INFO 2024-04-04 09:32:04,926 process.py process_mission():385 [37276] self.commandline = 'src/data/process_dorado.py --mission 2022.201.00 -v' INFO 2024-04-04 09:32:04,926 process.py process_mission():390 [37276] dorado_info[mission]["comment"] = 'Monterey Bay Diamond Mission - 20122G - ctdToUse = ctd1 ' INFO 2024-04-04 09:32:04,926 process.py process_mission():402 [37276] Processing Monterey Bay Diamond mission 2022.201.00 by user mccann on host MBARI2597.wifi.mbari.org INFO 2024-04-04 09:32:04,926 process.py download_process():152 [37276] Download and processing steps for 2022.201.00 INFO 2024-04-04 09:32:04,926 logs2netcdfs.py download_process_logs():664 [37276] src_dir = '/Volumes/AUVCTD/missionlogs/2022/2022201/2022.201.00' INFO 2024-04-04 09:32:04,926 logs2netcdfs.py download_process_logs():692 [37276] Rsyncing /Volumes/AUVCTD/missionlogs/2022/2022201/2022.201.00 to /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2022.201.00 INFO 2024-04-04 09:34:37,690 logs2netcdfs.py download_process_logs():700 [37276] Processing mission: dorado 2022.201.00 INFO 2024-04-04 09:34:37,691 logs2netcdfs.py download_process_logs():709 [37276] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2022.201.00/ctdDriver.log (28659654 bytes) INFO 2024-04-04 09:34:39,624 logs2netcdfs.py download_process_logs():709 [37276] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2022.201.00/ctdDriver2.log (28659549 bytes) INFO 2024-04-04 09:34:41,546 logs2netcdfs.py download_process_logs():709 [37276] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2022.201.00/gps.log (1457996 bytes) INFO 2024-04-04 09:34:41,687 logs2netcdfs.py download_process_logs():709 [37276] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2022.201.00/hydroscatlog.log (25070326 bytes) INFO 2024-04-04 09:34:43,933 logs2netcdfs.py download_process_logs():709 [37276] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2022.201.00/navigation.log (110438702 bytes) INFO 2024-04-04 09:34:51,286 logs2netcdfs.py download_process_logs():709 [37276] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2022.201.00/parosci.log (35663798 bytes) INFO 2024-04-04 09:34:53,840 logs2netcdfs.py download_process_logs():709 [37276] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2022.201.00/FLBBCD2K.log (27947223 bytes) INFO 2024-04-04 09:34:56,970 logs2netcdfs.py _process_log_file():644 [37276] Non-monotonic increasing time indices in /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2022.201.00/FLBBCD2K.log: [ 2 3642 3643 329425 329429 495983 495996 679182 679184 679185 708554 708561] INFO 2024-04-04 09:34:57,053 logs2netcdfs.py download_process_logs():709 [37276] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2022.201.00/tailCone.log (17908235 bytes) WARNING 2024-04-04 09:34:58,597 logs2netcdfs.py _create_variable():493 [37276] rudderCurrent: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (373078,) and arg 1 with shape (373077,). INFO 2024-04-04 09:34:58,597 logs2netcdfs.py _create_variable():494 [37276] len(data) (373077) does not match shape of rudderCurrent.shape[0] (373078) WARNING 2024-04-04 09:34:58,597 logs2netcdfs.py _create_variable():499 [37276] rudderCurrent data is short by one, appending the last value: 0 WARNING 2024-04-04 09:34:58,616 logs2netcdfs.py _create_variable():493 [37276] propCurrent1: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (373078,) and arg 1 with shape (373077,). INFO 2024-04-04 09:34:58,616 logs2netcdfs.py _create_variable():494 [37276] len(data) (373077) does not match shape of propCurrent1.shape[0] (373078) WARNING 2024-04-04 09:34:58,616 logs2netcdfs.py _create_variable():499 [37276] propCurrent1 data is short by one, appending the last value: 0.0 WARNING 2024-04-04 09:34:58,635 logs2netcdfs.py _create_variable():493 [37276] propCurrent2: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (373078,) and arg 1 with shape (373077,). INFO 2024-04-04 09:34:58,635 logs2netcdfs.py _create_variable():494 [37276] len(data) (373077) does not match shape of propCurrent2.shape[0] (373078) WARNING 2024-04-04 09:34:58,635 logs2netcdfs.py _create_variable():499 [37276] propCurrent2 data is short by one, appending the last value: 0 WARNING 2024-04-04 09:34:58,654 logs2netcdfs.py _create_variable():493 [37276] propRpm: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (373078,) and arg 1 with shape (373077,). INFO 2024-04-04 09:34:58,654 logs2netcdfs.py _create_variable():494 [37276] len(data) (373077) does not match shape of propRpm.shape[0] (373078) WARNING 2024-04-04 09:34:58,654 logs2netcdfs.py _create_variable():499 [37276] propRpm data is short by one, appending the last value: 0 WARNING 2024-04-04 09:34:58,676 logs2netcdfs.py _create_variable():493 [37276] elevatorAngle: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (373078,) and arg 1 with shape (373077,). INFO 2024-04-04 09:34:58,677 logs2netcdfs.py _create_variable():494 [37276] len(data) (373077) does not match shape of elevatorAngle.shape[0] (373078) WARNING 2024-04-04 09:34:58,677 logs2netcdfs.py _create_variable():499 [37276] elevatorAngle data is short by one, appending the last value: 0.00852570403367281 WARNING 2024-04-04 09:34:58,701 logs2netcdfs.py _create_variable():493 [37276] rudderAngle: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (373078,) and arg 1 with shape (373077,). INFO 2024-04-04 09:34:58,701 logs2netcdfs.py _create_variable():494 [37276] len(data) (373077) does not match shape of rudderAngle.shape[0] (373078) WARNING 2024-04-04 09:34:58,701 logs2netcdfs.py _create_variable():499 [37276] rudderAngle data is short by one, appending the last value: 0.17032304406166077 WARNING 2024-04-04 09:34:58,720 logs2netcdfs.py _create_variable():493 [37276] propPwm: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (373078,) and arg 1 with shape (373077,). INFO 2024-04-04 09:34:58,720 logs2netcdfs.py _create_variable():494 [37276] len(data) (373077) does not match shape of propPwm.shape[0] (373078) WARNING 2024-04-04 09:34:58,720 logs2netcdfs.py _create_variable():499 [37276] propPwm data is short by one, appending the last value: 0 WARNING 2024-04-04 09:34:58,733 logs2netcdfs.py _create_variable():493 [37276] propTemp: shape mismatch: objects cannot be broadcast to a single shape. Mismatch is between arg 0 with shape (373078,) and arg 1 with shape (373077,). INFO 2024-04-04 09:34:58,733 logs2netcdfs.py _create_variable():494 [37276] len(data) (373077) does not match shape of propTemp.shape[0] (373078) WARNING 2024-04-04 09:34:58,733 logs2netcdfs.py _create_variable():499 [37276] propTemp data is short by one, appending the last value: 0 INFO 2024-04-04 09:34:59,068 logs2netcdfs.py download_process_logs():709 [37276] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2022.201.00/biolume.log (20847158 bytes) INFO 2024-04-04 09:35:00,924 logs2netcdfs.py write_variables():523 [37276] Expanding original timeTag to time60Hz variable for raw data INFO 2024-04-04 09:35:01,470 logs2netcdfs.py download_process_logs():726 [37276] Time to process: 23.78 seconds INFO 2024-04-04 09:35:01,470 process.py download_process():181 [37276] Processing file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2022.201.00/lopc.bin (60407356 bytes) INFO 2024-04-04 09:35:01,471 lopcToNetCDF.py main():2282 [37276] Processing begun: Thu Apr 4 09:35:01 2024 INFO 2024-04-04 09:35:01,471 lopcToNetCDF.py constructTimestampList():1300 [37276] parosci_nc = /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/parosci.nc INFO 2024-04-04 09:35:01,471 lopcToNetCDF.py constructTimestampList():1301 [37276] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2024-04-04 09:35:01,471 lopcToNetCDF.py constructTimestampList():1304 [37276] /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/parosci.nc INFO 2024-04-04 09:35:01,474 lopcToNetCDF.py constructTimestampList():1321 [37276] From associated parosci.nc file: sensor_on_time = 1658347109.3, sensor_off_time = 1658421764.9 INFO 2024-04-04 09:35:01,474 lopcToNetCDF.py constructTimestampList():1325 [37276] Duration is 74655 seconds. Expecting to read 149310 L frames from the lopc.bin file. INFO 2024-04-04 09:35:01,474 lopcToNetCDF.py constructTimestampList():1335 [37276] recCount not passed in, assuming we'll have 149310 records from the lopc.bin file. INFO 2024-04-04 09:35:02,068 lopcToNetCDF.py main():2304 [37276] Examined sibling parosci.nc file to find startTime = 2022-07-20 19:58:29 Z and endTime = 2022-07-21 16:42:44 Z with 149310 records expected to be read from lopc.bin INFO 2024-04-04 09:35:02,068 lopcToNetCDF.py unpackLOPCbin():727 [37276] >>> Unpacking LOPC data from /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionlogs/2022.201.00/lopc.bin INFO 2024-04-04 09:35:02,068 lopcToNetCDF.py unpackLOPCbin():728 [37276] >>> Will write to NetCDF file /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/lopc.nc WARNING 2024-04-04 09:35:02,069 lopcToNetCDF.py readCframeData():667 [37276] Unable to parse a float from the string str[:70] = A085129 WARNING 2024-04-04 09:35:02,069 lopcToNetCDF.py readCframeData():667 [37276] Unable to parse a float from the string str[:70] = INFO 2024-04-04 09:35:02,069 lopcToNetCDF.py openNetCDFFile():1858 [37276] Will output NetCDF file to /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/lopc.nc INFO 2024-04-04 09:35:02,069 lopcToNetCDF.py openNetCDFFile():1888 [37276] missionName = 2022.201.00 INFO 2024-04-04 09:35:02,070 lopcToNetCDF.py openNetCDFFile():1907 [37276] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 INFO 2024-04-04 09:35:02,107 lopcToNetCDF.py unpackLOPCbin():953 [37276] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2024-04-04 09:35:02,108 lopcToNetCDF.py unpackLOPCbin():971 [37276] Count Count Count Error Error Error Error Error INFO 2024-04-04 09:35:02,108 lopcToNetCDF.py unpackLOPCbin():989 [37276] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2024-04-04 09:35:06,038 lopcToNetCDF.py unpackLOPCbin():1019 [37276] 10000 19801 12761 0 0 0 0 0 4.0 seconds, last L Frame: 149310 INFO 2024-04-04 09:35:09,588 lopcToNetCDF.py unpackLOPCbin():1019 [37276] 20000 29801 22110 0 0 0 0 0 3.5 seconds, last L Frame: 149310 INFO 2024-04-04 09:35:13,016 lopcToNetCDF.py unpackLOPCbin():1019 [37276] 30000 39801 29659 0 0 0 0 0 3.4 seconds, last L Frame: 149310 INFO 2024-04-04 09:35:17,683 lopcToNetCDF.py unpackLOPCbin():1019 [37276] 40000 49801 45448 0 0 0 0 0 4.7 seconds, last L Frame: 149310 INFO 2024-04-04 09:35:21,152 lopcToNetCDF.py unpackLOPCbin():1019 [37276] 50000 59801 55796 0 0 0 0 0 3.5 seconds, last L Frame: 149310 INFO 2024-04-04 09:35:25,751 lopcToNetCDF.py unpackLOPCbin():1019 [37276] 60000 4265 71532 0 0 0 0 0 4.6 seconds, last L Frame: 149310 INFO 2024-04-04 09:35:29,736 lopcToNetCDF.py unpackLOPCbin():1019 [37276] 70000 14265 84153 0 0 0 0 0 4.0 seconds, last L Frame: 149310 INFO 2024-04-04 09:35:33,678 lopcToNetCDF.py unpackLOPCbin():1019 [37276] 80000 24265 96772 0 0 0 0 0 3.9 seconds, last L Frame: 149310 INFO 2024-04-04 09:35:37,546 lopcToNetCDF.py unpackLOPCbin():1019 [37276] 90000 34265 108815 0 0 0 0 0 3.9 seconds, last L Frame: 149310 INFO 2024-04-04 09:35:40,953 lopcToNetCDF.py unpackLOPCbin():1019 [37276] 100000 44265 117941 0 0 0 0 0 3.4 seconds, last L Frame: 149310 INFO 2024-04-04 09:35:44,480 lopcToNetCDF.py unpackLOPCbin():1019 [37276] 110000 54265 128169 0 0 0 0 0 3.5 seconds, last L Frame: 149310 INFO 2024-04-04 09:35:47,880 lopcToNetCDF.py unpackLOPCbin():1019 [37276] 120000 64265 137502 0 0 0 0 0 3.4 seconds, last L Frame: 149310 INFO 2024-04-04 09:35:51,208 lopcToNetCDF.py unpackLOPCbin():1019 [37276] 130000 8729 145455 0 0 0 0 0 3.3 seconds, last L Frame: 149310 INFO 2024-04-04 09:35:55,208 lopcToNetCDF.py unpackLOPCbin():1019 [37276] 140000 18729 157624 0 0 0 0 0 4.0 seconds, last L Frame: 149310 INFO 2024-04-04 09:35:58,705 lopcToNetCDF.py main():2327 [37276] >>> Done reading file. INFO 2024-04-04 09:35:58,705 lopcToNetCDF.py main():2328 [37276] lFrameCount = 149307, mFrameCount = 167844 INFO 2024-04-04 09:35:58,705 lopcToNetCDF.py constructTimestampList():1300 [37276] parosci_nc = /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/parosci.nc INFO 2024-04-04 09:35:58,705 lopcToNetCDF.py constructTimestampList():1301 [37276] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2024-04-04 09:35:58,705 lopcToNetCDF.py constructTimestampList():1304 [37276] /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/parosci.nc INFO 2024-04-04 09:35:58,710 lopcToNetCDF.py constructTimestampList():1321 [37276] From associated parosci.nc file: sensor_on_time = 1658347109.3, sensor_off_time = 1658421764.9 INFO 2024-04-04 09:35:58,710 lopcToNetCDF.py constructTimestampList():1325 [37276] Duration is 74655 seconds. Expecting to read 149310 L frames from the lopc.bin file. INFO 2024-04-04 09:35:58,710 lopcToNetCDF.py constructTimestampList():1335 [37276] recCount not passed in, assuming we'll have 149310 records from the lopc.bin file. INFO 2024-04-04 09:35:58,716 lopcToNetCDF.py constructTimestampList():1344 [37276] Calling correctSampleCountList() with sampleCountList[0] = 9802 and len(sampleCountList) = 149307 INFO 2024-04-04 09:35:58,723 lopcToNetCDF.py correctSampleCountList():1724 [37276] Found overflows at indices: [ 55734 121270] INFO 2024-04-04 09:35:58,723 lopcToNetCDF.py correctSampleCountList():1729 [37276] Assigning values from slice starting at index 55734, i = 1 INFO 2024-04-04 09:35:58,727 lopcToNetCDF.py correctSampleCountList():1729 [37276] Assigning values from slice starting at index 121270, i = 2 INFO 2024-04-04 09:35:58,728 lopcToNetCDF.py correctSampleCountList():1737 [37276] Original sampleCountList = [ 9802 9803 9804 ... 159108 159109 159110] INFO 2024-04-04 09:35:58,728 lopcToNetCDF.py correctSampleCountList():1738 [37276] Found 0 0 values at indices: [] INFO 2024-04-04 09:35:58,728 lopcToNetCDF.py correctSampleCountList():1774 [37276] Found 0 stuck values at indices: [] INFO 2024-04-04 09:35:58,729 lopcToNetCDF.py deSpike():1574 [37276] d_sampleCountList = [1 1 1 ... 1 1 1] INFO 2024-04-04 09:35:58,729 lopcToNetCDF.py deSpike():1576 [37276] Found 0 spike indicators at indices: [] INFO 2024-04-04 09:35:58,729 lopcToNetCDF.py correctSampleCountList():1803 [37276] After despike() sampleCountList = [ 9802 9803 9804 ... 159108 159109 159110] INFO 2024-04-04 09:35:58,729 lopcToNetCDF.py constructTimestampList():1349 [37276] correctSampleCountList() returned correctedSampleCountList = [ 9802 9803 9804 ... 159108 159109 159110] with len(correctedSampleCountList) = 149307 INFO 2024-04-04 09:35:58,729 lopcToNetCDF.py constructTimestampList():1356 [37276] Subtracting 9802 from all values of correctedSampleCountList INFO 2024-04-04 09:35:58,729 lopcToNetCDF.py constructTimestampList():1361 [37276] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2024-04-04 09:35:58,729 lopcToNetCDF.py constructTimestampList():1365 [37276] New re-zeroed correctedSampleCountList = [0.00000e+00 5.00000e-01 1.00000e+00 ... 7.46530e+04 7.46535e+04 7.46540e+04] INFO 2024-04-04 09:35:58,730 lopcToNetCDF.py constructTimestampList():1376 [37276] timestampArray = [1.65834711e+09 1.65834711e+09 1.65834711e+09 ... 1.65842176e+09 1.65842176e+09 1.65842176e+09] INFO 2024-04-04 09:35:58,730 lopcToNetCDF.py constructTimestampList():1377 [37276] timestampArray[:2] = [1658347109.3 1658347109.8, ..., timestampArray[-2:] = 1658421762.8 1658421763.3] INFO 2024-04-04 09:35:58,836 lopcToNetCDF.py constructTimestampList():1388 [37276] timestampList[:2] = [1658347109.342189, 1658347109.842189], ..., timestampList[-2:] = [1658421762.842189, 1658421763.342189]] INFO 2024-04-04 09:35:58,836 lopcToNetCDF.py constructTimestampList():1392 [37276] Subsampling correctedSampleCountList (len = 149307) according to what got written to the netCDF file by the binning interval INFO 2024-04-04 09:35:58,836 lopcToNetCDF.py constructTimestampList():1396 [37276] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [149267, 149288] INFO 2024-04-04 09:35:58,836 lopcToNetCDF.py constructTimestampList():1420 [37276] len(subSampledCorrectedSampleCountList) = 7109 INFO 2024-04-04 09:35:58,836 lopcToNetCDF.py constructTimestampList():1437 [37276] len(timestampList) = 149307 INFO 2024-04-04 09:35:58,836 lopcToNetCDF.py constructTimestampList():1438 [37276] timestampList[:2] = [1658347109.342189, 1658347109.842189], ..., timestampList[-2:] = [1658421762.842189, 1658421763.342189]] INFO 2024-04-04 09:35:58,836 lopcToNetCDF.py constructTimestampList():1443 [37276] Subsampling timestampList (len = 149307) according to what got written to the netCDF file by the binning interval INFO 2024-04-04 09:35:58,837 lopcToNetCDF.py constructTimestampList():1453 [37276] Taking indices [[19, 40] ... [149266, 149287]] from timestampList to create subSampledTimestampList INFO 2024-04-04 09:35:58,841 lopcToNetCDF.py constructTimestampList():1458 [37276] len(subSampledTimestampList) = 7109 INFO 2024-04-04 09:35:58,841 lopcToNetCDF.py constructTimestampList():1470 [37276] Finding elements of cFrameEsecsList that != -9999 INFO 2024-04-04 09:35:58,888 lopcToNetCDF.py closeNetCDFFile():2103 [37276] Writing time axis for len(tsList) = 7109 INFO 2024-04-04 09:35:58,888 lopcToNetCDF.py closeNetCDFFile():2106 [37276] tsList[:1] = [1658347118.842189], ..., tsList[-2:] = [1658421743.342189, 1658421753.842189] INFO 2024-04-04 09:35:58,888 lopcToNetCDF.py closeNetCDFFile():2109 [37276] Begin time = 2022-07-20 19:58:38 Z INFO 2024-04-04 09:35:58,888 lopcToNetCDF.py closeNetCDFFile():2113 [37276] End time = 2022-07-21 16:42:33 Z INFO 2024-04-04 09:35:58,888 lopcToNetCDF.py closeNetCDFFile():2118 [37276] Writing time axis for len(cFrameEsecsList) = 7109 INFO 2024-04-04 09:35:58,888 lopcToNetCDF.py closeNetCDFFile():2121 [37276] cFrameEsecsList[:1] = [1.65835202e+09], ..., cFrameEsecsList[-2:] = [1.65836110e+09 1.65836111e+09] INFO 2024-04-04 09:35:58,888 lopcToNetCDF.py closeNetCDFFile():2125 [37276] Begin time = 2022-07-20 21:20:15 Z INFO 2024-04-04 09:35:58,888 lopcToNetCDF.py closeNetCDFFile():2129 [37276] End time = 2022-07-20 23:51:53 Z INFO 2024-04-04 09:35:58,893 lopcToNetCDF.py main():2369 [37276] Created file: /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/lopc.nc INFO 2024-04-04 09:35:58,893 lopcToNetCDF.py main():2372 [37276] Processing finished: Thu Apr 4 09:35:58 2024 Elapsed processing time from start of processing = 57 seconds INFO 2024-04-04 09:35:58,896 process.py calibrate():206 [37276] Calibration steps for 2022.201.00 INFO 2024-04-04 09:35:59,351 calibrate.py _nudge_pos():1584 [37276] 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 2024-04-04 09:35:59,352 calibrate.py _nudge_pos():1608 [37276] - - - 0 0.00 - - - INFO 2024-04-04 09:35:59,863 calibrate.py _nudge_pos():1703 [37276] 117: 0.020 0.0002006 -0.0003865 446 1.48 20.066 -48.278 2022-07-20T20:01:51.418345984 INFO 2024-04-04 09:36:06,104 calibrate.py _nudge_pos():1703 [37276] 1229: 0.130 0.0012039 0.0005839 7114 23.71 7.533 4.563 2022-07-20T20:44:05.414755328 INFO 2024-04-04 09:36:08,456 calibrate.py _nudge_pos():1703 [37276] 1640: 0.180 0.0000589 -0.0000129 20 0.06 137.891 -37.777 2022-07-20T20:50:59.416394240 INFO 2024-04-04 09:36:08,462 calibrate.py _nudge_pos():1703 [37276] 1641: 0.100 0.0011393 -0.0006438 7291 24.30 6.958 -4.909 2022-07-20T21:15:17.616500736 INFO 2024-04-04 09:36:09,150 calibrate.py _nudge_pos():1703 [37276] 1759: 0.200 0.0008386 -0.0002445 6800 22.66 5.493 -1.999 2022-07-20T21:39:54.615319552 INFO 2024-04-04 09:36:11,162 calibrate.py _nudge_pos():1703 [37276] 2109: 0.160 0.0008609 -0.0002751 7180 23.93 5.342 -2.131 2022-07-20T22:09:39.813025024 INFO 2024-04-04 09:36:11,644 calibrate.py _nudge_pos():1703 [37276] 2193: 0.070 0.0007784 -0.0002005 6616 22.05 5.243 -1.685 2022-07-20T22:33:06.016693248 INFO 2024-04-04 09:36:13,604 calibrate.py _nudge_pos():1703 [37276] 2540: 0.150 0.0008799 -0.0002123 7185 23.95 5.458 -1.643 2022-07-20T23:02:49.014549760 INFO 2024-04-04 09:36:14,080 calibrate.py _nudge_pos():1703 [37276] 2620: 0.050 0.0009001 -0.0002271 7541 25.13 5.321 -1.674 2022-07-20T23:29:16.215819008 INFO 2024-04-04 09:36:14,316 calibrate.py _nudge_pos():1703 [37276] 2661: 0.080 -0.0000340 -0.0000146 50 0.16 -30.914 -16.586 2022-07-20T23:30:06.212393984 INFO 2024-04-04 09:36:16,289 calibrate.py _nudge_pos():1703 [37276] 3007: 0.190 0.0008324 -0.0001431 6405 21.35 5.795 -1.242 2022-07-20T23:57:12.211005440 INFO 2024-04-04 09:36:16,985 calibrate.py _nudge_pos():1703 [37276] 3129: 0.110 0.0009638 -0.0001369 7400 24.67 5.808 -1.029 2022-07-21T00:23:53.411315712 INFO 2024-04-04 09:36:19,053 calibrate.py _nudge_pos():1703 [37276] 3492: 0.040 0.0011059 0.0002280 8161 27.20 6.043 1.553 2022-07-21T00:57:07.614703360 INFO 2024-04-04 09:36:19,191 calibrate.py _nudge_pos():1703 [37276] 3515: 0.160 0.0007515 0.0001226 7835 26.11 4.277 0.870 2022-07-21T01:23:36.615849472 INFO 2024-04-04 09:36:19,654 calibrate.py _nudge_pos():1703 [37276] 3596: 0.170 0.0000953 0.0000264 55 0.18 78.586 27.196 2022-07-21T01:25:07.619614976 INFO 2024-04-04 09:36:20,863 calibrate.py _nudge_pos():1703 [37276] 3804: 0.170 0.0000081 -0.0000043 15 0.05 25.638 -16.957 2022-07-21T01:28:37.615229696 INFO 2024-04-04 09:36:21,393 calibrate.py _nudge_pos():1703 [37276] 3896: 0.090 0.0006380 0.0000871 7801 26.00 3.646 0.621 2022-07-21T01:56:08.812114688 INFO 2024-04-04 09:36:21,596 calibrate.py _nudge_pos():1703 [37276] 3931: 0.010 0.0007161 0.0001564 8281 27.60 3.854 1.050 2022-07-21T02:24:19.016327936 INFO 2024-04-04 09:36:23,654 calibrate.py _nudge_pos():1703 [37276] 4283: 0.150 0.0006338 0.0001241 7115 23.71 3.970 0.970 2022-07-21T02:53:54.014732032 INFO 2024-04-04 09:36:23,945 calibrate.py _nudge_pos():1703 [37276] 4333: 0.060 0.0011815 0.0014838 7351 24.50 7.162 11.223 2022-07-21T03:19:13.210660096 INFO 2024-04-04 09:36:25,969 calibrate.py _nudge_pos():1703 [37276] 4682: 0.180 0.0015263 0.0017151 7625 25.41 8.918 12.505 2022-07-21T03:50:26.212350720 INFO 2024-04-04 09:36:26,401 calibrate.py _nudge_pos():1703 [37276] 4756: 0.100 0.0006659 0.0014280 7226 24.08 4.105 10.988 2022-07-21T04:15:44.418346496 INFO 2024-04-04 09:36:28,364 calibrate.py _nudge_pos():1703 [37276] 5098: 0.150 -0.0000292 -0.0000355 25 0.08 -54.141 -82.170 2022-07-21T04:21:30.414643968 INFO 2024-04-04 09:36:28,371 calibrate.py _nudge_pos():1703 [37276] 5099: 0.140 0.0000338 -0.0000536 15 0.05 107.463 -212.788 2022-07-21T04:21:33.414438400 INFO 2024-04-04 09:36:28,402 calibrate.py _nudge_pos():1703 [37276] 5104: 0.020 0.0002240 0.0006819 5376 17.92 1.856 7.052 2022-07-21T04:39:32.610508800 INFO 2024-04-04 09:36:30,450 calibrate.py _nudge_pos():1703 [37276] 5457: 0.170 0.0044301 0.0005283 8865 29.55 22.254 3.313 2022-07-21T05:14:57.614935808 INFO 2024-04-04 09:36:30,769 calibrate.py _nudge_pos():1703 [37276] 5512: 0.050 0.0030788 0.0007353 7211 24.03 19.009 5.669 2022-07-21T05:39:53.812439296 INFO 2024-04-04 09:36:32,852 calibrate.py _nudge_pos():1703 [37276] 5872: 0.190 0.0031553 0.0004420 7395 24.65 18.993 3.323 2022-07-21T06:10:31.816527360 INFO 2024-04-04 09:36:33,325 calibrate.py _nudge_pos():1703 [37276] 5952: 0.130 0.0036815 0.0003819 7850 26.16 20.870 2.705 2022-07-21T06:38:01.013549568 INFO 2024-04-04 09:36:35,812 calibrate.py _nudge_pos():1703 [37276] 6375: 0.060 0.0029076 -0.0005530 7696 25.65 16.809 -3.995 2022-07-21T07:10:42.219197696 INFO 2024-04-04 09:36:36,092 calibrate.py _nudge_pos():1703 [37276] 6420: 0.160 0.0028799 -0.0005883 7345 24.48 17.440 -4.453 2022-07-21T07:35:55.215550464 INFO 2024-04-04 09:36:38,316 calibrate.py _nudge_pos():1703 [37276] 6788: 0.110 0.0032852 -0.0007243 7760 25.86 18.826 -5.189 2022-07-21T08:07:54.414076416 INFO 2024-04-04 09:36:38,626 calibrate.py _nudge_pos():1703 [37276] 6839: 0.200 0.0030294 -0.0005685 7440 24.80 18.103 -4.248 2022-07-21T08:33:32.418715904 INFO 2024-04-04 09:36:41,075 calibrate.py _nudge_pos():1703 [37276] 7237: 0.190 0.0000843 -0.0001427 7720 25.73 0.485 -1.028 2022-07-21T09:05:53.615734784 INFO 2024-04-04 09:36:41,729 calibrate.py _nudge_pos():1703 [37276] 7346: 0.110 -0.0000485 0.0004154 7526 25.08 -0.287 3.069 2022-07-21T09:32:46.815223040 INFO 2024-04-04 09:36:41,797 calibrate.py _nudge_pos():1703 [37276] 7357: 0.100 -0.0000092 -0.0000274 190 0.63 -2.162 -8.053 2022-07-21T09:33:34.811934976 INFO 2024-04-04 09:36:43,643 calibrate.py _nudge_pos():1703 [37276] 7661: 0.020 -0.0000324 0.0002953 8186 27.28 -0.176 2.006 2022-07-21T10:05:55.019021824 INFO 2024-04-04 09:36:43,782 calibrate.py _nudge_pos():1703 [37276] 7683: 0.140 0.0001805 0.0002942 7430 24.76 1.081 2.201 2022-07-21T10:31:02.015785472 INFO 2024-04-04 09:36:46,121 calibrate.py _nudge_pos():1703 [37276] 8067: 0.080 0.0000540 0.0002437 7626 25.42 0.315 1.777 2022-07-21T11:02:50.215064832 INFO 2024-04-04 09:36:46,226 calibrate.py _nudge_pos():1703 [37276] 8084: 0.190 0.0001028 0.0003793 7105 23.68 0.644 2.968 2022-07-21T11:26:47.216623360 INFO 2024-04-04 09:36:48,460 calibrate.py _nudge_pos():1703 [37276] 8447: 0.100 0.0001059 0.0002817 7285 24.28 0.647 2.150 2022-07-21T11:57:06.412000000 INFO 2024-04-04 09:36:50,676 calibrate.py _nudge_pos():1703 [37276] 8804: 0.050 0.0004154 -0.0000703 7171 23.90 2.579 -0.545 2022-07-21T12:26:56.619362304 INFO 2024-04-04 09:36:58,473 calibrate.py _nudge_pos():1703 [37276] 10059: 0.020 0.0017411 -0.0022423 5116 17.05 15.151 -24.369 2022-07-21T13:04:53.813363712 INFO 2024-04-04 09:37:06,439 calibrate.py _nudge_pos():1703 [37276] 11334: 0.170 0.0009582 -0.0017026 4380 14.60 9.740 -21.614 2022-07-21T13:40:44.816010240 INFO 2024-04-04 09:37:14,483 calibrate.py _nudge_pos():1703 [37276] 12629: 0.090 0.0001981 -0.0000367 3730 12.43 2.365 -0.547 2022-07-21T14:14:45.016246784 INFO 2024-04-04 09:37:22,368 calibrate.py _nudge_pos():1703 [37276] 13887: 0.050 0.0001235 -0.0010859 4206 14.02 1.307 -14.355 2022-07-21T14:49:43.212510464 INFO 2024-04-04 09:37:45,079 calibrate.py _nudge_pos():1703 [37276] 17569: 0.150 -0.0001059 -0.0002532 2160 7.20 -2.183 -6.520 2022-07-21T15:58:16.410737152 INFO 2024-04-04 09:38:01,933 calibrate.py _nudge_pos():1760 [37276] 20199: - - - 1 0.00 - - INFO 2024-04-04 09:38:01,934 calibrate.py _nudge_pos():1766 [37276] Points in final series = 371952 INFO 2024-04-04 09:38:03,248 calibrate.py _hs2_process():2276 [37276] Number of bad hs2 points: 7 of 298444 INFO 2024-04-04 09:38:04,659 calibrate.py _geometric_depth_correction():3257 [37276] hs2: d_beg_time_diff: 1 seconds, d_end_time_diff: -1 seconds, INFO 2024-04-04 09:38:06,500 calibrate.py _geometric_depth_correction():3257 [37276] ctd1: d_beg_time_diff: 19 seconds, d_end_time_diff: -1 seconds, INFO 2024-04-04 09:38:07,890 calibrate.py _geometric_depth_correction():3257 [37276] ctd1: d_beg_time_diff: 19 seconds, d_end_time_diff: -1 seconds, INFO 2024-04-04 09:38:07,893 calibrate.py _ctd_process():2779 [37276] Performing range checking of ['ctd1_salinity'] in 2022.201.00/ctd1.nc INFO 2024-04-04 09:38:07,894 calibrate.py _range_qc_combined_nc():894 [37276] Setting 5 ctd1_salinity values to NaN INFO 2024-04-04 09:38:07,894 calibrate.py _range_qc_combined_nc():908 [37276] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2024-04-04 09:38:07,894 calibrate.py _range_qc_combined_nc():934 [37276] Done range checking ctd1 INFO 2024-04-04 09:38:09,618 calibrate.py _geometric_depth_correction():3257 [37276] ctd2: d_beg_time_diff: 19 seconds, d_end_time_diff: -1 seconds, INFO 2024-04-04 09:38:11,010 calibrate.py _geometric_depth_correction():3257 [37276] ctd2: d_beg_time_diff: 19 seconds, d_end_time_diff: -1 seconds, INFO 2024-04-04 09:38:11,013 calibrate.py _ctd_process():2779 [37276] Performing range checking of ['ctd2_salinity'] in 2022.201.00/ctd2.nc INFO 2024-04-04 09:38:11,014 calibrate.py _range_qc_combined_nc():894 [37276] Setting 4 ctd2_salinity values to NaN INFO 2024-04-04 09:38:11,014 calibrate.py _range_qc_combined_nc():908 [37276] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2024-04-04 09:38:11,014 calibrate.py _range_qc_combined_nc():934 [37276] Done range checking ctd2 ERROR 2024-04-04 09:38:11,015 calibrate.py process_logs():3378 [37276] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2022.201.00 INFO 2024-04-04 09:38:11,044 calibrate.py _biolume_process():2971 [37276] Checking for non-monotonic increasing time60hz INFO 2024-04-04 09:38:13,678 calibrate.py _biolume_process():2974 [37276] Removing non-monotonic increasing time60hz at indices: [4142580 4142581 4142582] INFO 2024-04-04 09:38:14,091 calibrate.py _geometric_depth_correction():3257 [37276] biolume: d_beg_time_diff: -4 seconds, d_end_time_diff: -1 seconds, INFO 2024-04-04 09:39:25,661 calibrate.py write_netcdf():3344 [37276] Writing calibrated instrument data to /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/dorado_2022.201.00_cal.nc INFO 2024-04-04 09:39:25,898 calibrate.py write_netcdf():3348 [37276] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_par, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, ecopuck_bbp700, ecopuck_cdom, ecopuck_chl, ecopuck_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, lopc_LCcount, lopc_countListSum, lopc_flowSpeed, lopc_nonTransCount, lopc_time, lopc_transCount, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2024-04-04 09:39:25,920 process.py align():230 [37276] Alignment steps for 2022.201.00 INFO 2024-04-04 09:39:26,015 align.py process_cal():145 [37276] Processing dorado_2022.201.00_cal.nc from /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00 INFO 2024-04-04 09:39:26,081 align.py process_cal():221 [37276] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2024-04-04 09:39:26,088 align.py process_cal():282 [37276] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2024-04-04 09:39:26,248 align.py process_cal():221 [37276] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2024-04-04 09:39:26,257 align.py process_cal():282 [37276] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2024-04-04 09:39:26,399 align.py process_cal():221 [37276] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2024-04-04 09:39:26,407 align.py process_cal():282 [37276] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2024-04-04 09:39:26,490 align.py process_cal():168 [37276] Skipping navigation_posx INFO 2024-04-04 09:39:26,491 align.py process_cal():168 [37276] Skipping navigation_posy INFO 2024-04-04 09:39:26,552 align.py process_cal():221 [37276] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2024-04-04 09:39:26,561 align.py process_cal():282 [37276] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2024-04-04 09:39:26,697 align.py process_cal():221 [37276] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:26,704 align.py process_cal():282 [37276] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:26,838 align.py process_cal():221 [37276] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:26,844 align.py process_cal():282 [37276] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:26,969 align.py process_cal():221 [37276] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:26,975 align.py process_cal():282 [37276] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:27,096 align.py process_cal():221 [37276] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:27,102 align.py process_cal():282 [37276] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:27,221 align.py process_cal():221 [37276] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:27,226 align.py process_cal():282 [37276] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:27,345 align.py process_cal():221 [37276] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:27,352 align.py process_cal():282 [37276] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:27,470 align.py process_cal():221 [37276] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:27,476 align.py process_cal():282 [37276] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:27,594 align.py process_cal():221 [37276] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:27,599 align.py process_cal():282 [37276] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:27,715 align.py process_cal():221 [37276] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:27,721 align.py process_cal():282 [37276] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:27,838 align.py process_cal():221 [37276] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:27,844 align.py process_cal():282 [37276] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:27,961 align.py process_cal():221 [37276] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:27,967 align.py process_cal():282 [37276] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:28,083 align.py process_cal():221 [37276] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:28,089 align.py process_cal():282 [37276] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:28,205 align.py process_cal():221 [37276] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:28,211 align.py process_cal():282 [37276] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:28,329 align.py process_cal():221 [37276] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:28,334 align.py process_cal():282 [37276] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:28,449 align.py process_cal():221 [37276] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:28,455 align.py process_cal():282 [37276] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:28,579 align.py process_cal():221 [37276] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:28,585 align.py process_cal():282 [37276] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:28,704 align.py process_cal():221 [37276] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:28,710 align.py process_cal():282 [37276] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:28,830 align.py process_cal():221 [37276] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:28,836 align.py process_cal():282 [37276] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:28,954 align.py process_cal():221 [37276] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:28,960 align.py process_cal():282 [37276] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:29,079 align.py process_cal():221 [37276] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:29,085 align.py process_cal():282 [37276] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:29,203 align.py process_cal():221 [37276] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:29,209 align.py process_cal():282 [37276] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:29,326 align.py process_cal():221 [37276] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:29,332 align.py process_cal():282 [37276] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:29,449 align.py process_cal():221 [37276] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2022.201.00_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2024-04-04 09:39:29,455 align.py process_cal():282 [37276] ctd2_par: instrument_sample_rate_hz = 4.00 INFO 2024-04-04 09:39:29,609 align.py process_cal():282 [37276] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2024-04-04 09:39:29,719 align.py process_cal():282 [37276] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2024-04-04 09:39:29,910 align.py process_cal():282 [37276] biolume_raw: instrument_sample_rate_hz = 58.98 INFO 2024-04-04 09:39:31,030 align.py process_cal():282 [37276] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2024-04-04 09:39:31,222 align.py process_cal():282 [37276] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2024-04-04 09:39:31,314 align.py process_cal():282 [37276] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2024-04-04 09:39:31,405 align.py process_cal():282 [37276] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2024-04-04 09:39:31,494 align.py process_cal():282 [37276] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2024-04-04 09:39:31,596 align.py process_cal():282 [37276] ecopuck_bbp700: instrument_sample_rate_hz = 10.40 INFO 2024-04-04 09:39:31,880 align.py process_cal():282 [37276] ecopuck_cdom: instrument_sample_rate_hz = 10.40 INFO 2024-04-04 09:39:32,140 align.py process_cal():282 [37276] ecopuck_chl: instrument_sample_rate_hz = 10.40 INFO 2024-04-04 09:39:32,402 align.py process_cal():282 [37276] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2024-04-04 09:39:32,553 align.py write_netcdf():367 [37276] Writing aligned data to /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/dorado_2022.201.00_align.nc INFO 2024-04-04 09:39:32,825 align.py write_netcdf():372 [37276] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_par, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, ecopuck_bbp700, ecopuck_cdom, ecopuck_chl, ecopuck_depth, ecopuck_latitude, ecopuck_longitude, ecopuck_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, lopc_LCcount, lopc_countListSum, lopc_depth, lopc_flowSpeed, lopc_latitude, lopc_longitude, lopc_nonTransCount, lopc_time, lopc_transCount, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2024-04-04 09:39:32,850 process.py resample():251 [37276] Resampling steps for 2022.201.00 INFO 2024-04-04 09:39:32,959 resample.py instruments_variables():234 [37276] Reading variables from /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/dorado_2022.201.00_align.nc mission netCDF file INFO 2024-04-04 09:39:32,982 resample.py instruments_variables():234 [37276] Reading variables from /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/dorado_2022.201.00_align.nc mission netCDF file INFO 2024-04-04 09:39:32,985 resample.py get_mission_start_end():808 [37276] navigation: 2022-07-20T19:59:05.429716992 to 2022-07-21T16:42:44.817938688 (0 days 00:00:00.099993088 before mission_end) INFO 2024-04-04 09:39:32,989 resample.py get_mission_start_end():808 [37276] hs2 : 2022-07-20T19:58:31.102068736 to 2022-07-21T16:42:44.787940864 (0 days 00:00:00.129990912 before mission_end) INFO 2024-04-04 09:39:32,993 resample.py get_mission_start_end():808 [37276] ctd1 : 2022-07-20T19:58:48.720861696 to 2022-07-21T16:42:44.817938688 (0 days 00:00:00.099993088 before mission_end) INFO 2024-04-04 09:39:32,996 resample.py get_mission_start_end():808 [37276] ctd2 : 2022-07-20T19:58:48.900849408 to 2022-07-21T16:42:44.827938048 (0 days 00:00:00.089993728 before mission_end) INFO 2024-04-04 09:39:32,998 resample.py get_mission_start_end():808 [37276] biolume : 2022-07-20T19:58:24.972454400 to 2022-07-21T16:42:44.197947136 (0 days 00:00:00.719984640 before mission_end) INFO 2024-04-04 09:39:32,999 resample.py get_mission_start_end():808 [37276] lopc : 2022-07-20T19:58:38.842189056 to 2022-07-21T16:42:33.842189056 (0 days 00:00:11.075742720 before mission_end) INFO 2024-04-04 09:39:33,005 resample.py get_mission_start_end():808 [37276] ecopuck : 2022-07-20T19:58:24.702507008 to 2022-07-21T16:42:44.917931776 (0 days 00:00:00 before mission_end) INFO 2024-04-04 09:39:33,010 resample.py get_mission_start_end():808 [37276] tailcone : 2022-07-20T19:58:34.101863168 to 2022-07-21T16:42:09.500358144 (0 days 00:00:35.417573632 before mission_end) INFO 2024-04-04 09:39:33,012 resample.py instruments_variables():234 [37276] Reading variables from /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/dorado_2022.201.00_align.nc mission netCDF file INFO 2024-04-04 09:39:33,012 resample.py resample_coordinates():248 [37276] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:33,245 resample.py resample_variable():703 [37276] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:33,311 resample.py resample_variable():703 [37276] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:33,373 resample.py resample_variable():703 [37276] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:33,432 resample.py resample_variable():703 [37276] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:33,490 resample.py resample_variable():703 [37276] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:33,546 resample.py resample_variable():703 [37276] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:33,604 resample.py resample_variable():703 [37276] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:33,658 resample.py resample_variable():703 [37276] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:33,710 resample.py resample_variable():703 [37276] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:33,764 resample.py resample_variable():703 [37276] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:33,819 resample.py resample_variable():703 [37276] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:33,875 resample.py resample_variable():703 [37276] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:33,929 resample.py resample_variable():703 [37276] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:33,982 resample.py resample_variable():703 [37276] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:34,036 resample.py resample_variable():703 [37276] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:34,087 resample.py resample_variable():703 [37276] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:34,136 resample.py resample_variable():703 [37276] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:34,191 resample.py resample_variable():703 [37276] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:34,244 resample.py resample_variable():703 [37276] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:34,296 resample.py resample_variable():703 [37276] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:34,348 resample.py resample_variable():703 [37276] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:34,399 resample.py resample_variable():703 [37276] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:34,449 resample.py resample_variable():703 [37276] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:34,499 resample.py resample_variable():703 [37276] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:34,548 resample.py resample_variable():703 [37276] Resampling ctd2_par with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:34,569 resample.py resample_variable():703 [37276] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:34,584 resample.py resample_variable():703 [37276] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:34,588 resample.py add_biolume_proxies():482 [37276] Adding biolume proxy variables computed from biolume_raw INFO 2024-04-04 09:39:36,369 resample.py add_biolume_proxies():522 [37276] Using flash_threshold = 1.0000e+11 INFO 2024-04-04 09:39:36,843 resample.py add_biolume_proxies():569 [37276] Computing flashes per liter: nbflash_high, nbflash_low INFO 2024-04-04 09:39:37,046 resample.py add_biolume_proxies():597 [37276] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2024-04-04 09:39:37,149 resample.py add_biolume_proxies():617 [37276] Saving Background bioluminescence (dinoflagellates proxy) INFO 2024-04-04 09:39:37,201 resample.py select_nighttime_bl_raw():411 [37276] Extracting biolume_raw data between sunset 2022-07-21 04:19:05.811166976 and sunrise 2022-07-21 11:59:05.817203200 INFO 2024-04-04 09:39:37,322 resample.py add_biolume_proxies():649 [37276] Using proxy_ratio_adinos = 3.9811e+13 INFO 2024-04-04 09:39:37,322 resample.py add_biolume_proxies():650 [37276] Using proxy_cal_factor = 0.004700 INFO 2024-04-04 09:39:37,439 resample.py resample_variable():703 [37276] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:37,446 resample.py resample_variable():703 [37276] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:37,453 resample.py resample_variable():703 [37276] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:37,459 resample.py resample_variable():703 [37276] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:37,469 resample.py resample_variable():703 [37276] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:37,587 resample.py resample_variable():703 [37276] Resampling ecopuck_bbp700 with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:37,732 resample.py resample_variable():703 [37276] Resampling ecopuck_cdom with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:37,880 resample.py resample_variable():703 [37276] Resampling ecopuck_chl with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:37,967 resample.py resample_variable():703 [37276] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2024-04-04 09:39:38,577 resample.py resample_mission():942 [37276] Saved resampled mission to /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/dorado_2022.201.00_1S.nc INFO 2024-04-04 09:39:46,215 create_products.py _get_best_ctd():376 [37276] ctdToUse = ctd1 INFO 2024-04-04 09:40:33,067 create_products.py gulper_odv():514 [37276] Wrote 20 Gulper data lines to /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionodvs/2022.201.00/dorado_2022.201.00_1S_Gulper.txt INFO 2024-04-04 09:40:33,067 process.py archive():307 [37276] Archiving steps for 2022.201.00 INFO 2024-04-04 09:40:33,073 archive.py copy_to_AUVTCD():54 [37276] Archiving /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/dorado_2022.201.00 files to /Volumes/AUVCTD/surveys/2022/netcdf INFO 2024-04-04 09:40:35,943 archive.py copy_to_AUVTCD():71 [37276] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/dorado_2022.201.00_1S.nc /Volumes/AUVCTD/surveys/2022/netcdf done. INFO 2024-04-04 09:40:58,531 archive.py copy_to_AUVTCD():71 [37276] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/dorado_2022.201.00_cal.nc /Volumes/AUVCTD/surveys/2022/netcdf done. INFO 2024-04-04 09:41:32,333 archive.py copy_to_AUVTCD():71 [37276] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/dorado_2022.201.00_align.nc /Volumes/AUVCTD/surveys/2022/netcdf done. INFO 2024-04-04 09:41:35,732 archive.py copy_to_AUVTCD():87 [37276] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2022/2022201/2022.201.00 done. INFO 2024-04-04 09:41:38,528 archive.py copy_to_AUVTCD():87 [37276] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2022/2022201/2022.201.00 done. INFO 2024-04-04 09:41:38,764 archive.py copy_to_AUVTCD():87 [37276] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/gps.nc /Volumes/AUVCTD/missionnetcdfs/2022/2022201/2022.201.00 done. INFO 2024-04-04 09:41:41,911 archive.py copy_to_AUVTCD():87 [37276] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2022/2022201/2022.201.00 done. INFO 2024-04-04 09:41:53,765 archive.py copy_to_AUVTCD():87 [37276] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2022/2022201/2022.201.00 done. INFO 2024-04-04 09:41:57,542 archive.py copy_to_AUVTCD():87 [37276] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2022/2022201/2022.201.00 done. INFO 2024-04-04 09:42:00,585 archive.py copy_to_AUVTCD():87 [37276] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/FLBBCD2K.nc /Volumes/AUVCTD/missionnetcdfs/2022/2022201/2022.201.00 done. INFO 2024-04-04 09:42:03,062 archive.py copy_to_AUVTCD():87 [37276] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2022/2022201/2022.201.00 done. INFO 2024-04-04 09:42:11,704 archive.py copy_to_AUVTCD():87 [37276] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2022/2022201/2022.201.00 done. INFO 2024-04-04 09:42:11,705 archive.py copy_to_AUVTCD():92 [37276] Archiving product files INFO 2024-04-04 09:42:11,841 archive.py copy_to_AUVTCD():101 [37276] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionodvs/2022.201.00/* /Volumes/AUVCTD/surveys/2022/odv done. INFO 2024-04-04 09:42:11,843 archive.py copy_to_AUVTCD():114 [37276] rsync /Users/mccann/GitHub/auv-python/data/auv_data/dorado/missionnetcdfs/2022.201.00/dorado_2022.201.00_processing.log /Volumes/AUVCTD/surveys/2022/netcdf