INFO 2025-06-26 15:28:01,839 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 15:28:01,839 process.py process_mission():434 [1] dorado_info[mission]["comment"] = AUVCTD mission - Kanna mission - Even though the thursdays runs (3 of them) are very short (~30mn each) the first one at leas had the gulper fired so it is of relevance for further science analysis. - ctdToUse = ctd1 INFO 2025-06-26 15:28:01,839 process.py process_mission():449 [1] Processing AUVCTD mission 2009.309.03 by user docker_user on host eae60d30a712 INFO 2025-06-26 15:28:01,839 process.py download_process():165 [1] Download and processing steps for 2009.309.03 INFO 2025-06-26 15:28:01,839 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2009/2009309/2009.309.03 INFO 2025-06-26 15:28:01,840 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2009/2009309/2009.309.03 to /data/auv_data/dorado/missionlogs/2009.309.03 INFO 2025-06-26 15:28:03,177 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2009.309.03 INFO 2025-06-26 15:28:03,177 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.309.03/ctdDriver.log (706510 bytes) INFO 2025-06-26 15:28:03,238 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.309.03/ctdDriver2.log (706061 bytes) INFO 2025-06-26 15:28:03,299 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.309.03/gps.log (20732 bytes) INFO 2025-06-26 15:28:03,308 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.309.03/hydroscatlog.log (681094 bytes) INFO 2025-06-26 15:28:03,386 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.309.03/navigation.log (2362958 bytes) INFO 2025-06-26 15:28:03,568 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.309.03/isuslog.log (46325 bytes) INFO 2025-06-26 15:28:03,577 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.309.03/parosci.log (833078 bytes) INFO 2025-06-26 15:28:03,651 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.309.03/tailCone.log (106747 bytes) INFO 2025-06-26 15:28:03,671 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2009.309.03/biolume.log (556108 bytes) INFO 2025-06-26 15:28:03,732 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 15:28:03,767 logs2netcdfs.py download_process_logs():807 [1] Time to process: 0.59 seconds INFO 2025-06-26 15:28:03,767 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2009.309.03/lopc.bin (1231816 bytes) INFO 2025-06-26 15:28:03,767 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 15:28:03 2025 INFO 2025-06-26 15:28:03,767 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2009.309.03/parosci.nc INFO 2025-06-26 15:28:03,767 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 15:28:03,767 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2009.309.03/parosci.nc INFO 2025-06-26 15:28:03,769 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1257447894.8, sensor_off_time = 1257449927.1 INFO 2025-06-26 15:28:03,769 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 2032 seconds. Expecting to read 4064 L frames from the lopc.bin file. INFO 2025-06-26 15:28:03,769 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 4064 records from the lopc.bin file. INFO 2025-06-26 15:28:03,794 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2009-11-05 19:04:54 Z and endTime = 2009-11-05 19:38:47 Z with 4064 records expected to be read from lopc.bin INFO 2025-06-26 15:28:03,794 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2009.309.03/lopc.bin INFO 2025-06-26 15:28:03,794 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2009.309.03/lopc.nc INFO 2025-06-26 15:28:03,794 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2009.309.03/lopc.nc INFO 2025-06-26 15:28:03,795 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2009.309.03 INFO 2025-06-26 15:28:03,795 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2025-06-26 15:28:03,826 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 15:28:03,826 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 15:28:03,826 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-26 15:28:05,105 lopcToNetCDF.py main():2345 [1] >>> Done reading file. INFO 2025-06-26 15:28:05,105 lopcToNetCDF.py main():2346 [1] lFrameCount = 4037, mFrameCount = 2082 INFO 2025-06-26 15:28:05,105 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2009.309.03/parosci.nc INFO 2025-06-26 15:28:05,105 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 15:28:05,105 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2009.309.03/parosci.nc INFO 2025-06-26 15:28:05,107 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1257447894.8, sensor_off_time = 1257449927.1 INFO 2025-06-26 15:28:05,107 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 2032 seconds. Expecting to read 4064 L frames from the lopc.bin file. INFO 2025-06-26 15:28:05,107 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 4064 records from the lopc.bin file. INFO 2025-06-26 15:28:05,107 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 20747 and len(sampleCountList) = 4069 INFO 2025-06-26 15:28:05,107 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [] INFO 2025-06-26 15:28:05,107 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [20747 20748 20749 ... 25358 25359 25360] INFO 2025-06-26 15:28:05,108 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 15:28:05,108 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-26 15:28:05,108 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [1 1 1 ... 1 1 1] INFO 2025-06-26 15:28:05,108 lopcToNetCDF.py deSpike():1590 [1] Found 1 spike indicators at indices: [7] INFO 2025-06-26 15:28:05,108 lopcToNetCDF.py deSpike():1595 [1] Identifying nature of spike value = 21299 at index = 7 INFO 2025-06-26 15:28:05,108 lopcToNetCDF.py deSpike():1714 [1] This is the last element in spike_indx. No need to deSpike(). INFO 2025-06-26 15:28:05,108 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [20747 20748 20749 ... 25358 25359 25360] INFO 2025-06-26 15:28:05,108 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [20747 20748 20749 ... 25358 25359 25360] with len(correctedSampleCountList) = 4069 INFO 2025-06-26 15:28:05,108 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 20747 from all values of correctedSampleCountList INFO 2025-06-26 15:28:05,108 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 15:28:05,108 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [0.0000e+00 5.0000e-01 1.0000e+00 ... 2.3055e+03 2.3060e+03 2.3065e+03] INFO 2025-06-26 15:28:05,109 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.25744789e+09 1.25744790e+09 1.25744790e+09 ... 1.25745020e+09 1.25745020e+09 1.25745020e+09] INFO 2025-06-26 15:28:05,109 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1257447894.8 1257447895.3, ..., timestampArray[-2:] = 1257450200.8 1257450201.3] INFO 2025-06-26 15:28:05,114 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1257447894.8213723), np.float64(1257447895.3213723)], ..., timestampList[-2:] = [np.float64(1257450200.8213723), np.float64(1257450201.3213723)]] INFO 2025-06-26 15:28:05,114 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 4069) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 15:28:05,114 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [4010, 4031] INFO 2025-06-26 15:28:05,114 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 192 INFO 2025-06-26 15:28:05,114 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 4069 INFO 2025-06-26 15:28:05,114 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1257447894.8213723), np.float64(1257447895.3213723)], ..., timestampList[-2:] = [np.float64(1257450200.8213723), np.float64(1257450201.3213723)]] INFO 2025-06-26 15:28:05,114 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 4069) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 15:28:05,114 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(4009), np.int32(4030)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 15:28:05,114 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 192 INFO 2025-06-26 15:28:05,114 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 ERROR 2025-06-26 15:28:05,115 lopcToNetCDF.py constructTimestampList():1501 [1] Cannot interpolate to cFrameEsecsListInterpolated: array of sample points is empty INFO 2025-06-26 15:28:05,118 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 192 INFO 2025-06-26 15:28:05,118 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1257448176.8213723)], ..., tsList[-2:] = [np.float64(1257450171.8213723), np.float64(1257450182.3213723)] INFO 2025-06-26 15:28:05,118 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2009-11-05 19:09:36 Z INFO 2025-06-26 15:28:05,118 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2009-11-05 19:43:02 Z INFO 2025-06-26 15:28:05,119 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 4037 INFO 2025-06-26 15:28:05,119 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [-9999], ..., cFrameEsecsList[-2:] = [-9999, -9999] INFO 2025-06-26 15:28:05,119 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 1969-12-31 21:13:21 Z INFO 2025-06-26 15:28:05,119 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 1969-12-31 21:13:21 Z INFO 2025-06-26 15:28:05,122 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2009.309.03/lopc.nc INFO 2025-06-26 15:28:05,122 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 15:28:05 2025 Elapsed processing time from start of processing = 1 seconds INFO 2025-06-26 15:28:05,123 process.py calibrate():227 [1] Calibration steps for 2009.309.03 INFO 2025-06-26 15:28:05,203 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 15:28:05,204 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 15:28:05,883 calibrate.py _nudge_pos():1806 [1] 101: 0.110 0.0018815 -0.0000569 8800 29.33 9.522 -0.360 2009-11-05T19:35:52.494113024 INFO 2025-06-26 15:28:07,485 calibrate.py _nudge_pos():1862 [1] 242: - - - 3 0.01 - - INFO 2025-06-26 15:28:07,485 calibrate.py _nudge_pos():1868 [1] Points in final series = 10003 WARNING 2025-06-26 15:28:07,503 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 8.33 Hz INFO 2025-06-26 15:28:07,593 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 7 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 15:28:07,688 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:28:07,751 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 27 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 15:28:07,753 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2009.309.03/ctd1.nc INFO 2025-06-26 15:28:07,754 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 15:28:07,754 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 15:28:07,754 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 15:28:07,839 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 15:28:07,903 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 28 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 15:28:07,905 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2009.309.03/ctd2.nc INFO 2025-06-26 15:28:07,906 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 15:28:07,906 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 15:28:07,906 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 15:28:07,915 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 15:28:08,003 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 180 1800 2160 2161 2162 5280 8280 8281 11940 11941 12960 12961 18060 18061 18062 32460 32461 32462 34860 34861 34862 117180 117181 117182] INFO 2025-06-26 15:28:08,023 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -1 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 15:28:08,028 calibrate.py process_logs():3548 [1] Error processing biolume: missing variable "No variable named 'avg_biolume'. Variables on the dataset include ['time', 'rrr', 'cal_striing', 'pump', 'flow', 'humidity', 'temperature', 'time60hz', 'raw']" ERROR 2025-06-26 15:28:08,037 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2009.309.03 INFO 2025-06-26 15:28:08,042 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2009.309.03/dorado_2009.309.03_cal.nc INFO 2025-06-26 15:28:08,092 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_depth, biolume_flow, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, 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 15:28:08,097 process.py align():251 [1] Alignment steps for 2009.309.03 INFO 2025-06-26 15:28:08,121 align.py process_cal():139 [1] Processing dorado_2009.309.03_cal.nc from /data/auv_data/dorado/missionnetcdfs/2009.309.03 INFO 2025-06-26 15:28:08,128 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:28:08,130 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:28:08,145 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:28:08,147 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:28:08,161 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:28:08,163 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:28:08,171 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 15:28:08,171 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 15:28:08,176 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 15:28:08,178 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 15:28:08,192 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.309.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:28:08,194 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:28:08,207 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.309.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:28:08,209 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:28:08,222 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2009.309.03_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:28:08,224 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:28:08,237 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.309.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:28:08,239 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:28:08,254 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.309.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:28:08,256 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:28:08,269 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.309.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:28:08,271 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:28:08,285 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.309.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:28:08,287 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:28:08,300 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.309.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:28:08,303 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:28:08,316 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.309.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:28:08,319 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:28:08,332 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.309.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:28:08,334 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:28:08,348 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.309.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:28:08,350 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:28:08,364 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.309.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:28:08,366 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:28:08,379 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2009.309.03_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:28:08,381 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:28:08,395 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.309.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:28:08,397 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:28:08,411 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.309.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:28:08,413 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:28:08,427 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.309.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:28:08,429 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:28:08,443 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.309.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:28:08,446 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:28:08,460 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.309.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:28:08,462 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:28:08,477 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.309.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:28:08,479 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:28:08,493 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2009.309.03_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 15:28:08,495 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 15:28:08,513 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:28:08,528 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:28:08,544 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.73 INFO 2025-06-26 15:28:08,560 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 1.00 INFO 2025-06-26 15:28:08,576 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 15:28:08,593 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 15:28:08,608 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 15:28:08,624 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 15:28:08,640 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 15:28:08,656 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 1.09 INFO 2025-06-26 15:28:08,668 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2009.309.03/dorado_2009.309.03_align.nc INFO 2025-06-26 15:28:08,730 align.py write_netcdf():342 [1] Data variables written: biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_time, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, 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 15:28:08,733 process.py resample():273 [1] Resampling steps for 2009.309.03 INFO 2025-06-26 15:28:08,733 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 15:28:08,757 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.309.03/dorado_2009.309.03_align.nc mission netCDF file INFO 2025-06-26 15:28:08,763 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.309.03/dorado_2009.309.03_align.nc mission netCDF file INFO 2025-06-26 15:28:08,764 resample.py get_mission_start_end():1145 [1] navigation: 2009-11-05T19:05:26.549198592 to 2009-11-05T19:38:47.092152064 (0 days 00:04:15.229220096 before mission_end) INFO 2025-06-26 15:28:08,765 resample.py get_mission_start_end():1145 [1] hs2 : 2009-11-05T19:05:02.610838528 to 2009-11-05T19:38:47.122149888 (0 days 00:04:15.199222272 before mission_end) INFO 2025-06-26 15:28:08,766 resample.py get_mission_start_end():1145 [1] ctd1 : 2009-11-05T19:05:22.149500160 to 2009-11-05T19:38:47.042155520 (0 days 00:04:15.279216640 before mission_end) INFO 2025-06-26 15:28:08,767 resample.py get_mission_start_end():1145 [1] ctd2 : 2009-11-05T19:05:23.209427456 to 2009-11-05T19:38:47.142148608 (0 days 00:04:15.179223552 before mission_end) INFO 2025-06-26 15:28:08,769 resample.py get_mission_start_end():1145 [1] isus : 2009-11-05T19:06:08.526323200 to 2009-11-05T19:38:46.392199936 (0 days 00:04:15.929172224 before mission_end) INFO 2025-06-26 15:28:08,770 resample.py get_mission_start_end():1145 [1] biolume : 2009-11-05T19:04:54.021392896 to 2009-11-05T19:38:46.412164352 (0 days 00:04:15.909207808 before mission_end) INFO 2025-06-26 15:28:08,771 resample.py get_mission_start_end():1145 [1] lopc : 2009-11-05T19:09:36.821372160 to 2009-11-05T19:43:02.321372160 (0 days 00:00:00 before mission_end) INFO 2025-06-26 15:28:08,772 resample.py get_mission_start_end():1145 [1] tailcone : 2009-11-05T19:04:59.061081600 to 2009-11-05T19:38:46.962161152 (0 days 00:04:15.359211008 before mission_end) INFO 2025-06-26 15:28:08,773 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2009.309.03/dorado_2009.309.03_align.nc mission netCDF file INFO 2025-06-26 15:28:08,773 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:08,820 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:08,831 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:08,842 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:08,852 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:08,863 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:08,874 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:08,885 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:08,896 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:08,905 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:08,914 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:08,923 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:08,932 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:08,941 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:08,950 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:08,959 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:08,968 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:08,978 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:08,988 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:08,999 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:09,010 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:09,020 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:09,030 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:09,040 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:09,049 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:09,057 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:09,066 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:09,075 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:09,082 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:09,090 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:09,098 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:09,106 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:09,116 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 15:28:09,233 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2009.309.03/dorado_2009.309.03_1S.nc INFO 2025-06-26 15:28:10,804 create_products.py gulper_odv():401 [1] No gulper times found for 2009.309.03 INFO 2025-06-26 15:28:10,804 process.py archive():337 [1] Archiving steps for 2009.309.03 INFO 2025-06-26 15:28:10,804 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2009.309.03/dorado_2009.309.03, BASE_PATH = /data/auv_data INFO 2025-06-26 15:28:10,804 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2009.309.03/dorado_2009.309.03 files to /Volumes/AUVCTD/surveys/2009/netcdf INFO 2025-06-26 15:28:10,806 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.309.03_1S.nc INFO 2025-06-26 15:28:10,814 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.03/dorado_2009.309.03_1S.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:28:10,815 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.309.03_cal.nc INFO 2025-06-26 15:28:10,829 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.03/dorado_2009.309.03_cal.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:28:10,830 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2009/netcdf/dorado_2009.309.03_align.nc INFO 2025-06-26 15:28:10,842 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.03/dorado_2009.309.03_align.nc /Volumes/AUVCTD/surveys/2009/netcdf done. INFO 2025-06-26 15:28:10,850 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.03/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009309/2009.309.03 done. INFO 2025-06-26 15:28:10,857 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.03/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009309/2009.309.03 done. INFO 2025-06-26 15:28:10,861 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.03/gps.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009309/2009.309.03 done. INFO 2025-06-26 15:28:10,867 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.03/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009309/2009.309.03 done. INFO 2025-06-26 15:28:10,877 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.03/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009309/2009.309.03 done. INFO 2025-06-26 15:28:10,881 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.03/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009309/2009.309.03 done. INFO 2025-06-26 15:28:10,889 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.03/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009309/2009.309.03 done. INFO 2025-06-26 15:28:10,894 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.03/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009309/2009.309.03 done. INFO 2025-06-26 15:28:10,904 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.03/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009309/2009.309.03 done. INFO 2025-06-26 15:28:10,915 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.03/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2009/2009309/2009.309.03 done. INFO 2025-06-26 15:28:10,915 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 15:28:10,915 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2009.309.03/dorado_2009.309.03_processing.log /Volumes/AUVCTD/surveys/2009/netcdf