1145 [1] lopc : 2013-03-22T20:10:57.813492224 to 2013-03-22T22:21:09.813492224 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:32:16,140 resample.py get_mission_start_end():1145 [1] tailcone : 2013-03-22T19:13:45.143641088 to 2013-03-22T21:24:09.197656576 (0 days 00:57:00.615835648 before mission_end) WARNING 2025-06-26 19:32:16,141 resample.py get_mission_start_end():1156 [1] Instrument tailcone has a gap > 5 minutes at the end of the mission: 0 days 00:57:00.615835648 INFO 2025-06-26 19:32:16,141 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.081.06/dorado_2013.081.06_align.nc mission netCDF file INFO 2025-06-26 19:32:16,142 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,244 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,244 resample.py resample_variable():1038 [1] Padding navigation_roll with 0 days 00:57:00.585837568 of NaNs to the end of mission INFO 2025-06-26 19:32:16,263 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,263 resample.py resample_variable():1038 [1] Padding navigation_pitch with 0 days 00:57:00.585837568 of NaNs to the end of mission INFO 2025-06-26 19:32:16,282 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,283 resample.py resample_variable():1038 [1] Padding navigation_yaw with 0 days 00:57:00.585837568 of NaNs to the end of mission INFO 2025-06-26 19:32:16,302 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,302 resample.py resample_variable():1038 [1] Padding navigation_mWaterSpeed with 0 days 00:57:00.585837568 of NaNs to the end of mission INFO 2025-06-26 19:32:16,320 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,320 resample.py resample_variable():1038 [1] Padding hs2_bbp420 with 0 days 00:57:00.715828736 of NaNs to the end of mission INFO 2025-06-26 19:32:16,337 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,337 resample.py resample_variable():1038 [1] Padding hs2_bbp700 with 0 days 00:57:00.715828736 of NaNs to the end of mission INFO 2025-06-26 19:32:16,354 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,354 resample.py resample_variable():1038 [1] Padding hs2_fl700 with 0 days 00:57:00.715828736 of NaNs to the end of mission INFO 2025-06-26 19:32:16,371 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,372 resample.py resample_variable():1038 [1] Padding ctd1_temperature with 0 days 00:57:00.705829376 of NaNs to the end of mission INFO 2025-06-26 19:32:16,388 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,388 resample.py resample_variable():1038 [1] Padding ctd1_conductivity with 0 days 00:57:00.705829376 of NaNs to the end of mission INFO 2025-06-26 19:32:16,405 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,405 resample.py resample_variable():1038 [1] Padding ctd1_salinity with 0 days 00:57:00.705829376 of NaNs to the end of mission INFO 2025-06-26 19:32:16,421 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,421 resample.py resample_variable():1038 [1] Padding ctd1_temperature_onboard with 0 days 00:57:00.705829376 of NaNs to the end of mission INFO 2025-06-26 19:32:16,437 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,438 resample.py resample_variable():1038 [1] Padding ctd1_conductivity_onboard with 0 days 00:57:00.705829376 of NaNs to the end of mission INFO 2025-06-26 19:32:16,454 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,454 resample.py resample_variable():1038 [1] Padding ctd1_salinity_onboard with 0 days 00:57:00.705829376 of NaNs to the end of mission INFO 2025-06-26 19:32:16,471 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,471 resample.py resample_variable():1038 [1] Padding ctd1_dissolvedO2 with 0 days 00:57:00.705829376 of NaNs to the end of mission INFO 2025-06-26 19:32:16,487 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,488 resample.py resample_variable():1038 [1] Padding ctd1_oxygen_mll with 0 days 00:57:00.705829376 of NaNs to the end of mission INFO 2025-06-26 19:32:16,504 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,504 resample.py resample_variable():1038 [1] Padding ctd1_oxygen_umolkg with 0 days 00:57:00.705829376 of NaNs to the end of mission INFO 2025-06-26 19:32:16,521 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,521 resample.py resample_variable():1038 [1] Padding ctd1_flow1 with 0 days 00:57:00.705829376 of NaNs to the end of mission INFO 2025-06-26 19:32:16,539 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,539 resample.py resample_variable():1038 [1] Padding ctd2_temperature with 0 days 00:57:00.715828736 of NaNs to the end of mission INFO 2025-06-26 19:32:16,557 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,557 resample.py resample_variable():1038 [1] Padding ctd2_conductivity with 0 days 00:57:00.715828736 of NaNs to the end of mission INFO 2025-06-26 19:32:16,574 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,574 resample.py resample_variable():1038 [1] Padding ctd2_salinity with 0 days 00:57:00.715828736 of NaNs to the end of mission INFO 2025-06-26 19:32:16,591 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,592 resample.py resample_variable():1038 [1] Padding ctd2_temperature_onboard with 0 days 00:57:00.715828736 of NaNs to the end of mission INFO 2025-06-26 19:32:16,609 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,609 resample.py resample_variable():1038 [1] Padding ctd2_conductivity_onboard with 0 days 00:57:00.715828736 of NaNs to the end of mission INFO 2025-06-26 19:32:16,626 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,627 resample.py resample_variable():1038 [1] Padding ctd2_salinity_onboard with 0 days 00:57:00.715828736 of NaNs to the end of mission INFO 2025-06-26 19:32:16,644 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,644 resample.py resample_variable():1038 [1] Padding ctd2_flow2 with 0 days 00:57:00.715828736 of NaNs to the end of mission INFO 2025-06-26 19:32:16,657 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,658 resample.py resample_variable():1038 [1] Padding isus_nitrate with 0 days 00:57:00.535841280 of NaNs to the end of mission INFO 2025-06-26 19:32:16,670 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,670 resample.py resample_variable():1038 [1] Padding isus_temp with 0 days 00:57:00.535841280 of NaNs to the end of mission INFO 2025-06-26 19:32:16,682 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,682 resample.py resample_variable():1038 [1] Padding isus_quality with 0 days 00:57:00.535841280 of NaNs to the end of mission INFO 2025-06-26 19:32:16,692 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,692 resample.py resample_variable():1038 [1] Padding biolume_flow with 0 days 00:57:01.325821184 of NaNs to the end of mission INFO 2025-06-26 19:32:16,702 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:16,702 resample.py resample_variable():1038 [1] Padding biolume_avg_biolume with 0 days 00:57:01.325821184 of NaNs to the end of mission INFO 2025-06-26 19:32:16,707 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:32:16,707 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:32:16,956 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:32:17,004 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:32:17,032 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:32:17,044 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:32:17,056 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:32:17,057 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:32:17,070 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:17,079 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:17,088 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:17,096 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:17,105 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:17,123 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:32:17,124 resample.py resample_variable():1038 [1] Padding tailcone_propRpm with 0 days 00:57:00.615835648 of NaNs to the end of mission INFO 2025-06-26 19:32:17,295 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.081.06/dorado_2013.081.06_1S.nc INFO 2025-06-26 19:32:18,966 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:32:29,245 create_products.py gulper_odv():522 [1] Wrote 9 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.081.06/dorado_2013.081.06_1S_Gulper.txt INFO 2025-06-26 19:32:29,245 process.py archive():337 [1] Archiving steps for 2013.081.06 INFO 2025-06-26 19:32:29,246 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.081.06/dorado_2013.081.06, BASE_PATH = /data/auv_data INFO 2025-06-26 19:32:29,247 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.081.06/dorado_2013.081.06 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:32:29,247 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.081.06_1S.nc INFO 2025-06-26 19:32:29,259 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.06/dorado_2013.081.06_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:32:29,260 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.081.06_cal.nc INFO 2025-06-26 19:32:29,314 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.06/dorado_2013.081.06_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:32:29,315 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.081.06_align.nc INFO 2025-06-26 19:32:29,395 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.06/dorado_2013.081.06_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:32:29,409 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.06/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013081/2013.081.06 done. INFO 2025-06-26 19:32:29,422 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.06/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013081/2013.081.06 done. INFO 2025-06-26 19:32:29,426 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.06/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013081/2013.081.06 done. INFO 2025-06-26 19:32:29,437 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.06/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013081/2013.081.06 done. INFO 2025-06-26 19:32:29,469 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.06/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013081/2013.081.06 done. INFO 2025-06-26 19:32:29,475 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.06/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013081/2013.081.06 done. INFO 2025-06-26 19:32:29,489 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.06/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013081/2013.081.06 done. INFO 2025-06-26 19:32:29,500 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.06/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013081/2013.081.06 done. INFO 2025-06-26 19:32:29,524 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.06/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013081/2013.081.06 done. INFO 2025-06-26 19:32:29,551 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.06/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013081/2013.081.06 done. INFO 2025-06-26 19:32:29,552 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:32:29,553 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.081.06_1S_Gulper.txt INFO 2025-06-26 19:32:29,557 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.081.06/dorado_2013.081.06_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 19:32:29,557 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.06/dorado_2013.081.06_processing.log /Volumes/AUVCTD/surveys/2013/netcdf