Execution of AUVprocess_main version 1.88 at 2019-12-18T23:43:37Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2019, ['351.00'], '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: 2019.351.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019351/2019.351.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2019/2019351/2019.351.00/ 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/2019/2019351/2019.351.00/navigation.nc') Creating vector time with 387226 elements. Creating vector mPos_x with 387226 elements. Creating vector time with 387226 elements. Creating vector mPos_y with 387226 elements. Creating vector time with 387226 elements. Creating vector mDepth with 387226 elements. Creating vector time with 387226 elements. Creating vector mGpsNorth with 387226 elements. Creating vector time with 387226 elements. Creating vector mGpsEast with 387226 elements. Creating vector time with 387226 elements. Creating vector mGpsValid with 387226 elements. Creating vector time with 387226 elements. Creating vector mPhi with 387226 elements. Creating vector time with 387226 elements. Creating vector mTheta with 387226 elements. Creating vector time with 387226 elements. Creating vector mPsi with 387226 elements. Creating vector time with 387226 elements. Creating vector mOmega_x with 387226 elements. Creating vector time with 387226 elements. Creating vector mOmega_y with 387226 elements. Creating vector time with 387226 elements. Creating vector mOmega_z with 387226 elements. Creating vector time with 387226 elements. Creating vector mPsaRange with 387226 elements. Creating vector time with 387226 elements. Creating vector mAltitude with 387226 elements. Creating vector time with 387226 elements. Creating vector multibeamAltitude with 387226 elements. Creating vector time with 387226 elements. Creating vector mDvlAltitude with 387226 elements. Creating vector time with 387226 elements. Creating vector mEchoAltitude with 387226 elements. Creating vector time with 387226 elements. Creating vector mEchoHorizRange with 387226 elements. Creating vector time with 387226 elements. Creating vector mEchoAltitudeLast with 387226 elements. Creating vector time with 387226 elements. Creating vector mEchoHorizRangeLast with 387226 elements. Creating vector time with 387226 elements. Creating vector mEchoNumOfPings with 387226 elements. Creating vector time with 387226 elements. Creating vector nadirCnts with 387226 elements. Creating vector time with 387226 elements. Creating vector obstacleCnts with 387226 elements. Creating vector time with 387226 elements. Creating vector nGoodNadirBeams with 387226 elements. Creating vector time with 387226 elements. Creating vector medianNadirBeamNo with 387226 elements. Creating vector time with 387226 elements. Creating vector mWaterSpeed with 387226 elements. Creating vector time with 387226 elements. Creating vector mDvlValid with 387226 elements. Creating vector time with 387226 elements. Creating vector mDvlNewData with 387226 elements. Creating vector time with 387226 elements. Creating vector mDeltaT with 387226 elements. Creating vector time with 387226 elements. Creating vector nfix with 387226 elements. Creating vector time with 387226 elements. Creating vector efix with 387226 elements. Creating vector time with 387226 elements. Creating vector filter_north with 387226 elements. Creating vector time with 387226 elements. Creating vector filter_east with 387226 elements. Creating vector time with 387226 elements. Creating vector filter_depth with 387226 elements. Creating vector time with 387226 elements. Creating vector north_current with 387226 elements. Creating vector time with 387226 elements. Creating vector east_current with 387226 elements. Creating vector time with 387226 elements. Creating vector speed_bias with 387226 elements. Creating vector time with 387226 elements. Creating vector heading_bias with 387226 elements. Creating vector time with 387226 elements. Creating vector latitude with 387226 elements. Creating vector time with 387226 elements. Creating vector longitude with 387226 elements. Creating vector time with 387226 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019351/2019.351.00/navigation.nc'); processNav(): median of positive valued depths = 36.4578 processNav(): Finding depths less than 255.2048 and times > 0 processNav(): length(Nav.depth) = 387226 processNav(): length(gindx) = 387226 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/2019/2019351/2019.351.00/gps.nc') Creating vector time with 6836 elements. Creating vector hours with 6836 elements. Creating vector time with 6836 elements. Creating vector minutes with 6836 elements. Creating vector time with 6836 elements. Creating vector seconds with 6836 elements. Creating vector time with 6836 elements. Creating vector centiSeconds with 6836 elements. Creating vector time with 6836 elements. Creating vector latitude with 6836 elements. Creating vector time with 6836 elements. Creating vector longitude with 6836 elements. Creating vector time with 6836 elements. Creating vector quality with 6836 elements. Creating vector time with 6836 elements. Creating vector numberOfSatellites with 6836 elements. Creating vector time with 6836 elements. Creating vector hdop with 6836 elements. Creating vector time with 6836 elements. Creating vector antennaHeight with 6836 elements. Creating vector time with 6836 elements. Creating vector geoHeight with 6836 elements. Creating vector time with 6836 elements. Creating vector dgpsDataAge with 6836 elements. Creating vector time with 6836 elements. Creating vector dgpsRSID with 6836 elements. Creating vector time with 6836 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019351/2019.351.00/gps.nc'); Processing depth data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019351/2019.351.00/parosci.nc') Creating vector time with 771081 elements. Creating vector depth with 771081 elements. Creating vector time with 771081 elements. Creating vector temp with 771081 elements. Creating vector time with 771081 elements. Creating vector pressure with 771081 elements. Creating vector time with 771081 elements. Creating vector temp_period with 771081 elements. Creating vector time with 771081 elements. Creating vector pres_period with 771081 elements. Creating vector time with 771081 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019351/2019.351.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.37374 max(Depth.data) = 202.7957 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.37374 max(Depth.data) = 202.7957 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/2019/2019351/2019.351.00/hydroscatlog.nc') Creating vector time with 309745 elements. Creating vector Seconds with 309745 elements. Creating vector time with 309745 elements. Creating vector HundrethsOfSeconds with 309745 elements. Creating vector time with 309745 elements. Creating vector Snorm1 with 309745 elements. Creating vector time with 309745 elements. Creating vector Snorm2 with 309745 elements. Creating vector time with 309745 elements. Creating vector Snorm3 with 309745 elements. Creating vector time with 309745 elements. Creating vector Gain_Status_1 with 309745 elements. Creating vector time with 309745 elements. Creating vector Gain_Status_2 with 309745 elements. Creating vector time with 309745 elements. Creating vector Gain_Status_3 with 309745 elements. Creating vector time with 309745 elements. Creating vector RawDepthValue with 309745 elements. Creating vector time with 309745 elements. Creating vector RawTempValue with 309745 elements. Creating vector time with 309745 elements. Creating vector Temperature with 309745 elements. Creating vector time with 309745 elements. Creating vector ErrorValue with 309745 elements. Creating vector time with 309745 elements. Creating vector bb470 with 309745 elements. Creating vector time with 309745 elements. Creating vector bb676 with 309745 elements. Creating vector time with 309745 elements. Creating vector fl676u with 309745 elements. Creating vector time with 309745 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019351/2019.351.00/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/2019/2019351/2019.351.00/ctdDriver.nc') Creating vector time with 309751 elements. Creating vector conductivity with 309751 elements. Creating vector time with 309751 elements. Creating vector temperature with 309751 elements. Creating vector time with 309751 elements. Creating vector cond_frequency with 309751 elements. Creating vector time with 309751 elements. Creating vector temp_frequency with 309751 elements. Creating vector time with 309751 elements. Creating vector spare with 309751 elements. Creating vector time with 309751 elements. Creating vector humidity with 309751 elements. Creating vector time with 309751 elements. Creating vector flow1 with 309751 elements. Creating vector time with 309751 elements. Creating vector CDOM with 309751 elements. Creating vector time with 309751 elements. Creating vector dissolvedO2 with 309751 elements. Creating vector time with 309751 elements. Creating vector salinity with 309751 elements. Creating vector time with 309751 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019351/2019.351.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2019/2019351/2019.351.00/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/2019/2019351/2019.351.00/ctdDriver2.nc') Creating vector time with 309816 elements. Creating vector conductivity with 309816 elements. Creating vector time with 309816 elements. Creating vector temperature with 309816 elements. Creating vector time with 309816 elements. Creating vector cond_frequency with 309816 elements. Creating vector time with 309816 elements. Creating vector temp_frequency with 309816 elements. Creating vector time with 309816 elements. Creating vector flow2 with 309816 elements. Creating vector time with 309816 elements. Creating vector spare with 309816 elements. Creating vector time with 309816 elements. Creating vector salinity with 309816 elements. Creating vector time with 309816 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019351/2019.351.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2019/2019351/2019.351.00/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/2019/2019351/2019.351.00/isuslog.nc') Creating vector time with 60072 elements. Creating vector isusNitrate with 60072 elements. Creating vector time with 60072 elements. Creating vector isusTemp with 60072 elements. Creating vector time with 60072 elements. Creating vector isusQuality with 60072 elements. Creating vector time with 60072 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019351/2019.351.00/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 71) In processBiolume (line 21) In processAUVmission (line 220) In AUVprocess_main (line 227)] [Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] [> In rmpath (line 71) In processBiolume (line 22) In processAUVmission (line 220) In AUVprocess_main (line 227)] loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019351/2019.351.00/biolume.nc') Creating vector time with 76174 elements. Creating vector rrr with 76174 elements. Creating vector time with 76174 elements. Creating vector cal_striing with 76174 elements. Creating vector time with 76174 elements. Creating vector avg_biolume with 76174 elements. Creating vector time with 76174 elements. Creating vector pump with 76174 elements. Creating vector time with 76174 elements. Creating vector system_voltage with 76174 elements. Creating vector time with 76174 elements. Creating vector flow with 76174 elements. Creating vector time with 76174 elements. Creating vector HV with 76174 elements. Creating vector time with 76174 elements. Creating vector reserved with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_0 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_1 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_2 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_3 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_4 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_5 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_6 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_7 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_8 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_9 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_10 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_11 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_12 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_13 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_14 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_15 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_16 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_17 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_18 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_19 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_20 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_21 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_22 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_23 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_24 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_25 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_26 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_27 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_28 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_29 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_30 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_31 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_32 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_33 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_34 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_35 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_36 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_37 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_38 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_39 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_40 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_41 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_42 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_43 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_44 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_45 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_46 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_47 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_48 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_49 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_50 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_51 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_52 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_53 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_54 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_55 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_56 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_57 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_58 with 76174 elements. Creating vector time with 76174 elements. Creating vector raw_59 with 76174 elements. Creating vector time with 76174 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019351/2019.351.00/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/2019/2019351/2019.351.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (7378 x 994) with 7333732 elements. Creating vector time with 7378 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (7378 x 994) with 7333732 elements. Creating vector time with 7378 elements. Creating vector bin with 994 elements. Creating matrix countList (7378 x 994) with 7333732 elements. Creating vector time with 7378 elements. Creating vector bin with 994 elements. Creating vector LCcount with 7378 elements. Creating vector time with 7378 elements. Creating vector transCount with 7378 elements. Creating vector time with 7378 elements. Creating vector nonTransCount with 7378 elements. Creating vector time with 7378 elements. Creating vector ai_mean with 7378 elements. Creating vector time with 7378 elements. Creating vector ai_min with 7378 elements. Creating vector time with 7378 elements. Creating vector ai_max with 7378 elements. Creating vector time with 7378 elements. Creating vector ai_std with 7378 elements. Creating vector time with 7378 elements. Creating vector esd_mean with 7378 elements. Creating vector time with 7378 elements. Creating vector esd_min with 7378 elements. Creating vector time with 7378 elements. Creating vector esd_max with 7378 elements. Creating vector time with 7378 elements. Creating vector esd_std with 7378 elements. Creating vector time with 7378 elements. Creating vector countSum with 7378 elements. Creating vector time with 7378 elements. Creating vector snapshot with 7378 elements. Creating vector time with 7378 elements. Creating vector threshold with 7378 elements. Creating vector time with 7378 elements. Creating vector sampleCount with 7378 elements. Creating vector time with 7378 elements. Creating vector flowCount with 7378 elements. Creating vector time with 7378 elements. Creating vector flowTime with 7378 elements. Creating vector time with 7378 elements. Creating vector bufferStatus with 7378 elements. Creating vector time with 7378 elements. Creating vector laserLevel with 7378 elements. Creating vector time with 7378 elements. Creating vector counter with 7378 elements. Creating vector time with 7378 elements. Creating vector counterPeriod with 7378 elements. Creating vector time with 7378 elements. Creating vector laserControl with 7378 elements. Creating vector time with 7378 elements. Creating vector countUnknownFrameCharacter with 7378 elements. Creating vector time with 7378 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 7378 elements. Creating vector time with 7378 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 7378 elements. Creating vector time with 7378 elements. Creating vector flowSpeed with 7378 elements. Creating vector time with 7378 elements. Creating vector countShortLFrameError with 7378 elements. Creating vector time with 7378 elements. Creating vector countGarbledLFrame with 7378 elements. Creating vector time with 7378 elements. Creating vector cFrameEsecs with 7378 elements. Creating vector time with 7378 elements. Creating vector correctedSampleCountList with 7378 elements. Creating vector time with 7378 elements. Creating vector time with 7378 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019351/2019.351.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019.351.00.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_2019.351.00.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 21 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_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 = 406 Gridding with nix = 1218, iZ = 403 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 385130 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 385130 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 120672 elements. *** Could not find start or end index in Met data read from http://elvis.shore.mbari.org/thredds/dodsC/agg/OS_MBARI-M1_R_M Looking for start days = 25552.858 since 1/1/1950 Looking for end days = 25553.7543 sIndx = eIndx = Met data goes from 20017.6042 to 25054.7292 No SWR data loaded from URL. Executing: /bin/rm -f ../results/2019351_GulperTimes.txt && touch ../results/2019351_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/2019/2019351/2019.351.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2019/2019351/2019.351.00/syslog -startEsecs 1576614934.6843 -surveyName Dorado389_2019_351_00_351_00 >> ../results/2019351_GulperTimes.txt Executing: removeGulpDups.py ../results/2019351_GulperTimes.txt Bottle: 0 Time: 1576616689.8841 Depth: 200.0115 Dist: 1.8295 Bottle: 1 Time: 1576616813.0856 Depth: 149.9192 Dist: 1.988 Bottle: 2 Time: 1576616933.2774 Depth: 99.9694 Dist: 2.1344 Bottle: 3 Time: 1576616990.0835 Depth: 79.9305 Dist: 2.1867 Bottle: 4 Time: 1576617041.28 Depth: 59.956 Dist: 2.2355 Bottle: 5 Time: 1576617092.0765 Depth: 39.9681 Dist: 2.2832 Bottle: 6 Time: 1576617127.4841 Depth: 29.9487 Dist: 2.3265 Bottle: 7 Time: 1576617161.2818 Depth: 19.9318 Dist: 2.3679 Bottle: 8 Time: 1576617195.4794 Depth: 9.9463 Dist: 2.4055 Bottle: 9 Time: 1576625505.4922 Depth: -0.022387 Dist: 3.396 Bottle: 10 Time: 1576655374.5777 Depth: 200.0305 Dist: 38.0109 Bottle: 11 Time: 1576655500.179 Depth: 149.9374 Dist: 38.1623 Bottle: 12 Time: 1576655616.1711 Depth: 99.9916 Dist: 38.3005 Bottle: 13 Time: 1576655671.9773 Depth: 79.9094 Dist: 38.3694 Bottle: 14 Time: 1576655725.5736 Depth: 59.9705 Dist: 38.4191 Bottle: 15 Time: 1576655782.3797 Depth: 39.9508 Dist: 38.4746 Bottle: 16 Time: 1576655815.9774 Depth: 29.9871 Dist: 38.5192 Bottle: 17 Time: 1576655852.1749 Depth: 19.9943 Dist: 38.5637 Bottle: 18 Time: 1576655883.9727 Depth: 9.8862 Dist: 38.6089 Bottle: 19 Time: 1576655922.3801 Depth: -0.13463 Dist: 38.6594 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_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 Did not add swr plot to the image. Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00_2column.png Elapsed time to save image: 15 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 SWR image not added to the plot. Printing biolume section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00_biolume.png Elapsed time to save image: 67 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 Did not add swr plot to the image. Printing two column section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00_lopc.png Elapsed time to save image: 17 seconds ************************************************************************* Calling plot_survey_stats to produce histogram and profile statistics plots... Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00_2column.png... Copied to /mbari/AUVCTD/surveys/2019/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00_biolume.png... Copied to /mbari/AUVCTD/surveys/2019/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00_lopc.png... Copied to /mbari/AUVCTD/surveys/2019/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2019/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2019/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2019/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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_351_00_351_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_351_00_351_00_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2019/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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_351_00_351_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_351_00_351_00_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2019/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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_351_00_351_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_351_00_351_00_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2019/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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_351_00_351_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_351_00_351_00_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2019/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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_351_00_351_00_Optical_Backscatter_420_nm.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_351_00_351_00_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2019/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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_351_00_351_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_351_00_351_00_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2019/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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_351_00_351_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_351_00_351_00_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2019/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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_351_00_351_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_351_00_351_00_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2019/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); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_351_00_351_00_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_351_00_351_00_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2019/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2019_351_00_351_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00.kml... Copied to /mbari/AUVCTD/surveys/2019/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2019_351_00_351_00_LOPC_Total_Count.kml' not found.] [> In create_data_products (line 419) In build_auv_survey (line 522) In AUVprocess_main (line 257)] ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 16 NaNs found in bbpRed. Interpolating anyway. Encountered 325 NaN values in array of lon that is 60038 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 59713 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 59713 are not equal to number of Lat lon points = 60038 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_2019_351_00_351_00.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00.txt... Copied to /mbari/AUVCTD/surveys/2019/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2019/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... 16 NaNs found in bbpRed. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00_decim.nc... Copied to /mbari/AUVCTD/surveys/2019/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_2019_351_00_351_00.nc... Copied to /mbari/AUVCTD/surveys/2019/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00_gridded.mat... Copied to /mbari/AUVCTD/surveys/2019/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019_351_00_351_00.mat... Copied to /mbari/AUVCTD/surveys/2019/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2019_351_00_351_00 processed" mccann@mbari.org < mail_Dorado389_2019_351_00_351_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2019.351.00.mat Processing time: 315 seconds