Execution of AUVprocess_main version 1.86 at 2018-05-24T04:35:37Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2011, ['166.00'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1') ************************************************************************* Processing data from SSDS via DODS server ************************************************************************* ************************************************************************* Processing AUV mission: 2011.166.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/ Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Processing DVL navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/navigation.nc') Creating vector time with 314731 elements. Creating vector mPos_x with 314731 elements. Creating vector time with 314731 elements. Creating vector mPos_y with 314731 elements. Creating vector time with 314731 elements. Creating vector mDepth with 314731 elements. Creating vector time with 314731 elements. Creating vector mGpsNorth with 314731 elements. Creating vector time with 314731 elements. Creating vector mGpsEast with 314731 elements. Creating vector time with 314731 elements. Creating vector mGpsValid with 314731 elements. Creating vector time with 314731 elements. Creating vector mPhi with 314731 elements. Creating vector time with 314731 elements. Creating vector mTheta with 314731 elements. Creating vector time with 314731 elements. Creating vector mPsi with 314731 elements. Creating vector time with 314731 elements. Creating vector mOmega_x with 314731 elements. Creating vector time with 314731 elements. Creating vector mOmega_y with 314731 elements. Creating vector time with 314731 elements. Creating vector mOmega_z with 314731 elements. Creating vector time with 314731 elements. Creating vector mPsaRange with 314731 elements. Creating vector time with 314731 elements. Creating vector mAltitude with 314731 elements. Creating vector time with 314731 elements. Creating vector mDvlAltitude with 314731 elements. Creating vector time with 314731 elements. Creating vector mEchoAltitude with 314731 elements. Creating vector time with 314731 elements. Creating vector mEchoHorizRange with 314731 elements. Creating vector time with 314731 elements. Creating vector mEchoAltitudeLast with 314731 elements. Creating vector time with 314731 elements. Creating vector mEchoHorizRangeLast with 314731 elements. Creating vector time with 314731 elements. Creating vector mEchoNumOfPings with 314731 elements. Creating vector time with 314731 elements. Creating vector mWaterSpeed with 314731 elements. Creating vector time with 314731 elements. Creating vector mDvlValid with 314731 elements. Creating vector time with 314731 elements. Creating vector mDvlNewData with 314731 elements. Creating vector time with 314731 elements. Creating vector mDeltaT with 314731 elements. Creating vector time with 314731 elements. Creating vector nfix with 314731 elements. Creating vector time with 314731 elements. Creating vector efix with 314731 elements. Creating vector time with 314731 elements. Creating vector filter_north with 314731 elements. Creating vector time with 314731 elements. Creating vector filter_east with 314731 elements. Creating vector time with 314731 elements. Creating vector filter_depth with 314731 elements. Creating vector time with 314731 elements. Creating vector north_current with 314731 elements. Creating vector time with 314731 elements. Creating vector east_current with 314731 elements. Creating vector time with 314731 elements. Creating vector speed_bias with 314731 elements. Creating vector time with 314731 elements. Creating vector heading_bias with 314731 elements. Creating vector time with 314731 elements. Creating vector latitude with 314731 elements. Creating vector time with 314731 elements. Creating vector longitude with 314731 elements. Creating vector time with 314731 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/navigation.nc'); [Warning: P-file /mbari/matlab/toolbox/matlab/strfun/num2str.p is older than MATLAB file /mbari/matlab/toolbox/matlab/strfun/num2str.m. /mbari/matlab/toolbox/matlab/strfun/num2str.p may be obsolete and may need to be regenerated. Type "help pcode" for information about generating P-files.] [> In processNav (line 62) In processAUVmission (line 60) In AUVprocess_main (line 225)] processNav(): median of positive valued depths = 17.2207 processNav(): Finding depths less than 120.5451 and times > 0 processNav(): length(Nav.depth) = 314731 processNav(): length(gindx) = 304533 Processing GPS navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/gps.nc') Creating vector time with 2335 elements. Creating vector hours with 2335 elements. Creating vector time with 2335 elements. Creating vector minutes with 2335 elements. Creating vector time with 2335 elements. Creating vector seconds with 2335 elements. Creating vector time with 2335 elements. Creating vector centiSeconds with 2335 elements. Creating vector time with 2335 elements. Creating vector latitude with 2335 elements. Creating vector time with 2335 elements. Creating vector longitude with 2335 elements. Creating vector time with 2335 elements. Creating vector quality with 2335 elements. Creating vector time with 2335 elements. Creating vector numberOfSatellites with 2335 elements. Creating vector time with 2335 elements. Creating vector hdop with 2335 elements. Creating vector time with 2335 elements. Creating vector antennaHeight with 2335 elements. Creating vector time with 2335 elements. Creating vector geoHeight with 2335 elements. Creating vector time with 2335 elements. Creating vector dgpsDataAge with 2335 elements. Creating vector time with 2335 elements. Creating vector dgpsRSID with 2335 elements. Creating vector time with 2335 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/gps.nc'); processGPS(): *** skipping bad position (lat,lon) = 24.5306, -108.4583 processGPS(): *** skipping bad position (lat,lon) = 24.5578, -108.4867 processGPS(): *** skipping bad position (lat,lon) = 24.585, -108.515 processGPS(): *** skipping bad position (lat,lon) = 24.6667, -108.6002 processGPS(): *** skipping bad position (lat,lon) = 24.6939, -108.6286 processGPS(): *** skipping bad position (lat,lon) = 24.7211, -108.657 processGPS(): *** skipping bad position (lat,lon) = 24.7484, -108.6855 processGPS(): *** skipping bad position (lat,lon) = 24.8302, -108.7707 processGPS(): *** skipping bad position (lat,lon) = 24.8574, -108.7991 processGPS(): *** skipping bad position (lat,lon) = 24.8847, -108.8275 processGPS(): *** skipping bad position (lat,lon) = 24.9119, -108.856 processGPS(): *** skipping bad position (lat,lon) = 24.9938, -108.9414 processGPS(): *** skipping bad position (lat,lon) = 25.021, -108.9698 processGPS(): *** skipping bad position (lat,lon) = 25.0483, -108.9982 processGPS(): *** skipping bad position (lat,lon) = 25.0756, -109.0267 processGPS(): *** skipping bad position (lat,lon) = 25.1575, -109.1122 processGPS(): *** skipping bad position (lat,lon) = 25.1848, -109.1407 processGPS(): *** skipping bad position (lat,lon) = 25.2121, -109.1692 processGPS(): *** skipping bad position (lat,lon) = 25.2394, -109.1977 processGPS(): *** skipping bad position (lat,lon) = 25.2667, -109.2262 processGPS(): *** skipping bad position (lat,lon) = 25.294, -109.2547 processGPS(): *** skipping bad position (lat,lon) = 25.3213, -109.2832 processGPS(): *** skipping bad position (lat,lon) = 25.3486, -109.3118 processGPS(): *** skipping bad position (lat,lon) = 25.376, -109.3404 processGPS(): *** skipping bad position (lat,lon) = 25.4033, -109.3689 processGPS(): *** skipping bad position (lat,lon) = 25.4852, -109.4545 processGPS(): *** skipping bad position (lat,lon) = 25.6492, -109.6259 processGPS(): *** skipping bad position (lat,lon) = 25.6766, -109.6545 processGPS(): *** skipping bad position (lat,lon) = 25.704, -109.6831 processGPS(): *** skipping bad position (lat,lon) = 25.7314, -109.7117 processGPS(): *** skipping bad position (lat,lon) = 25.8135, -109.7976 processGPS(): *** skipping bad position (lat,lon) = 25.8408, -109.8262 processGPS(): *** skipping bad position (lat,lon) = 25.8682, -109.8548 processGPS(): *** skipping bad position (lat,lon) = 25.8956, -109.8835 processGPS(): *** skipping bad position (lat,lon) = 25.9777, -109.9694 processGPS(): *** skipping bad position (lat,lon) = 26.0052, -109.9981 processGPS(): *** skipping bad position (lat,lon) = 26.0326, -110.0268 processGPS(): *** skipping bad position (lat,lon) = 26.0599, -110.0554 processGPS(): *** skipping bad position (lat,lon) = 26.0873, -110.0841 processGPS(): *** skipping bad position (lat,lon) = 26.1147, -110.1128 processGPS(): *** skipping bad position (lat,lon) = 26.1421, -110.1415 processGPS(): *** skipping bad position (lat,lon) = 26.1695, -110.1702 processGPS(): *** skipping bad position (lat,lon) = 26.1969, -110.1989 processGPS(): *** skipping bad position (lat,lon) = 26.2243, -110.2276 processGPS(): *** skipping bad position (lat,lon) = 26.2517, -110.2564 processGPS(): *** skipping bad position (lat,lon) = 26.3066, -110.3138 processGPS(): *** skipping bad position (lat,lon) = 26.334, -110.3426 processGPS(): *** skipping bad position (lat,lon) = 26.3614, -110.3713 processGPS(): *** skipping bad position (lat,lon) = 26.3888, -110.4001 processGPS(): *** skipping bad position (lat,lon) = 26.4711, -110.4863 processGPS(): *** skipping bad position (lat,lon) = 26.4985, -110.5151 processGPS(): *** skipping bad position (lat,lon) = 26.5809, -110.6015 processGPS(): *** skipping bad position (lat,lon) = 26.6357, -110.6591 processGPS(): *** skipping bad position (lat,lon) = 26.6632, -110.6879 processGPS(): *** skipping bad position (lat,lon) = 26.6906, -110.7167 processGPS(): *** skipping bad position (lat,lon) = 26.718, -110.7455 processGPS(): *** skipping bad position (lat,lon) = 26.8004, -110.8321 processGPS(): *** skipping bad position (lat,lon) = 26.8278, -110.8609 processGPS(): *** skipping bad position (lat,lon) = 26.8553, -110.8897 processGPS(): *** skipping bad position (lat,lon) = 26.8828, -110.9186 processGPS(): *** skipping bad position (lat,lon) = 27.0751, -111.1209 processGPS(): *** skipping bad position (lat,lon) = 27.1575, -111.2076 processGPS(): *** skipping bad position (lat,lon) = 27.1849, -111.2365 processGPS(): *** skipping bad position (lat,lon) = 27.2123, -111.2653 processGPS(): *** skipping bad position (lat,lon) = 27.2948, -111.3522 processGPS(): *** skipping bad position (lat,lon) = 27.3224, -111.3812 processGPS(): *** skipping bad position (lat,lon) = 27.3499, -111.4102 processGPS(): *** skipping bad position (lat,lon) = 27.3774, -111.4392 processGPS(): *** skipping bad position (lat,lon) = 27.4598, -111.5261 processGPS(): *** skipping bad position (lat,lon) = 27.4873, -111.5551 processGPS(): *** skipping bad position (lat,lon) = 27.5148, -111.5841 processGPS(): *** skipping bad position (lat,lon) = 27.5423, -111.6132 processGPS(): *** skipping bad position (lat,lon) = 27.5973, -111.6712 processGPS(): *** skipping bad position (lat,lon) = 27.6249, -111.7003 processGPS(): *** skipping bad position (lat,lon) = 27.6524, -111.7293 processGPS(): *** skipping bad position (lat,lon) = 27.6799, -111.7584 processGPS(): *** skipping bad position (lat,lon) = 27.7074, -111.7875 processGPS(): *** skipping bad position (lat,lon) = 27.7349, -111.8166 processGPS(): *** skipping bad position (lat,lon) = 27.7624, -111.8456 processGPS(): *** skipping bad position (lat,lon) = 27.7899, -111.8747 processGPS(): *** skipping bad position (lat,lon) = 27.8174, -111.9038 processGPS(): *** skipping bad position (lat,lon) = 27.8724, -111.9619 processGPS(): *** skipping bad position (lat,lon) = 27.9, -111.991 processGPS(): *** skipping bad position (lat,lon) = 27.9275, -112.0201 processGPS(): *** skipping bad position (lat,lon) = 27.955, -112.0493 processGPS(): *** skipping bad position (lat,lon) = 27.9825, -112.0784 processGPS(): *** skipping bad position (lat,lon) = 28.0052, -112.1028 processGPS(): *** skipping bad position (lat,lon) = 28.0032, -112.1031 processGPS(): *** skipping bad position (lat,lon) = 28.0247, -112.1263 processGPS(): *** skipping bad position (lat,lon) = 28.0521, -112.1554 processGPS(): *** skipping bad position (lat,lon) = 28.0795, -112.1844 processGPS(): *** skipping bad position (lat,lon) = 28.1069, -112.2134 processGPS(): *** skipping bad position (lat,lon) = 28.1343, -112.2424 processGPS(): *** skipping bad position (lat,lon) = 28.1617, -112.2714 processGPS(): *** skipping bad position (lat,lon) = 28.1891, -112.3005 processGPS(): *** skipping bad position (lat,lon) = 28.2166, -112.3297 processGPS(): *** skipping bad position (lat,lon) = 28.244, -112.3587 processGPS(): *** skipping bad position (lat,lon) = 28.2714, -112.3878 processGPS(): *** skipping bad position (lat,lon) = 28.2988, -112.4168 processGPS(): *** skipping bad position (lat,lon) = 28.3262, -112.4459 processGPS(): *** skipping bad position (lat,lon) = 28.3536, -112.475 processGPS(): *** skipping bad position (lat,lon) = 28.5454, -112.6788 processGPS(): *** skipping bad position (lat,lon) = 28.5729, -112.708 processGPS(): *** skipping bad position (lat,lon) = 28.6003, -112.7371 processGPS(): *** skipping bad position (lat,lon) = 28.6277, -112.7663 Processing depth data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/parosci.nc') Creating vector time with 533759 elements. Creating vector depth with 533759 elements. Creating vector time with 533759 elements. Creating vector temp with 533759 elements. Creating vector time with 533759 elements. Creating vector pressure with 533759 elements. Creating vector time with 533759 elements. Creating vector temp_period with 533759 elements. Creating vector time with 533759 elements. Creating vector pres_period with 533759 elements. Creating vector time with 533759 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.83669 max(Depth.data) = 249.6292 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.83669 max(Depth.data) = 249.6292 [Warning: P-file /mbari/matlab/toolbox/matlab/ops/unique.p is older than MATLAB file /mbari/matlab/toolbox/matlab/ops/unique.m. /mbari/matlab/toolbox/matlab/ops/unique.p may be obsolete and may need to be regenerated. Type "help pcode" for information about generating P-files.] [> In fix_depth_time (line 6) In processDepth (line 65) In processAUVmission (line 106) In AUVprocess_main (line 225)] Processing hs2 backscattering and chlorophyll fluorescence data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/hydroscatlog.nc') Creating vector time with 251784 elements. Creating vector Seconds with 251784 elements. Creating vector time with 251784 elements. Creating vector HundrethsOfSeconds with 251784 elements. Creating vector time with 251784 elements. Creating vector Snorm1 with 251784 elements. Creating vector time with 251784 elements. Creating vector Snorm2 with 251784 elements. Creating vector time with 251784 elements. Creating vector Snorm3 with 251784 elements. Creating vector time with 251784 elements. Creating vector Gain_Status_1 with 251784 elements. Creating vector time with 251784 elements. Creating vector Gain_Status_2 with 251784 elements. Creating vector time with 251784 elements. Creating vector Gain_Status_3 with 251784 elements. Creating vector time with 251784 elements. Creating vector RawDepthValue with 251784 elements. Creating vector time with 251784 elements. Creating vector RawTempValue with 251784 elements. Creating vector time with 251784 elements. Creating vector Temperature with 251784 elements. Creating vector time with 251784 elements. Creating vector ErrorValue with 251784 elements. Creating vector time with 251784 elements. Creating vector bb470 with 251784 elements. Creating vector time with 251784 elements. Creating vector bb676 with 251784 elements. Creating vector time with 251784 elements. Creating vector fl676u with 251784 elements. Creating vector time with 251784 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/hydroscatlog.nc'); Processing CTD #1 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/ctdDriver.nc') Creating vector time with 251770 elements. Creating vector conductivity with 251770 elements. Creating vector time with 251770 elements. Creating vector temperature with 251770 elements. Creating vector time with 251770 elements. Creating vector cond_frequency with 251770 elements. Creating vector time with 251770 elements. Creating vector temp_frequency with 251770 elements. Creating vector time with 251770 elements. Creating vector spare with 251770 elements. Creating vector time with 251770 elements. Creating vector humidity with 251770 elements. Creating vector time with 251770 elements. Creating vector flow1 with 251770 elements. Creating vector time with 251770 elements. Creating vector CDOM with 251770 elements. Creating vector time with 251770 elements. Creating vector dissolvedO2 with 251770 elements. Creating vector time with 251770 elements. Creating vector salinity with 251770 elements. Creating vector time with 251770 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/ctdDriver.cfg Oxygen calibration loaded from CTD config file (current method) Using constant flow rate offset for oxygen... Processing CTD #2 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/ctdDriver2.nc') Creating vector time with 251836 elements. Creating vector conductivity with 251836 elements. Creating vector time with 251836 elements. Creating vector temperature with 251836 elements. Creating vector time with 251836 elements. Creating vector cond_frequency with 251836 elements. Creating vector time with 251836 elements. Creating vector temp_frequency with 251836 elements. Creating vector time with 251836 elements. Creating vector flow2 with 251836 elements. Creating vector time with 251836 elements. Creating vector spare with 251836 elements. Creating vector time with 251836 elements. Creating vector salinity with 251836 elements. Creating vector time with 251836 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/ctdDriver2.cfg Processing ISUS data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/isuslog.nc') Creating vector time with 62558 elements. Creating vector isusNitrate with 62558 elements. Creating vector time with 62558 elements. Creating vector isusTemp with 62558 elements. Creating vector time with 62558 elements. Creating vector isusQuality with 62558 elements. Creating vector time with 62558 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/isuslog.nc'); Total lag applied to nitrate = 6 seconds Processing Biolume data... [Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 21) In processAUVmission (line 220) In AUVprocess_main (line 225)] [Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 22) In processAUVmission (line 220) In AUVprocess_main (line 225)] loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/biolume.nc') Creating vector time with 61927 elements. Creating vector rrr with 61927 elements. Creating vector time with 61927 elements. Creating vector cal_striing with 61927 elements. Creating vector time with 61927 elements. Creating vector avg_biolume with 61927 elements. Creating vector time with 61927 elements. Creating vector pump with 61927 elements. Creating vector time with 61927 elements. Creating vector system_voltage with 61927 elements. Creating vector time with 61927 elements. Creating vector flow with 61927 elements. Creating vector time with 61927 elements. Creating vector HV with 61927 elements. Creating vector time with 61927 elements. Creating vector reserved with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_0 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_1 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_2 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_3 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_4 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_5 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_6 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_7 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_8 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_9 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_10 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_11 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_12 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_13 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_14 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_15 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_16 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_17 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_18 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_19 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_20 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_21 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_22 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_23 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_24 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_25 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_26 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_27 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_28 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_29 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_30 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_31 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_32 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_33 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_34 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_35 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_36 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_37 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_38 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_39 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_40 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_41 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_42 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_43 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_44 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_45 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_46 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_47 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_48 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_49 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_50 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_51 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_52 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_53 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_54 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_55 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_56 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_57 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_58 with 61927 elements. Creating vector time with 61927 elements. Creating vector raw_59 with 61927 elements. Creating vector time with 61927 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/biolume.nc'); Processing LOPC plankton data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (4620 x 994) with 4592280 elements. Creating vector time with 4620 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (4620 x 994) with 4592280 elements. Creating vector time with 4620 elements. Creating vector bin with 994 elements. Creating matrix countList (4620 x 994) with 4592280 elements. Creating vector time with 4620 elements. Creating vector bin with 994 elements. Creating vector LCcount with 4620 elements. Creating vector time with 4620 elements. Creating vector transCount with 4620 elements. Creating vector time with 4620 elements. Creating vector nonTransCount with 4620 elements. Creating vector time with 4620 elements. Creating vector ai_mean with 4620 elements. Creating vector time with 4620 elements. Creating vector ai_min with 4620 elements. Creating vector time with 4620 elements. Creating vector ai_max with 4620 elements. Creating vector time with 4620 elements. Creating vector ai_std with 4620 elements. Creating vector time with 4620 elements. Creating vector esd_mean with 4620 elements. Creating vector time with 4620 elements. Creating vector esd_min with 4620 elements. Creating vector time with 4620 elements. Creating vector esd_max with 4620 elements. Creating vector time with 4620 elements. Creating vector esd_std with 4620 elements. Creating vector time with 4620 elements. Creating vector countSum with 4620 elements. Creating vector time with 4620 elements. Creating vector snapshot with 4620 elements. Creating vector time with 4620 elements. Creating vector threshold with 4620 elements. Creating vector time with 4620 elements. Creating vector sampleCount with 4620 elements. Creating vector time with 4620 elements. Creating vector flowCount with 4620 elements. Creating vector time with 4620 elements. Creating vector flowTime with 4620 elements. Creating vector time with 4620 elements. Creating vector bufferStatus with 4620 elements. Creating vector time with 4620 elements. Creating vector laserLevel with 4620 elements. Creating vector time with 4620 elements. Creating vector counter with 4620 elements. Creating vector time with 4620 elements. Creating vector counterPeriod with 4620 elements. Creating vector time with 4620 elements. Creating vector laserControl with 4620 elements. Creating vector time with 4620 elements. Creating vector countUnknownFrameCharacter with 4620 elements. Creating vector time with 4620 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 4620 elements. Creating vector time with 4620 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 4620 elements. Creating vector time with 4620 elements. Creating vector flowSpeed with 4620 elements. Creating vector time with 4620 elements. Creating vector countShortLFrameError with 4620 elements. Creating vector time with 4620 elements. Creating vector countGarbledLFrame with 4620 elements. Creating vector time with 4620 elements. Creating vector cFrameEsecs with 4620 elements. Creating vector time with 4620 elements. Creating vector correctedSampleCountList with 4620 elements. Creating vector time with 4620 elements. Creating vector time with 4620 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011.166.00.mat BL CTD1 CTD2 hs2 ISUS Nav gps lopc ************************************************************************* ************************************************************************* Calling build_auv_survey.m to construct survey file... SecondaryDissolvedO2 = [] Reading: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011.166.00.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 20 segments. [Warning: MATLAB has disabled some advanced graphics rendering features by switching to software OpenGL. For more information, click here.] Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00_nav_adjust.png [Warning: P-file /mbari/matlab/toolbox/matlab/imagesci/imformats.p is older than MATLAB file /mbari/matlab/toolbox/matlab/imagesci/imformats.m. /mbari/matlab/toolbox/matlab/imagesci/imformats.p may be obsolete and may need to be regenerated. Type "help pcode" for information about generating P-files.] [> In imwrite>parse_inputs (line 557) In imwrite (line 418) In writeRaster In printingGenerateOutput In alternatePrintPath In print (line 82) In create_data_products (line 99) In build_auv_survey (line 522) In AUVprocess_main (line 255)] [Warning: P-file /mbari/matlab/toolbox/matlab/timefun/datevec.p is older than MATLAB file /mbari/matlab/toolbox/matlab/timefun/datevec.m. /mbari/matlab/toolbox/matlab/timefun/datevec.p may be obsolete and may need to be regenerated. Type "help pcode" for information about generating P-files.] [> In datenum (line 103) In writepng (line 232) In imwrite (line 485) In writeRaster In printingGenerateOutput In alternatePrintPath In print (line 82) In create_data_products (line 99) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00.mat ************************************************************************* Calling plot_sections from ../viz to produce section plots ... Using median boxcar filter of vector... Using mean boxcar filter of vector... Number of profiles found = 362 Gridding with nix = 1086, iZ = 238 Using mean boxcar filter of vector... Using mean boxcar filter of vector... Using max boxcar filter of vector... Using max boxcar filter of vector... Using max boxcar filter of vector... Gridding... T S O Using median boxcar filter of vector... Using median boxcar filter of vector... Using median boxcar filter of vector... bbp420 bbp700 fl700_uncorr N BL BLflow LOPC count transCount nonTransCount LCcount Masking and filtering with median filter of size 5... cvarname = gT cvarname = gS cvarname = gO cvarname = gN cvarname = gF cvarname = gB420 cvarname = gB700 cvarname = gBL cvarname = gBLflow cvarname = gLOPCcount cvarname = gLOPCtransCount cvarname = gLOPCnonTransCount cvarname = gLOPCLCcount Encountered 0 NaN values in array of lon that is 302822 elements long ! gmt grdtrack -V ~/tmp/grdTrk.txt -GMonterey25.grd -bos >! ~/tmp/grdTrk.bath grdtrack: Warning: -b option with type s, S, or D are deprecated; Use f or d, with w to indicate swab grdtrack: Processing input grid(s) grdtrack: Output 1 columns via binary records using format f grdtrack: Sampled 302822 points from grid Monterey25.grd (2876 x 2447) Getting short wave radiation data from M1 for little plot above the biolume section plot Creating vector TIME with 118882 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 06/15/2011 13:29 to 06/16/2011 08:30 swr = 981.5000 923.9738 815.3347 649.5007 432.9239 221.8624 79.8187 8.9250 1.7667 1.7809 1.8541 1.6809 1.4000 1.6190 1.5699 1.6920 3.7518 45.9460 54.8401 202.6313 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2011166_GulperTimes.txt && touch ../results/2011166_GulperTimes.txt Getting mission start epoch seconds from: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2011/2011166/2011.166.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2011/2011166/2011.166.00/syslog -startEsecs 1308175612.8974 -surveyName Dorado389_2011_166_00_166_00 >> ../results/2011166_GulperTimes.txt Executing: removeGulpDups.py ../results/2011166_GulperTimes.txt Bottle: 0 Time: 1308177932 Depth: 2.5984 Dist: 1.9923 Bottle: 1 Time: 1308181714 Depth: 3.7202 Dist: 5.3495 Bottle: 3 Time: 1308182889 Depth: 2.0357 Dist: 6.5632 Bottle: 4 Time: 1308186489 Depth: 3.2628 Dist: 10.249 Bottle: 5 Time: 1308190089 Depth: 2.049 Dist: 13.954 Bottle: 6 Time: 1308193689 Depth: -0.4117 Dist: 17.6329 Bottle: 2 Time: 1308198548 Depth: 3.515 Dist: 23.1811 Bottle: 7 Time: 1308218776 Depth: 5.0276 Dist: 43.627 Bottle: 8 Time: 1308225976 Depth: 8.9643 Dist: 51.7031 Bottle: 9 Time: 1308233177 Depth: 18.1199 Dist: 58.782 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00_gridded.mat outvarstr = 'gF gT gN gS gD gO gB420 gB700 gBL gBLflow gLOPCcount gLOPCtransCount gLOPCnonTransCount gLOPCLCcount idist iZ auvnav distnav ilat ilon profDist profZ dists depths stride sdists sdepths fixLonSubIntrp fixLatSubIntrp GulperLocations bmask bdist bdepth fbdist fbdepth ' 2Column contouring gridded variable gD Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gS Drawing bottom contour from EM300 data 2Column contouring gridded variable gN Drawing bottom contour from EM300 data 2Column contouring gridded variable gO Drawing bottom contour from EM300 data 2Column contouring gridded variable gB420 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB700 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00_2column.png Elapsed time to save image: 12 seconds Biolume contouring gridded variable gD Drawing bottom contour from EM300 data Biolume contouring gridded variable gT Drawing bottom contour from EM300 data Biolume contouring gridded variable gS Drawing bottom contour from EM300 data Biolume contouring gridded variable gN Drawing bottom contour from EM300 data Biolume contouring gridded variable gO Drawing bottom contour from EM300 data Biolume contouring gridded variable gB420 Drawing bottom contour from EM300 data Biolume contouring gridded variable gB700 Drawing bottom contour from EM300 data Biolume contouring gridded variable gF Drawing bottom contour from EM300 data Biolume contouring gridded variable gBL Drawing bottom contour from EM300 data Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00_biolume.png Elapsed time to save image: 35 seconds 2Column contouring gridded variable gLOPCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCtransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCnonTransCount Drawing bottom contour from EM300 data 2Column contouring gridded variable gLOPCLCcount Drawing bottom contour from EM300 data 2Column contouring gridded variable gT Drawing bottom contour from EM300 data 2Column contouring gridded variable gB420 Drawing bottom contour from EM300 data 2Column contouring gridded variable gB700 Drawing bottom contour from EM300 data 2Column contouring gridded variable gF Drawing bottom contour from EM300 data 2Column contouring gridded variable gBL Drawing bottom contour from EM300 data Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00_lopc.png Elapsed time to save image: 9 seconds ************************************************************************* Calling plot_survey_stats to produce histogram and profile statistics plots... [Warning: P-file /mbari/matlab/toolbox/matlab/graph2d/subplot.p is older than MATLAB file /mbari/matlab/toolbox/matlab/graph2d/subplot.m. /mbari/matlab/toolbox/matlab/graph2d/subplot.p may be obsolete and may need to be regenerated. Type "help pcode" for information about generating P-files.] [> In plot_survey_stats (line 47) In create_data_products (line 128) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00_2column.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00_biolume.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00_lopc.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2011/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing KML files ... KML = write_kml(survey_shrt_filename_base, 'Temperature', jetplus, varlimits(1,:), ctd1.T, time.ctd1, auvnav, depth.ctd1, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_166_00_166_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_166_00_166_00_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2011/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Salinity', jetplus, varlimits(2,:), ctd1.S, time.ctd1, auvnav, depth.ctd1, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_166_00_166_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_166_00_166_00_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2011/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Nitrate', jetplus, varlimits(3,:), isus.nitrate, time.isus, auvnav, depth.isus, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_166_00_166_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_166_00_166_00_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2011/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Oxygen', jetplus, varlimits(4,:), ctd1.O2, time.ctd1, auvnav, depth.ctd1, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_166_00_166_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_166_00_166_00_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2011/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @420 nm', jetplus, varlimits(5,:), hs2.bbp420, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_166_00_166_00_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_166_00_166_00_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2011/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @700 nm', jetplus, varlimits(6,:), hs2.bbp700, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_166_00_166_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_166_00_166_00_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2011/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl700_uncorr, time.hs2, auvnav, depth.hs2, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_166_00_166_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_166_00_166_00_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2011/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Bioluminescence', jetplus, varlimits(8,:), biolume.biolume, time.biolume, auvnav, depth.biolume, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_166_00_166_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_166_00_166_00_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2011/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'LOPC Total Count', jetplus, varlimits(9,:), lopc.countSum, time.lopc, auvnav, depth.lopc, resultspath); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_166_00_166_00_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_166_00_166_00_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2011/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2011_166_00_166_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00.kml... Copied to /mbari/AUVCTD/surveys/2011/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2011_166_00_166_00_LOPC_Total_Count.kml' not found.] [> In create_data_products (line 414) In build_auv_survey (line 522) In AUVprocess_main (line 255)] ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 305 NaNs found in bbpBlue. Interpolating anyway. 445 NaNs found in bbpRed. Interpolating anyway. 58 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 337 NaN values in array of lon that is 62078 elements long ! gmt grdtrack -V ~/tmp/grdTrk.txt -GMonterey25.grd -bos >! ~/tmp/grdTrk.bath grdtrack: Warning: -b option with type s, S, or D are deprecated; Use f or d, with w to indicate swab grdtrack: Processing input grid(s) grdtrack: Output 1 columns via binary records using format f grdtrack: Sampled 61741 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 61741 are not equal to number of Lat lon points = 62078 AUV track probably goes outside of the range of the .grd file being used. Setting bottom depths to 1000 m Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00.txt... Copied to /mbari/AUVCTD/surveys/2011/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2011/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 305 NaNs found in bbpBlue. Interpolating anyway. 445 NaNs found in bbpRed. Interpolating anyway. 58 NaNs found in flRed_uncorr. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00_decim.nc... Copied to /mbari/AUVCTD/surveys/2011/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing netCDF file ... Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00.nc... Copied to /mbari/AUVCTD/surveys/2011/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00_gridded.mat... Copied to /mbari/AUVCTD/surveys/2011/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011_166_00_166_00.mat... Copied to /mbari/AUVCTD/surveys/2011/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2011_166_00_166_00 processed" mccann@mbari.org < mail_Dorado389_2011_166_00_166_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2011.166.00.mat Processing time: 392 seconds