INFO 2025-06-26 19:31:17,239 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 19:31:17,239 process.py process_mission():434 [1] dorado_info[mission]["comment"] = ECOHAB - CANON March 2013 - Outbound mission, JD's adaptive samping algorithm (niche model), 7 Gulpers fired - ctdToUse = ctd1 INFO 2025-06-26 19:31:17,239 process.py process_mission():449 [1] Processing CANON March 2013 mission 2013.081.05 by user docker_user on host eae60d30a712 INFO 2025-06-26 19:31:17,239 process.py download_process():165 [1] Download and processing steps for 2013.081.05 INFO 2025-06-26 19:31:17,239 logs2netcdfs.py download_process_logs():739 [1] src_dir = /Volumes/AUVCTD/missionlogs/2013/2013081/2013.081.05 INFO 2025-06-26 19:31:17,240 logs2netcdfs.py download_process_logs():768 [1] Rsyncing /Volumes/AUVCTD/missionlogs/2013/2013081/2013.081.05 to /data/auv_data/dorado/missionlogs/2013.081.05 INFO 2025-06-26 19:31:19,497 logs2netcdfs.py download_process_logs():779 [1] Processing mission: dorado 2013.081.05 INFO 2025-06-26 19:31:19,497 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.081.05/ctdDriver.log (4242822 bytes) INFO 2025-06-26 19:31:19,805 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.081.05/ctdDriver2.log (4242719 bytes) INFO 2025-06-26 19:31:20,126 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.081.05/gps.log (57596 bytes) INFO 2025-06-26 19:31:20,141 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.081.05/hydroscatlog.log (3715510 bytes) INFO 2025-06-26 19:31:20,540 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.081.05/navigation.log (15000118 bytes) INFO 2025-06-26 19:31:21,706 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.081.05/isuslog.log (328181 bytes) INFO 2025-06-26 19:31:21,741 logs2netcdfs.py _process_log_file():687 [1] Non-monotonic increasing time indices in /data/auv_data/dorado/missionlogs/2013.081.05/isuslog.log: [ 1 2 3 4 5 6 8 9 10 11] INFO 2025-06-26 19:31:21,742 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.081.05/parosci.log (5215574 bytes) INFO 2025-06-26 19:31:22,182 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.081.05/tailCone.log (2656075 bytes) INFO 2025-06-26 19:31:22,521 logs2netcdfs.py download_process_logs():788 [1] Processing file /data/auv_data/dorado/missionlogs/2013.081.05/biolume.log (3092898 bytes) INFO 2025-06-26 19:31:22,821 logs2netcdfs.py write_variables():575 [1] Expanding original timeTag to time60Hz variable for raw data INFO 2025-06-26 19:31:22,979 logs2netcdfs.py download_process_logs():807 [1] Time to process: 3.48 seconds INFO 2025-06-26 19:31:22,979 process.py download_process():198 [1] Processing file /data/auv_data/dorado/missionlogs/2013.081.05/lopc.bin (11254148 bytes) INFO 2025-06-26 19:31:22,979 lopcToNetCDF.py main():2297 [1] Processing begun: Thu Jun 26 19:31:22 2025 INFO 2025-06-26 19:31:22,980 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.081.05/parosci.nc INFO 2025-06-26 19:31:22,980 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:31:22,980 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.081.05/parosci.nc INFO 2025-06-26 19:31:22,983 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1363965137.9, sensor_off_time = 1363976202.1 INFO 2025-06-26 19:31:22,983 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 11064 seconds. Expecting to read 22128 L frames from the lopc.bin file. INFO 2025-06-26 19:31:22,984 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 22128 records from the lopc.bin file. INFO 2025-06-26 19:31:23,116 lopcToNetCDF.py main():2321 [1] Examined sibling parosci.nc file to find startTime = 2013-03-22 15:12:17 Z and endTime = 2013-03-22 18:16:42 Z with 22128 records expected to be read from lopc.bin INFO 2025-06-26 19:31:23,116 lopcToNetCDF.py unpackLOPCbin():723 [1] >>> Unpacking LOPC data from /data/auv_data/dorado/missionlogs/2013.081.05/lopc.bin INFO 2025-06-26 19:31:23,116 lopcToNetCDF.py unpackLOPCbin():724 [1] >>> Will write to NetCDF file /data/auv_data/dorado/missionnetcdfs/2013.081.05/lopc.nc INFO 2025-06-26 19:31:23,117 lopcToNetCDF.py openNetCDFFile():1861 [1] Will output NetCDF file to /data/auv_data/dorado/missionnetcdfs/2013.081.05/lopc.nc INFO 2025-06-26 19:31:23,117 lopcToNetCDF.py openNetCDFFile():1887 [1] missionName = 2013.081.05 INFO 2025-06-26 19:31:23,117 lopcToNetCDF.py openNetCDFFile():1910 [1] Writing bin axis for len(self.dataStructure['binSizeList']) = 994 WARNING 2025-06-26 19:31:23,120 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = A040310 WARNING 2025-06-26 19:31:23,120 lopcToNetCDF.py readCframeData():665 [1] Unable to parse a float from the string cstr[:70] = INFO 2025-06-26 19:31:23,207 lopcToNetCDF.py unpackLOPCbin():951 [1] L Frames sample M Frames ShortLFrame LBeforeMEnd MBeforeLEnd UnknownFrame Garbled L INFO 2025-06-26 19:31:23,207 lopcToNetCDF.py unpackLOPCbin():969 [1] Count Count Count Error Error Error Error Error INFO 2025-06-26 19:31:23,207 lopcToNetCDF.py unpackLOPCbin():987 [1] -------- -------- -------- ----------- ----------- ----------- ----------- ------------ ERROR 2025-06-26 19:31:23,544 lopcToNetCDF.py main():2340 [1] UnicodeDecodeError: 'utf-8' codec can't decode byte 0x8d in position 0: invalid start byte INFO 2025-06-26 19:31:23,544 lopcToNetCDF.py main():2341 [1] Failed to decode all of lopc.bin - resulting lopc.nc file likely incomplete INFO 2025-06-26 19:31:23,545 lopcToNetCDF.py constructTimestampList():1296 [1] parosci_nc = /data/auv_data/dorado/missionnetcdfs/2013.081.05/parosci.nc INFO 2025-06-26 19:31:23,545 lopcToNetCDF.py constructTimestampList():1297 [1] Using NetCDF4 to get start and end epoch seconds for this mission from this URL: INFO 2025-06-26 19:31:23,545 lopcToNetCDF.py constructTimestampList():1300 [1] /data/auv_data/dorado/missionnetcdfs/2013.081.05/parosci.nc INFO 2025-06-26 19:31:23,548 lopcToNetCDF.py constructTimestampList():1317 [1] From associated parosci.nc file: sensor_on_time = 1363965137.9, sensor_off_time = 1363976202.1 INFO 2025-06-26 19:31:23,548 lopcToNetCDF.py constructTimestampList():1322 [1] Duration is 11064 seconds. Expecting to read 22128 L frames from the lopc.bin file. INFO 2025-06-26 19:31:23,548 lopcToNetCDF.py constructTimestampList():1330 [1] recCount not passed in, assuming we'll have 22128 records from the lopc.bin file. INFO 2025-06-26 19:31:23,548 lopcToNetCDF.py constructTimestampList():1340 [1] Calling correctSampleCountList() with sampleCountList[0] = 1460 and len(sampleCountList) = 363 INFO 2025-06-26 19:31:23,549 lopcToNetCDF.py correctSampleCountList():1737 [1] Found overflows at indices: [] INFO 2025-06-26 19:31:23,549 lopcToNetCDF.py correctSampleCountList():1745 [1] Original sampleCountList = [1460 1461 1462 1463 1464 1465 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 1555 1556 1557 1558 1559 1560 1561 1562 1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 1576 1577 1578 1579 1580 1581 1582 1583 1584 1585 1586 1587 1588 1589 1590 1591 1592 1593 1594 1595 1596 1597 1598 1599 1600 1601 1602 1603 1604 1605 1606 1607 1608 1609 1610 1611 1612 1613 1614 1615 1616 1617 1618 1619 1620 1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 1652 1653 1654 1655 1656 1657 1658 1659 1660 1661 1662 1663 1664 1665 1666 1667 1668 1669 1670 1671 1672 1673 1674 1675 1676 1677 1678 1679 1680 1681 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691 1692 1693 1694 1695 1696 1697 1698 1699 1700 1701 1702 1703 1704 1705 1706 1707 1708 1709 1710 1711 1712 1713 1714 1715 1716 1717 1718 1719 1720 1721 1722 1723 1724 1725 1726 1727 1728 1729 1730 1731 1732 1733 1734 1735 1736 1737 1738 1739 1740 1741 1742 1743 1744 1745 1746 1747 1748 1749 1750 1751 1752 1753 1754 1755 1756 1757 1758 1759 1760 1761 1762 1763 1764 1765 1766 1767 1768 1769 1770 1771 1772 1773 1774 1775 1776 1777 1778 1779 1780 1781 1782 1783 1784 1785 1786 1787 1788 1789 1790 1791 1792 1793 1794 1795 1796 1797 1798 1799 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 1812 1813 1814 1815 1816 1817 1818 1819 1820 1821 1822 1823 1824 1825 1826 1827 1828 1829 1830 1831 1832 1833 1834 1835 1836 1837 1838 1839 1840 1841 1842 1843 1844 1845 1846 1847 1848 1849 1850 1851 1852 1853 1854 1855 1856 1857 1858 1859 1860 1861 1862 1863 1864 1865 1866 1867 1868 1869 1870 1871 1872 1873 1874 1875 1876 1877 1878 1879 1880 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 1891 1892 1893 1894 1895] INFO 2025-06-26 19:31:23,550 lopcToNetCDF.py correctSampleCountList():1746 [1] Found 0 0 values at indices: [] INFO 2025-06-26 19:31:23,550 lopcToNetCDF.py correctSampleCountList():1779 [1] Found 0 stuck values at indices: [] INFO 2025-06-26 19:31:23,550 lopcToNetCDF.py deSpike():1588 [1] d_sampleCountList = [ 1 1 1 1 1 74 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 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 19:31:23,551 lopcToNetCDF.py deSpike():1590 [1] Found 0 spike indicators at indices: [] INFO 2025-06-26 19:31:23,551 lopcToNetCDF.py correctSampleCountList():1805 [1] After despike() sampleCountList = [1460 1461 1462 1463 1464 1465 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 1555 1556 1557 1558 1559 1560 1561 1562 1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 1576 1577 1578 1579 1580 1581 1582 1583 1584 1585 1586 1587 1588 1589 1590 1591 1592 1593 1594 1595 1596 1597 1598 1599 1600 1601 1602 1603 1604 1605 1606 1607 1608 1609 1610 1611 1612 1613 1614 1615 1616 1617 1618 1619 1620 1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 1652 1653 1654 1655 1656 1657 1658 1659 1660 1661 1662 1663 1664 1665 1666 1667 1668 1669 1670 1671 1672 1673 1674 1675 1676 1677 1678 1679 1680 1681 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691 1692 1693 1694 1695 1696 1697 1698 1699 1700 1701 1702 1703 1704 1705 1706 1707 1708 1709 1710 1711 1712 1713 1714 1715 1716 1717 1718 1719 1720 1721 1722 1723 1724 1725 1726 1727 1728 1729 1730 1731 1732 1733 1734 1735 1736 1737 1738 1739 1740 1741 1742 1743 1744 1745 1746 1747 1748 1749 1750 1751 1752 1753 1754 1755 1756 1757 1758 1759 1760 1761 1762 1763 1764 1765 1766 1767 1768 1769 1770 1771 1772 1773 1774 1775 1776 1777 1778 1779 1780 1781 1782 1783 1784 1785 1786 1787 1788 1789 1790 1791 1792 1793 1794 1795 1796 1797 1798 1799 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 1812 1813 1814 1815 1816 1817 1818 1819 1820 1821 1822 1823 1824 1825 1826 1827 1828 1829 1830 1831 1832 1833 1834 1835 1836 1837 1838 1839 1840 1841 1842 1843 1844 1845 1846 1847 1848 1849 1850 1851 1852 1853 1854 1855 1856 1857 1858 1859 1860 1861 1862 1863 1864 1865 1866 1867 1868 1869 1870 1871 1872 1873 1874 1875 1876 1877 1878 1879 1880 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 1891 1892 1893 1894 1895] INFO 2025-06-26 19:31:23,553 lopcToNetCDF.py constructTimestampList():1347 [1] correctSampleCountList() returned correctedSampleCountList = [1460 1461 1462 1463 1464 1465 1539 1540 1541 1542 1543 1544 1545 1546 1547 1548 1549 1550 1551 1552 1553 1554 1555 1556 1557 1558 1559 1560 1561 1562 1563 1564 1565 1566 1567 1568 1569 1570 1571 1572 1573 1574 1575 1576 1577 1578 1579 1580 1581 1582 1583 1584 1585 1586 1587 1588 1589 1590 1591 1592 1593 1594 1595 1596 1597 1598 1599 1600 1601 1602 1603 1604 1605 1606 1607 1608 1609 1610 1611 1612 1613 1614 1615 1616 1617 1618 1619 1620 1621 1622 1623 1624 1625 1626 1627 1628 1629 1630 1631 1632 1633 1634 1635 1636 1637 1638 1639 1640 1641 1642 1643 1644 1645 1646 1647 1648 1649 1650 1651 1652 1653 1654 1655 1656 1657 1658 1659 1660 1661 1662 1663 1664 1665 1666 1667 1668 1669 1670 1671 1672 1673 1674 1675 1676 1677 1678 1679 1680 1681 1682 1683 1684 1685 1686 1687 1688 1689 1690 1691 1692 1693 1694 1695 1696 1697 1698 1699 1700 1701 1702 1703 1704 1705 1706 1707 1708 1709 1710 1711 1712 1713 1714 1715 1716 1717 1718 1719 1720 1721 1722 1723 1724 1725 1726 1727 1728 1729 1730 1731 1732 1733 1734 1735 1736 1737 1738 1739 1740 1741 1742 1743 1744 1745 1746 1747 1748 1749 1750 1751 1752 1753 1754 1755 1756 1757 1758 1759 1760 1761 1762 1763 1764 1765 1766 1767 1768 1769 1770 1771 1772 1773 1774 1775 1776 1777 1778 1779 1780 1781 1782 1783 1784 1785 1786 1787 1788 1789 1790 1791 1792 1793 1794 1795 1796 1797 1798 1799 1800 1801 1802 1803 1804 1805 1806 1807 1808 1809 1810 1811 1812 1813 1814 1815 1816 1817 1818 1819 1820 1821 1822 1823 1824 1825 1826 1827 1828 1829 1830 1831 1832 1833 1834 1835 1836 1837 1838 1839 1840 1841 1842 1843 1844 1845 1846 1847 1848 1849 1850 1851 1852 1853 1854 1855 1856 1857 1858 1859 1860 1861 1862 1863 1864 1865 1866 1867 1868 1869 1870 1871 1872 1873 1874 1875 1876 1877 1878 1879 1880 1881 1882 1883 1884 1885 1886 1887 1888 1889 1890 1891 1892 1893 1894 1895] with len(correctedSampleCountList) = 363 INFO 2025-06-26 19:31:23,554 lopcToNetCDF.py constructTimestampList():1358 [1] Subtracting 1460 from all values of correctedSampleCountList INFO 2025-06-26 19:31:23,554 lopcToNetCDF.py constructTimestampList():1363 [1] Constructing timestampArray from instrument corrected sampleCount and constant deltaT = 0.500000 INFO 2025-06-26 19:31:23,554 lopcToNetCDF.py constructTimestampList():1368 [1] New re-zeroed correctedSampleCountList = [ 0. 0.5 1. 1.5 2. 2.5 39.5 40. 40.5 41. 41.5 42. 42.5 43. 43.5 44. 44.5 45. 45.5 46. 46.5 47. 47.5 48. 48.5 49. 49.5 50. 50.5 51. 51.5 52. 52.5 53. 53.5 54. 54.5 55. 55.5 56. 56.5 57. 57.5 58. 58.5 59. 59.5 60. 60.5 61. 61.5 62. 62.5 63. 63.5 64. 64.5 65. 65.5 66. 66.5 67. 67.5 68. 68.5 69. 69.5 70. 70.5 71. 71.5 72. 72.5 73. 73.5 74. 74.5 75. 75.5 76. 76.5 77. 77.5 78. 78.5 79. 79.5 80. 80.5 81. 81.5 82. 82.5 83. 83.5 84. 84.5 85. 85.5 86. 86.5 87. 87.5 88. 88.5 89. 89.5 90. 90.5 91. 91.5 92. 92.5 93. 93.5 94. 94.5 95. 95.5 96. 96.5 97. 97.5 98. 98.5 99. 99.5 100. 100.5 101. 101.5 102. 102.5 103. 103.5 104. 104.5 105. 105.5 106. 106.5 107. 107.5 108. 108.5 109. 109.5 110. 110.5 111. 111.5 112. 112.5 113. 113.5 114. 114.5 115. 115.5 116. 116.5 117. 117.5 118. 118.5 119. 119.5 120. 120.5 121. 121.5 122. 122.5 123. 123.5 124. 124.5 125. 125.5 126. 126.5 127. 127.5 128. 128.5 129. 129.5 130. 130.5 131. 131.5 132. 132.5 133. 133.5 134. 134.5 135. 135.5 136. 136.5 137. 137.5 138. 138.5 139. 139.5 140. 140.5 141. 141.5 142. 142.5 143. 143.5 144. 144.5 145. 145.5 146. 146.5 147. 147.5 148. 148.5 149. 149.5 150. 150.5 151. 151.5 152. 152.5 153. 153.5 154. 154.5 155. 155.5 156. 156.5 157. 157.5 158. 158.5 159. 159.5 160. 160.5 161. 161.5 162. 162.5 163. 163.5 164. 164.5 165. 165.5 166. 166.5 167. 167.5 168. 168.5 169. 169.5 170. 170.5 171. 171.5 172. 172.5 173. 173.5 174. 174.5 175. 175.5 176. 176.5 177. 177.5 178. 178.5 179. 179.5 180. 180.5 181. 181.5 182. 182.5 183. 183.5 184. 184.5 185. 185.5 186. 186.5 187. 187.5 188. 188.5 189. 189.5 190. 190.5 191. 191.5 192. 192.5 193. 193.5 194. 194.5 195. 195.5 196. 196.5 197. 197.5 198. 198.5 199. 199.5 200. 200.5 201. 201.5 202. 202.5 203. 203.5 204. 204.5 205. 205.5 206. 206.5 207. 207.5 208. 208.5 209. 209.5 210. 210.5 211. 211.5 212. 212.5 213. 213.5 214. 214.5 215. 215.5 216. 216.5 217. 217.5] INFO 2025-06-26 19:31:23,556 lopcToNetCDF.py constructTimestampList():1379 [1] timestampArray = [1.36396514e+09 1.36396514e+09 1.36396514e+09 1.36396514e+09 1.36396514e+09 1.36396514e+09 1.36396518e+09 1.36396518e+09 1.36396518e+09 1.36396518e+09 1.36396518e+09 1.36396518e+09 1.36396518e+09 1.36396518e+09 1.36396518e+09 1.36396518e+09 1.36396518e+09 1.36396518e+09 1.36396518e+09 1.36396518e+09 1.36396518e+09 1.36396518e+09 1.36396519e+09 1.36396519e+09 1.36396519e+09 1.36396519e+09 1.36396519e+09 1.36396519e+09 1.36396519e+09 1.36396519e+09 1.36396519e+09 1.36396519e+09 1.36396519e+09 1.36396519e+09 1.36396519e+09 1.36396519e+09 1.36396519e+09 1.36396519e+09 1.36396519e+09 1.36396519e+09 1.36396519e+09 1.36396519e+09 1.36396520e+09 1.36396520e+09 1.36396520e+09 1.36396520e+09 1.36396520e+09 1.36396520e+09 1.36396520e+09 1.36396520e+09 1.36396520e+09 1.36396520e+09 1.36396520e+09 1.36396520e+09 1.36396520e+09 1.36396520e+09 1.36396520e+09 1.36396520e+09 1.36396520e+09 1.36396520e+09 1.36396520e+09 1.36396520e+09 1.36396521e+09 1.36396521e+09 1.36396521e+09 1.36396521e+09 1.36396521e+09 1.36396521e+09 1.36396521e+09 1.36396521e+09 1.36396521e+09 1.36396521e+09 1.36396521e+09 1.36396521e+09 1.36396521e+09 1.36396521e+09 1.36396521e+09 1.36396521e+09 1.36396521e+09 1.36396521e+09 1.36396521e+09 1.36396521e+09 1.36396522e+09 1.36396522e+09 1.36396522e+09 1.36396522e+09 1.36396522e+09 1.36396522e+09 1.36396522e+09 1.36396522e+09 1.36396522e+09 1.36396522e+09 1.36396522e+09 1.36396522e+09 1.36396522e+09 1.36396522e+09 1.36396522e+09 1.36396522e+09 1.36396522e+09 1.36396522e+09 1.36396522e+09 1.36396522e+09 1.36396523e+09 1.36396523e+09 1.36396523e+09 1.36396523e+09 1.36396523e+09 1.36396523e+09 1.36396523e+09 1.36396523e+09 1.36396523e+09 1.36396523e+09 1.36396523e+09 1.36396523e+09 1.36396523e+09 1.36396523e+09 1.36396523e+09 1.36396523e+09 1.36396523e+09 1.36396523e+09 1.36396523e+09 1.36396523e+09 1.36396524e+09 1.36396524e+09 1.36396524e+09 1.36396524e+09 1.36396524e+09 1.36396524e+09 1.36396524e+09 1.36396524e+09 1.36396524e+09 1.36396524e+09 1.36396524e+09 1.36396524e+09 1.36396524e+09 1.36396524e+09 1.36396524e+09 1.36396524e+09 1.36396524e+09 1.36396524e+09 1.36396524e+09 1.36396524e+09 1.36396525e+09 1.36396525e+09 1.36396525e+09 1.36396525e+09 1.36396525e+09 1.36396525e+09 1.36396525e+09 1.36396525e+09 1.36396525e+09 1.36396525e+09 1.36396525e+09 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1.36396535e+09 1.36396535e+09 1.36396535e+09 1.36396535e+09 1.36396535e+09 1.36396535e+09 1.36396535e+09 1.36396535e+09 1.36396535e+09 1.36396535e+09 1.36396535e+09 1.36396536e+09] INFO 2025-06-26 19:31:23,560 lopcToNetCDF.py constructTimestampList():1380 [1] timestampArray[:2] = [1363965137.9 1363965138.4, ..., timestampArray[-2:] = 1363965354.9 1363965355.4] INFO 2025-06-26 19:31:23,560 lopcToNetCDF.py constructTimestampList():1389 [1] timestampList[:2] = [np.float64(1363965137.9260833), np.float64(1363965138.4260833)], ..., timestampList[-2:] = [np.float64(1363965354.9260833), np.float64(1363965355.4260833)]] INFO 2025-06-26 19:31:23,560 lopcToNetCDF.py constructTimestampList():1394 [1] Subsampling correctedSampleCountList (len = 363) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 19:31:23,560 lopcToNetCDF.py constructTimestampList():1399 [1] lFrameCountWrittenList[:2] = [20, 41], ... lFrameCountWrittenList[-2:] = [335, 356] INFO 2025-06-26 19:31:23,560 lopcToNetCDF.py constructTimestampList():1420 [1] len(subSampledCorrectedSampleCountList) = 17 INFO 2025-06-26 19:31:23,560 lopcToNetCDF.py constructTimestampList():1439 [1] len(timestampList) = 363 INFO 2025-06-26 19:31:23,560 lopcToNetCDF.py constructTimestampList():1440 [1] timestampList[:2] = [np.float64(1363965137.9260833), np.float64(1363965138.4260833)], ..., timestampList[-2:] = [np.float64(1363965354.9260833), np.float64(1363965355.4260833)]] INFO 2025-06-26 19:31:23,560 lopcToNetCDF.py constructTimestampList():1446 [1] Subsampling timestampList (len = 363) according to what got written to the netCDF file by the binning interval INFO 2025-06-26 19:31:23,560 lopcToNetCDF.py constructTimestampList():1457 [1] Taking indices [[np.int32(19), np.int32(40)] ... [np.int32(334), np.int32(355)]] from timestampList to create subSampledTimestampList INFO 2025-06-26 19:31:23,560 lopcToNetCDF.py constructTimestampList():1463 [1] len(subSampledTimestampList) = 17 INFO 2025-06-26 19:31:23,561 lopcToNetCDF.py constructTimestampList():1477 [1] Finding elements of cFrameEsecsList that != -9999 ERROR 2025-06-26 19:31:23,561 lopcToNetCDF.py constructTimestampList():1501 [1] Cannot interpolate to cFrameEsecsListInterpolated: array of sample points is empty INFO 2025-06-26 19:31:23,562 lopcToNetCDF.py closeNetCDFFile():2096 [1] Writing time axis for len(tsList) = 17 INFO 2025-06-26 19:31:23,562 lopcToNetCDF.py closeNetCDFFile():2099 [1] tsList[:1] = [np.float64(1363965183.9260833)], ..., tsList[-2:] = [np.float64(1363965341.4260833), np.float64(1363965351.9260833)] INFO 2025-06-26 19:31:23,563 lopcToNetCDF.py closeNetCDFFile():2100 [1] Begin time = 2013-03-22 15:13:03 Z INFO 2025-06-26 19:31:23,563 lopcToNetCDF.py closeNetCDFFile():2103 [1] End time = 2013-03-22 15:15:51 Z INFO 2025-06-26 19:31:23,563 lopcToNetCDF.py closeNetCDFFile():2107 [1] Writing time axis for len(cFrameEsecsList) = 363 INFO 2025-06-26 19:31:23,563 lopcToNetCDF.py closeNetCDFFile():2111 [1] cFrameEsecsList[:1] = [-9999], ..., cFrameEsecsList[-2:] = [-9999, -9999] INFO 2025-06-26 19:31:23,563 lopcToNetCDF.py closeNetCDFFile():2116 [1] Begin time = 1969-12-31 21:13:21 Z INFO 2025-06-26 19:31:23,563 lopcToNetCDF.py closeNetCDFFile():2120 [1] End time = 1969-12-31 21:13:21 Z INFO 2025-06-26 19:31:23,567 lopcToNetCDF.py main():2381 [1] Created file: /data/auv_data/dorado/missionnetcdfs/2013.081.05/lopc.nc INFO 2025-06-26 19:31:23,567 lopcToNetCDF.py main():2384 [1] Processing finished: Thu Jun 26 19:31:23 2025 Elapsed processing time from start of processing = 0 seconds INFO 2025-06-26 19:31:23,567 process.py calibrate():227 [1] Calibration steps for 2013.081.05 INFO 2025-06-26 19:31:23,701 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 19:31:23,703 calibrate.py _nudge_pos():1711 [1] - - - 0 0.00 - - - INFO 2025-06-26 19:31:24,625 calibrate.py _nudge_pos():1806 [1] 131: 0.070 -0.0000396 -0.0000684 1490 4.96 -1.231 -2.555 2013-03-22T15:19:24.126886656 INFO 2025-06-26 19:31:25,286 calibrate.py _nudge_pos():1806 [1] 203: 0.070 0.0048727 -0.0020639 7465 24.88 30.226 -15.371 2013-03-22T15:45:28.129745152 INFO 2025-06-26 19:31:25,607 calibrate.py _nudge_pos():1806 [1] 238: 0.070 -0.0000236 0.0000242 15 0.05 -78.047 95.944 2013-03-22T15:46:05.127210496 INFO 2025-06-26 19:31:25,673 calibrate.py _nudge_pos():1806 [1] 245: 0.080 -0.0000195 0.0000302 25 0.08 -37.636 69.937 2013-03-22T15:46:16.126457088 INFO 2025-06-26 19:31:25,747 calibrate.py _nudge_pos():1806 [1] 253: 0.080 0.0063919 -0.0039113 9955 33.18 29.739 -21.843 2013-03-22T16:19:34.129584640 INFO 2025-06-26 19:31:26,412 calibrate.py _nudge_pos():1806 [1] 325: 0.080 0.0051375 -0.0047309 8215 27.38 28.972 -32.017 2013-03-22T16:48:10.132030208 INFO 2025-06-26 19:31:27,005 calibrate.py _nudge_pos():1806 [1] 389: 0.090 0.0044349 -0.0048779 8085 26.95 25.417 -33.543 2013-03-22T17:16:10.126942976 INFO 2025-06-26 19:31:27,618 calibrate.py _nudge_pos():1806 [1] 455: 0.090 0.0050290 -0.0046828 8375 27.91 27.830 -31.087 2013-03-22T17:45:10.127744768 INFO 2025-06-26 19:31:28,012 calibrate.py _nudge_pos():1806 [1] 498: 0.090 0.0043118 -0.0042390 7795 25.98 25.641 -30.234 2013-03-22T18:11:52.128000000 INFO 2025-06-26 19:31:30,703 calibrate.py _nudge_pos():1862 [1] 750: - - - 5 0.01 - - INFO 2025-06-26 19:31:30,703 calibrate.py _nudge_pos():1868 [1] Points in final series = 55139 INFO 2025-06-26 19:31:31,307 calibrate.py _geometric_depth_correction():3423 [1] hs2: d_beg_time_diff: 3 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:31:31,730 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:31:32,073 calibrate.py _geometric_depth_correction():3423 [1] ctd1: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:31:32,076 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd1_salinity'] in 2013.081.05/ctd1.nc INFO 2025-06-26 19:31:32,078 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd1_salinity values to NaN INFO 2025-06-26 19:31:32,078 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 19:31:32,078 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd1 INFO 2025-06-26 19:31:32,501 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:31:32,850 calibrate.py _geometric_depth_correction():3423 [1] ctd2: d_beg_time_diff: 17 seconds, d_end_time_diff: -1 seconds INFO 2025-06-26 19:31:32,853 calibrate.py _ctd_process():2919 [1] Performing range checking of ['ctd2_salinity'] in 2013.081.05/ctd2.nc INFO 2025-06-26 19:31:32,854 calibrate.py _range_qc_combined_nc():898 [1] Setting 0 ctd2_salinity values to NaN INFO 2025-06-26 19:31:32,854 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 19:31:32,854 calibrate.py _range_qc_combined_nc():936 [1] Done range checking ctd2 INFO 2025-06-26 19:31:33,350 calibrate.py _biolume_process():3128 [1] Checking for non-monotonic increasing time60hz INFO 2025-06-26 19:31:33,926 calibrate.py _geometric_depth_correction():3423 [1] biolume: d_beg_time_diff: -2 seconds, d_end_time_diff: -1 seconds ERROR 2025-06-26 19:31:33,959 calibrate.py process_logs():3542 [1] Error processing ecopuck: ecopuck has no orig_data - likely a missing or zero-sized .log file in missionlogs/2013.081.05 INFO 2025-06-26 19:31:34,005 calibrate.py write_netcdf():3508 [1] Writing calibrated instrument data to /data/auv_data/dorado/missionnetcdfs/2013.081.05/dorado_2013.081.05_cal.nc INFO 2025-06-26 19:31:34,110 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 19:31:34,116 process.py align():251 [1] Alignment steps for 2013.081.05 INFO 2025-06-26 19:31:34,153 align.py process_cal():139 [1] Processing dorado_2013.081.05_cal.nc from /data/auv_data/dorado/missionnetcdfs/2013.081.05 INFO 2025-06-26 19:31:34,173 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:31:34,177 align.py process_cal():249 [1] navigation_roll: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:31:34,220 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:31:34,224 align.py process_cal():249 [1] navigation_pitch: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:31:34,270 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:31:34,274 align.py process_cal():249 [1] navigation_yaw: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:31:34,298 align.py process_cal():161 [1] Skipping navigation_posx INFO 2025-06-26 19:31:34,299 align.py process_cal():161 [1] Skipping navigation_posy INFO 2025-06-26 19:31:34,315 align.py process_cal():206 [1] Using pitch corrected navigation_depth: mDepth from navigation.nc INFO 2025-06-26 19:31:34,319 align.py process_cal():249 [1] navigation_mWaterSpeed: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:31:34,361 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:34,364 align.py process_cal():249 [1] hs2_bbp420: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:34,402 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:34,405 align.py process_cal():249 [1] hs2_bbp700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:34,444 align.py process_cal():206 [1] Using pitch corrected hs2_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to hs2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:34,447 align.py process_cal():249 [1] hs2_fl700: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:34,485 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:34,489 align.py process_cal():249 [1] ctd1_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:34,527 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:34,531 align.py process_cal():249 [1] ctd1_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:34,568 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:34,571 align.py process_cal():249 [1] ctd1_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:34,610 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:34,613 align.py process_cal():249 [1] ctd1_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:34,652 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:34,656 align.py process_cal():249 [1] ctd1_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:34,695 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:34,699 align.py process_cal():249 [1] ctd1_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:34,738 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:34,742 align.py process_cal():249 [1] ctd1_dissolvedO2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:34,781 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:34,784 align.py process_cal():249 [1] ctd1_oxygen_mll: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:34,822 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:34,827 align.py process_cal():249 [1] ctd1_oxygen_umolkg: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:34,865 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:34,869 align.py process_cal():249 [1] ctd1_flow1: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:34,907 align.py process_cal():206 [1] Using pitch corrected ctd1_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to ctd1_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:34,910 align.py process_cal():249 [1] ctd1_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:34,949 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:34,953 align.py process_cal():249 [1] ctd2_temperature: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:34,991 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:34,994 align.py process_cal():249 [1] ctd2_conductivity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:35,034 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:35,037 align.py process_cal():249 [1] ctd2_salinity: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:35,075 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:35,079 align.py process_cal():249 [1] ctd2_temperature_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:35,121 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:35,124 align.py process_cal():249 [1] ctd2_conductivity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:35,163 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:35,167 align.py process_cal():249 [1] ctd2_salinity_onboard: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:35,206 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:35,210 align.py process_cal():249 [1] ctd2_flow2: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:35,248 align.py process_cal():206 [1] Using pitch corrected ctd2_depth: Variable depth_filtdepth from dorado_2013.081.05_cal.nc linearly interpolated to ctd2_time and corrected for pitch using SensorOffset(x=4.5, y=0.0) INFO 2025-06-26 19:31:35,252 align.py process_cal():249 [1] ctd2_depth: instrument_sample_rate_hz = 4.00 INFO 2025-06-26 19:31:35,302 align.py process_cal():249 [1] isus_nitrate: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:31:35,340 align.py process_cal():249 [1] isus_temp: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:31:35,378 align.py process_cal():249 [1] isus_quality: instrument_sample_rate_hz = 0.93 INFO 2025-06-26 19:31:35,418 align.py process_cal():249 [1] biolume_flow: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:31:35,458 align.py process_cal():249 [1] biolume_avg_biolume: instrument_sample_rate_hz = 0.98 INFO 2025-06-26 19:31:35,518 align.py process_cal():249 [1] biolume_raw: instrument_sample_rate_hz = 58.99 INFO 2025-06-26 19:31:35,822 align.py process_cal():249 [1] lopc_countListSum: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 19:31:35,855 align.py process_cal():249 [1] lopc_transCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 19:31:35,888 align.py process_cal():249 [1] lopc_nonTransCount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 19:31:35,922 align.py process_cal():249 [1] lopc_LCcount: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 19:31:35,954 align.py process_cal():249 [1] lopc_flowSpeed: instrument_sample_rate_hz = 0.10 INFO 2025-06-26 19:31:35,989 align.py process_cal():249 [1] tailcone_propRpm: instrument_sample_rate_hz = 5.00 INFO 2025-06-26 19:31:36,022 align.py write_netcdf():337 [1] Writing aligned data to /data/auv_data/dorado/missionnetcdfs/2013.081.05/dorado_2013.081.05_align.nc INFO 2025-06-26 19:31:36,134 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 19:31:36,137 process.py resample():273 [1] Resampling steps for 2013.081.05 INFO 2025-06-26 19:31:36,138 resample.py resample_mission():1185 [1] Using depth_threshold = 10.00 m INFO 2025-06-26 19:31:36,174 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.081.05/dorado_2013.081.05_align.nc mission netCDF file INFO 2025-06-26 19:31:36,180 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.081.05/dorado_2013.081.05_align.nc mission netCDF file INFO 2025-06-26 19:31:36,181 resample.py get_mission_start_end():1145 [1] navigation: 2013-03-22T15:12:54.583572224 to 2013-03-22T18:16:42.128133888 (0 days 00:00:00.079994368 before mission_end) INFO 2025-06-26 19:31:36,183 resample.py get_mission_start_end():1145 [1] hs2 : 2013-03-22T15:12:21.785819136 to 2013-03-22T18:16:42.118134272 (0 days 00:00:00.089993984 before mission_end) INFO 2025-06-26 19:31:36,185 resample.py get_mission_start_end():1145 [1] ctd1 : 2013-03-22T15:12:35.084908032 to 2013-03-22T18:16:42.078137088 (0 days 00:00:00.129991168 before mission_end) INFO 2025-06-26 19:31:36,186 resample.py get_mission_start_end():1145 [1] ctd2 : 2013-03-22T15:12:35.534877184 to 2013-03-22T18:16:42.028140544 (0 days 00:00:00.179987712 before mission_end) INFO 2025-06-26 19:31:36,188 resample.py get_mission_start_end():1145 [1] isus : 2013-03-22T15:13:16.842047488 to 2013-03-22T18:16:41.518175488 (0 days 00:00:00.689952768 before mission_end) INFO 2025-06-26 19:31:36,189 resample.py get_mission_start_end():1145 [1] biolume : 2013-03-22T15:12:15.746198528 to 2013-03-22T18:16:41.188163840 (0 days 00:00:01.019964416 before mission_end) INFO 2025-06-26 19:31:36,190 resample.py get_mission_start_end():1145 [1] lopc : 2013-03-22T15:13:03.926083328 to 2013-03-22T15:15:51.926083328 (0 days 03:00:50.282044928 before mission_end) WARNING 2025-06-26 19:31:36,191 resample.py get_mission_start_end():1156 [1] Instrument lopc has a gap > 5 minutes at the end of the mission: 0 days 03:00:50.282044928 INFO 2025-06-26 19:31:36,192 resample.py get_mission_start_end():1145 [1] tailcone : 2013-03-22T15:12:17.646102784 to 2013-03-22T18:16:42.208128256 (0 days 00:00:00 before mission_end) INFO 2025-06-26 19:31:36,193 resample.py instruments_variables():235 [1] Reading variables from /data/auv_data/dorado/missionnetcdfs/2013.081.05/dorado_2013.081.05_align.nc mission netCDF file INFO 2025-06-26 19:31:36,194 resample.py resample_coordinates():249 [1] Resampling coordinates depth, latitude and longitude with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,328 resample.py resample_variable():1031 [1] Resampling navigation_roll with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,354 resample.py resample_variable():1031 [1] Resampling navigation_pitch with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,379 resample.py resample_variable():1031 [1] Resampling navigation_yaw with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,403 resample.py resample_variable():1031 [1] Resampling navigation_mWaterSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,426 resample.py resample_variable():1031 [1] Resampling hs2_bbp420 with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,448 resample.py resample_variable():1031 [1] Resampling hs2_bbp700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,469 resample.py resample_variable():1031 [1] Resampling hs2_fl700 with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,491 resample.py resample_variable():1031 [1] Resampling ctd1_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,511 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,532 resample.py resample_variable():1031 [1] Resampling ctd1_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,551 resample.py resample_variable():1031 [1] Resampling ctd1_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,571 resample.py resample_variable():1031 [1] Resampling ctd1_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,592 resample.py resample_variable():1031 [1] Resampling ctd1_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,612 resample.py resample_variable():1031 [1] Resampling ctd1_dissolvedO2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,632 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_mll with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,652 resample.py resample_variable():1031 [1] Resampling ctd1_oxygen_umolkg with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,672 resample.py resample_variable():1031 [1] Resampling ctd1_flow1 with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,694 resample.py resample_variable():1031 [1] Resampling ctd2_temperature with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,716 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,738 resample.py resample_variable():1031 [1] Resampling ctd2_salinity with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,760 resample.py resample_variable():1031 [1] Resampling ctd2_temperature_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,782 resample.py resample_variable():1031 [1] Resampling ctd2_conductivity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,804 resample.py resample_variable():1031 [1] Resampling ctd2_salinity_onboard with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,826 resample.py resample_variable():1031 [1] Resampling ctd2_flow2 with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,840 resample.py resample_variable():1031 [1] Resampling isus_nitrate with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,853 resample.py resample_variable():1031 [1] Resampling isus_temp with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,865 resample.py resample_variable():1031 [1] Resampling isus_quality with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,877 resample.py resample_variable():1031 [1] Resampling biolume_flow with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,887 resample.py resample_variable():1031 [1] Resampling biolume_avg_biolume with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:36,891 resample.py set_proxy_parameters():520 [1] Setting biolume proxy parameters for period4 INFO 2025-06-26 19:31:36,891 resample.py add_biolume_proxies():549 [1] Adding biolume proxy variables computed from biolume_raw INFO 2025-06-26 19:31:37,262 resample.py add_biolume_proxies():595 [1] Using flash_threshold = 1.0000e+11 INFO 2025-06-26 19:31:37,334 resample.py add_biolume_proxies():638 [1] Computing flashes per liter: nbflash_high, nbflash_low INFO 2025-06-26 19:31:37,378 resample.py add_biolume_proxies():666 [1] Saving flash intensity: biolume_intflash - the upper bound of the background envelope INFO 2025-06-26 19:31:37,398 resample.py add_biolume_proxies():683 [1] Saving Background bioluminescence (dinoflagellates proxy) INFO 2025-06-26 19:31:37,416 resample.py select_nighttime_bl_raw():432 [1] No sunset or sunrise found during this mission. INFO 2025-06-26 19:31:37,416 resample.py add_biolume_proxies():694 [1] No nighttime_bl_raw data to compute adinos, diatoms, hdinos proxies INFO 2025-06-26 19:31:37,432 resample.py resample_variable():1031 [1] Resampling lopc_countListSum with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:37,433 resample.py resample_variable():1038 [1] Padding lopc_countListSum with 0 days 03:00:50.282044928 of NaNs to the end of mission INFO 2025-06-26 19:31:37,444 resample.py resample_variable():1031 [1] Resampling lopc_transCount with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:37,444 resample.py resample_variable():1038 [1] Padding lopc_transCount with 0 days 03:00:50.282044928 of NaNs to the end of mission INFO 2025-06-26 19:31:37,453 resample.py resample_variable():1031 [1] Resampling lopc_nonTransCount with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:37,454 resample.py resample_variable():1038 [1] Padding lopc_nonTransCount with 0 days 03:00:50.282044928 of NaNs to the end of mission INFO 2025-06-26 19:31:37,463 resample.py resample_variable():1031 [1] Resampling lopc_LCcount with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:37,463 resample.py resample_variable():1038 [1] Padding lopc_LCcount with 0 days 03:00:50.282044928 of NaNs to the end of mission INFO 2025-06-26 19:31:37,474 resample.py resample_variable():1031 [1] Resampling lopc_flowSpeed with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:37,474 resample.py resample_variable():1038 [1] Padding lopc_flowSpeed with 0 days 03:00:50.282044928 of NaNs to the end of mission INFO 2025-06-26 19:31:37,502 resample.py resample_variable():1031 [1] Resampling tailcone_propRpm with frequency 1S following 3 point median filter INFO 2025-06-26 19:31:37,705 resample.py resample_mission():1297 [1] Saved resampled mission to /data/auv_data/dorado/missionnetcdfs/2013.081.05/dorado_2013.081.05_1S.nc INFO 2025-06-26 19:31:39,911 create_products.py _get_best_ctd():380 [1] ctdToUse = ctd1 INFO 2025-06-26 19:31:48,373 create_products.py gulper_odv():522 [1] Wrote 7 Gulper data lines to /data/auv_data/dorado/missionodvs/2013.081.05/dorado_2013.081.05_1S_Gulper.txt INFO 2025-06-26 19:31:48,373 process.py archive():337 [1] Archiving steps for 2013.081.05 INFO 2025-06-26 19:31:48,373 process.py archive():347 [1] nc_file_base = /data/auv_data/dorado/missionnetcdfs/2013.081.05/dorado_2013.081.05, BASE_PATH = /data/auv_data INFO 2025-06-26 19:31:48,374 archive.py copy_to_AUVTCD():60 [1] Archiving /data/auv_data/dorado/missionnetcdfs/2013.081.05/dorado_2013.081.05 files to /Volumes/AUVCTD/surveys/2013/netcdf INFO 2025-06-26 19:31:48,375 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.081.05_1S.nc INFO 2025-06-26 19:31:48,390 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.05/dorado_2013.081.05_1S.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:31:48,391 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.081.05_cal.nc INFO 2025-06-26 19:31:48,467 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.05/dorado_2013.081.05_cal.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:31:48,467 archive.py copy_to_AUVTCD():78 [1] Removing /Volumes/AUVCTD/surveys/2013/netcdf/dorado_2013.081.05_align.nc INFO 2025-06-26 19:31:48,577 archive.py copy_to_AUVTCD():82 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.05/dorado_2013.081.05_align.nc /Volumes/AUVCTD/surveys/2013/netcdf done. INFO 2025-06-26 19:31:48,595 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.05/ctdDriver.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013081/2013.081.05 done. INFO 2025-06-26 19:31:48,611 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.05/ctdDriver2.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013081/2013.081.05 done. INFO 2025-06-26 19:31:48,615 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.05/gps.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013081/2013.081.05 done. INFO 2025-06-26 19:31:48,629 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.05/hydroscatlog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013081/2013.081.05 done. INFO 2025-06-26 19:31:48,670 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.05/navigation.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013081/2013.081.05 done. INFO 2025-06-26 19:31:48,676 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.05/isuslog.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013081/2013.081.05 done. INFO 2025-06-26 19:31:48,694 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.05/parosci.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013081/2013.081.05 done. INFO 2025-06-26 19:31:48,707 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.05/tailCone.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013081/2013.081.05 done. INFO 2025-06-26 19:31:48,739 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.05/biolume.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013081/2013.081.05 done. INFO 2025-06-26 19:31:48,745 archive.py copy_to_AUVTCD():108 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.05/lopc.nc /Volumes/AUVCTD/missionnetcdfs/2013/2013081/2013.081.05 done. INFO 2025-06-26 19:31:48,745 archive.py copy_to_AUVTCD():116 [1] Archiving product files INFO 2025-06-26 19:31:48,746 archive.py copy_to_AUVTCD():133 [1] Removing /Volumes/AUVCTD/surveys/2013/odv/dorado_2013.081.05_1S_Gulper.txt INFO 2025-06-26 19:31:48,751 archive.py copy_to_AUVTCD():136 [1] copyfile /data/auv_data/dorado/missionodvs/2013.081.05/dorado_2013.081.05_1S_Gulper.txt /Volumes/AUVCTD/surveys/2013/odv done. INFO 2025-06-26 19:31:48,751 archive.py copy_to_AUVTCD():161 [1] copyfile /data/auv_data/dorado/missionnetcdfs/2013.081.05/dorado_2013.081.05_processing.log /Volumes/AUVCTD/surveys/2013/netcdf