INFO 2025-06-26 16:21:31,953 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 16:21:31,953 process.py process_mission():434 [1] dorado_info[mission]["comment"] = Inner-bay survey third one for BloomEx in October 2010 - Tight survey around stell drifters - ctdToUse = ctd1 INFO 2025-06-26 16:21:31,953 process.py process_mission():449 [1] Processing AUVCTD mission 2010.279.02 by user docker_user on host eae60d30a712 INFO 2025-06-26 16:21:31,953 process.py download_process():165 [1] Download and processing steps for 2010.279.02 INFO 2025-06-26 16:21:31,953 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2010/2010279/2010.279.02 INFO 2025-06-26 16:21:31,954 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2010/2010279/2010.279.02 to /data/auv_data/dorado/missionlogs/2010.279.02 INFO 2025-06-26 16:21:38,810 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2010.279.02 INFO 2025-06-26 16:21:38,811 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.279.02/ctdDriver.log (19223051 bytes) INFO 2025-06-26 16:21:40,163 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.279.02/ctdDriver.log: [ 91 226 241 306 437 795 1035 1190 1923 2261 2294 2309 2372 2831 3992 4054 4199 4211 6019 6872 8252 8835 13632 15232 17277 19412 20426 20632 24400 27131 29996 30751 32137 33145 34071 37419 38634 39449 43257 45752 47507 49503 49530 49886 51478 52231 54557 54975 55276 61710 66741 67237 67417 69522 72019 77613 79341 79605 81109 81349 85499 87554 90233 91941 93445 93949 97158 99683 99796 116151 116824 118502 118907 119948 125519 134536 138647 141530 142202 146153 146966 153652 159666 160028 173615 177672 182902 183805 185048 189656 192681 196113 196336] INFO 2025-06-26 16:21:40,220 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.279.02/ctdDriver2.log (19222655 bytes) INFO 2025-06-26 16:21:41,666 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.279.02/ctdDriver2.log: [ 86 222 237 545 613 837 1031 1505 2257 2480 2940 3139 3654 3836 4050 4207 6015 7963 8273 8344 13448 15288 19332 19408 20628 21328 24396 24880 26991 27127 28306 29992 32133 35138 37415 38630 39445 39609 39707 47503 49499 57005 61706 62852 63674 65331 67233 67447 72274 77609 78713 79337 79601 81105 81345 82580 85495 87550 88160 90229 91937 93945 97154 99792 101151 104477 116147 116820 118498 118903 134532 138643 141526 141961 141997 146962 155418 155472 157166 159662 160024 173611 177668 179009 179401 183801 189652 192677 196109 196332] INFO 2025-06-26 16:21:41,731 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.279.02/gps.log (420836 bytes) INFO 2025-06-26 16:21:41,784 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.279.02/hydroscatlog.log (16819426 bytes) INFO 2025-06-26 16:21:43,496 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2010.279.02/hydroscatlog.log: [ 1 112 173 482 595 875 1447 1516 1518 1562 1590 2003 2374 2912 3153 3582 4073 5606 6323 6575 8116 8356 9134 10232 10974 11960 12050 12055 13502 15014 15368 16742 19410 20497 25445 29067 30063 32204 33432 34566 38696 39879 39887 40846 42063 47015 51497 54536 54822 57007 60040 60995 61467 65384 65431 67466 69356 73844 79566 79920 79995 87868 88206 93484 97707 99837 105652 108684 112839 113258 114697 116178 126686 132749 133709 136819 141410 141977 142214 144604 147662 155179 159887 161157 168705 169878 172529 173613 173826 181111 182534 185957 188044 189646 192018 196322 196753] INFO 2025-06-26 16:21:43,552 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.279.02/navigation.log (58969682 bytes) INFO 2025-06-26 16:21:47,981 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.279.02/isuslog.log (1243829 bytes) INFO 2025-06-26 16:21:48,107 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.279.02/parosci.log (21951446 bytes) INFO 2025-06-26 16:21:49,984 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.279.02/tailCone.log (11993947 bytes) INFO 2025-06-26 16:21:51,536 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2010.279.02/biolume.log (13988558 bytes) INFO 2025-06-26 16:21:53,038 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 16:21:53,766 logs2netcdfs.py download_process_logs():807 [1] Time to process: 14.96 seconds INFO 2025-06-26 16:21:53,767 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2010.279.02/lopc.bin (178343000 bytes) INFO 2025-06-26 16:21:53,767 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 16:21:53 2025 INFO 2025-06-26 16:21:53,767 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2010.279.02/parosci.nc INFO 2025-06-26 16:21:53,767 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 16:21:53,767 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2010.279.02/parosci.nc INFO 2025-06-26 16:21:53,770 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1286401904.0, sensor_off_time = 1286451987.9 INFO 2025-06-26 16:21:53,771 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 50083 seconds. Expecting to read 100166 L frames from the lopc.bin file. INFO 2025-06-26 16:21:53,771 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 100166 records from the lopc.bin file. INFO 2025-06-26 16:21:54,363 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2010-10-06 21:51:44 Z and endTime = 2010-10-07 11:46:27 Z with 100166 records expected to be read from lopc.bin INFO 2025-06-26 16:21:54,364 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2010.279.02/lopc.bin INFO 2025-06-26 16:21:54,364 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2010.279.02/lopc.nc INFO 2025-06-26 16:21:54,364 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2010.279.02/lopc.nc INFO 2025-06-26 16:21:54,365 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2010.279.02 INFO 2025-06-26 16:21:54,365 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 16:21:54,369 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A0214901 WARNING 2025-06-26 16:21:54,370 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 16:21:54,529 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 16:21:54,529 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 16:21:54,529 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 16:21:54,772 lopcToNetCDF.py main():2340 [1] UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb6 in position 0: invalid start byte INFO 2025-06-26 16:21:54,772 lopcToNetCDF.py main():2341 [1] Failed to decode all of lopc.bin - resulting lopc.nc file likely incomplete INFO 2025-06-26 16:21:54,772 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2010.279.02/parosci.nc INFO 2025-06-26 16:21:54,772 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 16:21:54,772 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2010.279.02/parosci.nc INFO 2025-06-26 16:21:54,776 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1286401904.0, sensor_off_time = 1286451987.9 INFO 2025-06-26 16:21:54,776 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 50083 seconds. Expecting to read 100166 L frames from the lopc.bin file. INFO 2025-06-26 16:21:54,776 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 100166 records from the lopc.bin file. INFO 2025-06-26 16:21:54,776 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 1950 and len(sampleCountList) = 201 INFO 2025-06-26 16:21:54,776 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [] INFO 2025-06-26 16:21:54,776 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [1950 1951 2476 2477 2478 2479 2480 2481 2482 2483 2484 2485 2486 2487 2488 2489 2490 2491 2492 2493 2494 2495 2496 2497 2498 2499 2500 2501 2502 2503 2504 2505 2506 2507 2508 2509 2510 2511 2512 2513 2514 2515 2516 2517 2518 2519 2520 2521 2522 2523 2524 2525 2526 2527 2528 2529 2530 2531 2532 2533 2534 2535 2536 2537 2538 2539 2540 2541 2542 2543 2544 2545 2546 2547 2548 2549 2550 2551 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 2562 2563 2564 2565 2566 2567 2568 2569 2570 2571 2572 2573 2574 2575 2576 2577 2578 2579 2580 2581 2582 2583 2584 2585 2586 2587 2588 2589 2590 2591 2592 2593 2594 2595 2596 2597 2598 2599 2600 2601 2602 2603 2604 2605 2606 2607 2608 2609 2610 2611 2612 2613 2614 2615 2616 2617 2618 2619 2620 2621 2622 2623 2624 2625 2626 2627 2628 2629 2630 2631 2632 2633 2634 2635 2636 2637 2638 2639 2640 2641 2642 2643 2644 2645 2646 2647 2648 2649 2650 2651 2652 2653 2654 2655 2656 2657 2658 2659 2660 2661 2662 2663 2664 2665 2666 2667 2668 2669 2670 2671 2672 2673 2674] INFO 2025-06-26 16:21:54,777 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 16:21:54,777 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-26 16:21:54,777 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [ 1 525 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 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 16:21:54,778 lopcToNetCDF.py deSpike():1590 [1] Found 1 spike indicators at indices: [2] INFO 2025-06-26 16:21:54,778 lopcToNetCDF.py deSpike():1595 [1] Identifying nature of spike value = 2476 at index = 2 INFO 2025-06-26 16:21:54,778 lopcToNetCDF.py deSpike():1714 [1] This is the last element in spike_indx. No need to deSpike(). INFO 2025-06-26 16:21:54,778 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [1950 1951 2476 2477 2478 2479 2480 2481 2482 2483 2484 2485 2486 2487 2488 2489 2490 2491 2492 2493 2494 2495 2496 2497 2498 2499 2500 2501 2502 2503 2504 2505 2506 2507 2508 2509 2510 2511 2512 2513 2514 2515 2516 2517 2518 2519 2520 2521 2522 2523 2524 2525 2526 2527 2528 2529 2530 2531 2532 2533 2534 2535 2536 2537 2538 2539 2540 2541 2542 2543 2544 2545 2546 2547 2548 2549 2550 2551 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 2562 2563 2564 2565 2566 2567 2568 2569 2570 2571 2572 2573 2574 2575 2576 2577 2578 2579 2580 2581 2582 2583 2584 2585 2586 2587 2588 2589 2590 2591 2592 2593 2594 2595 2596 2597 2598 2599 2600 2601 2602 2603 2604 2605 2606 2607 2608 2609 2610 2611 2612 2613 2614 2615 2616 2617 2618 2619 2620 2621 2622 2623 2624 2625 2626 2627 2628 2629 2630 2631 2632 2633 2634 2635 2636 2637 2638 2639 2640 2641 2642 2643 2644 2645 2646 2647 2648 2649 2650 2651 2652 2653 2654 2655 2656 2657 2658 2659 2660 2661 2662 2663 2664 2665 2666 2667 2668 2669 2670 2671 2672 2673 2674] INFO 2025-06-26 16:21:54,779 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [1950 1951 2476 2477 2478 2479 2480 2481 2482 2483 2484 2485 2486 2487 2488 2489 2490 2491 2492 2493 2494 2495 2496 2497 2498 2499 2500 2501 2502 2503 2504 2505 2506 2507 2508 2509 2510 2511 2512 2513 2514 2515 2516 2517 2518 2519 2520 2521 2522 2523 2524 2525 2526 2527 2528 2529 2530 2531 2532 2533 2534 2535 2536 2537 2538 2539 2540 2541 2542 2543 2544 2545 2546 2547 2548 2549 2550 2551 2552 2553 2554 2555 2556 2557 2558 2559 2560 2561 2562 2563 2564 2565 2566 2567 2568 2569 2570 2571 2572 2573 2574 2575 2576 2577 2578 2579 2580 2581 2582 2583 2584 2585 2586 2587 2588 2589 2590 2591 2592 2593 2594 2595 2596 2597 2598 2599 2600 2601 2602 2603 2604 2605 2606 2607 2608 2609 2610 2611 2612 2613 2614 2615 2616 2617 2618 2619 2620 2621 2622 2623 2624 2625 2626 2627 2628 2629 2630 2631 2632 2633 2634 2635 2636 2637 2638 2639 2640 2641 2642 2643 2644 2645 2646 2647 2648 2649 2650 2651 2652 2653 2654 2655 2656 2657 2658 2659 2660 2661 2662 2663 2664 2665 2666 2667 2668 2669 2670 2671 2672 2673 2674] with len(correctedSampleCountList) = 201 INFO 2025-06-26 16:21:54,780 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 1950 from all values of correctedSampleCountList INFO 2025-06-26 16:21:54,780 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 16:21:54,780 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [ 0. 0.5 263. 263.5 264. 264.5 265. 265.5 266. 266.5 267. 267.5 268. 268.5 269. 269.5 270. 270.5 271. 271.5 272. 272.5 273. 273.5 274. 274.5 275. 275.5 276. 276.5 277. 277.5 278. 278.5 279. 279.5 280. 280.5 281. 281.5 282. 282.5 283. 283.5 284. 284.5 285. 285.5 286. 286.5 287. 287.5 288. 288.5 289. 289.5 290. 290.5 291. 291.5 292. 292.5 293. 293.5 294. 294.5 295. 295.5 296. 296.5 297. 297.5 298. 298.5 299. 299.5 300. 300.5 301. 301.5 302. 302.5 303. 303.5 304. 304.5 305. 305.5 306. 306.5 307. 307.5 308. 308.5 309. 309.5 310. 310.5 311. 311.5 312. 312.5 313. 313.5 314. 314.5 315. 315.5 316. 316.5 317. 317.5 318. 318.5 319. 319.5 320. 320.5 321. 321.5 322. 322.5 323. 323.5 324. 324.5 325. 325.5 326. 326.5 327. 327.5 328. 328.5 329. 329.5 330. 330.5 331. 331.5 332. 332.5 333. 333.5 334. 334.5 335. 335.5 336. 336.5 337. 337.5 338. 338.5 339. 339.5 340. 340.5 341. 341.5 342. 342.5 343. 343.5 344. 344.5 345. 345.5 346. 346.5 347. 347.5 348. 348.5 349. 349.5 350. 350.5 351. 351.5 352. 352.5 353. 353.5 354. 354.5 355. 355.5 356. 356.5 357. 357.5 358. 358.5 359. 359.5 360. 360.5 361. 361.5 362. ] INFO 2025-06-26 16:21:54,781 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.28640190e+09 1.28640190e+09 1.28640217e+09 1.28640217e+09 1.28640217e+09 1.28640217e+09 1.28640217e+09 1.28640217e+09 1.28640217e+09 1.28640217e+09 1.28640217e+09 1.28640217e+09 1.28640217e+09 1.28640217e+09 1.28640217e+09 1.28640217e+09 1.28640217e+09 1.28640217e+09 1.28640218e+09 1.28640218e+09 1.28640218e+09 1.28640218e+09 1.28640218e+09 1.28640218e+09 1.28640218e+09 1.28640218e+09 1.28640218e+09 1.28640218e+09 1.28640218e+09 1.28640218e+09 1.28640218e+09 1.28640218e+09 1.28640218e+09 1.28640218e+09 1.28640218e+09 1.28640218e+09 1.28640218e+09 1.28640218e+09 1.28640219e+09 1.28640219e+09 1.28640219e+09 1.28640219e+09 1.28640219e+09 1.28640219e+09 1.28640219e+09 1.28640219e+09 1.28640219e+09 1.28640219e+09 1.28640219e+09 1.28640219e+09 1.28640219e+09 1.28640219e+09 1.28640219e+09 1.28640219e+09 1.28640219e+09 1.28640219e+09 1.28640219e+09 1.28640219e+09 1.28640220e+09 1.28640220e+09 1.28640220e+09 1.28640220e+09 1.28640220e+09 1.28640220e+09 1.28640220e+09 1.28640220e+09 1.28640220e+09 1.28640220e+09 1.28640220e+09 1.28640220e+09 1.28640220e+09 1.28640220e+09 1.28640220e+09 1.28640220e+09 1.28640220e+09 1.28640220e+09 1.28640220e+09 1.28640220e+09 1.28640221e+09 1.28640221e+09 1.28640221e+09 1.28640221e+09 1.28640221e+09 1.28640221e+09 1.28640221e+09 1.28640221e+09 1.28640221e+09 1.28640221e+09 1.28640221e+09 1.28640221e+09 1.28640221e+09 1.28640221e+09 1.28640221e+09 1.28640221e+09 1.28640221e+09 1.28640221e+09 1.28640221e+09 1.28640221e+09 1.28640222e+09 1.28640222e+09 1.28640222e+09 1.28640222e+09 1.28640222e+09 1.28640222e+09 1.28640222e+09 1.28640222e+09 1.28640222e+09 1.28640222e+09 1.28640222e+09 1.28640222e+09 1.28640222e+09 1.28640222e+09 1.28640222e+09 1.28640222e+09 1.28640222e+09 1.28640222e+09 1.28640222e+09 1.28640222e+09 1.28640223e+09 1.28640223e+09 1.28640223e+09 1.28640223e+09 1.28640223e+09 1.28640223e+09 1.28640223e+09 1.28640223e+09 1.28640223e+09 1.28640223e+09 1.28640223e+09 1.28640223e+09 1.28640223e+09 1.28640223e+09 1.28640223e+09 1.28640223e+09 1.28640223e+09 1.28640223e+09 1.28640223e+09 1.28640223e+09 1.28640224e+09 1.28640224e+09 1.28640224e+09 1.28640224e+09 1.28640224e+09 1.28640224e+09 1.28640224e+09 1.28640224e+09 1.28640224e+09 1.28640224e+09 1.28640224e+09 1.28640224e+09 1.28640224e+09 1.28640224e+09 1.28640224e+09 1.28640224e+09 1.28640224e+09 1.28640224e+09 1.28640224e+09 1.28640224e+09 1.28640225e+09 1.28640225e+09 1.28640225e+09 1.28640225e+09 1.28640225e+09 1.28640225e+09 1.28640225e+09 1.28640225e+09 1.28640225e+09 1.28640225e+09 1.28640225e+09 1.28640225e+09 1.28640225e+09 1.28640225e+09 1.28640225e+09 1.28640225e+09 1.28640225e+09 1.28640225e+09 1.28640225e+09 1.28640225e+09 1.28640226e+09 1.28640226e+09 1.28640226e+09 1.28640226e+09 1.28640226e+09 1.28640226e+09 1.28640226e+09 1.28640226e+09 1.28640226e+09 1.28640226e+09 1.28640226e+09 1.28640226e+09 1.28640226e+09 1.28640226e+09 1.28640226e+09 1.28640226e+09 1.28640226e+09 1.28640226e+09 1.28640226e+09 1.28640226e+09 1.28640227e+09 1.28640227e+09 1.28640227e+09] INFO 2025-06-26 16:21:54,783 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1286401904.0 1286401904.5, ..., timestampArray[-2:] = 1286402265.5 1286402266.0] INFO 2025-06-26 16:21:54,784 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1286401904.049983), np.float64(1286401904.549983)], ..., timestampList[-2:] = [np.float64(1286402265.549983), np.float64(1286402266.049983)]] INFO 2025-06-26 16:21:54,784 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 201) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 16:21:54,784 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [167, 188] INFO 2025-06-26 16:21:54,784 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 9 INFO 2025-06-26 16:21:54,784 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 201 INFO 2025-06-26 16:21:54,784 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1286401904.049983), np.float64(1286401904.549983)], ..., timestampList[-2:] = [np.float64(1286402265.549983), np.float64(1286402266.049983)]] INFO 2025-06-26 16:21:54,784 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 201) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 16:21:54,784 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(166), np.int32(187)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 16:21:54,784 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 9 INFO 2025-06-26 16:21:54,784 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 INFO 2025-06-26 16:21:54,785 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 9 INFO 2025-06-26 16:21:54,786 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1286402175.549983)], ..., tsList[-2:] = [np.float64(1286402249.049983), np.float64(1286402259.549983)] INFO 2025-06-26 16:21:54,786 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2010-10-06 21:56:15 Z INFO 2025-06-26 16:21:54,786 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2010-10-06 21:57:39 Z INFO 2025-06-26 16:21:54,786 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 9 INFO 2025-06-26 16:21:54,786 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [1.286402e+09], ..., cFrameEsecsList[-2:] = [1.286402e+09 1.286402e+09] INFO 2025-06-26 16:21:54,786 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 2010-10-06 21:53:21 Z INFO 2025-06-26 16:21:54,786 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 2010-10-06 21:53:21 Z INFO 2025-06-26 16:21:54,790 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2010.279.02/lopc.nc INFO 2025-06-26 16:21:54,790 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 16:21:54 2025 Elapsed processing time from start of processing = 1 seconds INFO 2025-06-26 16:21:54,791 process.py calibrate():227 [1] Calibration steps for 2010.279.02 INFO 2025-06-26 16:21:55,156 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 16:21:55,158 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 16:21:56,009 calibrate.py _nudge_pos():1806 [1] 124: 0.050 0.0034161 -0.0052769 7850 26.33 19.237 -37.142 2010-10-06T22:20:04.323506432 INFO 2025-06-26 16:21:56,901 calibrate.py _nudge_pos():1806 [1] 212: 0.060 -0.0032448 -0.0028390 8039 26.85 -17.915 -19.596 2010-10-06T22:48:22.317185792 INFO 2025-06-26 16:21:57,737 calibrate.py _nudge_pos():1806 [1] 292: 0.070 0.0005736 -0.0017196 7480 24.98 3.404 -12.756 2010-10-06T23:14:40.319085312 INFO 2025-06-26 16:21:58,759 calibrate.py _nudge_pos():1806 [1] 392: 0.060 -0.0019011 -0.0045948 6512 21.73 -12.971 -39.181 2010-10-06T23:38:04.322904320 INFO 2025-06-26 16:22:00,133 calibrate.py _nudge_pos():1806 [1] 529: 0.060 -0.0009845 -0.0008401 8787 29.33 -4.976 -5.308 2010-10-07T00:09:40.323019520 INFO 2025-06-26 16:22:00,897 calibrate.py _nudge_pos():1806 [1] 605: 0.070 0.0008431 -0.0016256 3853 12.85 9.728 -23.447 2010-10-07T00:23:46.325064448 INFO 2025-06-26 16:22:02,564 calibrate.py _nudge_pos():1806 [1] 766: 0.070 0.0008184 -0.0024157 3277 10.93 11.100 -40.954 2010-10-07T00:37:22.319164928 INFO 2025-06-26 16:22:03,344 calibrate.py _nudge_pos():1806 [1] 842: 0.070 0.0022736 -0.0033161 9064 30.25 11.144 -20.315 2010-10-07T01:08:52.319691264 INFO 2025-06-26 16:22:03,969 calibrate.py _nudge_pos():1806 [1] 903: 0.070 0.0009863 -0.0036494 8927 29.80 4.907 -22.695 2010-10-07T01:39:40.323094016 INFO 2025-06-26 16:22:04,963 calibrate.py _nudge_pos():1806 [1] 999: 0.070 0.0013199 -0.0039121 8338 27.81 7.035 -26.064 2010-10-07T02:09:04.322252032 INFO 2025-06-26 16:22:05,742 calibrate.py _nudge_pos():1806 [1] 1074: 0.070 -0.0012974 -0.0041226 6638 22.16 -8.677 -34.467 2010-10-07T02:32:28.326071040 INFO 2025-06-26 16:22:06,552 calibrate.py _nudge_pos():1806 [1] 1152: 0.080 -0.0015614 -0.0033981 8099 27.01 -8.569 -23.309 2010-10-07T03:00:46.319750656 INFO 2025-06-26 16:22:07,425 calibrate.py _nudge_pos():1806 [1] 1234: 0.080 -0.0003364 -0.0008005 6667 22.24 -2.242 -6.669 2010-10-07T03:24:22.322747648 INFO 2025-06-26 16:22:08,206 calibrate.py _nudge_pos():1806 [1] 1307: 0.090 0.0014367 -0.0032796 7734 25.80 8.256 -23.557 2010-10-07T03:51:22.321770240 INFO 2025-06-26 16:22:08,676 calibrate.py _nudge_pos():1806 [1] 1352: 0.090 -0.0000730 0.0000422 45 0.15 -73.802 53.350 2010-10-07T03:52:15.318139904 INFO 2025-06-26 16:22:09,319 calibrate.py _nudge_pos():1806 [1] 1413: 0.090 0.0008074 -0.0032824 8516 28.41 4.212 -21.407 2010-10-07T04:21:40.317229056 INFO 2025-06-26 16:22:10,078 calibrate.py _nudge_pos():1806 [1] 1485: 0.090 0.0004327 -0.0038454 9267 30.91 2.075 -23.050 2010-10-07T04:53:46.325288192 INFO 2025-06-26 16:22:10,932 calibrate.py _nudge_pos():1806 [1] 1566: 0.090 0.0000695 -0.0001194 470 1.56 6.589 -14.148 2010-10-07T04:56:40.323368704 INFO 2025-06-26 16:22:11,531 calibrate.py _nudge_pos():1806 [1] 1622: 0.090 0.0009294 -0.0032818 8270 27.58 4.995 -22.049 2010-10-07T05:25:10.326225408 INFO 2025-06-26 16:22:12,405 calibrate.py _nudge_pos():1806 [1] 1704: 0.090 0.0010687 -0.0042442 7151 23.85 6.643 -32.979 2010-10-07T05:50:22.322646528 INFO 2025-06-26 16:22:13,598 calibrate.py _nudge_pos():1806 [1] 1812: 0.100 -0.0002526 -0.0043591 7499 25.01 -1.497 -32.293 2010-10-07T06:17:10.322491136 INFO 2025-06-26 16:22:14,687 calibrate.py _nudge_pos():1806 [1] 1911: 0.100 -0.0025939 -0.0017777 8323 27.76 -13.847 -11.865 2010-10-07T06:46:34.321648896 INFO 2025-06-26 16:22:15,543 calibrate.py _nudge_pos():1806 [1] 1991: 0.100 0.0037094 -0.0049820 8358 27.88 19.722 -33.112 2010-10-07T07:15:46.321628672 INFO 2025-06-26 16:22:16,446 calibrate.py _nudge_pos():1806 [1] 2074: 0.100 0.0024221 -0.0033308 7775 25.93 13.845 -23.803 2010-10-07T07:43:04.319418112 INFO 2025-06-26 16:22:17,278 calibrate.py _nudge_pos():1806 [1] 2151: 0.110 -0.0015775 -0.0047825 7258 24.23 -9.650 -36.575 2010-10-07T08:08:34.324605440 INFO 2025-06-26 16:22:18,118 calibrate.py _nudge_pos():1806 [1] 2227: 0.110 -0.0009397 -0.0031759 9039 30.15 -4.620 -19.521 2010-10-07T08:39:58.325542656 INFO 2025-06-26 16:22:18,959 calibrate.py _nudge_pos():1806 [1] 2303: 0.110 0.0001357 -0.0037422 6312 21.05 0.956 -32.948 2010-10-07T09:02:16.323883520 INFO 2025-06-26 16:22:19,771 calibrate.py _nudge_pos():1806 [1] 2377: 0.120 -0.0001869 -0.0039819 10035 33.48 -0.828 -22.038 2010-10-07T09:36:58.321256960 INFO 2025-06-26 16:22:20,795 calibrate.py _nudge_pos():1806 [1] 2470: 0.120 -0.0015525 -0.0006750 6288 20.96 -10.976 -5.966 2010-10-07T09:59:28.318775552 INFO 2025-06-26 16:22:20,864 calibrate.py _nudge_pos():1806 [1] 2476: 0.120 0.0000023 -0.0000097 60 0.20 1.700 -9.112 2010-10-07T09:59:45.317611264 INFO 2025-06-26 16:22:21,904 calibrate.py _nudge_pos():1806 [1] 2570: 0.110 0.0023886 -0.0039606 6284 20.96 16.888 -35.008 2010-10-07T10:22:16.325060864 INFO 2025-06-26 16:22:22,822 calibrate.py _nudge_pos():1806 [1] 2644: 0.120 0.0006325 -0.0005492 1313 4.38 21.404 -23.235 2010-10-07T10:27:52.322043392 INFO 2025-06-26 16:22:23,646 calibrate.py _nudge_pos():1806 [1] 2719: 0.120 -0.0000377 -0.0039648 7633 25.46 -0.219 -28.852 2010-10-07T10:54:34.322298880 INFO 2025-06-26 16:22:57,160 calibrate.py _nudge_pos():1862 [1] 5783: - - - 3 0.01 - - INFO 2025-06-26 16:22:57,160 calibrate.py _nudge_pos():1868 [1] Points in final series = 249861 WARNING 2025-06-26 16:22:57,514 calibrate.py _depth_process():2193 [1] Expected sample_rate to be 10 Hz, instead it's 9.09 Hz INFO 2025-06-26 16:23:22,688 calibrate.py _hs2_process():2400 [1] Number of bad hs2 points: 18 of 200122 INFO 2025-06-26 16:23:24,196 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 6 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:23:38,514 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:23:40,038 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:23:40,042 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2010.279.02/ctd1.nc INFO 2025-06-26 16:23:40,043 calibrate.py _range_qc_combined_nc():898 [1] Setting 66 ctd1_salinity values to NaN INFO 2025-06-26 16:23:40,044 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 16:23:40,044 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 16:23:51,360 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:23:52,850 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 26 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 16:23:52,854 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2010.279.02/ctd2.nc INFO 2025-06-26 16:23:52,856 calibrate.py _range_qc_combined_nc():898 [1] Setting 358 ctd2_salinity values to NaN INFO 2025-06-26 16:23:52,856 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 16:23:52,856 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 16:23:52,929 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 16:23:55,191 calibrate.py _biolume_process():3131 [1] Removing non-monotonic increasing time60hz at indices: [ 60 61 62 ... 2903646 2903647 2903648] INFO 2025-06-26 16:23:55,634 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 16:24:41,703 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2010.279.02 INFO 2025-06-26 16:24:41,894 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2010.279.02/dorado_2010.279.02_cal.nc INFO 2025-06-26 16:25:04,190 calibrate.py write_netcdf():3512 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, depth_filtdepth, depth_filtpres, depth_time, gps_latitude, gps_longitude, gps_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_time, isus_nitrate, isus_quality, isus_temp, isus_time, lopc_LCcount, lopc_countListSum, lopc_flowSpeed, lopc_nonTransCount, lopc_time, lopc_transCount, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_posx, navigation_posy, navigation_roll, navigation_time, navigation_yaw, nudged_latitude, nudged_longitude, tailcone_propRpm, tailcone_time, time INFO 2025-06-26 16:25:04,197 process.py align():251 [1] Alignment steps for 2010.279.02 INFO 2025-06-26 16:25:04,281 align.py process_cal():139 [1] Processing dorado_2010.279.02_cal.nc from /data/auv_data/dorado/missionnetcdfs/2010.279.02 INFO 2025-06-26 16:25:04,348 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:25:04,355 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 16:25:04,522 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:25:04,531 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 16:25:04,688 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:25:04,699 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 16:25:04,794 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 16:25:04,794 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 16:25:04,854 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 16:25:04,864 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 16:25:05,018 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:05,027 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:05,161 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:05,169 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:05,306 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:05,314 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:05,450 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:05,458 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:05,601 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:05,610 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:05,746 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:05,754 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:05,889 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:05,897 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:06,034 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:06,043 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:06,180 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:06,188 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:06,323 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:06,333 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:06,470 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:06,479 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:06,615 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:06,624 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:06,762 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:06,770 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:06,907 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:06,915 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:07,059 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:07,068 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:07,205 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:07,214 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:07,357 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:07,365 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:07,507 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:07,516 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:07,657 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:07,667 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:07,807 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:07,816 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:07,956 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:07,965 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:08,102 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2010.279.02_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 16:25:08,109 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 16:25:08,276 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 16:25:08,383 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 16:25:08,491 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.78 INFO 2025-06-26 16:25:08,603 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 16:25:08,727 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 16:25:08,978 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.95 INFO 2025-06-26 16:25:10,419 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 16:25:10,511 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 16:25:10,607 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 16:25:10,699 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 16:25:10,794 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 16:25:10,896 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 4.99 INFO 2025-06-26 16:25:11,005 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2010.279.02/dorado_2010.279.02_align.nc INFO 2025-06-26 16:25:11,318 align.py write_netcdf():342 [1] Data variables written: biolume_avg_biolume, biolume_depth, biolume_flow, biolume_latitude, biolume_longitude, biolume_raw, biolume_time, biolume_time60hz, ctd1_conductivity, ctd1_conductivity_onboard, ctd1_depth, ctd1_dissolvedO2, ctd1_flow1, ctd1_latitude, ctd1_longitude, ctd1_oxygen_mll, ctd1_oxygen_umolkg, ctd1_salinity, ctd1_salinity_onboard, ctd1_temperature, ctd1_temperature_onboard, ctd1_time, ctd2_conductivity, ctd2_conductivity_onboard, ctd2_depth, ctd2_flow2, ctd2_latitude, ctd2_longitude, ctd2_salinity, ctd2_salinity_onboard, ctd2_temperature, ctd2_temperature_onboard, ctd2_time, hs2_bbp420, hs2_bbp700, hs2_depth, hs2_fl700, hs2_latitude, hs2_longitude, hs2_time, isus_depth, isus_latitude, isus_longitude, isus_nitrate, isus_quality, isus_temp, isus_time, lopc_LCcount, lopc_countListSum, lopc_depth, lopc_flowSpeed, lopc_latitude, lopc_longitude, lopc_nonTransCount, lopc_time, lopc_transCount, navigation_depth, navigation_latitude, navigation_longitude, navigation_mWaterSpeed, navigation_pitch, navigation_roll, navigation_time, navigation_yaw, tailcone_depth, tailcone_latitude, tailcone_longitude, tailcone_propRpm, tailcone_time INFO 2025-06-26 16:25:11,326 process.py resample():273 [1] Resampling steps for 2010.279.02 INFO 2025-06-26 16:25:11,327 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 16:25:11,408 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.279.02/dorado_2010.279.02_align.nc mission netCDF file INFO 2025-06-26 16:25:11,417 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.279.02/dorado_2010.279.02_align.nc mission netCDF file INFO 2025-06-26 16:25:11,419 resample.py get_mission_start_end():1145 [1] navigation: 2010-10-06T21:52:32.516662784 to 2010-10-07T11:46:27.919003136 (0 days 00:00:00.019998464 before mission_end) INFO 2025-06-26 16:25:11,422 resample.py get_mission_start_end():1145 [1] hs2 : 2010-10-06T21:51:50.169563648 to 2010-10-07T11:46:27.759013888 (0 days 00:00:00.179987712 before mission_end) INFO 2025-06-26 16:25:11,424 resample.py get_mission_start_end():1145 [1] ctd1 : 2010-10-06T21:52:10.318183680 to 2010-10-07T11:46:27.739015424 (0 days 00:00:00.199986176 before mission_end) INFO 2025-06-26 16:25:11,427 resample.py get_mission_start_end():1145 [1] ctd2 : 2010-10-06T21:52:10.988137728 to 2010-10-07T11:46:27.749014528 (0 days 00:00:00.189987072 before mission_end) INFO 2025-06-26 16:25:11,429 resample.py get_mission_start_end():1145 [1] isus : 2010-10-06T21:53:05.234421504 to 2010-10-07T11:46:26.959068672 (0 days 00:00:00.979932928 before mission_end) INFO 2025-06-26 16:25:11,430 resample.py get_mission_start_end():1145 [1] biolume : 2010-10-06T21:51:41.780104448 to 2010-10-07T11:46:27.119023616 (0 days 00:00:00.819977984 before mission_end) INFO 2025-06-26 16:25:11,432 resample.py get_mission_start_end():1145 [1] lopc : 2010-10-06T21:56:15.549982976 to 2010-10-06T21:57:39.549982976 (0 days 13:48:48.389018624 before mission_end) WARNING 2025-06-26 16:25:11,433 resample.py get_mission_start_end():1156 [1] Instrument lopc has a gap > 5 minutes at the end of the mission: 0 days 13:48:48.389018624 INFO 2025-06-26 16:25:11,435 resample.py get_mission_start_end():1145 [1] tailcone : 2010-10-06T21:51:45.539880960 to 2010-10-07T11:46:27.939001600 (0 days 00:00:00 before mission_end) INFO 2025-06-26 16:25:11,435 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2010.279.02/dorado_2010.279.02_align.nc mission netCDF file INFO 2025-06-26 16:25:11,436 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:11,962 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:12,048 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:12,132 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:12,214 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:12,285 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:12,357 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:12,427 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:12,497 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:12,562 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:12,632 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:12,697 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:12,762 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:12,828 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:12,892 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:12,957 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:13,024 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:13,091 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:13,159 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:13,230 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:13,305 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:13,374 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:13,445 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:13,515 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:13,587 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:13,617 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:13,641 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:13,666 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:13,691 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:13,715 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:13,723 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 16:25:13,723 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 16:25:15,675 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 16:25:16,318 resample.py add_biolume_proxies():633 [1] Zero flow values found: 54 of 50087 - replaced with 350 ml/s INFO 2025-06-26 16:25:16,319 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 16:25:16,545 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 16:25:16,631 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 16:25:16,693 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 16:25:16,694 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 16:25:16,723 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:16,723 resample.py resample_variable():1038 [1] Padding lopc_countListSum with 0 days 13:48:48.389018624 of NaNs to the end of mission INFO 2025-06-26 16:25:16,735 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:16,736 resample.py resample_variable():1038 [1] Padding lopc_transCount with 0 days 13:48:48.389018624 of NaNs to the end of mission INFO 2025-06-26 16:25:16,747 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:16,747 resample.py resample_variable():1038 [1] Padding lopc_nonTransCount with 0 days 13:48:48.389018624 of NaNs to the end of mission INFO 2025-06-26 16:25:16,758 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:16,758 resample.py resample_variable():1038 [1] Padding lopc_LCcount with 0 days 13:48:48.389018624 of NaNs to the end of mission INFO 2025-06-26 16:25:16,769 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:16,770 resample.py resample_variable():1038 [1] Padding lopc_flowSpeed with 0 days 13:48:48.389018624 of NaNs to the end of mission INFO 2025-06-26 16:25:16,845 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 16:25:17,285 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2010.279.02/dorado_2010.279.02_1S.nc INFO 2025-06-26 16:25:21,979 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 16:25:37,056 create_products.py gulper_odv():522 [1] Wrote 10 Gulper data lines to /data/auv_data/dorado/missionodvs/2010.279.02/dorado_2010.279.02_1S_Gulper.txt INFO 2025-06-26 16:25:37,056 process.py archive():337 [1] Archiving steps for 2010.279.02 INFO 2025-06-26 16:25:37,056 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2010.279.02/dorado_2010.279.02, BASE_PATH = /data/auv_data INFO 2025-06-26 16:25:37,058 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2010.279.02/dorado_2010.279.02 files to /Volumes/AUVCTD/surveys/2010/netcdf INFO 2025-06-26 16:25:37,059 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.279.02_1S.nc INFO 2025-06-26 16:25:37,108 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.279.02/dorado_2010.279.02_1S.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:25:37,109 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.279.02_cal.nc INFO 2025-06-26 16:25:37,414 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.279.02/dorado_2010.279.02_cal.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:25:37,415 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2010/netcdf/dorado_2010.279.02_align.nc INFO 2025-06-26 16:25:37,848 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.279.02/dorado_2010.279.02_align.nc /Volumes/AUVCTD/surveys/2010/netcdf done. INFO 2025-06-26 16:25:37,900 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.279.02/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010279/2010.279.02 done. INFO 2025-06-26 16:25:37,950 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.279.02/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010279/2010.279.02 done. INFO 2025-06-26 16:25:37,956 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.279.02/gps.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010279/2010.279.02 done. INFO 2025-06-26 16:25:38,002 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.279.02/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010279/2010.279.02 done. INFO 2025-06-26 16:25:38,156 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.279.02/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010279/2010.279.02 done. INFO 2025-06-26 16:25:38,165 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.279.02/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010279/2010.279.02 done. INFO 2025-06-26 16:25:38,225 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.279.02/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010279/2010.279.02 done. INFO 2025-06-26 16:25:38,266 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.279.02/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010279/2010.279.02 done. INFO 2025-06-26 16:25:38,402 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.279.02/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010279/2010.279.02 done. INFO 2025-06-26 16:25:38,408 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.279.02/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2010/2010279/2010.279.02 done. INFO 2025-06-26 16:25:38,408 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 16:25:38,410 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2010/odv/dorado_2010.279.02_1S_Gulper.txt INFO 2025-06-26 16:25:38,415 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2010.279.02/dorado_2010.279.02_1S_Gulper.txt /Volumes/AUVCTD/surveys/2010/odv done. INFO 2025-06-26 16:25:38,415 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2010.279.02/dorado_2010.279.02_processing.log /Volumes/AUVCTD/surveys/2010/netcdf