Execution of AUVprocess_main version 1.88 at 2021-07-29T17:23:41Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2018, ['079.00'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd2') ************************************************************************* Processing data from SSDS via DODS server ************************************************************************* ************************************************************************* Processing AUV mission: 2018.079.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018079/2018.079.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2018/2018079/2018.079.00/ Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd.cvs/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/2018/2018079/2018.079.00/navigation.nc') Creating vector time with 175964 elements. Creating vector mPos_x with 175964 elements. Creating vector time with 175964 elements. Creating vector mPos_y with 175964 elements. Creating vector time with 175964 elements. Creating vector mDepth with 175964 elements. Creating vector time with 175964 elements. Creating vector mGpsNorth with 175964 elements. Creating vector time with 175964 elements. Creating vector mGpsEast with 175964 elements. Creating vector time with 175964 elements. Creating vector mGpsValid with 175964 elements. Creating vector time with 175964 elements. Creating vector mPhi with 175964 elements. Creating vector time with 175964 elements. Creating vector mTheta with 175964 elements. Creating vector time with 175964 elements. Creating vector mPsi with 175964 elements. Creating vector time with 175964 elements. Creating vector mOmega_x with 175964 elements. Creating vector time with 175964 elements. Creating vector mOmega_y with 175964 elements. Creating vector time with 175964 elements. Creating vector mOmega_z with 175964 elements. Creating vector time with 175964 elements. Creating vector mPsaRange with 175964 elements. Creating vector time with 175964 elements. Creating vector mAltitude with 175964 elements. Creating vector time with 175964 elements. Creating vector multibeamAltitude with 175964 elements. Creating vector time with 175964 elements. Creating vector mDvlAltitude with 175964 elements. Creating vector time with 175964 elements. Creating vector mEchoAltitude with 175964 elements. Creating vector time with 175964 elements. Creating vector mEchoHorizRange with 175964 elements. Creating vector time with 175964 elements. Creating vector mEchoAltitudeLast with 175964 elements. Creating vector time with 175964 elements. Creating vector mEchoHorizRangeLast with 175964 elements. Creating vector time with 175964 elements. Creating vector mEchoNumOfPings with 175964 elements. Creating vector time with 175964 elements. Creating vector nadirCnts with 175964 elements. Creating vector time with 175964 elements. Creating vector obstacleCnts with 175964 elements. Creating vector time with 175964 elements. Creating vector nGoodNadirBeams with 175964 elements. Creating vector time with 175964 elements. Creating vector medianNadirBeamNo with 175964 elements. Creating vector time with 175964 elements. Creating vector mWaterSpeed with 175964 elements. Creating vector time with 175964 elements. Creating vector mDvlValid with 175964 elements. Creating vector time with 175964 elements. Creating vector mDvlNewData with 175964 elements. Creating vector time with 175964 elements. Creating vector mDeltaT with 175964 elements. Creating vector time with 175964 elements. Creating vector nfix with 175964 elements. Creating vector time with 175964 elements. Creating vector efix with 175964 elements. Creating vector time with 175964 elements. Creating vector filter_north with 175964 elements. Creating vector time with 175964 elements. Creating vector filter_east with 175964 elements. Creating vector time with 175964 elements. Creating vector filter_depth with 175964 elements. Creating vector time with 175964 elements. Creating vector north_current with 175964 elements. Creating vector time with 175964 elements. Creating vector east_current with 175964 elements. Creating vector time with 175964 elements. Creating vector speed_bias with 175964 elements. Creating vector time with 175964 elements. Creating vector heading_bias with 175964 elements. Creating vector time with 175964 elements. Creating vector latitude with 175964 elements. Creating vector time with 175964 elements. Creating vector longitude with 175964 elements. Creating vector time with 175964 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018079/2018.079.00/navigation.nc'); processNav(): median of positive valued depths = 39.4129 processNav(): Finding depths less than 275.89 and times > 0 processNav(): length(Nav.depth) = 175964 processNav(): length(gindx) = 175964 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/2018/2018079/2018.079.00/gps.nc') Creating vector time with 3244 elements. Creating vector hours with 3244 elements. Creating vector time with 3244 elements. Creating vector minutes with 3244 elements. Creating vector time with 3244 elements. Creating vector seconds with 3244 elements. Creating vector time with 3244 elements. Creating vector centiSeconds with 3244 elements. Creating vector time with 3244 elements. Creating vector latitude with 3244 elements. Creating vector time with 3244 elements. Creating vector longitude with 3244 elements. Creating vector time with 3244 elements. Creating vector quality with 3244 elements. Creating vector time with 3244 elements. Creating vector numberOfSatellites with 3244 elements. Creating vector time with 3244 elements. Creating vector hdop with 3244 elements. Creating vector time with 3244 elements. Creating vector antennaHeight with 3244 elements. Creating vector time with 3244 elements. Creating vector geoHeight with 3244 elements. Creating vector time with 3244 elements. Creating vector dgpsDataAge with 3244 elements. Creating vector time with 3244 elements. Creating vector dgpsRSID with 3244 elements. Creating vector time with 3244 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018079/2018.079.00/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/2018/2018079/2018.079.00/parosci.nc') Creating vector time with 345490 elements. Creating vector depth with 345490 elements. Creating vector time with 345490 elements. Creating vector temp with 345490 elements. Creating vector time with 345490 elements. Creating vector pressure with 345490 elements. Creating vector time with 345490 elements. Creating vector temp_period with 345490 elements. Creating vector time with 345490 elements. Creating vector pres_period with 345490 elements. Creating vector time with 345490 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018079/2018.079.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.3223 max(Depth.data) = 103.2705 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.3223 max(Depth.data) = 103.2705 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/2018/2018079/2018.079.00/hydroscatlog.nc') Creating vector time with 139440 elements. Creating vector Seconds with 139440 elements. Creating vector time with 139440 elements. Creating vector HundrethsOfSeconds with 139440 elements. Creating vector time with 139440 elements. Creating vector Snorm1 with 139440 elements. Creating vector time with 139440 elements. Creating vector Snorm2 with 139440 elements. Creating vector time with 139440 elements. Creating vector Snorm3 with 139440 elements. Creating vector time with 139440 elements. Creating vector Gain_Status_1 with 139440 elements. Creating vector time with 139440 elements. Creating vector Gain_Status_2 with 139440 elements. Creating vector time with 139440 elements. Creating vector Gain_Status_3 with 139440 elements. Creating vector time with 139440 elements. Creating vector RawDepthValue with 139440 elements. Creating vector time with 139440 elements. Creating vector RawTempValue with 139440 elements. Creating vector time with 139440 elements. Creating vector Temperature with 139440 elements. Creating vector time with 139440 elements. Creating vector ErrorValue with 139440 elements. Creating vector time with 139440 elements. Creating vector bb470 with 139440 elements. Creating vector time with 139440 elements. Creating vector bb676 with 139440 elements. Creating vector time with 139440 elements. Creating vector fl676u with 139440 elements. Creating vector time with 139440 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018079/2018.079.00/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/2018/2018079/2018.079.00/ctdDriver.nc') Creating vector time with 139558 elements. Creating vector conductivity with 139558 elements. Creating vector time with 139558 elements. Creating vector temperature with 139558 elements. Creating vector time with 139558 elements. Creating vector cond_frequency with 139558 elements. Creating vector time with 139558 elements. Creating vector temp_frequency with 139558 elements. Creating vector time with 139558 elements. Creating vector spare with 139558 elements. Creating vector time with 139558 elements. Creating vector humidity with 139558 elements. Creating vector time with 139558 elements. Creating vector flow1 with 139558 elements. Creating vector time with 139558 elements. Creating vector CDOM with 139558 elements. Creating vector time with 139558 elements. Creating vector dissolvedO2 with 139558 elements. Creating vector time with 139558 elements. Creating vector salinity with 139558 elements. Creating vector time with 139558 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018079/2018.079.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2018/2018079/2018.079.00/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/2018/2018079/2018.079.00/ctdDriver2.nc') Creating vector time with 139626 elements. Creating vector conductivity with 139626 elements. Creating vector time with 139626 elements. Creating vector temperature with 139626 elements. Creating vector time with 139626 elements. Creating vector cond_frequency with 139626 elements. Creating vector time with 139626 elements. Creating vector temp_frequency with 139626 elements. Creating vector time with 139626 elements. Creating vector flow2 with 139626 elements. Creating vector time with 139626 elements. Creating vector spare with 139626 elements. Creating vector time with 139626 elements. Creating vector salinity with 139626 elements. Creating vector time with 139626 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018079/2018.079.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2018/2018079/2018.079.00/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/2018/2018079/2018.079.00/isuslog.nc') Creating vector time with 27443 elements. Creating vector isusNitrate with 27443 elements. Creating vector time with 27443 elements. Creating vector isusTemp with 27443 elements. Creating vector time with 27443 elements. Creating vector isusQuality with 27443 elements. Creating vector time with 27443 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018079/2018.079.00/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/2018/2018079/2018.079.00/biolume.nc') Creating vector time with 34605 elements. Creating vector rrr with 34605 elements. Creating vector time with 34605 elements. Creating vector cal_striing with 34605 elements. Creating vector time with 34605 elements. Creating vector avg_biolume with 34605 elements. Creating vector time with 34605 elements. Creating vector pump with 34605 elements. Creating vector time with 34605 elements. Creating vector system_voltage with 34605 elements. Creating vector time with 34605 elements. Creating vector flow with 34605 elements. Creating vector time with 34605 elements. Creating vector HV with 34605 elements. Creating vector time with 34605 elements. Creating vector reserved with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_0 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_1 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_2 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_3 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_4 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_5 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_6 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_7 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_8 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_9 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_10 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_11 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_12 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_13 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_14 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_15 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_16 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_17 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_18 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_19 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_20 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_21 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_22 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_23 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_24 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_25 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_26 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_27 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_28 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_29 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_30 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_31 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_32 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_33 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_34 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_35 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_36 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_37 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_38 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_39 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_40 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_41 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_42 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_43 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_44 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_45 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_46 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_47 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_48 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_49 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_50 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_51 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_52 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_53 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_54 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_55 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_56 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_57 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_58 with 34605 elements. Creating vector time with 34605 elements. Creating vector raw_59 with 34605 elements. Creating vector time with 34605 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018079/2018.079.00/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/2018/2018079/2018.079.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (3349 x 994) with 3328906 elements. Creating vector time with 3349 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (3349 x 994) with 3328906 elements. Creating vector time with 3349 elements. Creating vector bin with 994 elements. Creating matrix countList (3349 x 994) with 3328906 elements. Creating vector time with 3349 elements. Creating vector bin with 994 elements. Creating vector LCcount with 3349 elements. Creating vector time with 3349 elements. Creating vector transCount with 3349 elements. Creating vector time with 3349 elements. Creating vector nonTransCount with 3349 elements. Creating vector time with 3349 elements. Creating vector ai_mean with 3349 elements. Creating vector time with 3349 elements. Creating vector ai_min with 3349 elements. Creating vector time with 3349 elements. Creating vector ai_max with 3349 elements. Creating vector time with 3349 elements. Creating vector ai_std with 3349 elements. Creating vector time with 3349 elements. Creating vector esd_mean with 3349 elements. Creating vector time with 3349 elements. Creating vector esd_min with 3349 elements. Creating vector time with 3349 elements. Creating vector esd_max with 3349 elements. Creating vector time with 3349 elements. Creating vector esd_std with 3349 elements. Creating vector time with 3349 elements. Creating vector countSum with 3349 elements. Creating vector time with 3349 elements. Creating vector snapshot with 3349 elements. Creating vector time with 3349 elements. Creating vector threshold with 3349 elements. Creating vector time with 3349 elements. Creating vector sampleCount with 3349 elements. Creating vector time with 3349 elements. Creating vector flowCount with 3349 elements. Creating vector time with 3349 elements. Creating vector flowTime with 3349 elements. Creating vector time with 3349 elements. Creating vector bufferStatus with 3349 elements. Creating vector time with 3349 elements. Creating vector laserLevel with 3349 elements. Creating vector time with 3349 elements. Creating vector counter with 3349 elements. Creating vector time with 3349 elements. Creating vector counterPeriod with 3349 elements. Creating vector time with 3349 elements. Creating vector laserControl with 3349 elements. Creating vector time with 3349 elements. Creating vector countUnknownFrameCharacter with 3349 elements. Creating vector time with 3349 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 3349 elements. Creating vector time with 3349 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 3349 elements. Creating vector time with 3349 elements. Creating vector flowSpeed with 3349 elements. Creating vector time with 3349 elements. Creating vector countShortLFrameError with 3349 elements. Creating vector time with 3349 elements. Creating vector countGarbledLFrame with 3349 elements. Creating vector time with 3349 elements. Creating vector cFrameEsecs with 3349 elements. Creating vector time with 3349 elements. Creating vector correctedSampleCountList with 3349 elements. Creating vector time with 3349 elements. Creating vector time with 3349 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018079/2018.079.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018.079.00.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.cvs/src/matlab/doradosdp/results/Dorado389_2018.079.00.mat has_par2 = 0 Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 13 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_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 = 178 Gridding with nix = 534, iZ = 204 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 175827 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 175827 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 145548 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 03/20/2018 09:30 to 03/20/2018 21:30 swr = 56.6639 133.6931 121.2970 63.5215 56.4580 47.7365 49.3083 67.4363 56.0313 19.9200 3.4601 1.8201 1.6333 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2018079_GulperTimes.txt && touch ../results/2018079_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/2018/2018079/2018.079.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2018/2018079/2018.079.00/syslog -startEsecs 1521570130.9281 -surveyName Dorado389_2018_079_00_079_00 >> ../results/2018079_GulperTimes.txt Executing: removeGulpDups.py ../results/2018079_GulperTimes.txt Bottle: 0 Time: 1521571412.5203 Depth: 100.0651 Dist: 1.3638 Bottle: 1 Time: 1521571481.1256 Depth: 79.9627 Dist: 1.4318 Bottle: 2 Time: 1521571550.7208 Depth: 59.9929 Dist: 1.5106 Bottle: 3 Time: 1521571616.9263 Depth: 39.9129 Dist: 1.5869 Bottle: 4 Time: 1521571659.7234 Depth: 29.9634 Dist: 1.6265 Bottle: 5 Time: 1521571700.3206 Depth: 19.9924 Dist: 1.6657 Bottle: 6 Time: 1521571749.5272 Depth: 9.9576 Dist: 1.7267 Bottle: 7 Time: 1521571796.324 Depth: -0.027082 Dist: 1.7755 Bottle: 8 Time: 1521602553.727 Depth: 100.011 Dist: 35.4104 Bottle: 9 Time: 1521602625.3221 Depth: 79.8991 Dist: 35.4774 Bottle: 10 Time: 1521602691.3276 Depth: 59.9911 Dist: 35.5269 Bottle: 11 Time: 1521602764.9225 Depth: 39.9723 Dist: 35.6106 Bottle: 12 Time: 1521602807.3296 Depth: 29.9755 Dist: 35.6618 Bottle: 13 Time: 1521602852.5265 Depth: 19.9167 Dist: 35.708 Bottle: 14 Time: 1521602899.5233 Depth: 9.9358 Dist: 35.7555 Bottle: 15 Time: 1521602950.7298 Depth: 0.30778 Dist: 35.7972 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_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.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00_2column.png Elapsed time to save image: 11 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.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00_biolume.png Elapsed time to save image: 45 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.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00_lopc.png Elapsed time to save image: 10 seconds ************************************************************************* Calling plot_survey_stats to produce histogram and profile statistics plots... Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00_2column.png... Copied to /mbari/AUVCTD/surveys/2018/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00_biolume.png... Copied to /mbari/AUVCTD/surveys/2018/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00_lopc.png... Copied to /mbari/AUVCTD/surveys/2018/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2018/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2018/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2018/images/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd2 temperature... Interpolating ctd2 salinity... 47 NaNs found in bbpBlue. Interpolating anyway. 106 NaNs found in bbpRed. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00_decim.nc... Copied to /mbari/AUVCTD/surveys/2018/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2018_079_00_079_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2018_079_00_079_00_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2018_079_00_079_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2018_079_00_079_00_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2018_079_00_079_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2018_079_00_079_00_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2018_079_00_079_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2018_079_00_079_00_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2018_079_00_079_00_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2018_079_00_079_00_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2018_079_00_079_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2018_079_00_079_00_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2018_079_00_079_00_Chlorophyll_Fluorescence.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2018_079_00_079_00_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2018_079_00_079_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2018_079_00_079_00_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/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.cvs/src/matlab/doradosdp/results//Dorado389_2018_079_00_079_00_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2018_079_00_079_00_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Creating Dorado389_2018_079_00_079_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00.kml... Copied to /mbari/AUVCTD/surveys/2018/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2018_079_00_079_00_LOPC_Total_Count.kml' not found.] [> In create_data_products (line 445) In build_auv_survey (line 530) In AUVprocess_main (line 257)] ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00.mat ... Iterpolating to isus time values... Interpolating ctd2 temperature... Interpolating ctd2 salinity... 47 NaNs found in bbpBlue. Interpolating anyway. 106 NaNs found in bbpRed. Interpolating anyway. Encountered 23 NaN values in array of lon that is 27385 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 27362 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 27362 are not equal to number of Lat lon points = 27385 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.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00.txt Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00.txt... Copied to /mbari/AUVCTD/surveys/2018/odv/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2018/odv/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ ************************************************************************* Writing netCDF file ... Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00.nc... Copied to /mbari/AUVCTD/surveys/2018/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00_gridded.mat... Copied to /mbari/AUVCTD/surveys/2018/mat/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_079_00_079_00.mat... Copied to /mbari/AUVCTD/surveys/2018/mat/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ permalink_url.sh http://dods.mbari.org/cgi-bin/nph-nc/data/auvctd/surveys/2018/netcdf/Dorado389_2018_079_00_079_00.nc ************************************************************************* Composing email to send to auvctd@listserver.mbari.org ... !mail -s "Survey Dorado389_2018_079_00_079_00 processed" auvctd@listserver.mbari.org < mail_Dorado389_2018_079_00_079_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018.079.00.mat Processing time: 250 seconds