INFO 2025-06-27 03:22:42,826 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2015 --end_year 2025 --num_cores 1 -v --noinput --clobber INFO 2025-06-27 03:22:42,826 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Engineering test mssion out to M2 and back, with nightime profile at M1 and dayttime profiles at C1 and M2. Gulper samples were discarded. No HS2 (this will be getting reinstalled before next run with new calibrations). We were carrying the FLBB instrument for fluorescence and backscatter. No water flow through LOPC or CDOM - ctdToUse = ctd1 INFO 2025-06-27 03:22:42,826 process.py process_mission():449 [1] Processing AUVCTD mission 2020.323.01 by user docker_user on host 355841a7028c INFO 2025-06-27 03:22:42,826 process.py download_process():165 [1] Download and processing steps for 2020.323.01 INFO 2025-06-27 03:22:42,826 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2020/2020323/2020.323.01 INFO 2025-06-27 03:22:42,826 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2020/2020323/2020.323.01 to /data/auv_data/dorado/missionlogs/2020.323.01 INFO 2025-06-27 03:23:01,091 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2020.323.01 INFO 2025-06-27 03:23:01,091 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.323.01/ctdDriver.log (63426726 bytes) INFO 2025-06-27 03:23:05,768 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.323.01/ctdDriver2.log (63423357 bytes) INFO 2025-06-27 03:23:10,464 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.323.01/gps.log (1654484 bytes) INFO 2025-06-27 03:23:10,645 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.323.01/navigation.log (244429022 bytes) INFO 2025-06-27 03:23:29,231 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.323.01/isuslog.log (4102485 bytes) INFO 2025-06-27 03:23:29,652 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.323.01/parosci.log (78911366 bytes) INFO 2025-06-27 03:23:36,257 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.323.01/FLBBCD2K.log (61721919 bytes) INFO 2025-06-27 03:23:44,363 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2020.323.01/FLBBCD2K.log: [ 2 5 10 21 24 26 29 31 35 38 43 51 60 221 223 229 231 239 9453 9455 9457 9458 9462 9464 9468 9470 9475 9480 9482 9489 963692 1665834 1665835 1665837 1665839 1665841 1665842 1665844 1665864 1665871] INFO 2025-06-27 03:23:44,609 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.323.01/tailCone.log (39644875 bytes) INFO 2025-06-27 03:23:49,705 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2020.323.01/biolume.log (46126282 bytes) INFO 2025-06-27 03:23:54,580 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-27 03:23:56,932 logs2netcdfs.py download_process_logs():807 [1] Time to process: 55.84 seconds INFO 2025-06-27 03:23:56,932 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2020.323.01/lopc.bin (92945335 bytes) INFO 2025-06-27 03:23:56,932 lopcToNetCDF.py main():2297 [1] Processing begun: Fri Jun 27 03:23:56 2025 INFO 2025-06-27 03:23:56,932 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2020.323.01/parosci.nc INFO 2025-06-27 03:23:56,932 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-27 03:23:56,932 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2020.323.01/parosci.nc INFO 2025-06-27 03:23:56,936 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1605728595.7, sensor_off_time = 1605893785.9 INFO 2025-06-27 03:23:56,936 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 165190 seconds. Expecting to read 330380 L frames from the lopc.bin file. INFO 2025-06-27 03:23:56,936 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 330380 records from the lopc.bin file. INFO 2025-06-27 03:23:58,915 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2020-11-18 19:43:15 Z and endTime = 2020-11-20 17:36:25 Z with 330380 records expected to be read from lopc.bin INFO 2025-06-27 03:23:58,915 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2020.323.01/lopc.bin INFO 2025-06-27 03:23:58,915 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2020.323.01/lopc.nc INFO 2025-06-27 03:23:58,916 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2020.323.01/lopc.nc INFO 2025-06-27 03:23:58,916 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2020.323.01 INFO 2025-06-27 03:23:58,917 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-27 03:23:58,946 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-27 03:23:58,946 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-27 03:23:58,946 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-27 03:24:01,414 lopcToNetCDF.py unpackLOPCbin():1013 [1] 10000 10000 20 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:03,904 lopcToNetCDF.py unpackLOPCbin():1013 [1] 20000 20000 30 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:06,363 lopcToNetCDF.py unpackLOPCbin():1013 [1] 30000 30000 38 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:08,874 lopcToNetCDF.py unpackLOPCbin():1013 [1] 40000 40000 42 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:11,416 lopcToNetCDF.py unpackLOPCbin():1013 [1] 50000 50000 44 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:13,953 lopcToNetCDF.py unpackLOPCbin():1013 [1] 60000 60000 51 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:16,470 lopcToNetCDF.py unpackLOPCbin():1013 [1] 70000 4464 58 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:18,971 lopcToNetCDF.py unpackLOPCbin():1013 [1] 80000 14464 63 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:21,497 lopcToNetCDF.py unpackLOPCbin():1013 [1] 90000 24464 69 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:24,015 lopcToNetCDF.py unpackLOPCbin():1013 [1] 100000 34464 74 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:26,595 lopcToNetCDF.py unpackLOPCbin():1013 [1] 110000 44464 80 0 0 0 0 0 2.6 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:29,108 lopcToNetCDF.py unpackLOPCbin():1013 [1] 120000 54464 87 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:31,607 lopcToNetCDF.py unpackLOPCbin():1013 [1] 130000 64464 92 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:34,082 lopcToNetCDF.py unpackLOPCbin():1013 [1] 140000 8928 94 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:36,590 lopcToNetCDF.py unpackLOPCbin():1013 [1] 150000 18928 108 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:39,091 lopcToNetCDF.py unpackLOPCbin():1013 [1] 160000 28928 134 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:41,612 lopcToNetCDF.py unpackLOPCbin():1013 [1] 170000 38928 134 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:44,191 lopcToNetCDF.py unpackLOPCbin():1013 [1] 180000 48928 144 0 0 0 0 0 2.6 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:46,720 lopcToNetCDF.py unpackLOPCbin():1013 [1] 190000 58928 152 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:49,216 lopcToNetCDF.py unpackLOPCbin():1013 [1] 200000 3392 159 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:51,757 lopcToNetCDF.py unpackLOPCbin():1013 [1] 210000 13392 162 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:54,557 lopcToNetCDF.py unpackLOPCbin():1013 [1] 220000 23392 169 0 0 0 0 0 2.8 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:57,103 lopcToNetCDF.py unpackLOPCbin():1013 [1] 230000 33392 181 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:24:59,640 lopcToNetCDF.py unpackLOPCbin():1013 [1] 240000 43392 185 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:25:02,176 lopcToNetCDF.py unpackLOPCbin():1013 [1] 250000 53392 191 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:25:04,714 lopcToNetCDF.py unpackLOPCbin():1013 [1] 260000 63392 197 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:25:07,250 lopcToNetCDF.py unpackLOPCbin():1013 [1] 270000 7856 212 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:25:09,825 lopcToNetCDF.py unpackLOPCbin():1013 [1] 280000 17856 224 0 0 0 0 0 2.6 seconds, last L Frame: 330380 INFO 2025-06-27 03:25:12,373 lopcToNetCDF.py unpackLOPCbin():1013 [1] 290000 27856 231 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:25:14,894 lopcToNetCDF.py unpackLOPCbin():1013 [1] 300000 37856 256 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:25:17,388 lopcToNetCDF.py unpackLOPCbin():1013 [1] 310000 47856 270 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:25:19,921 lopcToNetCDF.py unpackLOPCbin():1013 [1] 320000 57856 278 0 0 0 0 0 2.5 seconds, last L Frame: 330380 INFO 2025-06-27 03:25:22,503 lopcToNetCDF.py unpackLOPCbin():1013 [1] 330000 2320 310 0 0 0 0 0 2.6 seconds, last L Frame: 330380 INFO 2025-06-27 03:25:22,593 lopcToNetCDF.py main():2345 [1] >>> Done reading file. INFO 2025-06-27 03:25:22,593 lopcToNetCDF.py main():2346 [1] lFrameCount = 330363, mFrameCount = 311 INFO 2025-06-27 03:25:22,593 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2020.323.01/parosci.nc INFO 2025-06-27 03:25:22,593 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-27 03:25:22,593 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2020.323.01/parosci.nc INFO 2025-06-27 03:25:22,597 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1605728595.7, sensor_off_time = 1605893785.9 INFO 2025-06-27 03:25:22,597 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 165190 seconds. Expecting to read 330380 L frames from the lopc.bin file. INFO 2025-06-27 03:25:22,597 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 330380 records from the lopc.bin file. INFO 2025-06-27 03:25:22,597 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 1 and len(sampleCountList) = 330363 INFO 2025-06-27 03:25:22,628 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [ 65535 131071 196607 262143 327679] INFO 2025-06-27 03:25:22,629 lopcToNetCDF.py correctSampleCountList():1740 [1] Assigning values from slice starting at index 65535, i = 1 INFO 2025-06-27 03:25:22,643 lopcToNetCDF.py correctSampleCountList():1740 [1] Assigning values from slice starting at index 131071, i = 2 INFO 2025-06-27 03:25:22,654 lopcToNetCDF.py correctSampleCountList():1740 [1] Assigning values from slice starting at index 196607, i = 3 INFO 2025-06-27 03:25:22,660 lopcToNetCDF.py correctSampleCountList():1740 [1] Assigning values from slice starting at index 262143, i = 4 INFO 2025-06-27 03:25:22,663 lopcToNetCDF.py correctSampleCountList():1740 [1] Assigning values from slice starting at index 327679, i = 5 INFO 2025-06-27 03:25:22,664 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [ 1 2 3 ... 330366 330367 330368] INFO 2025-06-27 03:25:22,664 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-27 03:25:22,665 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-27 03:25:22,666 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [1 1 1 ... 1 1 1] INFO 2025-06-27 03:25:22,667 lopcToNetCDF.py deSpike():1590 [1] Found 0 spike indicators at indices: [] INFO 2025-06-27 03:25:22,667 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [ 1 2 3 ... 330366 330367 330368] INFO 2025-06-27 03:25:22,667 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [ 1 2 3 ... 330366 330367 330368] with len(correctedSampleCountList) = 330363 INFO 2025-06-27 03:25:22,667 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 1 from all values of correctedSampleCountList INFO 2025-06-27 03:25:22,667 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-27 03:25:22,668 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [0.000000e+00 5.000000e-01 1.000000e+00 ... 1.651825e+05 1.651830e+05 1.651835e+05] INFO 2025-06-27 03:25:22,670 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.60572860e+09 1.60572860e+09 1.60572860e+09 ... 1.60589378e+09 1.60589378e+09 1.60589378e+09] INFO 2025-06-27 03:25:22,670 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1605728595.7 1605728596.2, ..., timestampArray[-2:] = 1605893778.7 1605893779.2] INFO 2025-06-27 03:25:23,010 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1605728595.679727), np.float64(1605728596.179727)], ..., timestampList[-2:] = [np.float64(1605893778.679727), np.float64(1605893779.179727)]] INFO 2025-06-27 03:25:23,011 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 330363) according to what got written to the netCDF file by the binning interval INFO 2025-06-27 03:25:23,011 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [330329, 330350] INFO 2025-06-27 03:25:23,013 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 15731 INFO 2025-06-27 03:25:23,013 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 330363 INFO 2025-06-27 03:25:23,013 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1605728595.679727), np.float64(1605728596.179727)], ..., timestampList[-2:] = [np.float64(1605893778.679727), np.float64(1605893779.179727)]] INFO 2025-06-27 03:25:23,013 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 330363) according to what got written to the netCDF file by the binning interval INFO 2025-06-27 03:25:23,016 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(330328), np.int32(330349)]] from timestampList to create subSampledTimestampList INFO 2025-06-27 03:25:23,033 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 15731 INFO 2025-06-27 03:25:23,038 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 INFO 2025-06-27 03:25:23,107 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 15731 INFO 2025-06-27 03:25:23,107 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1605728605.179727)], ..., tsList[-2:] = [np.float64(1605893762.179727), np.float64(1605893772.679727)] INFO 2025-06-27 03:25:23,107 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2020-11-18 19:43:25 Z INFO 2025-06-27 03:25:23,107 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2020-11-20 17:36:12 Z INFO 2025-06-27 03:25:23,107 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 15731 INFO 2025-06-27 03:25:23,107 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [1.60572861e+09], ..., cFrameEsecsList[-2:] = [1.60572992e+09 1.60572993e+09] INFO 2025-06-27 03:25:23,108 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 2020-11-18 19:43:25 Z INFO 2025-06-27 03:25:23,108 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 2020-11-18 20:05:27 Z INFO 2025-06-27 03:25:23,113 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2020.323.01/lopc.nc INFO 2025-06-27 03:25:23,113 lopcToNetCDF.py main():2384 [1] Processing finished: Fri Jun 27 03:25:23 2025 Elapsed processing time from start of processing = 86 seconds INFO 2025-06-27 03:25:23,126 process.py calibrate():227 [1] Calibration steps for 2020.323.01 INFO 2025-06-27 03:25:24,336 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 2025-06-27 03:25:24,339 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-27 03:25:25,283 calibrate.py _nudge_pos():1806 [1] 106: 0.080 -0.0003444 0.0003180 7836 26.12 -1.957 2.256 2020-11-18T20:11:03.765455360 INFO 2025-06-27 03:25:27,905 calibrate.py _nudge_pos():1806 [1] 330: 0.160 -0.0005017 -0.0000613 3750 12.50 -5.957 -0.909 2020-11-18T20:27:16.758800640 INFO 2025-06-27 03:25:28,126 calibrate.py _nudge_pos():1806 [1] 348: 0.080 -0.0000145 0.0000933 91 0.30 -7.152 57.625 2020-11-18T20:27:51.966388992 INFO 2025-06-27 03:25:30,501 calibrate.py _nudge_pos():1806 [1] 553: 0.160 0.0002999 -0.0000739 11051 36.83 1.208 -0.372 2020-11-18T21:08:05.961019136 INFO 2025-06-27 03:25:33,167 calibrate.py _nudge_pos():1806 [1] 782: 0.050 -0.0066911 -0.0003588 18256 60.85 -16.317 -1.093 2020-11-18T22:12:45.365261568 INFO 2025-06-27 03:25:34,996 calibrate.py _nudge_pos():1806 [1] 939: 0.040 -0.0000344 0.0000179 25 0.08 -63.732 41.536 2020-11-18T22:15:26.364232192 INFO 2025-06-27 03:25:35,928 calibrate.py _nudge_pos():1806 [1] 1018: 0.070 -0.0048885 -0.0005155 15651 52.17 -13.907 -1.831 2020-11-18T23:08:54.564455424 INFO 2025-06-27 03:25:36,117 calibrate.py _nudge_pos():1806 [1] 1034: 0.080 -0.0000210 0.0000031 25 0.08 -38.894 7.134 2020-11-18T23:09:14.563085568 INFO 2025-06-27 03:25:38,573 calibrate.py _nudge_pos():1806 [1] 1246: 0.120 -0.0037271 -0.0005958 15286 50.95 -10.857 -2.167 2020-11-19T00:03:42.759198976 INFO 2025-06-27 03:25:41,224 calibrate.py _nudge_pos():1806 [1] 1472: 0.150 -0.0019323 0.0001225 13916 46.38 -6.183 0.489 2020-11-19T00:53:50.963122944 INFO 2025-06-27 03:25:44,119 calibrate.py _nudge_pos():1806 [1] 1718: 0.010 -0.0034414 0.0004941 15627 52.09 -9.807 1.758 2020-11-19T01:50:01.362234624 INFO 2025-06-27 03:25:46,882 calibrate.py _nudge_pos():1806 [1] 1952: 0.030 -0.0040643 0.0005699 14165 47.22 -12.778 2.237 2020-11-19T02:41:07.562185472 INFO 2025-06-27 03:25:49,759 calibrate.py _nudge_pos():1806 [1] 2194: 0.110 -0.0002687 0.0000764 4395 14.65 -2.723 0.966 2020-11-19T02:59:47.565459968 INFO 2025-06-27 03:25:54,863 calibrate.py _nudge_pos():1806 [1] 2612: 0.030 -0.0003066 0.0008538 6766 22.55 -2.018 7.016 2020-11-19T03:29:17.764193024 INFO 2025-06-27 03:26:41,330 calibrate.py _nudge_pos():1806 [1] 6463: 0.200 -0.0007332 0.0005032 5115 17.05 -6.385 5.470 2020-11-19T04:50:30.960356352 INFO 2025-06-27 03:26:41,490 calibrate.py _nudge_pos():1806 [1] 6476: 0.200 -0.0000496 0.0000011 45 0.15 -50.243 1.404 2020-11-19T04:50:51.958917888 INFO 2025-06-27 03:26:58,797 calibrate.py _nudge_pos():1806 [1] 7909: 0.120 -0.0046316 0.0042065 14591 48.63 -14.138 16.027 2020-11-19T06:03:22.360894976 INFO 2025-06-27 03:27:01,360 calibrate.py _nudge_pos():1806 [1] 8116: 0.160 0.0000326 -0.0000198 30 0.10 49.992 -37.885 2020-11-19T06:06:54.366371328 INFO 2025-06-27 03:27:01,502 calibrate.py _nudge_pos():1806 [1] 8128: 0.150 -0.0033321 0.0049491 14341 47.80 -10.349 19.186 2020-11-19T06:54:53.559133184 INFO 2025-06-27 03:27:04,243 calibrate.py _nudge_pos():1806 [1] 8354: 0.020 -0.0035480 0.0031634 15722 52.40 -10.053 11.186 2020-11-19T07:51:02.958313728 INFO 2025-06-27 03:27:07,306 calibrate.py _nudge_pos():1806 [1] 8596: 0.040 -0.0031861 0.0041831 14341 47.80 -9.897 16.216 2020-11-19T08:42:52.165318144 INFO 2025-06-27 03:27:10,338 calibrate.py _nudge_pos():1806 [1] 8843: 0.100 -0.0016216 0.0053810 15781 52.60 -4.578 18.956 2020-11-19T09:39:34.362252032 INFO 2025-06-27 03:27:13,214 calibrate.py _nudge_pos():1806 [1] 9073: 0.160 -0.0014664 0.0052332 17371 57.90 -3.761 16.748 2020-11-19T10:41:17.558565632 INFO 2025-06-27 03:27:16,005 calibrate.py _nudge_pos():1806 [1] 9304: 0.160 -0.0000551 -0.0000532 15 0.05 -175.469 -211.361 2020-11-19T10:45:10.562603776 INFO 2025-06-27 03:27:16,042 calibrate.py _nudge_pos():1806 [1] 9307: 0.020 -0.0011665 0.0034008 16822 56.07 -3.090 11.239 2020-11-19T11:41:16.961989632 INFO 2025-06-27 03:27:18,875 calibrate.py _nudge_pos():1806 [1] 9532: 0.070 0.0014017 0.0011602 15861 52.87 3.938 4.066 2020-11-19T12:37:53.159334144 INFO 2025-06-27 03:27:21,612 calibrate.py _nudge_pos():1806 [1] 9752: 0.180 0.0008809 0.0008379 18261 60.87 2.150 2.551 2020-11-19T13:42:26.364001536 INFO 2025-06-27 03:27:24,524 calibrate.py _nudge_pos():1806 [1] 9983: 0.020 0.0024093 0.0010644 17012 56.70 6.312 3.478 2020-11-19T14:42:58.765164800 INFO 2025-06-27 03:27:27,604 calibrate.py _nudge_pos():1806 [1] 10225: 0.110 0.0013611 0.0015350 18206 60.68 3.332 4.687 2020-11-19T15:47:40.959216384 INFO 2025-06-27 03:27:30,529 calibrate.py _nudge_pos():1806 [1] 10452: 0.050 -0.0010872 0.0000447 7531 25.10 -6.435 0.330 2020-11-19T16:16:33.160552448 INFO 2025-06-27 03:27:30,543 calibrate.py _nudge_pos():1806 [1] 10453: 0.070 0.0000192 -0.0000223 160 0.53 5.389 -7.801 2020-11-19T16:17:05.158360576 INFO 2025-06-27 03:27:33,109 calibrate.py _nudge_pos():1806 [1] 10654: 0.150 -0.0007541 0.0006567 7000 23.33 -4.803 5.216 2020-11-19T16:43:45.158753024 INFO 2025-06-27 03:27:35,763 calibrate.py _nudge_pos():1806 [1] 10862: 0.030 0.0010044 0.0005521 14362 47.87 3.117 2.137 2020-11-19T17:35:04.557799680 INFO 2025-06-27 03:27:38,856 calibrate.py _nudge_pos():1806 [1] 11099: 0.050 0.0015276 -0.0010950 15591 51.97 4.367 -3.905 2020-11-19T18:30:58.758021120 INFO 2025-06-27 03:27:42,029 calibrate.py _nudge_pos():1806 [1] 11336: 0.080 0.0013804 -0.0008329 15046 50.15 4.089 -3.078 2020-11-19T19:25:03.965709312 INFO 2025-06-27 03:27:45,273 calibrate.py _nudge_pos():1806 [1] 11584: 0.120 0.0004152 0.0016721 14741 49.13 1.255 6.306 2020-11-19T20:18:19.166822912 INFO 2025-06-27 03:27:48,865 calibrate.py _nudge_pos():1806 [1] 11855: 0.180 0.0022961 0.0048413 15411 51.37 6.639 17.464 2020-11-19T21:14:11.367181568 INFO 2025-06-27 03:27:52,042 calibrate.py _nudge_pos():1806 [1] 12099: 0.200 0.0028017 0.0046905 14601 48.67 8.549 17.859 2020-11-19T22:06:54.560487936 INFO 2025-06-27 03:27:54,736 calibrate.py _nudge_pos():1806 [1] 12304: 0.040 -0.0004473 0.0045928 14041 46.80 -1.419 18.185 2020-11-19T22:57:06.964124160 INFO 2025-06-27 03:27:57,607 calibrate.py _nudge_pos():1806 [1] 12518: 0.100 0.0025850 0.0063478 16691 55.63 6.899 21.143 2020-11-19T23:56:18.160850432 INFO 2025-06-27 03:28:00,865 calibrate.py _nudge_pos():1806 [1] 12760: 0.130 0.0004634 0.0034829 14316 47.72 1.442 13.525 2020-11-20T00:48:02.358198528 INFO 2025-06-27 03:28:03,974 calibrate.py _nudge_pos():1806 [1] 12986: 0.190 -0.0025202 0.0020855 15746 52.48 -7.129 7.363 2020-11-20T01:44:16.567049216 INFO 2025-06-27 03:28:06,964 calibrate.py _nudge_pos():1806 [1] 13212: 0.060 -0.0010831 0.0027970 17760 59.20 -2.716 8.755 2020-11-20T02:47:13.958280448 INFO 2025-06-27 03:28:10,250 calibrate.py _nudge_pos():1806 [1] 13458: 0.190 0.0005166 0.0007717 7500 25.00 3.068 5.721 2020-11-20T03:16:19.958671104 INFO 2025-06-27 03:28:13,111 calibrate.py _nudge_pos():1806 [1] 13670: 0.070 0.0017883 0.0010915 18176 60.58 4.381 3.338 2020-11-20T04:20:26.365174016 INFO 2025-06-27 03:28:16,067 calibrate.py _nudge_pos():1806 [1] 13890: 0.110 0.0012517 -0.0016181 15146 50.48 3.680 -5.939 2020-11-20T05:14:34.562657280 INFO 2025-06-27 03:28:19,117 calibrate.py _nudge_pos():1806 [1] 14116: 0.150 0.0014461 -0.0016203 15496 51.65 4.156 -5.813 2020-11-20T06:09:58.764933888 INFO 2025-06-27 03:28:22,430 calibrate.py _nudge_pos():1806 [1] 14360: 0.010 0.0005658 -0.0020047 15881 52.93 1.586 -7.018 2020-11-20T07:06:58.160689152 INFO 2025-06-27 03:28:26,209 calibrate.py _nudge_pos():1806 [1] 14634: 0.090 -0.0000206 -0.0038663 18086 60.28 -0.051 -11.884 2020-11-20T08:11:48.364192000 INFO 2025-06-27 03:28:29,675 calibrate.py _nudge_pos():1806 [1] 14887: 0.200 0.0003671 -0.0032735 18250 60.83 0.896 -9.971 2020-11-20T09:16:50.566872832 INFO 2025-06-27 03:28:33,068 calibrate.py _nudge_pos():1806 [1] 15130: 0.060 0.0002166 -0.0008423 5225 17.41 1.846 -8.963 2020-11-20T09:38:17.758694144 INFO 2025-06-27 03:28:37,084 calibrate.py _nudge_pos():1806 [1] 15423: 0.020 -0.0000287 -0.0000632 126 0.42 -10.211 -28.090 2020-11-20T09:43:34.966963968 INFO 2025-06-27 03:29:06,089 calibrate.py _nudge_pos():1806 [1] 17462: 0.200 -0.0001958 -0.0002556 9895 32.98 -0.881 -1.436 2020-11-20T10:50:31.961780992 INFO 2025-06-27 03:29:09,317 calibrate.py _nudge_pos():1806 [1] 17689: 0.060 0.0018471 0.0004275 14481 48.27 5.677 1.641 2020-11-20T11:42:34.357882112 INFO 2025-06-27 03:29:13,872 calibrate.py _nudge_pos():1806 [1] 18013: 0.050 0.0003334 0.0001088 12111 40.37 1.225 0.499 2020-11-20T12:28:19.559822848 INFO 2025-06-27 03:29:20,503 calibrate.py _nudge_pos():1806 [1] 18488: 0.090 0.0008276 0.0001075 13381 44.60 2.753 0.447 2020-11-20T13:20:49.764019200 INFO 2025-06-27 03:29:24,240 calibrate.py _nudge_pos():1806 [1] 18751: 0.180 0.0000678 0.0000776 1259 4.19 2.398 3.428 2020-11-20T13:29:23.758808064 INFO 2025-06-27 03:29:27,334 calibrate.py _nudge_pos():1806 [1] 18964: 0.150 -0.0000195 0.0000225 20 0.06 -45.644 65.921 2020-11-20T13:32:59.764010752 INFO 2025-06-27 03:29:27,607 calibrate.py _nudge_pos():1806 [1] 18983: 0.160 0.0026211 -0.0006183 14416 48.05 8.094 -2.384 2020-11-20T14:21:20.965264896 INFO 2025-06-27 03:29:30,967 calibrate.py _nudge_pos():1806 [1] 19217: 0.180 0.0004060 0.0001161 1100 3.66 16.446 5.872 2020-11-20T14:28:53.964232192 INFO 2025-06-27 03:29:34,385 calibrate.py _nudge_pos():1806 [1] 19457: 0.020 0.0001159 0.0005374 14901 49.67 0.346 2.005 2020-11-20T15:22:33.363688192 INFO 2025-06-27 03:29:38,116 calibrate.py _nudge_pos():1806 [1] 19715: 0.060 0.0018392 0.0029633 14936 49.78 5.484 11.030 2020-11-20T16:16:37.561445376 INFO 2025-06-27 03:29:41,995 calibrate.py _nudge_pos():1806 [1] 19983: 0.090 0.0025683 0.0021001 7686 25.62 14.877 15.189 2020-11-20T16:46:41.957836032 INFO 2025-06-27 03:30:25,332 calibrate.py _nudge_pos():1862 [1] 22927: - - - 4 0.01 - - INFO 2025-06-27 03:30:25,332 calibrate.py _nudge_pos():1868 [1] Points in final series = 824852 INFO 2025-06-27 03:30:33,133 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 10 seconds, d_end_time_diff: 0 seconds INFO 2025-06-27 03:30:38,125 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 10 seconds, d_end_time_diff: 0 seconds INFO 2025-06-27 03:30:38,133 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2020.323.01/ctd1.nc INFO 2025-06-27 03:30:38,135 calibrate.py _range_qc_combined_nc():898 [1] Setting 1 ctd1_salinity values to NaN INFO 2025-06-27 03:30:38,136 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 2025-06-27 03:30:38,136 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-27 03:30:44,103 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: 0 seconds INFO 2025-06-27 03:30:49,091 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 18 seconds, d_end_time_diff: 0 seconds INFO 2025-06-27 03:30:49,098 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2020.323.01/ctd2.nc INFO 2025-06-27 03:30:49,101 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-27 03:30:49,101 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 2025-06-27 03:30:49,101 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-27 03:30:49,333 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-27 03:30:57,259 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [64620 64680] INFO 2025-06-27 03:30:58,950 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -5 seconds, d_end_time_diff: -1 seconds INFO 2025-06-27 03:35:07,441 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2020.323.01/dorado_2020.323.01_cal.nc INFO 2025-06-27 03:35:08,522 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_par, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, ecopuck_bbp700, ecopuck_cdom, ecopuck_chl, ecopuck_time, gps_latitude, gps_longitude, gps_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 2025-06-27 03:35:08,533 process.py align():251 [1] Alignment steps for 2020.323.01 INFO 2025-06-27 03:35:08,748 align.py process_cal():139 [1] Processing dorado_2020.323.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2020.323.01 INFO 2025-06-27 03:35:08,981 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-27 03:35:09,004 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-27 03:35:09,618 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-27 03:35:09,659 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-27 03:35:10,212 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-27 03:35:10,263 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-27 03:35:10,616 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-27 03:35:10,617 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-27 03:35:10,870 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-27 03:35:10,908 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-27 03:35:11,427 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.323.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:35:11,459 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:35:11,946 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.323.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:35:11,972 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:35:12,431 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.323.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:35:12,459 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:35:12,915 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.323.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:35:12,937 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:35:13,378 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.323.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:35:13,411 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:35:13,883 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.323.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:35:13,908 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:35:14,363 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.323.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:35:14,385 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:35:14,921 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.323.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:35:14,943 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:35:15,433 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.323.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:35:15,457 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:35:15,963 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.323.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:35:15,986 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:35:16,448 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2020.323.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:35:16,474 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:35:16,927 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.323.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:35:16,949 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:35:17,408 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.323.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:35:17,432 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:35:17,882 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.323.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:35:17,909 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:35:18,435 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.323.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:35:18,460 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:35:18,968 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.323.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:35:19,000 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:35:19,605 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.323.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:35:19,636 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:35:20,136 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.323.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:35:20,166 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:35:20,672 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.323.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:35:20,692 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:35:21,126 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2020.323.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-27 03:35:21,153 align.py process_cal():249 [1] ctd2_par: instrument_sample_rate_hz = 4.00 INFO 2025-06-27 03:35:21,749 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-27 03:35:22,233 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-27 03:35:22,597 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-27 03:35:22,973 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-27 03:35:23,359 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-27 03:35:24,157 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-27 03:35:28,881 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-27 03:35:29,173 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-27 03:35:29,474 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-27 03:35:29,761 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-27 03:35:30,051 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-27 03:35:30,412 align.py process_cal():249 [1] ecopuck_bbp700: instrument_sample_rate_hz = 10.38 INFO 2025-06-27 03:35:31,508 align.py process_cal():249 [1] ecopuck_cdom: instrument_sample_rate_hz = 10.38 INFO 2025-06-27 03:35:32,471 align.py process_cal():249 [1] ecopuck_chl: instrument_sample_rate_hz = 10.38 INFO 2025-06-27 03:35:33,542 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-27 03:35:33,856 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2020.323.01/dorado_2020.323.01_align.nc INFO 2025-06-27 03:35:34,891 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_par, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, ecopuck_bbp700, ecopuck_cdom, ecopuck_chl, ecopuck_depth, ecopuck_latitude, ecopuck_longitude, ecopuck_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 2025-06-27 03:35:34,899 process.py resample():273 [1] Resampling steps for 2020.323.01 INFO 2025-06-27 03:35:34,900 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-27 03:35:35,085 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2020.323.01/dorado_2020.323.01_align.nc mission netCDF file INFO 2025-06-27 03:35:35,102 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2020.323.01/dorado_2020.323.01_align.nc mission netCDF file INFO 2025-06-27 03:35:35,106 resample.py get_mission_start_end():1145 [1] navigation: 2020-11-18T19:43:52.057234944 to 2020-11-20T17:36:25.763431424 (0 days 00:00:00.159988736 before mission_end) INFO 2025-06-27 03:35:35,110 resample.py get_mission_start_end():1145 [1] ctd1 : 2020-11-18T19:43:25.749037312 to 2020-11-20T17:36:25.873423616 (0 days 00:00:00.049996544 before mission_end) INFO 2025-06-27 03:35:35,114 resample.py get_mission_start_end():1145 [1] ctd2 : 2020-11-18T19:43:34.478439424 to 2020-11-20T17:36:25.923420160 (0 days 00:00:00 before mission_end) INFO 2025-06-27 03:35:35,117 resample.py get_mission_start_end():1145 [1] isus : 2020-11-18T19:44:34.114353920 to 2020-11-20T17:36:25.113475840 (0 days 00:00:00.809944320 before mission_end) INFO 2025-06-27 03:35:35,120 resample.py get_mission_start_end():1145 [1] biolume : 2020-11-18T19:43:10.940017408 to 2020-11-20T17:36:24.963451904 (0 days 00:00:00.959968256 before mission_end) INFO 2025-06-27 03:35:35,123 resample.py get_mission_start_end():1145 [1] lopc : 2020-11-18T19:43:25.179727104 to 2020-11-20T17:36:12.679727104 (0 days 00:00:13.243693056 before mission_end) INFO 2025-06-27 03:35:35,131 resample.py get_mission_start_end():1145 [1] ecopuck : 2020-11-18T19:43:10.660070912 to 2020-11-20T17:36:25.913420800 (0 days 00:00:00.009999360 before mission_end) INFO 2025-06-27 03:35:35,138 resample.py get_mission_start_end():1145 [1] tailcone : 2020-11-18T19:43:21.069357824 to 2020-11-20T17:36:25.833426432 (0 days 00:00:00.089993728 before mission_end) INFO 2025-06-27 03:35:35,140 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2020.323.01/dorado_2020.323.01_align.nc mission netCDF file INFO 2025-06-27 03:35:35,140 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:36,889 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:37,158 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:37,412 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:37,675 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:37,949 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:38,189 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:38,442 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:38,654 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:38,873 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:39,098 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:39,339 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:39,552 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:39,780 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:40,012 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:40,247 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:40,490 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:40,740 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:40,986 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:41,237 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:41,524 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:41,791 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:42,024 resample.py resample_variable():1031 [1] Resampling ctd2_par with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:42,116 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:42,184 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:42,246 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:42,310 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:42,376 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:42,395 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-27 03:35:42,395 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-27 03:35:48,990 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-27 03:35:51,192 resample.py add_biolume_proxies():633 [1] Zero flow values found: 3 of 165195 - replaced with 350 ml/s INFO 2025-06-27 03:35:51,193 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-27 03:35:51,991 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-27 03:35:52,374 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-27 03:35:52,577 resample.py select_nighttime_bl_raw():408 [1] Extracting biolume_raw data between sunset 2020-11-19 01:53:52.163040512 and sunrise 2020-11-19 13:43:52.361493248 INFO 2025-06-27 03:35:53,207 resample.py select_nighttime_bl_raw():408 [1] Extracting biolume_raw data between sunset 2020-11-20 01:53:52.564207616 and sunrise 2020-11-20 13:43:52.762660352 INFO 2025-06-27 03:35:53,771 resample.py add_biolume_proxies():700 [1] No hs2_fl700 data. Not computing adinos, diatoms, and hdinos INFO 2025-06-27 03:35:53,827 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:53,854 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:53,883 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:53,908 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:53,966 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:54,513 resample.py resample_variable():1031 [1] Resampling ecopuck_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:55,128 resample.py resample_variable():1031 [1] Resampling ecopuck_cdom with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:55,802 resample.py resample_variable():1031 [1] Resampling ecopuck_chl with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:56,110 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-27 03:35:57,265 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2020.323.01/dorado_2020.323.01_1S.nc INFO 2025-06-27 03:36:04,173 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-27 03:36:28,148 create_products.py gulper_odv():522 [1] Wrote 20 Gulper data lines to /data/auv_data/dorado/missionodvs/2020.323.01/dorado_2020.323.01_1S_Gulper.txt INFO 2025-06-27 03:36:28,148 process.py archive():337 [1] Archiving steps for 2020.323.01 INFO 2025-06-27 03:36:28,148 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2020.323.01/dorado_2020.323.01, BASE_PATH = /data/auv_data INFO 2025-06-27 03:36:28,151 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2020.323.01/dorado_2020.323.01 files to /Volumes/AUVCTD/surveys/2020/netcdf INFO 2025-06-27 03:36:28,153 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2020/netcdf/dorado_2020.323.01_1S.nc INFO 2025-06-27 03:36:28,475 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.323.01/dorado_2020.323.01_1S.nc /Volumes/AUVCTD/surveys/2020/netcdf done. INFO 2025-06-27 03:36:28,479 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2020/netcdf/dorado_2020.323.01_cal.nc INFO 2025-06-27 03:36:30,245 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.323.01/dorado_2020.323.01_cal.nc /Volumes/AUVCTD/surveys/2020/netcdf done. INFO 2025-06-27 03:36:30,253 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2020/netcdf/dorado_2020.323.01_align.nc INFO 2025-06-27 03:36:32,370 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.323.01/dorado_2020.323.01_align.nc /Volumes/AUVCTD/surveys/2020/netcdf done. INFO 2025-06-27 03:36:32,644 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.323.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020323/2020.323.01 done. INFO 2025-06-27 03:36:32,902 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.323.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020323/2020.323.01 done. INFO 2025-06-27 03:36:32,920 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.323.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020323/2020.323.01 done. INFO 2025-06-27 03:36:33,705 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.323.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020323/2020.323.01 done. INFO 2025-06-27 03:36:33,727 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.323.01/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020323/2020.323.01 done. INFO 2025-06-27 03:36:33,986 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.323.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020323/2020.323.01 done. INFO 2025-06-27 03:36:34,267 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.323.01/FLBBCD2K.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020323/2020.323.01 done. INFO 2025-06-27 03:36:34,447 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.323.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020323/2020.323.01 done. INFO 2025-06-27 03:36:35,091 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.323.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020323/2020.323.01 done. INFO 2025-06-27 03:36:35,767 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.323.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2020/2020323/2020.323.01 done. INFO 2025-06-27 03:36:35,767 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-27 03:36:35,771 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2020/odv/dorado_2020.323.01_1S_Gulper.txt INFO 2025-06-27 03:36:35,791 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2020.323.01/dorado_2020.323.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2020/odv done. INFO 2025-06-27 03:36:35,792 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2020.323.01/dorado_2020.323.01_processing.log /Volumes/AUVCTD/surveys/2020/netcdf