INFO 2025-06-26 20:30:29,827 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 20:30:29,827 process.py process_mission():434 [1] dorado_info[mission]["comment"] = CANON-ECOHAB September 2014 with rhodamine sensor on ctdDriver2, channel 1 - ctdToUse = ctd1 INFO 2025-06-26 20:30:29,827 process.py process_mission():449 [1] Processing CANON September 2014 mission 2014.266.05 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:30:29,827 process.py download_process():165 [1] Download and processing steps for 2014.266.05 INFO 2025-06-26 20:30:29,827 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2014/2014266/2014.266.05 INFO 2025-06-26 20:30:29,827 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2014/2014266/2014.266.05 to /data/auv_data/dorado/missionlogs/2014.266.05 INFO 2025-06-26 20:30:32,647 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2014.266.05 INFO 2025-06-26 20:30:32,647 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.266.05/ctdDriver.log (2337990 bytes) INFO 2025-06-26 20:30:32,814 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.266.05/ctdDriver2.log (2337892 bytes) WARNING 2025-06-26 20:30:32,933 logs2netcdfs.py _read_data():216 [1] unpack requires a buffer of 8 bytes, b = b'\n' at record 24346, for time in file /data/auv_data/dorado/missionlogs/2014.266.05/ctdDriver2.log INFO 2025-06-26 20:30:32,933 logs2netcdfs.py _read_data():224 [1] bytes read = 2337899 file size = 2337892 INFO 2025-06-26 20:30:32,933 logs2netcdfs.py _read_data():229 [1] Tried to read 8 bytes, but only 7 bytes remaining INFO 2025-06-26 20:30:32,933 logs2netcdfs.py _read_data():235 [1] Successfully unpacked 24346 records WARNING 2025-06-26 20:30:32,939 logs2netcdfs.py _create_variable():536 [1] conductivity: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (24347,) and arg 1 with shape (24346,). INFO 2025-06-26 20:30:32,939 logs2netcdfs.py _create_variable():537 [1] len(data) (24346) does not match shape of conductivity.shape[0] (24347) WARNING 2025-06-26 20:30:32,939 logs2netcdfs.py _create_variable():544 [1] conductivity data is short by one, appending the last value: 4.346113083612477 WARNING 2025-06-26 20:30:32,942 logs2netcdfs.py _create_variable():536 [1] temperature: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (24347,) and arg 1 with shape (24346,). INFO 2025-06-26 20:30:32,942 logs2netcdfs.py _create_variable():537 [1] len(data) (24346) does not match shape of temperature.shape[0] (24347) WARNING 2025-06-26 20:30:32,942 logs2netcdfs.py _create_variable():544 [1] temperature data is short by one, appending the last value: 17.383847053690033 WARNING 2025-06-26 20:30:32,945 logs2netcdfs.py _create_variable():536 [1] cond_frequency: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (24347,) and arg 1 with shape (24346,). INFO 2025-06-26 20:30:32,945 logs2netcdfs.py _create_variable():537 [1] len(data) (24346) does not match shape of cond_frequency.shape[0] (24347) WARNING 2025-06-26 20:30:32,945 logs2netcdfs.py _create_variable():544 [1] cond_frequency data is short by one, appending the last value: 6329.2734375 WARNING 2025-06-26 20:30:32,947 logs2netcdfs.py _create_variable():536 [1] temp_frequency: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (24347,) and arg 1 with shape (24346,). INFO 2025-06-26 20:30:32,947 logs2netcdfs.py _create_variable():537 [1] len(data) (24346) does not match shape of temp_frequency.shape[0] (24347) WARNING 2025-06-26 20:30:32,948 logs2netcdfs.py _create_variable():544 [1] temp_frequency data is short by one, appending the last value: 8545.75 WARNING 2025-06-26 20:30:32,950 logs2netcdfs.py _create_variable():536 [1] rhodamine: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (24347,) and arg 1 with shape (24346,). INFO 2025-06-26 20:30:32,950 logs2netcdfs.py _create_variable():537 [1] len(data) (24346) does not match shape of rhodamine.shape[0] (24347) WARNING 2025-06-26 20:30:32,950 logs2netcdfs.py _create_variable():544 [1] rhodamine data is short by one, appending the last value: 0.0 WARNING 2025-06-26 20:30:32,952 logs2netcdfs.py _create_variable():536 [1] spare1: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (24347,) and arg 1 with shape (24346,). INFO 2025-06-26 20:30:32,953 logs2netcdfs.py _create_variable():537 [1] len(data) (24346) does not match shape of spare1.shape[0] (24347) WARNING 2025-06-26 20:30:32,953 logs2netcdfs.py _create_variable():544 [1] spare1 data is short by one, appending the last value: 0.0 WARNING 2025-06-26 20:30:32,955 logs2netcdfs.py _create_variable():536 [1] spare2: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (24347,) and arg 1 with shape (24346,). INFO 2025-06-26 20:30:32,955 logs2netcdfs.py _create_variable():537 [1] len(data) (24346) does not match shape of spare2.shape[0] (24347) WARNING 2025-06-26 20:30:32,955 logs2netcdfs.py _create_variable():544 [1] spare2 data is short by one, appending the last value: 0.0 WARNING 2025-06-26 20:30:32,958 logs2netcdfs.py _create_variable():536 [1] flow2: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (24347,) and arg 1 with shape (24346,). INFO 2025-06-26 20:30:32,958 logs2netcdfs.py _create_variable():537 [1] len(data) (24346) does not match shape of flow2.shape[0] (24347) WARNING 2025-06-26 20:30:32,958 logs2netcdfs.py _create_variable():544 [1] flow2 data is short by one, appending the last value: 0.0 WARNING 2025-06-26 20:30:32,960 logs2netcdfs.py _create_variable():536 [1] spare3: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (24347,) and arg 1 with shape (24346,). INFO 2025-06-26 20:30:32,960 logs2netcdfs.py _create_variable():537 [1] len(data) (24346) does not match shape of spare3.shape[0] (24347) WARNING 2025-06-26 20:30:32,960 logs2netcdfs.py _create_variable():544 [1] spare3 data is short by one, appending the last value: 0.0 WARNING 2025-06-26 20:30:32,963 logs2netcdfs.py _create_variable():536 [1] spare4: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (24347,) and arg 1 with shape (24346,). INFO 2025-06-26 20:30:32,963 logs2netcdfs.py _create_variable():537 [1] len(data) (24346) does not match shape of spare4.shape[0] (24347) WARNING 2025-06-26 20:30:32,963 logs2netcdfs.py _create_variable():544 [1] spare4 data is short by one, appending the last value: 0.0 WARNING 2025-06-26 20:30:32,965 logs2netcdfs.py _create_variable():536 [1] salinity: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (24347,) and arg 1 with shape (24346,). INFO 2025-06-26 20:30:32,965 logs2netcdfs.py _create_variable():537 [1] len(data) (24346) does not match shape of salinity.shape[0] (24347) WARNING 2025-06-26 20:30:32,965 logs2netcdfs.py _create_variable():544 [1] salinity data is short by one, appending the last value: 33.42516438060392 INFO 2025-06-26 20:30:32,996 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2014.266.05/ctdDriver2.log: [24346] INFO 2025-06-26 20:30:33,003 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.266.05/gps.log (84668 bytes) INFO 2025-06-26 20:30:33,021 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.266.05/hydroscatlog.log (2051890 bytes) INFO 2025-06-26 20:30:33,237 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.266.05/navigation.log (8738370 bytes) INFO 2025-06-26 20:30:33,863 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.266.05/isuslog.log (151669 bytes) INFO 2025-06-26 20:30:33,882 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2014.266.05/isuslog.log: [ 1 2 3 4 6 7 8 9 10 11 13 14 15 16 17 18 19] INFO 2025-06-26 20:30:33,883 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.266.05/parosci.log (2880326 bytes) INFO 2025-06-26 20:30:34,128 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.266.05/tailCone.log (1466635 bytes) INFO 2025-06-26 20:30:34,319 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2014.266.05/biolume.log (1710386 bytes) INFO 2025-06-26 20:30:34,492 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:30:34,582 logs2netcdfs.py download_process_logs():807 [1] Time to process: 1.94 seconds INFO 2025-06-26 20:30:34,583 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2014.266.05/lopc.bin (8803546 bytes) INFO 2025-06-26 20:30:34,583 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:30:34 2025 INFO 2025-06-26 20:30:34,583 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.266.05/parosci.nc INFO 2025-06-26 20:30:34,583 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:30:34,583 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.266.05/parosci.nc INFO 2025-06-26 20:30:34,586 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1411506993.7, sensor_off_time = 1411513104.9 INFO 2025-06-26 20:30:34,586 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 6111 seconds. Expecting to read 12222 L frames from the lopc.bin file. INFO 2025-06-26 20:30:34,586 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 12222 records from the lopc.bin file. INFO 2025-06-26 20:30:34,658 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2014-09-23 21:16:33 Z and endTime = 2014-09-23 22:58:24 Z with 12222 records expected to be read from lopc.bin INFO 2025-06-26 20:30:34,659 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2014.266.05/lopc.bin INFO 2025-06-26 20:30:34,659 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2014.266.05/lopc.nc INFO 2025-06-26 20:30:34,659 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2014.266.05/lopc.nc INFO 2025-06-26 20:30:34,659 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2014.266.05 INFO 2025-06-26 20:30:34,660 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 20:30:34,663 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 20:30:34,729 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:30:34,729 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:30:34,729 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-26 20:30:44,692 lopcToNetCDF.py unpackLOPCbin():1013 [1] 10000 52607 27082 1 0 0 0 0 10.0 seconds, last L Frame: 12222 INFO 2025-06-26 20:30:47,327 lopcToNetCDF.py main():2345 [1] >>> Done reading file. INFO 2025-06-26 20:30:47,327 lopcToNetCDF.py main():2346 [1] lFrameCount = 12230, mFrameCount = 33508 INFO 2025-06-26 20:30:47,327 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2014.266.05/parosci.nc INFO 2025-06-26 20:30:47,327 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:30:47,328 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2014.266.05/parosci.nc INFO 2025-06-26 20:30:47,331 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1411506993.7, sensor_off_time = 1411513104.9 INFO 2025-06-26 20:30:47,331 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 6111 seconds. Expecting to read 12222 L frames from the lopc.bin file. INFO 2025-06-26 20:30:47,331 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 12222 records from the lopc.bin file. INFO 2025-06-26 20:30:47,331 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 29171 and len(sampleCountList) = 12230 INFO 2025-06-26 20:30:47,333 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [] INFO 2025-06-26 20:30:47,333 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [29171 29172 29173 ... 54835 54836 54837] INFO 2025-06-26 20:30:47,333 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 20:30:47,334 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-26 20:30:47,334 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [1 1 1 ... 1 1 1] INFO 2025-06-26 20:30:47,334 lopcToNetCDF.py deSpike():1590 [1] Found 1 spike indicators at indices: [5] INFO 2025-06-26 20:30:47,334 lopcToNetCDF.py deSpike():1595 [1] Identifying nature of spike value = 42613 at index = 5 INFO 2025-06-26 20:30:47,334 lopcToNetCDF.py deSpike():1714 [1] This is the last element in spike_indx. No need to deSpike(). INFO 2025-06-26 20:30:47,335 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [29171 29172 29173 ... 54835 54836 54837] INFO 2025-06-26 20:30:47,335 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [29171 29172 29173 ... 54835 54836 54837] with len(correctedSampleCountList) = 12230 INFO 2025-06-26 20:30:47,335 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 29171 from all values of correctedSampleCountList INFO 2025-06-26 20:30:47,335 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 20:30:47,335 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [0.00000e+00 5.00000e-01 1.00000e+00 ... 1.28320e+04 1.28325e+04 1.28330e+04] INFO 2025-06-26 20:30:47,336 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.41150699e+09 1.41150699e+09 1.41150699e+09 ... 1.41151983e+09 1.41151983e+09 1.41151983e+09] INFO 2025-06-26 20:30:47,337 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1411506993.7 1411506994.2, ..., timestampArray[-2:] = 1411519826.2 1411519826.7] INFO 2025-06-26 20:30:47,352 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1411506993.7427742), np.float64(1411506994.2427742)], ..., timestampList[-2:] = [np.float64(1411519826.2427742), np.float64(1411519826.7427742)]] INFO 2025-06-26 20:30:47,352 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 12230) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 20:30:47,352 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [12200, 12221] INFO 2025-06-26 20:30:47,352 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 582 INFO 2025-06-26 20:30:47,352 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 12230 INFO 2025-06-26 20:30:47,352 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1411506993.7427742), np.float64(1411506994.2427742)], ..., timestampList[-2:] = [np.float64(1411519826.2427742), np.float64(1411519826.7427742)]] INFO 2025-06-26 20:30:47,353 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 12230) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 20:30:47,353 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(12199), np.int32(12220)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 20:30:47,354 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 582 INFO 2025-06-26 20:30:47,354 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 INFO 2025-06-26 20:30:47,366 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 582 INFO 2025-06-26 20:30:47,366 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1411513721.7427742)], ..., tsList[-2:] = [np.float64(1411519811.7427742), np.float64(1411519822.2427742)] INFO 2025-06-26 20:30:47,367 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2014-09-23 23:08:41 Z INFO 2025-06-26 20:30:47,367 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2014-09-24 00:50:22 Z INFO 2025-06-26 20:30:47,367 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 582 INFO 2025-06-26 20:30:47,367 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [1.4115131e+09], ..., cFrameEsecsList[-2:] = [1.4115131e+09 1.4115131e+09] INFO 2025-06-26 20:30:47,367 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 2014-09-23 22:58:23 Z INFO 2025-06-26 20:30:47,367 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 2014-09-23 22:58:23 Z INFO 2025-06-26 20:30:47,372 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2014.266.05/lopc.nc INFO 2025-06-26 20:30:47,372 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 20:30:47 2025 Elapsed processing time from start of processing = 12 seconds INFO 2025-06-26 20:30:47,372 process.py calibrate():227 [1] Calibration steps for 2014.266.05 INFO 2025-06-26 20:30:47,498 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 20:30:47,500 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:30:48,312 calibrate.py _nudge_pos():1806 [1] 119: 0.100 -0.0013481 0.0006911 3955 13.18 -15.183 9.716 2014-09-23T21:31:40.130682368 INFO 2025-06-26 20:30:48,404 calibrate.py _nudge_pos():1806 [1] 128: 0.090 -0.0001355 0.0002302 120 0.40 -50.701 107.478 2014-09-23T21:32:12.138489600 INFO 2025-06-26 20:30:49,200 calibrate.py _nudge_pos():1806 [1] 208: 0.100 -0.0005205 -0.0000809 1450 4.83 -15.997 -3.104 2014-09-23T21:38:22.133143552 INFO 2025-06-26 20:30:50,086 calibrate.py _nudge_pos():1806 [1] 301: 0.090 -0.0007021 0.0002914 1400 4.66 -22.350 11.577 2014-09-23T21:44:34.137659392 INFO 2025-06-26 20:30:51,182 calibrate.py _nudge_pos():1806 [1] 418: 0.100 -0.0006895 0.0002481 1310 4.36 -23.459 10.535 2014-09-23T21:50:52.131765248 INFO 2025-06-26 20:30:52,242 calibrate.py _nudge_pos():1806 [1] 532: 0.090 -0.0004954 0.0002580 1775 5.91 -12.436 8.086 2014-09-23T21:58:40.139704320 INFO 2025-06-26 20:30:52,991 calibrate.py _nudge_pos():1806 [1] 612: 0.100 -0.0007291 0.0001663 1345 4.48 -24.159 6.880 2014-09-23T22:04:28.135865088 INFO 2025-06-26 20:30:53,679 calibrate.py _nudge_pos():1806 [1] 685: 0.100 -0.0002149 0.0000705 1945 6.48 -4.923 2.016 2014-09-23T22:12:10.134215936 INFO 2025-06-26 20:30:54,401 calibrate.py _nudge_pos():1806 [1] 758: 0.100 -0.0011787 0.0009793 1850 6.16 -28.391 29.442 2014-09-23T22:19:34.133799680 INFO 2025-06-26 20:30:54,981 calibrate.py _nudge_pos():1806 [1] 819: 0.110 0.0001944 0.0000092 2035 6.78 4.256 0.251 2014-09-23T22:27:22.131739904 INFO 2025-06-26 20:30:55,240 calibrate.py _nudge_pos():1806 [1] 846: 0.100 -0.0000095 -0.0000170 35 0.11 -12.424 -27.823 2014-09-23T22:27:55.139478784 INFO 2025-06-26 20:30:55,418 calibrate.py _nudge_pos():1806 [1] 864: 0.100 0.0000311 -0.0000049 35 0.11 40.751 -8.017 2014-09-23T22:28:19.137834496 INFO 2025-06-26 20:30:55,603 calibrate.py _nudge_pos():1806 [1] 884: 0.100 -0.0007886 0.0000938 2080 6.93 -16.893 2.507 2014-09-23T22:35:34.138034944 INFO 2025-06-26 20:30:55,881 calibrate.py _nudge_pos():1806 [1] 913: 0.100 -0.0000010 -0.0000678 25 0.08 -1.913 -156.951 2014-09-23T22:36:07.135774720 INFO 2025-06-26 20:30:56,353 calibrate.py _nudge_pos():1806 [1] 963: 0.110 -0.0002345 0.0000400 820 2.73 -12.753 2.712 2014-09-23T22:39:40.131183360 INFO 2025-06-26 20:30:56,798 calibrate.py _nudge_pos():1806 [1] 1010: 0.100 -0.0000104 -0.0000093 80 0.26 -5.859 -6.522 2014-09-23T22:40:42.136935680 INFO 2025-06-26 20:30:57,137 calibrate.py _nudge_pos():1806 [1] 1047: 0.100 -0.0006337 0.0003622 2025 6.75 -13.943 9.949 2014-09-23T22:48:04.136656640 INFO 2025-06-26 20:30:57,192 calibrate.py _nudge_pos():1806 [1] 1053: 0.110 -0.0000137 -0.0000339 60 0.20 -10.367 -31.969 2014-09-23T22:48:21.135492096 INFO 2025-06-26 20:30:57,613 calibrate.py _nudge_pos():1806 [1] 1099: 0.110 -0.0000041 -0.0000120 25 0.08 -7.547 -27.797 2014-09-23T22:49:11.132067328 INFO 2025-06-26 20:30:57,855 calibrate.py _nudge_pos():1806 [1] 1125: 0.110 -0.0008795 0.0001292 2450 8.16 -15.993 2.933 2014-09-23T22:57:46.136786944 INFO 2025-06-26 20:30:58,227 calibrate.py _nudge_pos():1862 [1] 1117: - - - 3 0.01 - - INFO 2025-06-26 20:30:58,227 calibrate.py _nudge_pos():1868 [1] Points in final series = 30333 INFO 2025-06-26 20:30:58,522 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:30:58,767 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:30:58,955 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:30:58,957 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2014.266.05/ctd1.nc INFO 2025-06-26 20:30:58,958 calibrate.py _range_qc_combined_nc():898 [1] Setting 2 ctd1_salinity values to NaN INFO 2025-06-26 20:30:58,958 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 20:30:58,958 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:30:59,185 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:30:59,368 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:30:59,370 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2014.266.05/ctd2.nc INFO 2025-06-26 20:30:59,371 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:30:59,371 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 20:30:59,371 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 20:30:59,602 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:30:59,858 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60 61 62 63 64 65 66] INFO 2025-06-26 20:30:59,915 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -3 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:31:05,442 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2014.266.05 INFO 2025-06-26 20:31:05,470 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2014.266.05/dorado_2014.266.05_cal.nc INFO 2025-06-26 20:31:05,574 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 20:31:05,580 process.py align():251 [1] Alignment steps for 2014.266.05 INFO 2025-06-26 20:31:05,610 align.py process_cal():139 [1] Processing dorado_2014.266.05_cal.nc from /data/auv_data/dorado/missionnetcdfs/2014.266.05 INFO 2025-06-26 20:31:05,622 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:31:05,624 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:31:05,652 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:31:05,655 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:31:05,681 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:31:05,684 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:31:05,699 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:31:05,700 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:31:05,710 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:31:05,713 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:31:05,739 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:05,741 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:05,766 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:05,768 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:05,792 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:05,794 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:05,818 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:05,820 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:05,844 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:05,847 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:05,872 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:05,875 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:05,899 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:05,902 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:05,927 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:05,930 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:05,955 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:05,958 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:05,983 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:05,986 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:06,010 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:06,013 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:06,038 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:06,041 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:06,066 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:06,069 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:06,093 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:06,095 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:06,120 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:06,122 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:06,147 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:06,150 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:06,175 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:06,177 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:06,202 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:06,205 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:06,230 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:06,233 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:06,258 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:06,262 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:06,288 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:06,291 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:06,317 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2014.266.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:31:06,320 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:31:06,352 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:31:06,379 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:31:06,403 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 20:31:06,432 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:31:06,459 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:31:06,498 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 59.00 INFO 2025-06-26 20:31:06,675 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:31:06,702 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:31:06,732 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:31:06,759 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:31:06,786 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:31:06,812 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:31:06,836 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2014.266.05/dorado_2014.266.05_align.nc INFO 2025-06-26 20:31:06,926 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 20:31:06,928 process.py resample():273 [1] Resampling steps for 2014.266.05 INFO 2025-06-26 20:31:06,929 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:31:06,960 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.266.05/dorado_2014.266.05_align.nc mission netCDF file INFO 2025-06-26 20:31:06,966 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.266.05/dorado_2014.266.05_align.nc mission netCDF file INFO 2025-06-26 20:31:06,967 resample.py get_mission_start_end():1145 [1] navigation: 2014-09-23T21:17:18.349718528 to 2014-09-23T22:58:24.734142720 (0 days 01:51:57.508631552 before mission_end) WARNING 2025-06-26 20:31:06,968 resample.py get_mission_start_end():1156 [1] Instrument navigation has a gap > 5 minutes at the end of the mission: 0 days 01:51:57.508631552 INFO 2025-06-26 20:31:06,969 resample.py get_mission_start_end():1145 [1] hs2 : 2014-09-23T21:16:38.572443392 to 2014-09-23T22:58:24.754141440 (0 days 01:51:57.488632832 before mission_end) WARNING 2025-06-26 20:31:06,970 resample.py get_mission_start_end():1156 [1] Instrument hs2 has a gap > 5 minutes at the end of the mission: 0 days 01:51:57.488632832 INFO 2025-06-26 20:31:06,971 resample.py get_mission_start_end():1145 [1] ctd1 : 2014-09-23T21:16:58.351088640 to 2014-09-23T22:58:24.734142720 (0 days 01:51:57.508631552 before mission_end) WARNING 2025-06-26 20:31:06,972 resample.py get_mission_start_end():1156 [1] Instrument ctd1 has a gap > 5 minutes at the end of the mission: 0 days 01:51:57.508631552 INFO 2025-06-26 20:31:06,973 resample.py get_mission_start_end():1145 [1] ctd2 : 2014-09-23T21:16:58.331089920 to 2014-09-23T22:58:24.734142720 (0 days 01:51:57.508631552 before mission_end) WARNING 2025-06-26 20:31:06,973 resample.py get_mission_start_end():1156 [1] Instrument ctd2 has a gap > 5 minutes at the end of the mission: 0 days 01:51:57.508631552 INFO 2025-06-26 20:31:06,974 resample.py get_mission_start_end():1145 [1] isus : 2014-09-23T21:17:31.558813696 to 2014-09-23T22:58:24.764140544 (0 days 01:51:57.478633728 before mission_end) WARNING 2025-06-26 20:31:06,975 resample.py get_mission_start_end():1156 [1] Instrument isus has a gap > 5 minutes at the end of the mission: 0 days 01:51:57.478633728 INFO 2025-06-26 20:31:06,976 resample.py get_mission_start_end():1145 [1] biolume : 2014-09-23T21:16:30.992928512 to 2014-09-23T22:58:24.284139520 (0 days 01:51:57.958634752 before mission_end) WARNING 2025-06-26 20:31:06,977 resample.py get_mission_start_end():1156 [1] Instrument biolume has a gap > 5 minutes at the end of the mission: 0 days 01:51:57.958634752 INFO 2025-06-26 20:31:06,978 resample.py get_mission_start_end():1145 [1] lopc : 2014-09-23T23:08:41.742774272 to 2014-09-24T00:50:22.242774272 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:31:06,980 resample.py get_mission_start_end():1145 [1] tailcone : 2014-09-23T21:16:36.152609280 to 2014-09-23T22:58:24.744142080 (0 days 01:51:57.498632192 before mission_end) WARNING 2025-06-26 20:31:06,981 resample.py get_mission_start_end():1156 [1] Instrument tailcone has a gap > 5 minutes at the end of the mission: 0 days 01:51:57.498632192 INFO 2025-06-26 20:31:06,981 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2014.266.05/dorado_2014.266.05_align.nc mission netCDF file INFO 2025-06-26 20:31:06,982 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,073 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,073 resample.py resample_variable():1038 [1] Padding navigation_roll with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,094 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,094 resample.py resample_variable():1038 [1] Padding navigation_pitch with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,114 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,114 resample.py resample_variable():1038 [1] Padding navigation_yaw with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,135 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,135 resample.py resample_variable():1038 [1] Padding navigation_mWaterSpeed with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,155 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,155 resample.py resample_variable():1038 [1] Padding hs2_bbp420 with 0 days 01:51:57.488632832 of NaNs to the end of mission INFO 2025-06-26 20:31:07,176 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,176 resample.py resample_variable():1038 [1] Padding hs2_bbp700 with 0 days 01:51:57.488632832 of NaNs to the end of mission INFO 2025-06-26 20:31:07,196 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,196 resample.py resample_variable():1038 [1] Padding hs2_fl700 with 0 days 01:51:57.488632832 of NaNs to the end of mission INFO 2025-06-26 20:31:07,214 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,215 resample.py resample_variable():1038 [1] Padding ctd1_temperature with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,232 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,232 resample.py resample_variable():1038 [1] Padding ctd1_conductivity with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,248 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,249 resample.py resample_variable():1038 [1] Padding ctd1_salinity with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,266 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,266 resample.py resample_variable():1038 [1] Padding ctd1_temperature_onboard with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,283 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,283 resample.py resample_variable():1038 [1] Padding ctd1_conductivity_onboard with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,299 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,300 resample.py resample_variable():1038 [1] Padding ctd1_salinity_onboard with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,317 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,317 resample.py resample_variable():1038 [1] Padding ctd1_dissolvedO2 with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,334 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,334 resample.py resample_variable():1038 [1] Padding ctd1_oxygen_mll with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,350 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,351 resample.py resample_variable():1038 [1] Padding ctd1_oxygen_umolkg with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,368 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,368 resample.py resample_variable():1038 [1] Padding ctd1_flow1 with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,387 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,387 resample.py resample_variable():1038 [1] Padding ctd2_temperature with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,405 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,406 resample.py resample_variable():1038 [1] Padding ctd2_conductivity with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,424 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,424 resample.py resample_variable():1038 [1] Padding ctd2_salinity with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,442 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,442 resample.py resample_variable():1038 [1] Padding ctd2_temperature_onboard with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,460 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,460 resample.py resample_variable():1038 [1] Padding ctd2_conductivity_onboard with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,479 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,479 resample.py resample_variable():1038 [1] Padding ctd2_salinity_onboard with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,496 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,497 resample.py resample_variable():1038 [1] Padding ctd2_flow2 with 0 days 01:51:57.508631552 of NaNs to the end of mission INFO 2025-06-26 20:31:07,509 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,510 resample.py resample_variable():1038 [1] Padding isus_nitrate with 0 days 01:51:57.478633728 of NaNs to the end of mission INFO 2025-06-26 20:31:07,522 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,522 resample.py resample_variable():1038 [1] Padding isus_temp with 0 days 01:51:57.478633728 of NaNs to the end of mission INFO 2025-06-26 20:31:07,533 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,533 resample.py resample_variable():1038 [1] Padding isus_quality with 0 days 01:51:57.478633728 of NaNs to the end of mission INFO 2025-06-26 20:31:07,544 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,544 resample.py resample_variable():1038 [1] Padding biolume_flow with 0 days 01:51:57.958634752 of NaNs to the end of mission INFO 2025-06-26 20:31:07,554 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,554 resample.py resample_variable():1038 [1] Padding biolume_avg_biolume with 0 days 01:51:57.958634752 of NaNs to the end of mission INFO 2025-06-26 20:31:07,559 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:31:07,559 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:31:07,799 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:31:07,859 resample.py add_biolume_proxies():633 [1] Zero flow values found: 6115 of 6115 - replaced with 350 ml/s INFO 2025-06-26 20:31:07,860 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:31:07,896 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:31:07,913 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:31:07,932 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:31:07,932 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:31:07,955 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,969 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,983 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:07,998 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:08,012 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:08,040 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:31:08,040 resample.py resample_variable():1038 [1] Padding tailcone_propRpm with 0 days 01:51:57.498632192 of NaNs to the end of mission INFO 2025-06-26 20:31:08,327 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2014.266.05/dorado_2014.266.05_1S.nc INFO 2025-06-26 20:31:10,938 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:31:37,473 create_products.py gulper_odv():522 [1] Wrote 20 Gulper data lines to /data/auv_data/dorado/missionodvs/2014.266.05/dorado_2014.266.05_1S_Gulper.txt INFO 2025-06-26 20:31:37,474 process.py archive():337 [1] Archiving steps for 2014.266.05 INFO 2025-06-26 20:31:37,474 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2014.266.05/dorado_2014.266.05, BASE_PATH = /data/auv_data INFO 2025-06-26 20:31:37,476 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2014.266.05/dorado_2014.266.05 files to /Volumes/AUVCTD/surveys/2014/netcdf INFO 2025-06-26 20:31:37,477 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.266.05_1S.nc INFO 2025-06-26 20:31:37,491 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.266.05/dorado_2014.266.05_1S.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:31:37,492 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.266.05_cal.nc INFO 2025-06-26 20:31:37,545 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.266.05/dorado_2014.266.05_cal.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:31:37,546 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2014/netcdf/dorado_2014.266.05_align.nc INFO 2025-06-26 20:31:37,624 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.266.05/dorado_2014.266.05_align.nc /Volumes/AUVCTD/surveys/2014/netcdf done. INFO 2025-06-26 20:31:37,640 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.266.05/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014266/2014.266.05 done. INFO 2025-06-26 20:31:37,654 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.266.05/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014266/2014.266.05 done. INFO 2025-06-26 20:31:37,661 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.266.05/gps.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014266/2014.266.05 done. INFO 2025-06-26 20:31:37,673 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.266.05/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014266/2014.266.05 done. INFO 2025-06-26 20:31:37,702 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.266.05/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014266/2014.266.05 done. INFO 2025-06-26 20:31:37,708 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.266.05/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014266/2014.266.05 done. INFO 2025-06-26 20:31:37,723 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.266.05/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014266/2014.266.05 done. INFO 2025-06-26 20:31:37,735 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.266.05/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014266/2014.266.05 done. INFO 2025-06-26 20:31:37,761 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.266.05/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014266/2014.266.05 done. INFO 2025-06-26 20:31:37,790 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.266.05/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2014/2014266/2014.266.05 done. INFO 2025-06-26 20:31:37,791 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:31:37,792 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2014/odv/dorado_2014.266.05_1S_Gulper.txt INFO 2025-06-26 20:31:37,798 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2014.266.05/dorado_2014.266.05_1S_Gulper.txt /Volumes/AUVCTD/surveys/2014/odv done. INFO 2025-06-26 20:31:37,799 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2014.266.05/dorado_2014.266.05_processing.log /Volumes/AUVCTD/surveys/2014/netcdf