INFO 2025-06-26 20:11:36,929 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 20:11:36,929 process.py process_mission():434 [1] dorado_info[mission]["comment"] = SIMZ October 2013 in Soquel Bight - ctdToUse = ctd1 INFO 2025-06-26 20:11:36,930 process.py process_mission():449 [1] Processing SIMZ October 2013 mission 2013.301.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 20:11:36,930 process.py download_process():165 [1] Download and processing steps for 2013.301.02 INFO 2025-06-26 20:11:36,930 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013301/2013.301.02 INFO 2025-06-26 20:11:36,930 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013301/2013.301.02 to /data/auv_data/dorado/missionlogs/2013.301.02 INFO 2025-06-26 20:11:37,564 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.301.02 INFO 2025-06-26 20:11:37,564 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.301.02/ctdDriver.log (124134 bytes) INFO 2025-06-26 20:11:37,580 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.301.02/ctdDriver2.log (124127 bytes) INFO 2025-06-26 20:11:37,594 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.301.02/gps.log (25916 bytes) INFO 2025-06-26 20:11:37,603 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.301.02/hydroscatlog.log (116026 bytes) INFO 2025-06-26 20:11:37,622 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.301.02/navigation.log (425270 bytes) INFO 2025-06-26 20:11:37,664 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.301.02/parosci.log (163862 bytes) INFO 2025-06-26 20:11:37,681 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.301.02/tailCone.log (83707 bytes) INFO 2025-06-26 20:11:37,696 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.301.02/biolume.log (100390 bytes) INFO 2025-06-26 20:11:37,710 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 20:11:37,717 logs2netcdfs.py download_process_logs():807 [1] Time to process: 0.15 seconds INFO 2025-06-26 20:11:37,717 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.301.02/lopc.bin (396182 bytes) INFO 2025-06-26 20:11:37,717 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 20:11:37 2025 INFO 2025-06-26 20:11:37,717 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.301.02/parosci.nc INFO 2025-06-26 20:11:37,717 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:11:37,717 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.301.02/parosci.nc INFO 2025-06-26 20:11:37,718 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1382974069.0, sensor_off_time = 1382974415.2 INFO 2025-06-26 20:11:37,719 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 346 seconds. Expecting to read 692 L frames from the lopc.bin file. INFO 2025-06-26 20:11:37,719 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 692 records from the lopc.bin file. INFO 2025-06-26 20:11:37,723 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-10-28 15:27:49 Z and endTime = 2013-10-28 15:33:35 Z with 692 records expected to be read from lopc.bin INFO 2025-06-26 20:11:37,723 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.301.02/lopc.bin INFO 2025-06-26 20:11:37,723 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.301.02/lopc.nc INFO 2025-06-26 20:11:37,723 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.301.02/lopc.nc INFO 2025-06-26 20:11:37,723 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.301.02 INFO 2025-06-26 20:11:37,724 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 20:11:37,726 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 20:11:37,774 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 20:11:37,774 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 20:11:37,774 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ INFO 2025-06-26 20:11:38,225 lopcToNetCDF.py main():2345 [1] >>> Done reading file. INFO 2025-06-26 20:11:38,225 lopcToNetCDF.py main():2346 [1] lFrameCount = 702, mFrameCount = 1355 INFO 2025-06-26 20:11:38,225 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.301.02/parosci.nc INFO 2025-06-26 20:11:38,225 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 20:11:38,225 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.301.02/parosci.nc INFO 2025-06-26 20:11:38,227 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1382974069.0, sensor_off_time = 1382974415.2 INFO 2025-06-26 20:11:38,227 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 346 seconds. Expecting to read 692 L frames from the lopc.bin file. INFO 2025-06-26 20:11:38,227 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 692 records from the lopc.bin file. INFO 2025-06-26 20:11:38,227 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 1595 and len(sampleCountList) = 702 INFO 2025-06-26 20:11:38,227 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [] INFO 2025-06-26 20:11:38,227 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [ 1595 1596 1597 1598 1599 1600 1601 22983 22984 22985 22986 22987 22988 22989 22990 22991 22992 22993 22994 22995 22996 22997 22998 22999 23000 23001 23002 23003 23004 23005 23006 23007 23008 23009 23010 23011 23012 23013 23014 23015 23016 23017 23018 23019 23020 23021 23022 23023 23024 23025 23026 23027 23028 23029 23030 23031 23032 23033 23034 23035 23036 23037 23038 23039 23040 23041 23042 23043 23044 23045 23046 23047 23048 23049 23050 23051 23052 23053 23054 23055 23056 23057 23058 23059 23060 23061 23062 23063 23064 23065 23066 23067 23068 23069 23070 23071 23072 23073 23074 23075 23076 23077 23078 23079 23080 23081 23082 23083 23084 23085 23086 23087 23088 23089 23090 23091 23092 23093 23094 23095 23096 23097 23098 23099 23100 23101 23102 23103 23104 23105 23106 23107 23108 23109 23110 23111 23112 23113 23114 23115 23116 23117 23118 23119 23120 23121 23122 23123 23124 23125 23126 23127 23128 23129 23130 23131 23132 23133 23134 23135 23136 23137 23138 23139 23140 23141 23142 23143 23144 23145 23146 23147 23148 23149 23150 23151 23152 23153 23154 23155 23156 23157 23158 23159 23160 23161 23162 23163 23164 23165 23166 23167 23168 23169 23170 23171 23172 23173 23174 23175 23176 23177 23178 23179 23180 23181 23182 23183 23184 23185 23186 23187 23188 23189 23190 23191 23192 23193 23194 23195 23196 23197 23198 23199 23200 23201 23202 23203 23204 23205 23206 23207 23208 23209 23210 23211 23212 23213 23214 23215 23216 23217 23218 23219 23220 23221 23222 23223 23224 23225 23226 23227 23228 23229 23230 23231 23232 23233 23234 23235 23236 23237 23238 23239 23240 23241 23242 23243 23244 23245 23246 23247 23248 23249 23250 23251 23252 23253 23254 23255 23256 23257 23258 23259 23260 23261 23262 23263 23264 23265 23266 23267 23268 23269 23270 23271 23272 23273 23274 23275 23276 23277 23278 23279 23280 23281 23282 23283 23284 23285 23286 23287 23288 23289 23290 23291 23292 23293 23294 23295 23296 23297 23298 23299 23300 23301 23302 23303 23304 23305 23306 23307 23308 23309 23310 23311 23312 23313 23314 23315 23316 23317 23318 23319 23320 23321 23322 23323 23324 23325 23326 23327 23328 23329 23330 23331 23332 23333 23334 23335 23336 23337 23338 23339 23340 23341 23342 23343 23344 23345 23346 23347 23348 23349 23350 23351 23352 23353 23354 23355 23356 23357 23358 23359 23360 23361 23362 23363 23364 23365 23366 23367 23368 23369 23370 23371 23372 23373 23374 23375 23376 23377 23378 23379 23380 23381 23382 23383 23384 23385 23386 23387 23388 23389 23390 23391 23392 23393 23394 23395 23396 23397 23398 23399 23400 23401 23402 23403 23404 23405 23406 23407 23408 23409 23410 23411 23412 23413 23414 23415 23416 23417 23418 23419 23420 23421 23422 23423 23424 23425 23426 23427 23428 23429 23430 23431 23432 23433 23434 23435 23436 23437 23438 23439 23440 23441 23442 23443 23444 23445 23446 23447 23448 23449 23450 23451 23452 23453 23454 23455 23456 23457 23458 23459 23460 23461 23462 23463 23464 23465 23466 23467 23468 23469 23470 23471 23472 23473 23474 23475 23476 23477 23478 23479 23480 23481 23482 23483 23484 23485 23486 23487 23488 23489 23490 23491 23492 23493 23494 23495 23496 23497 23498 23499 23500 23501 23502 23503 23504 23505 23506 23507 23508 23509 23510 23511 23512 23513 23514 23515 23516 23517 23518 23519 23520 23521 23522 23523 23524 23525 23526 23527 23528 23529 23530 23531 23532 23533 23534 23535 23536 23537 23538 23539 23540 23541 23542 23543 23544 23545 23546 23547 23548 23549 23550 23551 23552 23553 23554 23555 23556 23557 23558 23559 23560 23561 23562 23563 23564 23565 23566 23567 23568 23569 23570 23571 23572 23573 23574 23575 23576 23577 23578 23579 23580 23581 23582 23583 23584 23585 23586 23587 23588 23589 23590 23591 23592 23593 23594 23595 23596 23597 23598 23599 23600 23601 23602 23603 23604 23605 23606 23607 23608 23609 23610 23611 23612 23613 23614 23615 23616 23617 23618 23619 23620 23621 23622 23623 23624 23625 23626 23627 23628 23629 23630 23631 23632 23633 23634 23635 23636 23637 23638 23639 23640 23641 23642 23643 23644 23645 23646 23647 23648 23649 23650 23651 23652 23653 23654 23655 23656 23657 23658 23659 23660 23661 23662 23663 23664 23665 23666 23667 23668 23669 23670 23671 23672 23673 23674 23675 23676 23677] INFO 2025-06-26 20:11:38,230 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 20:11:38,230 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-26 20:11:38,230 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [ 1 1 1 1 1 1 21382 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 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 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 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 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 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 20:11:38,232 lopcToNetCDF.py deSpike():1590 [1] Found 1 spike indicators at indices: [7] INFO 2025-06-26 20:11:38,232 lopcToNetCDF.py deSpike():1595 [1] Identifying nature of spike value = 22983 at index = 7 INFO 2025-06-26 20:11:38,232 lopcToNetCDF.py deSpike():1714 [1] This is the last element in spike_indx. No need to deSpike(). INFO 2025-06-26 20:11:38,232 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [ 1595 1596 1597 1598 1599 1600 1601 22983 22984 22985 22986 22987 22988 22989 22990 22991 22992 22993 22994 22995 22996 22997 22998 22999 23000 23001 23002 23003 23004 23005 23006 23007 23008 23009 23010 23011 23012 23013 23014 23015 23016 23017 23018 23019 23020 23021 23022 23023 23024 23025 23026 23027 23028 23029 23030 23031 23032 23033 23034 23035 23036 23037 23038 23039 23040 23041 23042 23043 23044 23045 23046 23047 23048 23049 23050 23051 23052 23053 23054 23055 23056 23057 23058 23059 23060 23061 23062 23063 23064 23065 23066 23067 23068 23069 23070 23071 23072 23073 23074 23075 23076 23077 23078 23079 23080 23081 23082 23083 23084 23085 23086 23087 23088 23089 23090 23091 23092 23093 23094 23095 23096 23097 23098 23099 23100 23101 23102 23103 23104 23105 23106 23107 23108 23109 23110 23111 23112 23113 23114 23115 23116 23117 23118 23119 23120 23121 23122 23123 23124 23125 23126 23127 23128 23129 23130 23131 23132 23133 23134 23135 23136 23137 23138 23139 23140 23141 23142 23143 23144 23145 23146 23147 23148 23149 23150 23151 23152 23153 23154 23155 23156 23157 23158 23159 23160 23161 23162 23163 23164 23165 23166 23167 23168 23169 23170 23171 23172 23173 23174 23175 23176 23177 23178 23179 23180 23181 23182 23183 23184 23185 23186 23187 23188 23189 23190 23191 23192 23193 23194 23195 23196 23197 23198 23199 23200 23201 23202 23203 23204 23205 23206 23207 23208 23209 23210 23211 23212 23213 23214 23215 23216 23217 23218 23219 23220 23221 23222 23223 23224 23225 23226 23227 23228 23229 23230 23231 23232 23233 23234 23235 23236 23237 23238 23239 23240 23241 23242 23243 23244 23245 23246 23247 23248 23249 23250 23251 23252 23253 23254 23255 23256 23257 23258 23259 23260 23261 23262 23263 23264 23265 23266 23267 23268 23269 23270 23271 23272 23273 23274 23275 23276 23277 23278 23279 23280 23281 23282 23283 23284 23285 23286 23287 23288 23289 23290 23291 23292 23293 23294 23295 23296 23297 23298 23299 23300 23301 23302 23303 23304 23305 23306 23307 23308 23309 23310 23311 23312 23313 23314 23315 23316 23317 23318 23319 23320 23321 23322 23323 23324 23325 23326 23327 23328 23329 23330 23331 23332 23333 23334 23335 23336 23337 23338 23339 23340 23341 23342 23343 23344 23345 23346 23347 23348 23349 23350 23351 23352 23353 23354 23355 23356 23357 23358 23359 23360 23361 23362 23363 23364 23365 23366 23367 23368 23369 23370 23371 23372 23373 23374 23375 23376 23377 23378 23379 23380 23381 23382 23383 23384 23385 23386 23387 23388 23389 23390 23391 23392 23393 23394 23395 23396 23397 23398 23399 23400 23401 23402 23403 23404 23405 23406 23407 23408 23409 23410 23411 23412 23413 23414 23415 23416 23417 23418 23419 23420 23421 23422 23423 23424 23425 23426 23427 23428 23429 23430 23431 23432 23433 23434 23435 23436 23437 23438 23439 23440 23441 23442 23443 23444 23445 23446 23447 23448 23449 23450 23451 23452 23453 23454 23455 23456 23457 23458 23459 23460 23461 23462 23463 23464 23465 23466 23467 23468 23469 23470 23471 23472 23473 23474 23475 23476 23477 23478 23479 23480 23481 23482 23483 23484 23485 23486 23487 23488 23489 23490 23491 23492 23493 23494 23495 23496 23497 23498 23499 23500 23501 23502 23503 23504 23505 23506 23507 23508 23509 23510 23511 23512 23513 23514 23515 23516 23517 23518 23519 23520 23521 23522 23523 23524 23525 23526 23527 23528 23529 23530 23531 23532 23533 23534 23535 23536 23537 23538 23539 23540 23541 23542 23543 23544 23545 23546 23547 23548 23549 23550 23551 23552 23553 23554 23555 23556 23557 23558 23559 23560 23561 23562 23563 23564 23565 23566 23567 23568 23569 23570 23571 23572 23573 23574 23575 23576 23577 23578 23579 23580 23581 23582 23583 23584 23585 23586 23587 23588 23589 23590 23591 23592 23593 23594 23595 23596 23597 23598 23599 23600 23601 23602 23603 23604 23605 23606 23607 23608 23609 23610 23611 23612 23613 23614 23615 23616 23617 23618 23619 23620 23621 23622 23623 23624 23625 23626 23627 23628 23629 23630 23631 23632 23633 23634 23635 23636 23637 23638 23639 23640 23641 23642 23643 23644 23645 23646 23647 23648 23649 23650 23651 23652 23653 23654 23655 23656 23657 23658 23659 23660 23661 23662 23663 23664 23665 23666 23667 23668 23669 23670 23671 23672 23673 23674 23675 23676 23677] INFO 2025-06-26 20:11:38,235 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [ 1595 1596 1597 1598 1599 1600 1601 22983 22984 22985 22986 22987 22988 22989 22990 22991 22992 22993 22994 22995 22996 22997 22998 22999 23000 23001 23002 23003 23004 23005 23006 23007 23008 23009 23010 23011 23012 23013 23014 23015 23016 23017 23018 23019 23020 23021 23022 23023 23024 23025 23026 23027 23028 23029 23030 23031 23032 23033 23034 23035 23036 23037 23038 23039 23040 23041 23042 23043 23044 23045 23046 23047 23048 23049 23050 23051 23052 23053 23054 23055 23056 23057 23058 23059 23060 23061 23062 23063 23064 23065 23066 23067 23068 23069 23070 23071 23072 23073 23074 23075 23076 23077 23078 23079 23080 23081 23082 23083 23084 23085 23086 23087 23088 23089 23090 23091 23092 23093 23094 23095 23096 23097 23098 23099 23100 23101 23102 23103 23104 23105 23106 23107 23108 23109 23110 23111 23112 23113 23114 23115 23116 23117 23118 23119 23120 23121 23122 23123 23124 23125 23126 23127 23128 23129 23130 23131 23132 23133 23134 23135 23136 23137 23138 23139 23140 23141 23142 23143 23144 23145 23146 23147 23148 23149 23150 23151 23152 23153 23154 23155 23156 23157 23158 23159 23160 23161 23162 23163 23164 23165 23166 23167 23168 23169 23170 23171 23172 23173 23174 23175 23176 23177 23178 23179 23180 23181 23182 23183 23184 23185 23186 23187 23188 23189 23190 23191 23192 23193 23194 23195 23196 23197 23198 23199 23200 23201 23202 23203 23204 23205 23206 23207 23208 23209 23210 23211 23212 23213 23214 23215 23216 23217 23218 23219 23220 23221 23222 23223 23224 23225 23226 23227 23228 23229 23230 23231 23232 23233 23234 23235 23236 23237 23238 23239 23240 23241 23242 23243 23244 23245 23246 23247 23248 23249 23250 23251 23252 23253 23254 23255 23256 23257 23258 23259 23260 23261 23262 23263 23264 23265 23266 23267 23268 23269 23270 23271 23272 23273 23274 23275 23276 23277 23278 23279 23280 23281 23282 23283 23284 23285 23286 23287 23288 23289 23290 23291 23292 23293 23294 23295 23296 23297 23298 23299 23300 23301 23302 23303 23304 23305 23306 23307 23308 23309 23310 23311 23312 23313 23314 23315 23316 23317 23318 23319 23320 23321 23322 23323 23324 23325 23326 23327 23328 23329 23330 23331 23332 23333 23334 23335 23336 23337 23338 23339 23340 23341 23342 23343 23344 23345 23346 23347 23348 23349 23350 23351 23352 23353 23354 23355 23356 23357 23358 23359 23360 23361 23362 23363 23364 23365 23366 23367 23368 23369 23370 23371 23372 23373 23374 23375 23376 23377 23378 23379 23380 23381 23382 23383 23384 23385 23386 23387 23388 23389 23390 23391 23392 23393 23394 23395 23396 23397 23398 23399 23400 23401 23402 23403 23404 23405 23406 23407 23408 23409 23410 23411 23412 23413 23414 23415 23416 23417 23418 23419 23420 23421 23422 23423 23424 23425 23426 23427 23428 23429 23430 23431 23432 23433 23434 23435 23436 23437 23438 23439 23440 23441 23442 23443 23444 23445 23446 23447 23448 23449 23450 23451 23452 23453 23454 23455 23456 23457 23458 23459 23460 23461 23462 23463 23464 23465 23466 23467 23468 23469 23470 23471 23472 23473 23474 23475 23476 23477 23478 23479 23480 23481 23482 23483 23484 23485 23486 23487 23488 23489 23490 23491 23492 23493 23494 23495 23496 23497 23498 23499 23500 23501 23502 23503 23504 23505 23506 23507 23508 23509 23510 23511 23512 23513 23514 23515 23516 23517 23518 23519 23520 23521 23522 23523 23524 23525 23526 23527 23528 23529 23530 23531 23532 23533 23534 23535 23536 23537 23538 23539 23540 23541 23542 23543 23544 23545 23546 23547 23548 23549 23550 23551 23552 23553 23554 23555 23556 23557 23558 23559 23560 23561 23562 23563 23564 23565 23566 23567 23568 23569 23570 23571 23572 23573 23574 23575 23576 23577 23578 23579 23580 23581 23582 23583 23584 23585 23586 23587 23588 23589 23590 23591 23592 23593 23594 23595 23596 23597 23598 23599 23600 23601 23602 23603 23604 23605 23606 23607 23608 23609 23610 23611 23612 23613 23614 23615 23616 23617 23618 23619 23620 23621 23622 23623 23624 23625 23626 23627 23628 23629 23630 23631 23632 23633 23634 23635 23636 23637 23638 23639 23640 23641 23642 23643 23644 23645 23646 23647 23648 23649 23650 23651 23652 23653 23654 23655 23656 23657 23658 23659 23660 23661 23662 23663 23664 23665 23666 23667 23668 23669 23670 23671 23672 23673 23674 23675 23676 23677] with len(correctedSampleCountList) = 702 INFO 2025-06-26 20:11:38,237 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 1595 from all values of correctedSampleCountList INFO 2025-06-26 20:11:38,237 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 20:11:38,237 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [0.00000e+00 5.00000e-01 1.00000e+00 1.50000e+00 2.00000e+00 2.50000e+00 3.00000e+00 1.06940e+04 1.06945e+04 1.06950e+04 1.06955e+04 1.06960e+04 1.06965e+04 1.06970e+04 1.06975e+04 1.06980e+04 1.06985e+04 1.06990e+04 1.06995e+04 1.07000e+04 1.07005e+04 1.07010e+04 1.07015e+04 1.07020e+04 1.07025e+04 1.07030e+04 1.07035e+04 1.07040e+04 1.07045e+04 1.07050e+04 1.07055e+04 1.07060e+04 1.07065e+04 1.07070e+04 1.07075e+04 1.07080e+04 1.07085e+04 1.07090e+04 1.07095e+04 1.07100e+04 1.07105e+04 1.07110e+04 1.07115e+04 1.07120e+04 1.07125e+04 1.07130e+04 1.07135e+04 1.07140e+04 1.07145e+04 1.07150e+04 1.07155e+04 1.07160e+04 1.07165e+04 1.07170e+04 1.07175e+04 1.07180e+04 1.07185e+04 1.07190e+04 1.07195e+04 1.07200e+04 1.07205e+04 1.07210e+04 1.07215e+04 1.07220e+04 1.07225e+04 1.07230e+04 1.07235e+04 1.07240e+04 1.07245e+04 1.07250e+04 1.07255e+04 1.07260e+04 1.07265e+04 1.07270e+04 1.07275e+04 1.07280e+04 1.07285e+04 1.07290e+04 1.07295e+04 1.07300e+04 1.07305e+04 1.07310e+04 1.07315e+04 1.07320e+04 1.07325e+04 1.07330e+04 1.07335e+04 1.07340e+04 1.07345e+04 1.07350e+04 1.07355e+04 1.07360e+04 1.07365e+04 1.07370e+04 1.07375e+04 1.07380e+04 1.07385e+04 1.07390e+04 1.07395e+04 1.07400e+04 1.07405e+04 1.07410e+04 1.07415e+04 1.07420e+04 1.07425e+04 1.07430e+04 1.07435e+04 1.07440e+04 1.07445e+04 1.07450e+04 1.07455e+04 1.07460e+04 1.07465e+04 1.07470e+04 1.07475e+04 1.07480e+04 1.07485e+04 1.07490e+04 1.07495e+04 1.07500e+04 1.07505e+04 1.07510e+04 1.07515e+04 1.07520e+04 1.07525e+04 1.07530e+04 1.07535e+04 1.07540e+04 1.07545e+04 1.07550e+04 1.07555e+04 1.07560e+04 1.07565e+04 1.07570e+04 1.07575e+04 1.07580e+04 1.07585e+04 1.07590e+04 1.07595e+04 1.07600e+04 1.07605e+04 1.07610e+04 1.07615e+04 1.07620e+04 1.07625e+04 1.07630e+04 1.07635e+04 1.07640e+04 1.07645e+04 1.07650e+04 1.07655e+04 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1.08490e+04 1.08495e+04 1.08500e+04 1.08505e+04 1.08510e+04 1.08515e+04 1.08520e+04 1.08525e+04 1.08530e+04 1.08535e+04 1.08540e+04 1.08545e+04 1.08550e+04 1.08555e+04 1.08560e+04 1.08565e+04 1.08570e+04 1.08575e+04 1.08580e+04 1.08585e+04 1.08590e+04 1.08595e+04 1.08600e+04 1.08605e+04 1.08610e+04 1.08615e+04 1.08620e+04 1.08625e+04 1.08630e+04 1.08635e+04 1.08640e+04 1.08645e+04 1.08650e+04 1.08655e+04 1.08660e+04 1.08665e+04 1.08670e+04 1.08675e+04 1.08680e+04 1.08685e+04 1.08690e+04 1.08695e+04 1.08700e+04 1.08705e+04 1.08710e+04 1.08715e+04 1.08720e+04 1.08725e+04 1.08730e+04 1.08735e+04 1.08740e+04 1.08745e+04 1.08750e+04 1.08755e+04 1.08760e+04 1.08765e+04 1.08770e+04 1.08775e+04 1.08780e+04 1.08785e+04 1.08790e+04 1.08795e+04 1.08800e+04 1.08805e+04 1.08810e+04 1.08815e+04 1.08820e+04 1.08825e+04 1.08830e+04 1.08835e+04 1.08840e+04 1.08845e+04 1.08850e+04 1.08855e+04 1.08860e+04 1.08865e+04 1.08870e+04 1.08875e+04 1.08880e+04 1.08885e+04 1.08890e+04 1.08895e+04 1.08900e+04 1.08905e+04 1.08910e+04 1.08915e+04 1.08920e+04 1.08925e+04 1.08930e+04 1.08935e+04 1.08940e+04 1.08945e+04 1.08950e+04 1.08955e+04 1.08960e+04 1.08965e+04 1.08970e+04 1.08975e+04 1.08980e+04 1.08985e+04 1.08990e+04 1.08995e+04 1.09000e+04 1.09005e+04 1.09010e+04 1.09015e+04 1.09020e+04 1.09025e+04 1.09030e+04 1.09035e+04 1.09040e+04 1.09045e+04 1.09050e+04 1.09055e+04 1.09060e+04 1.09065e+04 1.09070e+04 1.09075e+04 1.09080e+04 1.09085e+04 1.09090e+04 1.09095e+04 1.09100e+04 1.09105e+04 1.09110e+04 1.09115e+04 1.09120e+04 1.09125e+04 1.09130e+04 1.09135e+04 1.09140e+04 1.09145e+04 1.09150e+04 1.09155e+04 1.09160e+04 1.09165e+04 1.09170e+04 1.09175e+04 1.09180e+04 1.09185e+04 1.09190e+04 1.09195e+04 1.09200e+04 1.09205e+04 1.09210e+04 1.09215e+04 1.09220e+04 1.09225e+04 1.09230e+04 1.09235e+04 1.09240e+04 1.09245e+04 1.09250e+04 1.09255e+04 1.09260e+04 1.09265e+04 1.09270e+04 1.09275e+04 1.09280e+04 1.09285e+04 1.09290e+04 1.09295e+04 1.09300e+04 1.09305e+04 1.09310e+04 1.09315e+04 1.09320e+04 1.09325e+04 1.09330e+04 1.09335e+04 1.09340e+04 1.09345e+04 1.09350e+04 1.09355e+04 1.09360e+04 1.09365e+04 1.09370e+04 1.09375e+04 1.09380e+04 1.09385e+04 1.09390e+04 1.09395e+04 1.09400e+04 1.09405e+04 1.09410e+04 1.09415e+04 1.09420e+04 1.09425e+04 1.09430e+04 1.09435e+04 1.09440e+04 1.09445e+04 1.09450e+04 1.09455e+04 1.09460e+04 1.09465e+04 1.09470e+04 1.09475e+04 1.09480e+04 1.09485e+04 1.09490e+04 1.09495e+04 1.09500e+04 1.09505e+04 1.09510e+04 1.09515e+04 1.09520e+04 1.09525e+04 1.09530e+04 1.09535e+04 1.09540e+04 1.09545e+04 1.09550e+04 1.09555e+04 1.09560e+04 1.09565e+04 1.09570e+04 1.09575e+04 1.09580e+04 1.09585e+04 1.09590e+04 1.09595e+04 1.09600e+04 1.09605e+04 1.09610e+04 1.09615e+04 1.09620e+04 1.09625e+04 1.09630e+04 1.09635e+04 1.09640e+04 1.09645e+04 1.09650e+04 1.09655e+04 1.09660e+04 1.09665e+04 1.09670e+04 1.09675e+04 1.09680e+04 1.09685e+04 1.09690e+04 1.09695e+04 1.09700e+04 1.09705e+04 1.09710e+04 1.09715e+04 1.09720e+04 1.09725e+04 1.09730e+04 1.09735e+04 1.09740e+04 1.09745e+04 1.09750e+04 1.09755e+04 1.09760e+04 1.09765e+04 1.09770e+04 1.09775e+04 1.09780e+04 1.09785e+04 1.09790e+04 1.09795e+04 1.09800e+04 1.09805e+04 1.09810e+04 1.09815e+04 1.09820e+04 1.09825e+04 1.09830e+04 1.09835e+04 1.09840e+04 1.09845e+04 1.09850e+04 1.09855e+04 1.09860e+04 1.09865e+04 1.09870e+04 1.09875e+04 1.09880e+04 1.09885e+04 1.09890e+04 1.09895e+04 1.09900e+04 1.09905e+04 1.09910e+04 1.09915e+04 1.09920e+04 1.09925e+04 1.09930e+04 1.09935e+04 1.09940e+04 1.09945e+04 1.09950e+04 1.09955e+04 1.09960e+04 1.09965e+04 1.09970e+04 1.09975e+04 1.09980e+04 1.09985e+04 1.09990e+04 1.09995e+04 1.10000e+04 1.10005e+04 1.10010e+04 1.10015e+04 1.10020e+04 1.10025e+04 1.10030e+04 1.10035e+04 1.10040e+04 1.10045e+04 1.10050e+04 1.10055e+04 1.10060e+04 1.10065e+04 1.10070e+04 1.10075e+04 1.10080e+04 1.10085e+04 1.10090e+04 1.10095e+04 1.10100e+04 1.10105e+04 1.10110e+04 1.10115e+04 1.10120e+04 1.10125e+04 1.10130e+04 1.10135e+04 1.10140e+04 1.10145e+04 1.10150e+04 1.10155e+04 1.10160e+04 1.10165e+04 1.10170e+04 1.10175e+04 1.10180e+04 1.10185e+04 1.10190e+04 1.10195e+04 1.10200e+04 1.10205e+04 1.10210e+04 1.10215e+04 1.10220e+04 1.10225e+04 1.10230e+04 1.10235e+04 1.10240e+04 1.10245e+04 1.10250e+04 1.10255e+04 1.10260e+04 1.10265e+04 1.10270e+04 1.10275e+04 1.10280e+04 1.10285e+04 1.10290e+04 1.10295e+04 1.10300e+04 1.10305e+04 1.10310e+04 1.10315e+04 1.10320e+04 1.10325e+04 1.10330e+04 1.10335e+04 1.10340e+04 1.10345e+04 1.10350e+04 1.10355e+04 1.10360e+04 1.10365e+04 1.10370e+04 1.10375e+04 1.10380e+04 1.10385e+04 1.10390e+04 1.10395e+04 1.10400e+04 1.10405e+04 1.10410e+04] INFO 2025-06-26 20:11:38,243 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.38297407e+09 1.38297407e+09 1.38297407e+09 1.38297407e+09 1.38297407e+09 1.38297407e+09 1.38297407e+09 1.38298476e+09 1.38298476e+09 1.38298476e+09 1.38298476e+09 1.38298477e+09 1.38298477e+09 1.38298477e+09 1.38298477e+09 1.38298477e+09 1.38298477e+09 1.38298477e+09 1.38298477e+09 1.38298477e+09 1.38298477e+09 1.38298477e+09 1.38298477e+09 1.38298477e+09 1.38298477e+09 1.38298477e+09 1.38298477e+09 1.38298477e+09 1.38298477e+09 1.38298477e+09 1.38298477e+09 1.38298478e+09 1.38298478e+09 1.38298478e+09 1.38298478e+09 1.38298478e+09 1.38298478e+09 1.38298478e+09 1.38298478e+09 1.38298478e+09 1.38298478e+09 1.38298478e+09 1.38298478e+09 1.38298478e+09 1.38298478e+09 1.38298478e+09 1.38298478e+09 1.38298478e+09 1.38298478e+09 1.38298478e+09 1.38298478e+09 1.38298479e+09 1.38298479e+09 1.38298479e+09 1.38298479e+09 1.38298479e+09 1.38298479e+09 1.38298479e+09 1.38298479e+09 1.38298479e+09 1.38298479e+09 1.38298479e+09 1.38298479e+09 1.38298479e+09 1.38298479e+09 1.38298479e+09 1.38298479e+09 1.38298479e+09 1.38298479e+09 1.38298479e+09 1.38298479e+09 1.38298480e+09 1.38298480e+09 1.38298480e+09 1.38298480e+09 1.38298480e+09 1.38298480e+09 1.38298480e+09 1.38298480e+09 1.38298480e+09 1.38298480e+09 1.38298480e+09 1.38298480e+09 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1.38298510e+09 1.38298510e+09 1.38298510e+09 1.38298510e+09 1.38298510e+09 1.38298510e+09 1.38298510e+09 1.38298510e+09 1.38298510e+09 1.38298510e+09 1.38298510e+09 1.38298510e+09 1.38298510e+09 1.38298510e+09 1.38298511e+09 1.38298511e+09 1.38298511e+09 1.38298511e+09 1.38298511e+09 1.38298511e+09 1.38298511e+09 1.38298511e+09 1.38298511e+09 1.38298511e+09 1.38298511e+09] INFO 2025-06-26 20:11:38,249 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1382974069.0 1382974069.5, ..., timestampArray[-2:] = 1382985109.5 1382985110.0] INFO 2025-06-26 20:11:38,250 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1382974069.0202882), np.float64(1382974069.5202882)], ..., timestampList[-2:] = [np.float64(1382985109.5202882), np.float64(1382985110.0202882)]] INFO 2025-06-26 20:11:38,250 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 702) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 20:11:38,250 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [671, 692] INFO 2025-06-26 20:11:38,250 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 33 INFO 2025-06-26 20:11:38,250 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 702 INFO 2025-06-26 20:11:38,250 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1382974069.0202882), np.float64(1382974069.5202882)], ..., timestampList[-2:] = [np.float64(1382985109.5202882), np.float64(1382985110.0202882)]] INFO 2025-06-26 20:11:38,250 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 702) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 20:11:38,250 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(670), np.int32(691)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 20:11:38,250 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 33 INFO 2025-06-26 20:11:38,250 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 INFO 2025-06-26 20:11:38,252 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 33 INFO 2025-06-26 20:11:38,252 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1382984769.0202882)], ..., tsList[-2:] = [np.float64(1382985094.5202882), np.float64(1382985105.0202882)] INFO 2025-06-26 20:11:38,252 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2013-10-28 18:26:09 Z INFO 2025-06-26 20:11:38,252 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2013-10-28 18:31:45 Z INFO 2025-06-26 20:11:38,252 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 33 INFO 2025-06-26 20:11:38,252 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [1.3829744e+09], ..., cFrameEsecsList[-2:] = [1.3829744e+09 1.3829744e+09] INFO 2025-06-26 20:11:38,252 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 2013-10-28 15:33:17 Z INFO 2025-06-26 20:11:38,252 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 2013-10-28 15:33:17 Z INFO 2025-06-26 20:11:38,256 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2013.301.02/lopc.nc INFO 2025-06-26 20:11:38,256 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 20:11:38 2025 Elapsed processing time from start of processing = 0 seconds INFO 2025-06-26 20:11:38,256 process.py calibrate():227 [1] Calibration steps for 2013.301.02 INFO 2025-06-26 20:11:38,313 calibrate.py _navigation_process():1584 [1] Bypassing Nav QC depth check INFO 2025-06-26 20:11:38,316 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 20:11:38,318 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 20:11:41,201 calibrate.py _nudge_pos():1862 [1] 311: - - - 4 0.01 - - INFO 2025-06-26 20:11:41,201 calibrate.py _nudge_pos():1868 [1] Points in final series = 1362 INFO 2025-06-26 20:11:41,236 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 4 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:11:41,269 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 24 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:11:41,281 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 24 seconds, d_end_time_diff: 0 seconds INFO 2025-06-26 20:11:41,282 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.301.02/ctd1.nc INFO 2025-06-26 20:11:41,283 calibrate.py _range_qc_combined_nc():898 [1] Setting 168 ctd1_salinity values to NaN INFO 2025-06-26 20:11:41,283 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 20:11:41,284 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 20:11:41,309 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:11:41,321 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 24 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 20:11:41,322 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.301.02/ctd2.nc INFO 2025-06-26 20:11:41,323 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 20:11:41,323 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 20:11:41,323 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 ERROR 2025-06-26 20:11:41,324 calibrate.py process_logs():3542 [1] Error processing isus: isus has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.301.02 INFO 2025-06-26 20:11:41,325 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 20:11:41,344 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 20:11:41,362 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.301.02 INFO 2025-06-26 20:11:41,367 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.301.02/dorado_2013.301.02_cal.nc INFO 2025-06-26 20:11:41,411 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 20:11:41,416 process.py align():251 [1] Alignment steps for 2013.301.02 INFO 2025-06-26 20:11:41,439 align.py process_cal():139 [1] Processing dorado_2013.301.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.301.02 INFO 2025-06-26 20:11:41,443 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:11:41,445 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:11:41,456 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:11:41,457 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:11:41,467 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:11:41,468 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:11:41,474 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 20:11:41,474 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 20:11:41,477 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 20:11:41,479 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:11:41,488 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,489 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,499 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,501 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,509 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,511 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,520 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,521 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,531 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,532 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,541 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,543 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,554 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,555 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,564 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,566 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,574 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,576 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,585 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,586 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,595 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,597 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,606 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,608 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,617 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,618 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,628 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,629 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,638 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,640 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,650 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,651 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,661 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,662 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,672 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,673 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,682 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,684 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,694 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,695 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,705 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,706 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,716 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.301.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 20:11:41,717 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 20:11:41,730 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:11:41,743 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 20:11:41,755 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 20:11:41,775 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:11:41,788 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:11:41,801 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:11:41,814 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:11:41,827 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 20:11:41,840 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 20:11:41,850 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.301.02/dorado_2013.301.02_align.nc INFO 2025-06-26 20:11:41,902 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 20:11:41,905 process.py resample():273 [1] Resampling steps for 2013.301.02 INFO 2025-06-26 20:11:41,905 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 20:11:41,927 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.301.02/dorado_2013.301.02_align.nc mission netCDF file INFO 2025-06-26 20:11:41,932 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.301.02/dorado_2013.301.02_align.nc mission netCDF file INFO 2025-06-26 20:11:41,933 resample.py get_mission_start_end():1145 [1] navigation: 2013-10-28T15:28:24.337869056 to 2013-10-28T15:33:35.126578432 (0 days 02:58:09.893709824 before mission_end) WARNING 2025-06-26 20:11:41,934 resample.py get_mission_start_end():1156 [1] Instrument navigation has a gap > 5 minutes at the end of the mission: 0 days 02:58:09.893709824 INFO 2025-06-26 20:11:41,935 resample.py get_mission_start_end():1145 [1] hs2 : 2013-10-28T15:27:53.140006144 to 2013-10-28T15:33:35.126578432 (0 days 02:58:09.893709824 before mission_end) WARNING 2025-06-26 20:11:41,936 resample.py get_mission_start_end():1156 [1] Instrument hs2 has a gap > 5 minutes at the end of the mission: 0 days 02:58:09.893709824 INFO 2025-06-26 20:11:41,936 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-10-28T15:28:13.938581248 to 2013-10-28T15:33:35.166575616 (0 days 02:58:09.853712640 before mission_end) WARNING 2025-06-26 20:11:41,937 resample.py get_mission_start_end():1156 [1] Instrument ctd1 has a gap > 5 minutes at the end of the mission: 0 days 02:58:09.853712640 INFO 2025-06-26 20:11:41,938 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-10-28T15:28:13.818589440 to 2013-10-28T15:33:35.046583808 (0 days 02:58:09.973704448 before mission_end) WARNING 2025-06-26 20:11:41,939 resample.py get_mission_start_end():1156 [1] Instrument ctd2 has a gap > 5 minutes at the end of the mission: 0 days 02:58:09.973704448 INFO 2025-06-26 20:11:41,940 resample.py get_mission_start_end():1145 [1] biolume : 2013-10-28T15:27:46.560422400 to 2013-10-28T15:33:34.436591360 (0 days 02:58:10.583696896 before mission_end) WARNING 2025-06-26 20:11:41,941 resample.py get_mission_start_end():1156 [1] Instrument biolume has a gap > 5 minutes at the end of the mission: 0 days 02:58:10.583696896 INFO 2025-06-26 20:11:41,942 resample.py get_mission_start_end():1145 [1] lopc : 2013-10-28T18:26:09.020288256 to 2013-10-28T18:31:45.020288256 (0 days 00:00:00 before mission_end) INFO 2025-06-26 20:11:41,943 resample.py get_mission_start_end():1145 [1] tailcone : 2013-10-28T15:27:48.750306816 to 2013-10-28T15:33:35.136577536 (0 days 02:58:09.883710720 before mission_end) WARNING 2025-06-26 20:11:41,943 resample.py get_mission_start_end():1156 [1] Instrument tailcone has a gap > 5 minutes at the end of the mission: 0 days 02:58:09.883710720 INFO 2025-06-26 20:11:41,944 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.301.02/dorado_2013.301.02_align.nc mission netCDF file INFO 2025-06-26 20:11:41,944 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:41,973 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:41,973 resample.py resample_variable():1038 [1] Padding navigation_roll with 0 days 02:58:09.893709824 of NaNs to the end of mission INFO 2025-06-26 20:11:41,983 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:41,983 resample.py resample_variable():1038 [1] Padding navigation_pitch with 0 days 02:58:09.893709824 of NaNs to the end of mission INFO 2025-06-26 20:11:41,991 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:41,992 resample.py resample_variable():1038 [1] Padding navigation_yaw with 0 days 02:58:09.893709824 of NaNs to the end of mission INFO 2025-06-26 20:11:42,000 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,000 resample.py resample_variable():1038 [1] Padding navigation_mWaterSpeed with 0 days 02:58:09.893709824 of NaNs to the end of mission INFO 2025-06-26 20:11:42,010 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,010 resample.py resample_variable():1038 [1] Padding hs2_bbp420 with 0 days 02:58:09.893709824 of NaNs to the end of mission INFO 2025-06-26 20:11:42,019 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,019 resample.py resample_variable():1038 [1] Padding hs2_bbp700 with 0 days 02:58:09.893709824 of NaNs to the end of mission INFO 2025-06-26 20:11:42,027 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,028 resample.py resample_variable():1038 [1] Padding hs2_fl700 with 0 days 02:58:09.893709824 of NaNs to the end of mission INFO 2025-06-26 20:11:42,036 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,036 resample.py resample_variable():1038 [1] Padding ctd1_temperature with 0 days 02:58:09.853712640 of NaNs to the end of mission INFO 2025-06-26 20:11:42,044 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,044 resample.py resample_variable():1038 [1] Padding ctd1_conductivity with 0 days 02:58:09.853712640 of NaNs to the end of mission INFO 2025-06-26 20:11:42,053 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,053 resample.py resample_variable():1038 [1] Padding ctd1_salinity with 0 days 02:58:09.853712640 of NaNs to the end of mission INFO 2025-06-26 20:11:42,061 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,061 resample.py resample_variable():1038 [1] Padding ctd1_temperature_onboard with 0 days 02:58:09.853712640 of NaNs to the end of mission INFO 2025-06-26 20:11:42,069 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,069 resample.py resample_variable():1038 [1] Padding ctd1_conductivity_onboard with 0 days 02:58:09.853712640 of NaNs to the end of mission INFO 2025-06-26 20:11:42,078 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,078 resample.py resample_variable():1038 [1] Padding ctd1_salinity_onboard with 0 days 02:58:09.853712640 of NaNs to the end of mission INFO 2025-06-26 20:11:42,086 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,087 resample.py resample_variable():1038 [1] Padding ctd1_dissolvedO2 with 0 days 02:58:09.853712640 of NaNs to the end of mission INFO 2025-06-26 20:11:42,095 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,095 resample.py resample_variable():1038 [1] Padding ctd1_oxygen_mll with 0 days 02:58:09.853712640 of NaNs to the end of mission INFO 2025-06-26 20:11:42,103 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,103 resample.py resample_variable():1038 [1] Padding ctd1_oxygen_umolkg with 0 days 02:58:09.853712640 of NaNs to the end of mission INFO 2025-06-26 20:11:42,111 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,111 resample.py resample_variable():1038 [1] Padding ctd1_flow1 with 0 days 02:58:09.853712640 of NaNs to the end of mission INFO 2025-06-26 20:11:42,121 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,121 resample.py resample_variable():1038 [1] Padding ctd2_temperature with 0 days 02:58:09.973704448 of NaNs to the end of mission INFO 2025-06-26 20:11:42,130 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,131 resample.py resample_variable():1038 [1] Padding ctd2_conductivity with 0 days 02:58:09.973704448 of NaNs to the end of mission INFO 2025-06-26 20:11:42,140 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,140 resample.py resample_variable():1038 [1] Padding ctd2_salinity with 0 days 02:58:09.973704448 of NaNs to the end of mission INFO 2025-06-26 20:11:42,149 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,149 resample.py resample_variable():1038 [1] Padding ctd2_temperature_onboard with 0 days 02:58:09.973704448 of NaNs to the end of mission INFO 2025-06-26 20:11:42,157 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,157 resample.py resample_variable():1038 [1] Padding ctd2_conductivity_onboard with 0 days 02:58:09.973704448 of NaNs to the end of mission INFO 2025-06-26 20:11:42,166 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,166 resample.py resample_variable():1038 [1] Padding ctd2_salinity_onboard with 0 days 02:58:09.973704448 of NaNs to the end of mission INFO 2025-06-26 20:11:42,175 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,175 resample.py resample_variable():1038 [1] Padding ctd2_flow2 with 0 days 02:58:09.973704448 of NaNs to the end of mission INFO 2025-06-26 20:11:42,182 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,182 resample.py resample_variable():1038 [1] Padding biolume_flow with 0 days 02:58:10.583696896 of NaNs to the end of mission INFO 2025-06-26 20:11:42,189 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,189 resample.py resample_variable():1038 [1] Padding biolume_avg_biolume with 0 days 02:58:10.583696896 of NaNs to the end of mission INFO 2025-06-26 20:11:42,193 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 20:11:42,193 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 20:11:42,207 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 20:11:42,213 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 20:11:42,218 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 20:11:42,220 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 20:11:42,223 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 20:11:42,223 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 20:11:42,235 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,243 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,251 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,259 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,266 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,275 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 20:11:42,275 resample.py resample_variable():1038 [1] Padding tailcone_propRpm with 0 days 02:58:09.883710720 of NaNs to the end of mission INFO 2025-06-26 20:11:42,391 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.301.02/dorado_2013.301.02_1S.nc INFO 2025-06-26 20:11:44,322 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 20:11:46,040 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.301.02/dorado_2013.301.02_1S_Gulper.txt INFO 2025-06-26 20:11:46,040 process.py archive():337 [1] Archiving steps for 2013.301.02 INFO 2025-06-26 20:11:46,040 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.301.02/dorado_2013.301.02, BASE_PATH = /data/auv_data INFO 2025-06-26 20:11:46,042 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.301.02/dorado_2013.301.02 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 20:11:46,042 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.301.02_1S.nc INFO 2025-06-26 20:11:46,048 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.301.02/dorado_2013.301.02_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:11:46,049 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.301.02_cal.nc INFO 2025-06-26 20:11:46,059 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.301.02/dorado_2013.301.02_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:11:46,060 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.301.02_align.nc INFO 2025-06-26 20:11:46,070 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.301.02/dorado_2013.301.02_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 20:11:46,078 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.301.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013301/2013.301.02 done. INFO 2025-06-26 20:11:46,083 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.301.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013301/2013.301.02 done. INFO 2025-06-26 20:11:46,086 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.301.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013301/2013.301.02 done. INFO 2025-06-26 20:11:46,091 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.301.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013301/2013.301.02 done. INFO 2025-06-26 20:11:46,096 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.301.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013301/2013.301.02 done. INFO 2025-06-26 20:11:46,102 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.301.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013301/2013.301.02 done. INFO 2025-06-26 20:11:46,106 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.301.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013301/2013.301.02 done. INFO 2025-06-26 20:11:46,112 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.301.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013301/2013.301.02 done. INFO 2025-06-26 20:11:46,119 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.301.02/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013301/2013.301.02 done. INFO 2025-06-26 20:11:46,119 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 20:11:46,120 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.301.02_1S_Gulper.txt INFO 2025-06-26 20:11:46,125 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.301.02/dorado_2013.301.02_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 20:11:46,125 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.301.02/dorado_2013.301.02_processing.log /Volumes/AUVCTD/surveys/2013/netcdf