INFO 2025-06-26 20:10:45,247 process.py process_mission():429 [1] commandline = src/data/process_dorado.py --start_year 2005 --end_year 2014 --num_cores 1 -v --noinput --clobber INFO 2025-06-26 20:10:45,247 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ October 2013 in Soquel Bight - ctdToUse = ctd1 INFO 2025-06-26 20:10:45,247 process.py process_mission():449 [1] Processing SIMZ October 2013 mission 2013.298.01 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:10:45,247 process.py download_process():165 [1] Download and processing steps for 2013.298.01 INFO 2025-06-26 20:10:45,247 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013298/2013.298.01 INFO 2025-06-26 20:10:45,247 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013298/2013.298.01 to /data/auv_data/dorado/missionlogs/2013.298.01 INFO 2025-06-26 20:10:48,606 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.298.01 INFO 2025-06-26 20:10:48,606 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.298.01/ctdDriver.log (5270694 bytes) INFO 2025-06-26 20:10:48,983 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.298.01/ctdDriver2.log (5270687 bytes) INFO 2025-06-26 20:10:49,369 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.298.01/gps.log (63644 bytes) INFO 2025-06-26 20:10:49,384 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.298.01/hydroscatlog.log (4616158 bytes) INFO 2025-06-26 20:10:49,853 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.298.01/navigation.log (18654982 bytes) INFO 2025-06-26 20:10:51,195 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.298.01/parosci.log (6482822 bytes) INFO 2025-06-26 20:10:51,731 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.298.01/parosci.log: [134546] INFO 2025-06-26 20:10:51,751 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.298.01/tailCone.log (3300043 bytes) INFO 2025-06-26 20:10:52,165 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.298.01/biolume.log (3842942 bytes) INFO 2025-06-26 20:10:52,538 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:10:52,730 logs2netcdfs.py download_process_logs():807 [1] Time to process: 4.12 seconds INFO 2025-06-26 20:10:52,731 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.298.01/lopc.bin (26547287 bytes) INFO 2025-06-26 20:10:52,731 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:10:52 2025 INFO 2025-06-26 20:10:52,731 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.298.01/parosci.nc INFO 2025-06-26 20:10:52,731 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:10:52,731 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.298.01/parosci.nc INFO 2025-06-26 20:10:52,734 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1382728344.2, sensor_off_time = 1382742093.9 INFO 2025-06-26 20:10:52,735 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 13749 seconds. Expecting to read 27498 L frames from the lopc.bin file. INFO 2025-06-26 20:10:52,735 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 27498 records from the lopc.bin file. INFO 2025-06-26 20:10:52,897 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-10-25 19:12:24 Z and endTime = 2013-10-25 23:01:33 Z with 27498 records expected to be read from lopc.bin INFO 2025-06-26 20:10:52,898 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.298.01/lopc.bin INFO 2025-06-26 20:10:52,898 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.298.01/lopc.nc INFO 2025-06-26 20:10:52,898 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.298.01/lopc.nc INFO 2025-06-26 20:10:52,899 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.298.01 INFO 2025-06-26 20:10:52,899 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 20:10:52,902 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 20:10:52,966 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:10:52,966 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:10:52,967 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 20:10:53,035 lopcToNetCDF.py main():2340 [1] UnicodeDecodeError: 'utf-8' codec can't decode byte 0xba in position 0: invalid start byte INFO 2025-06-26 20:10:53,035 lopcToNetCDF.py main():2341 [1] Failed to decode all of lopc.bin - resulting lopc.nc file likely incomplete INFO 2025-06-26 20:10:53,035 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.298.01/parosci.nc INFO 2025-06-26 20:10:53,035 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:10:53,035 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.298.01/parosci.nc INFO 2025-06-26 20:10:53,039 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1382728344.2, sensor_off_time = 1382742093.9 INFO 2025-06-26 20:10:53,039 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 13749 seconds. Expecting to read 27498 L frames from the lopc.bin file. INFO 2025-06-26 20:10:53,039 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 27498 records from the lopc.bin file. INFO 2025-06-26 20:10:53,039 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 12458 and len(sampleCountList) = 134 INFO 2025-06-26 20:10:53,039 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [] INFO 2025-06-26 20:10:53,039 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [12458 12459 12460 24225 24226 24227 24228 24229 24230 24231 24232 24233 24234 24235 24236 24237 24238 24239 24240 24241 24242 24243 24244 24245 24246 24247 24248 24249 24250 24251 24252 24253 24254 24255 24256 24257 24258 24259 24260 24261 24262 24263 24264 24265 24266 24267 24268 24269 24270 24271 24272 24273 24274 24275 24276 24277 24278 24279 24280 24281 24282 24283 24284 24285 24286 24287 24288 24289 24290 24291 24292 24293 24294 24295 24296 24297 24298 24299 24300 24301 24302 24303 24304 24305 24306 24307 24308 24309 24310 24311 24312 24313 24314 24315 24316 24317 24318 24319 24320 24321 24322 24323 24324 24325 24326 24327 24328 24329 24330 24331 24332 24333 24334 24335 24336 24337 24338 24339 24340 24341 24342 24343 24344 24345 24346 24347 24348 24349 24350 24351 24352 24353 24354 24355] INFO 2025-06-26 20:10:53,040 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 20:10:53,040 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-26 20:10:53,040 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [ 1 1 11765 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1] INFO 2025-06-26 20:10:53,040 lopcToNetCDF.py deSpike():1590 [1] Found 1 spike indicators at indices: [3] INFO 2025-06-26 20:10:53,040 lopcToNetCDF.py deSpike():1595 [1] Identifying nature of spike value = 24225 at index = 3 INFO 2025-06-26 20:10:53,041 lopcToNetCDF.py deSpike():1714 [1] This is the last element in spike_indx. No need to deSpike(). INFO 2025-06-26 20:10:53,041 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [12458 12459 12460 24225 24226 24227 24228 24229 24230 24231 24232 24233 24234 24235 24236 24237 24238 24239 24240 24241 24242 24243 24244 24245 24246 24247 24248 24249 24250 24251 24252 24253 24254 24255 24256 24257 24258 24259 24260 24261 24262 24263 24264 24265 24266 24267 24268 24269 24270 24271 24272 24273 24274 24275 24276 24277 24278 24279 24280 24281 24282 24283 24284 24285 24286 24287 24288 24289 24290 24291 24292 24293 24294 24295 24296 24297 24298 24299 24300 24301 24302 24303 24304 24305 24306 24307 24308 24309 24310 24311 24312 24313 24314 24315 24316 24317 24318 24319 24320 24321 24322 24323 24324 24325 24326 24327 24328 24329 24330 24331 24332 24333 24334 24335 24336 24337 24338 24339 24340 24341 24342 24343 24344 24345 24346 24347 24348 24349 24350 24351 24352 24353 24354 24355] INFO 2025-06-26 20:10:53,041 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [12458 12459 12460 24225 24226 24227 24228 24229 24230 24231 24232 24233 24234 24235 24236 24237 24238 24239 24240 24241 24242 24243 24244 24245 24246 24247 24248 24249 24250 24251 24252 24253 24254 24255 24256 24257 24258 24259 24260 24261 24262 24263 24264 24265 24266 24267 24268 24269 24270 24271 24272 24273 24274 24275 24276 24277 24278 24279 24280 24281 24282 24283 24284 24285 24286 24287 24288 24289 24290 24291 24292 24293 24294 24295 24296 24297 24298 24299 24300 24301 24302 24303 24304 24305 24306 24307 24308 24309 24310 24311 24312 24313 24314 24315 24316 24317 24318 24319 24320 24321 24322 24323 24324 24325 24326 24327 24328 24329 24330 24331 24332 24333 24334 24335 24336 24337 24338 24339 24340 24341 24342 24343 24344 24345 24346 24347 24348 24349 24350 24351 24352 24353 24354 24355] with len(correctedSampleCountList) = 134 INFO 2025-06-26 20:10:53,042 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 12458 from all values of correctedSampleCountList INFO 2025-06-26 20:10:53,042 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 20:10:53,042 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [0.0000e+00 5.0000e-01 1.0000e+00 5.8835e+03 5.8840e+03 5.8845e+03 5.8850e+03 5.8855e+03 5.8860e+03 5.8865e+03 5.8870e+03 5.8875e+03 5.8880e+03 5.8885e+03 5.8890e+03 5.8895e+03 5.8900e+03 5.8905e+03 5.8910e+03 5.8915e+03 5.8920e+03 5.8925e+03 5.8930e+03 5.8935e+03 5.8940e+03 5.8945e+03 5.8950e+03 5.8955e+03 5.8960e+03 5.8965e+03 5.8970e+03 5.8975e+03 5.8980e+03 5.8985e+03 5.8990e+03 5.8995e+03 5.9000e+03 5.9005e+03 5.9010e+03 5.9015e+03 5.9020e+03 5.9025e+03 5.9030e+03 5.9035e+03 5.9040e+03 5.9045e+03 5.9050e+03 5.9055e+03 5.9060e+03 5.9065e+03 5.9070e+03 5.9075e+03 5.9080e+03 5.9085e+03 5.9090e+03 5.9095e+03 5.9100e+03 5.9105e+03 5.9110e+03 5.9115e+03 5.9120e+03 5.9125e+03 5.9130e+03 5.9135e+03 5.9140e+03 5.9145e+03 5.9150e+03 5.9155e+03 5.9160e+03 5.9165e+03 5.9170e+03 5.9175e+03 5.9180e+03 5.9185e+03 5.9190e+03 5.9195e+03 5.9200e+03 5.9205e+03 5.9210e+03 5.9215e+03 5.9220e+03 5.9225e+03 5.9230e+03 5.9235e+03 5.9240e+03 5.9245e+03 5.9250e+03 5.9255e+03 5.9260e+03 5.9265e+03 5.9270e+03 5.9275e+03 5.9280e+03 5.9285e+03 5.9290e+03 5.9295e+03 5.9300e+03 5.9305e+03 5.9310e+03 5.9315e+03 5.9320e+03 5.9325e+03 5.9330e+03 5.9335e+03 5.9340e+03 5.9345e+03 5.9350e+03 5.9355e+03 5.9360e+03 5.9365e+03 5.9370e+03 5.9375e+03 5.9380e+03 5.9385e+03 5.9390e+03 5.9395e+03 5.9400e+03 5.9405e+03 5.9410e+03 5.9415e+03 5.9420e+03 5.9425e+03 5.9430e+03 5.9435e+03 5.9440e+03 5.9445e+03 5.9450e+03 5.9455e+03 5.9460e+03 5.9465e+03 5.9470e+03 5.9475e+03 5.9480e+03 5.9485e+03] INFO 2025-06-26 20:10:53,043 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.38272834e+09 1.38272834e+09 1.38272835e+09 1.38273423e+09 1.38273423e+09 1.38273423e+09 1.38273423e+09 1.38273423e+09 1.38273423e+09 1.38273423e+09 1.38273423e+09 1.38273423e+09 1.38273423e+09 1.38273423e+09 1.38273423e+09 1.38273423e+09 1.38273423e+09 1.38273423e+09 1.38273424e+09 1.38273424e+09 1.38273424e+09 1.38273424e+09 1.38273424e+09 1.38273424e+09 1.38273424e+09 1.38273424e+09 1.38273424e+09 1.38273424e+09 1.38273424e+09 1.38273424e+09 1.38273424e+09 1.38273424e+09 1.38273424e+09 1.38273424e+09 1.38273424e+09 1.38273424e+09 1.38273424e+09 1.38273424e+09 1.38273425e+09 1.38273425e+09 1.38273425e+09 1.38273425e+09 1.38273425e+09 1.38273425e+09 1.38273425e+09 1.38273425e+09 1.38273425e+09 1.38273425e+09 1.38273425e+09 1.38273425e+09 1.38273425e+09 1.38273425e+09 1.38273425e+09 1.38273425e+09 1.38273425e+09 1.38273425e+09 1.38273425e+09 1.38273425e+09 1.38273426e+09 1.38273426e+09 1.38273426e+09 1.38273426e+09 1.38273426e+09 1.38273426e+09 1.38273426e+09 1.38273426e+09 1.38273426e+09 1.38273426e+09 1.38273426e+09 1.38273426e+09 1.38273426e+09 1.38273426e+09 1.38273426e+09 1.38273426e+09 1.38273426e+09 1.38273426e+09 1.38273426e+09 1.38273426e+09 1.38273427e+09 1.38273427e+09 1.38273427e+09 1.38273427e+09 1.38273427e+09 1.38273427e+09 1.38273427e+09 1.38273427e+09 1.38273427e+09 1.38273427e+09 1.38273427e+09 1.38273427e+09 1.38273427e+09 1.38273427e+09 1.38273427e+09 1.38273427e+09 1.38273427e+09 1.38273427e+09 1.38273427e+09 1.38273427e+09 1.38273428e+09 1.38273428e+09 1.38273428e+09 1.38273428e+09 1.38273428e+09 1.38273428e+09 1.38273428e+09 1.38273428e+09 1.38273428e+09 1.38273428e+09 1.38273428e+09 1.38273428e+09 1.38273428e+09 1.38273428e+09 1.38273428e+09 1.38273428e+09 1.38273428e+09 1.38273428e+09 1.38273428e+09 1.38273428e+09 1.38273429e+09 1.38273429e+09 1.38273429e+09 1.38273429e+09 1.38273429e+09 1.38273429e+09 1.38273429e+09 1.38273429e+09 1.38273429e+09 1.38273429e+09 1.38273429e+09 1.38273429e+09 1.38273429e+09 1.38273429e+09 1.38273429e+09 1.38273429e+09] INFO 2025-06-26 20:10:53,044 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1382728344.2 1382728344.7, ..., timestampArray[-2:] = 1382734292.2 1382734292.7] INFO 2025-06-26 20:10:53,044 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1382728344.2250113), np.float64(1382728344.7250113)], ..., timestampList[-2:] = [np.float64(1382734292.2250113), np.float64(1382734292.7250113)]] INFO 2025-06-26 20:10:53,045 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 134) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 20:10:53,045 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [104, 125] INFO 2025-06-26 20:10:53,045 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 6 INFO 2025-06-26 20:10:53,045 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 134 INFO 2025-06-26 20:10:53,045 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1382728344.2250113), np.float64(1382728344.7250113)], ..., timestampList[-2:] = [np.float64(1382734292.2250113), np.float64(1382734292.7250113)]] INFO 2025-06-26 20:10:53,045 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 134) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 20:10:53,045 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(103), np.int32(124)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 20:10:53,045 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 6 INFO 2025-06-26 20:10:53,045 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 ERROR 2025-06-26 20:10:53,045 lopcToNetCDF.py constructTimestampList():1501 [1] Cannot interpolate to cFrameEsecsListInterpolated: array of sample points is empty INFO 2025-06-26 20:10:53,046 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 6 INFO 2025-06-26 20:10:53,046 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1382734235.7250113)], ..., tsList[-2:] = [np.float64(1382734277.7250113), np.float64(1382734288.2250113)] INFO 2025-06-26 20:10:53,046 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2013-10-25 20:50:35 Z INFO 2025-06-26 20:10:53,046 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2013-10-25 20:51:28 Z INFO 2025-06-26 20:10:53,047 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 134 INFO 2025-06-26 20:10:53,047 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [-9999], ..., cFrameEsecsList[-2:] = [-9999, -9999] INFO 2025-06-26 20:10:53,047 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 1969-12-31 21:13:21 Z INFO 2025-06-26 20:10:53,047 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 1969-12-31 21:13:21 Z INFO 2025-06-26 20:10:53,050 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2013.298.01/lopc.nc INFO 2025-06-26 20:10:53,050 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 20:10:53 2025 Elapsed processing time from start of processing = 0 seconds INFO 2025-06-26 20:10:53,051 process.py calibrate():227 [1] Calibration steps for 2013.298.01 INFO 2025-06-26 20:10:53,264 calibrate.py _nudge_pos():1680 [1] seg# end_sec_diff end_lon_diff end_lat_diff len(segi) seg_min u_drift (cm/s) v_drift (cm/s) start datetime of segment INFO 2025-06-26 20:10:53,266 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:10:53,882 calibrate.py _nudge_pos():1806 [1] 96: 0.040 -0.0006333 0.0016298 7635 25.45 -3.688 11.868 2013-10-25T19:39:22.124177664 INFO 2025-06-26 20:10:54,269 calibrate.py _nudge_pos():1806 [1] 137: 0.040 -0.0006296 0.0021825 8590 28.63 -3.260 14.125 2013-10-25T20:08:40.123746304 INFO 2025-06-26 20:10:54,685 calibrate.py _nudge_pos():1806 [1] 181: 0.040 -0.0006116 0.0023374 8665 28.88 -3.140 14.997 2013-10-25T20:38:16.132081408 INFO 2025-06-26 20:10:54,733 calibrate.py _nudge_pos():1806 [1] 186: 0.040 -0.0000133 0.0000224 90 0.30 -6.662 13.973 2013-10-25T20:38:38.130574592 INFO 2025-06-26 20:10:55,238 calibrate.py _nudge_pos():1806 [1] 239: 0.050 -0.0002872 0.0005946 2180 7.26 -5.861 15.168 2013-10-25T20:46:46.127144448 INFO 2025-06-26 20:10:55,812 calibrate.py _nudge_pos():1806 [1] 299: 0.050 0.0003130 0.0003585 4325 14.41 3.219 4.609 2013-10-25T21:02:10.123846400 INFO 2025-06-26 20:10:56,312 calibrate.py _nudge_pos():1806 [1] 351: 0.050 -0.0006316 -0.0001100 4515 15.05 -6.223 -1.354 2013-10-25T21:18:04.128492544 INFO 2025-06-26 20:10:56,797 calibrate.py _nudge_pos():1806 [1] 402: 0.050 -0.0007827 -0.0004141 5900 19.66 -5.900 -3.902 2013-10-25T21:38:34.124231936 INFO 2025-06-26 20:10:57,140 calibrate.py _nudge_pos():1806 [1] 438: 0.060 -0.0008363 -0.0004166 7055 23.51 -5.271 -3.283 2013-10-25T22:02:40.125174272 INFO 2025-06-26 20:10:57,474 calibrate.py _nudge_pos():1806 [1] 473: 0.050 -0.0010076 -0.0003539 7525 25.08 -5.953 -2.615 2013-10-25T22:28:19.129745152 INFO 2025-06-26 20:10:57,541 calibrate.py _nudge_pos():1806 [1] 480: 0.060 0.0000125 0.0000202 25 0.08 23.244 46.790 2013-10-25T22:28:30.128991744 INFO 2025-06-26 20:10:57,779 calibrate.py _nudge_pos():1806 [1] 504: 0.060 -0.0006173 0.0000073 4825 16.08 -5.688 0.084 2013-10-25T22:44:58.131309056 INFO 2025-06-26 20:10:58,215 calibrate.py _nudge_pos():1806 [1] 548: 0.070 -0.0003232 -0.0001077 3145 10.48 -4.569 -1.905 2013-10-25T22:56:10.125274112 INFO 2025-06-26 20:11:01,324 calibrate.py _nudge_pos():1862 [1] 834: - - - 4 0.01 - - INFO 2025-06-26 20:11:01,324 calibrate.py _nudge_pos():1868 [1] Points in final series = 68576 INFO 2025-06-26 20:11:03,994 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 7 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:11:04,517 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:11:04,929 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:11:04,931 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.298.01/ctd1.nc INFO 2025-06-26 20:11:04,932 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 20:11:04,932 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd1_salinity', Range(min=30, max=40))] INFO 2025-06-26 20:11:04,932 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:11:05,438 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:11:05,860 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:11:05,862 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.298.01/ctd2.nc INFO 2025-06-26 20:11:05,863 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:11:05,864 calibrate.py _range_qc_combined_nc():910 [1] Checked for data outside of these variables and ranges: [('ctd2_salinity', Range(min=30, max=40))] INFO 2025-06-26 20:11:05,864 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 20:11:05,864 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.298.01 INFO 2025-06-26 20:11:05,875 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:11:06,457 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [60] INFO 2025-06-26 20:11:06,578 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -3 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:11:19,111 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.298.01 INFO 2025-06-26 20:11:19,230 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.298.01/dorado_2013.298.01_cal.nc INFO 2025-06-26 20:11:19,341 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, lopc_LCcount, lopc_countListSum, lopc_flowSpeed, lopc_nonTransCount, lopc_time, lopc_transCount, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 20:11:19,346 process.py align():251 [1] Alignment steps for 2013.298.01 INFO 2025-06-26 20:11:19,381 align.py process_cal():139 [1] Processing dorado_2013.298.01_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.298.01 INFO 2025-06-26 20:11:19,403 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:11:19,406 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:11:19,455 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:11:19,459 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:11:19,509 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:11:19,513 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:11:19,542 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:11:19,542 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:11:19,561 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:11:19,564 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:11:19,613 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:19,617 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:19,660 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:19,664 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:19,707 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:19,710 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:19,752 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:19,756 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:19,799 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:19,803 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:19,846 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:19,850 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:19,895 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:19,898 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:19,940 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:19,944 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:19,987 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:19,990 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:20,035 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:20,039 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:20,084 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:20,088 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:20,140 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:20,144 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:20,188 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:20,192 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:20,235 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:20,238 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:20,283 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:20,287 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:20,330 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:20,334 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:20,379 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:20,383 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:20,427 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:20,431 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:20,476 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:20,479 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:20,523 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:20,527 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:20,572 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:20,576 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:20,619 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.298.01_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:20,623 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:20,681 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:11:20,723 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:11:20,791 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 20:11:21,143 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:11:21,180 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:11:21,216 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:11:21,251 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:11:21,287 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:11:21,323 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:11:21,359 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.298.01/dorado_2013.298.01_align.nc INFO 2025-06-26 20:11:21,478 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, lopc_LCcount, lopc_countListSum, lopc_depth, lopc_flowSpeed, lopc_latitude, lopc_longitude, lopc_nonTransCount, lopc_time, lopc_transCount, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 20:11:21,480 process.py resample():273 [1] Resampling steps for 2013.298.01 INFO 2025-06-26 20:11:21,481 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:11:21,513 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.298.01/dorado_2013.298.01_align.nc mission netCDF file INFO 2025-06-26 20:11:21,519 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.298.01/dorado_2013.298.01_align.nc mission netCDF file INFO 2025-06-26 20:11:21,520 resample.py get_mission_start_end():1145 [1] navigation: 2013-10-25T19:12:58.932633600 to 2013-10-25T23:01:33.923092480 (0 days 00:00:00.099993088 before mission_end) INFO 2025-06-26 20:11:21,522 resample.py get_mission_start_end():1145 [1] hs2 : 2013-10-25T19:12:31.604505856 to 2013-10-25T23:01:34.023085568 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:11:21,524 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-10-25T19:12:50.323223552 to 2013-10-25T23:01:33.783101952 (0 days 00:00:00.239983616 before mission_end) INFO 2025-06-26 20:11:21,525 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-10-25T19:12:50.553207808 to 2013-10-25T23:01:33.993087744 (0 days 00:00:00.029997824 before mission_end) INFO 2025-06-26 20:11:21,527 resample.py get_mission_start_end():1145 [1] biolume : 2013-10-25T19:12:21.125189632 to 2013-10-25T23:01:32.663144704 (0 days 00:00:01.359940864 before mission_end) INFO 2025-06-26 20:11:21,528 resample.py get_mission_start_end():1145 [1] lopc : 2013-10-25T20:50:35.725011456 to 2013-10-25T20:51:28.225011456 (0 days 02:10:05.798074112 before mission_end) WARNING 2025-06-26 20:11:21,529 resample.py get_mission_start_end():1156 [1] Instrument lopc has a gap > 5 minutes at the end of the mission: 0 days 02:10:05.798074112 INFO 2025-06-26 20:11:21,530 resample.py get_mission_start_end():1145 [1] tailcone : 2013-10-25T19:12:26.004889600 to 2013-10-25T23:01:34.003087104 (0 days 00:00:00.019998464 before mission_end) INFO 2025-06-26 20:11:21,530 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.298.01/dorado_2013.298.01_align.nc mission netCDF file INFO 2025-06-26 20:11:21,531 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:21,695 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:21,723 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:21,750 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:21,778 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:21,804 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:21,828 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:21,852 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:21,877 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:21,899 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:21,922 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:21,944 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:21,966 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:21,989 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:22,012 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:22,035 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:22,057 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:22,079 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:22,103 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:22,127 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:22,151 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:22,174 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:22,198 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:22,221 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:22,245 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:22,257 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:22,268 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:22,272 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:11:22,272 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:11:22,756 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:11:22,855 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:11:22,903 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:11:22,925 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:11:22,944 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:11:22,944 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:11:22,959 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:22,959 resample.py resample_variable():1038 [1] Padding lopc_countListSum with 0 days 02:10:05.798074112 of NaNs to the end of mission INFO 2025-06-26 20:11:22,969 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:22,969 resample.py resample_variable():1038 [1] Padding lopc_transCount with 0 days 02:10:05.798074112 of NaNs to the end of mission INFO 2025-06-26 20:11:22,978 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:22,978 resample.py resample_variable():1038 [1] Padding lopc_nonTransCount with 0 days 02:10:05.798074112 of NaNs to the end of mission INFO 2025-06-26 20:11:22,987 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:22,987 resample.py resample_variable():1038 [1] Padding lopc_LCcount with 0 days 02:10:05.798074112 of NaNs to the end of mission INFO 2025-06-26 20:11:22,996 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:22,996 resample.py resample_variable():1038 [1] Padding lopc_flowSpeed with 0 days 02:10:05.798074112 of NaNs to the end of mission INFO 2025-06-26 20:11:23,024 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:23,219 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.298.01/dorado_2013.298.01_1S.nc INFO 2025-06-26 20:11:25,770 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:11:36,445 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.298.01/dorado_2013.298.01_1S_Gulper.txt INFO 2025-06-26 20:11:36,445 process.py archive():337 [1] Archiving steps for 2013.298.01 INFO 2025-06-26 20:11:36,445 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.298.01/dorado_2013.298.01, BASE_PATH = /data/auv_data INFO 2025-06-26 20:11:36,445 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.298.01/dorado_2013.298.01 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 20:11:36,447 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.298.01_1S.nc INFO 2025-06-26 20:11:36,463 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.01/dorado_2013.298.01_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:11:36,464 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.298.01_cal.nc INFO 2025-06-26 20:11:36,559 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.01/dorado_2013.298.01_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:11:36,560 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.298.01_align.nc INFO 2025-06-26 20:11:36,697 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.01/dorado_2013.298.01_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:11:36,718 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.01/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013298/2013.298.01 done. INFO 2025-06-26 20:11:36,736 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.01/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013298/2013.298.01 done. INFO 2025-06-26 20:11:36,740 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.01/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013298/2013.298.01 done. INFO 2025-06-26 20:11:36,756 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.01/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013298/2013.298.01 done. INFO 2025-06-26 20:11:36,808 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.01/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013298/2013.298.01 done. INFO 2025-06-26 20:11:36,829 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.01/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013298/2013.298.01 done. INFO 2025-06-26 20:11:36,845 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.01/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013298/2013.298.01 done. INFO 2025-06-26 20:11:36,884 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.01/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013298/2013.298.01 done. INFO 2025-06-26 20:11:36,889 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.01/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013298/2013.298.01 done. INFO 2025-06-26 20:11:36,889 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:11:36,890 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.298.01_1S_Gulper.txt INFO 2025-06-26 20:11:36,895 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.298.01/dorado_2013.298.01_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 20:11:36,895 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.298.01/dorado_2013.298.01_processing.log /Volumes/AUVCTD/surveys/2013/netcdf