Execution of AUVprocess_main version 1.88 at 2020-11-24T21:34:43Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2020, ['286.00'], '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: 2020.286.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020286/2020.286.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2020/2020286/2020.286.00/ 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/2020/2020286/2020.286.00/navigation.nc') Creating vector time with 385947 elements. Creating vector mPos_x with 385947 elements. Creating vector time with 385947 elements. Creating vector mPos_y with 385947 elements. Creating vector time with 385947 elements. Creating vector mDepth with 385947 elements. Creating vector time with 385947 elements. Creating vector mGpsNorth with 385947 elements. Creating vector time with 385947 elements. Creating vector mGpsEast with 385947 elements. Creating vector time with 385947 elements. Creating vector mGpsValid with 385947 elements. Creating vector time with 385947 elements. Creating vector mPhi with 385947 elements. Creating vector time with 385947 elements. Creating vector mTheta with 385947 elements. Creating vector time with 385947 elements. Creating vector mPsi with 385947 elements. Creating vector time with 385947 elements. Creating vector mOmega_x with 385947 elements. Creating vector time with 385947 elements. Creating vector mOmega_y with 385947 elements. Creating vector time with 385947 elements. Creating vector mOmega_z with 385947 elements. Creating vector time with 385947 elements. Creating vector mPsaRange with 385947 elements. Creating vector time with 385947 elements. Creating vector mAltitude with 385947 elements. Creating vector time with 385947 elements. Creating vector multibeamAltitude with 385947 elements. Creating vector time with 385947 elements. Creating vector mDvlAltitude with 385947 elements. Creating vector time with 385947 elements. Creating vector mEchoAltitude with 385947 elements. Creating vector time with 385947 elements. Creating vector mEchoHorizRange with 385947 elements. Creating vector time with 385947 elements. Creating vector mEchoAltitudeLast with 385947 elements. Creating vector time with 385947 elements. Creating vector mEchoHorizRangeLast with 385947 elements. Creating vector time with 385947 elements. Creating vector mEchoNumOfPings with 385947 elements. Creating vector time with 385947 elements. Creating vector nadirCnts with 385947 elements. Creating vector time with 385947 elements. Creating vector obstacleCnts with 385947 elements. Creating vector time with 385947 elements. Creating vector nGoodNadirBeams with 385947 elements. Creating vector time with 385947 elements. Creating vector medianNadirBeamNo with 385947 elements. Creating vector time with 385947 elements. Creating vector mWaterSpeed with 385947 elements. Creating vector time with 385947 elements. Creating vector mDvlValid with 385947 elements. Creating vector time with 385947 elements. Creating vector mDvlNewData with 385947 elements. Creating vector time with 385947 elements. Creating vector mDeltaT with 385947 elements. Creating vector time with 385947 elements. Creating vector nfix with 385947 elements. Creating vector time with 385947 elements. Creating vector efix with 385947 elements. Creating vector time with 385947 elements. Creating vector filter_north with 385947 elements. Creating vector time with 385947 elements. Creating vector filter_east with 385947 elements. Creating vector time with 385947 elements. Creating vector filter_depth with 385947 elements. Creating vector time with 385947 elements. Creating vector north_current with 385947 elements. Creating vector time with 385947 elements. Creating vector east_current with 385947 elements. Creating vector time with 385947 elements. Creating vector speed_bias with 385947 elements. Creating vector time with 385947 elements. Creating vector heading_bias with 385947 elements. Creating vector time with 385947 elements. Creating vector latitude with 385947 elements. Creating vector time with 385947 elements. Creating vector longitude with 385947 elements. Creating vector time with 385947 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020286/2020.286.00/navigation.nc'); processNav(): median of positive valued depths = 37.1497 processNav(): Finding depths less than 260.0478 and times > 0 processNav(): length(Nav.depth) = 385947 processNav(): length(gindx) = 385947 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/2020/2020286/2020.286.00/gps.nc') Creating vector time with 20211 elements. Creating vector hours with 20211 elements. Creating vector time with 20211 elements. Creating vector minutes with 20211 elements. Creating vector time with 20211 elements. Creating vector seconds with 20211 elements. Creating vector time with 20211 elements. Creating vector centiSeconds with 20211 elements. Creating vector time with 20211 elements. Creating vector latitude with 20211 elements. Creating vector time with 20211 elements. Creating vector longitude with 20211 elements. Creating vector time with 20211 elements. Creating vector quality with 20211 elements. Creating vector time with 20211 elements. Creating vector numberOfSatellites with 20211 elements. Creating vector time with 20211 elements. Creating vector hdop with 20211 elements. Creating vector time with 20211 elements. Creating vector antennaHeight with 20211 elements. Creating vector time with 20211 elements. Creating vector geoHeight with 20211 elements. Creating vector time with 20211 elements. Creating vector dgpsDataAge with 20211 elements. Creating vector time with 20211 elements. Creating vector dgpsRSID with 20211 elements. Creating vector time with 20211 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020286/2020.286.00/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/2020/2020286/2020.286.00/parosci.nc') Creating vector time with 768543 elements. Creating vector depth with 768543 elements. Creating vector time with 768543 elements. Creating vector temp with 768543 elements. Creating vector time with 768543 elements. Creating vector pressure with 768543 elements. Creating vector time with 768543 elements. Creating vector temp_period with 768543 elements. Creating vector time with 768543 elements. Creating vector pres_period with 768543 elements. Creating vector time with 768543 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020286/2020.286.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.30387 max(Depth.data) = 202.9131 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.30387 max(Depth.data) = 202.9131 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/2020/2020286/2020.286.00/hydroscatlog.nc') Creating vector time with 308659 elements. Creating vector Seconds with 308659 elements. Creating vector time with 308659 elements. Creating vector HundrethsOfSeconds with 308659 elements. Creating vector time with 308659 elements. Creating vector Snorm1 with 308659 elements. Creating vector time with 308659 elements. Creating vector Snorm2 with 308659 elements. Creating vector time with 308659 elements. Creating vector Snorm3 with 308659 elements. Creating vector time with 308659 elements. Creating vector Gain_Status_1 with 308659 elements. Creating vector time with 308659 elements. Creating vector Gain_Status_2 with 308659 elements. Creating vector time with 308659 elements. Creating vector Gain_Status_3 with 308659 elements. Creating vector time with 308659 elements. Creating vector RawDepthValue with 308659 elements. Creating vector time with 308659 elements. Creating vector RawTempValue with 308659 elements. Creating vector time with 308659 elements. Creating vector Temperature with 308659 elements. Creating vector time with 308659 elements. Creating vector ErrorValue with 308659 elements. Creating vector time with 308659 elements. Creating vector bb470 with 308659 elements. Creating vector time with 308659 elements. Creating vector bb676 with 308659 elements. Creating vector time with 308659 elements. Creating vector fl676u with 308659 elements. Creating vector time with 308659 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020286/2020.286.00/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/2020/2020286/2020.286.00/ctdDriver.nc') Creating vector time with 308730 elements. Creating vector conductivity with 308730 elements. Creating vector time with 308730 elements. Creating vector temperature with 308730 elements. Creating vector time with 308730 elements. Creating vector cond_frequency with 308730 elements. Creating vector time with 308730 elements. Creating vector temp_frequency with 308730 elements. Creating vector time with 308730 elements. Creating vector spare with 308730 elements. Creating vector time with 308730 elements. Creating vector humidity with 308730 elements. Creating vector time with 308730 elements. Creating vector flow1 with 308730 elements. Creating vector time with 308730 elements. Creating vector CDOM with 308730 elements. Creating vector time with 308730 elements. Creating vector dissolvedO2 with 308730 elements. Creating vector time with 308730 elements. Creating vector salinity with 308730 elements. Creating vector time with 308730 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020286/2020.286.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2020/2020286/2020.286.00/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/2020/2020286/2020.286.00/ctdDriver2.nc') Creating vector time with 308603 elements. Creating vector conductivity with 308603 elements. Creating vector time with 308603 elements. Creating vector temperature with 308603 elements. Creating vector time with 308603 elements. Creating vector cond_frequency with 308603 elements. Creating vector time with 308603 elements. Creating vector temp_frequency with 308603 elements. Creating vector time with 308603 elements. Creating vector flow2 with 308603 elements. Creating vector time with 308603 elements. Creating vector par with 308603 elements. Creating vector time with 308603 elements. Creating vector spare with 308603 elements. Creating vector time with 308603 elements. Creating vector salinity with 308603 elements. Creating vector time with 308603 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020286/2020.286.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2020/2020286/2020.286.00/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/2020/2020286/2020.286.00/isuslog.nc') Creating vector time with 60051 elements. Creating vector isusNitrate with 60051 elements. Creating vector time with 60051 elements. Creating vector isusTemp with 60051 elements. Creating vector time with 60051 elements. Creating vector isusQuality with 60051 elements. Creating vector time with 60051 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020286/2020.286.00/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/2020/2020286/2020.286.00/biolume.nc') Creating vector time with 75921 elements. Creating vector rrr with 75921 elements. Creating vector time with 75921 elements. Creating vector cal_striing with 75921 elements. Creating vector time with 75921 elements. Creating vector avg_biolume with 75921 elements. Creating vector time with 75921 elements. Creating vector pump with 75921 elements. Creating vector time with 75921 elements. Creating vector system_voltage with 75921 elements. Creating vector time with 75921 elements. Creating vector flow with 75921 elements. Creating vector time with 75921 elements. Creating vector HV with 75921 elements. Creating vector time with 75921 elements. Creating vector reserved with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_0 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_1 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_2 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_3 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_4 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_5 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_6 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_7 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_8 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_9 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_10 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_11 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_12 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_13 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_14 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_15 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_16 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_17 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_18 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_19 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_20 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_21 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_22 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_23 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_24 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_25 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_26 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_27 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_28 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_29 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_30 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_31 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_32 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_33 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_34 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_35 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_36 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_37 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_38 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_39 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_40 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_41 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_42 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_43 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_44 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_45 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_46 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_47 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_48 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_49 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_50 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_51 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_52 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_53 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_54 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_55 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_56 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_57 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_58 with 75921 elements. Creating vector time with 75921 elements. Creating vector raw_59 with 75921 elements. Creating vector time with 75921 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020286/2020.286.00/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/2020/2020286/2020.286.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (7354 x 994) with 7309876 elements. Creating vector time with 7354 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (7354 x 994) with 7309876 elements. Creating vector time with 7354 elements. Creating vector bin with 994 elements. Creating matrix countList (7354 x 994) with 7309876 elements. Creating vector time with 7354 elements. Creating vector bin with 994 elements. Creating vector LCcount with 7354 elements. Creating vector time with 7354 elements. Creating vector transCount with 7354 elements. Creating vector time with 7354 elements. Creating vector nonTransCount with 7354 elements. Creating vector time with 7354 elements. Creating vector ai_mean with 7354 elements. Creating vector time with 7354 elements. Creating vector ai_min with 7354 elements. Creating vector time with 7354 elements. Creating vector ai_max with 7354 elements. Creating vector time with 7354 elements. Creating vector ai_std with 7354 elements. Creating vector time with 7354 elements. Creating vector esd_mean with 7354 elements. Creating vector time with 7354 elements. Creating vector esd_min with 7354 elements. Creating vector time with 7354 elements. Creating vector esd_max with 7354 elements. Creating vector time with 7354 elements. Creating vector esd_std with 7354 elements. Creating vector time with 7354 elements. Creating vector countSum with 7354 elements. Creating vector time with 7354 elements. Creating vector snapshot with 7354 elements. Creating vector time with 7354 elements. Creating vector threshold with 7354 elements. Creating vector time with 7354 elements. Creating vector sampleCount with 7354 elements. Creating vector time with 7354 elements. Creating vector flowCount with 7354 elements. Creating vector time with 7354 elements. Creating vector flowTime with 7354 elements. Creating vector time with 7354 elements. Creating vector bufferStatus with 7354 elements. Creating vector time with 7354 elements. Creating vector laserLevel with 7354 elements. Creating vector time with 7354 elements. Creating vector counter with 7354 elements. Creating vector time with 7354 elements. Creating vector counterPeriod with 7354 elements. Creating vector time with 7354 elements. Creating vector laserControl with 7354 elements. Creating vector time with 7354 elements. Creating vector countUnknownFrameCharacter with 7354 elements. Creating vector time with 7354 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 7354 elements. Creating vector time with 7354 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 7354 elements. Creating vector time with 7354 elements. Creating vector flowSpeed with 7354 elements. Creating vector time with 7354 elements. Creating vector countShortLFrameError with 7354 elements. Creating vector time with 7354 elements. Creating vector countGarbledLFrame with 7354 elements. Creating vector time with 7354 elements. Creating vector cFrameEsecs with 7354 elements. Creating vector time with 7354 elements. Creating vector correctedSampleCountList with 7354 elements. Creating vector time with 7354 elements. Creating vector time with 7354 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020286/2020.286.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020.286.00.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_2020.286.00.mat has_par2 = 0 Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 31 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_286_00_286_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_286_00_286_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_286_00_286_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 = 278 Gridding with nix = 834, 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 385866 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 385866 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 140704 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 10/12/2020 10:29 to 10/13/2020 09:30 swr = 515.0881 659.3325 766.0897 728.7378 636.2961 472.6825 305.8807 77.0789 14.1751 3.6521 3.3534 3.6890 2.9189 2.7044 2.8290 3.0000 2.7711 2.7289 3.0000 3.0144 3.1489 59.1514 188.0218 270.5123 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_286_00_286_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2020286_GulperTimes.txt && touch ../results/2020286_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/2020/2020286/2020.286.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2020/2020286/2020.286.00/syslog -startEsecs 1602529563.0559 -surveyName Dorado389_2020_286_00_286_00 >> ../results/2020286_GulperTimes.txt Executing: removeGulpDups.py ../results/2020286_GulperTimes.txt Bottle: 0 Time: 1602530613.054 Depth: 149.9947 Dist: 0.8175 Bottle: 1 Time: 1602530795.2515 Depth: 99.9691 Dist: 0.9862 Bottle: 2 Time: 1602530914.3933 Depth: 59.9329 Dist: 1.094 Bottle: 3 Time: 1602531062.4532 Depth: 19.9672 Dist: 1.2298 Bottle: 4 Time: 1602531130.4485 Depth: 4.968 Dist: 1.2875 Bottle: 5 Time: 1602536019.2536 Depth: 5.0315 Dist: 5.5942 Bottle: 6 Time: 1602540001.2508 Depth: 5.0345 Dist: 9.6678 Bottle: 7 Time: 1602543768.2528 Depth: 0.036176 Dist: 13.7268 Bottle: 8 Time: 1602547651.8567 Depth: 5.0557 Dist: 17.6362 Bottle: 9 Time: 1602551816.4514 Depth: 5.0301 Dist: 21.9677 Bottle: 10 Time: 1602555322.0513 Depth: 5.059 Dist: 25.8174 Bottle: 11 Time: 1602559215.0546 Depth: 5.0718 Dist: 29.9226 Bottle: 12 Time: 1602563183.6527 Depth: -0.068571 Dist: 33.9505 Bottle: 13 Time: 1602569127.8555 Depth: 5.0487 Dist: 39.8414 Bottle: 14 Time: 1602573124.3917 Depth: 5.0748 Dist: 44.1935 Bottle: 15 Time: 1602578377.4519 Depth: 5.0397 Dist: 48.7616 Bottle: 16 Time: 1602582412.0555 Depth: -0.034676 Dist: 52.8332 Bottle: 17 Time: 1602586348.0559 Depth: -0.021814 Dist: 54.5555 Bottle: 18 Time: 1602590315.0541 Depth: -0.0032234 Dist: 56.4415 Bottle: 19 Time: 1602594288.2519 Depth: 5.0588 Dist: 60.0139 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_286_00_286_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_2020_286_00_286_00_2column.png Elapsed time to save image: 21 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_2020_286_00_286_00_biolume.png Elapsed time to save image: 53 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_2020_286_00_286_00_lopc.png Elapsed time to save image: 12 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_2020_286_00_286_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_286_00_286_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_286_00_286_00_2column.png... Copied to /mbari/AUVCTD/surveys/2020/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_2020_286_00_286_00_biolume.png... Copied to /mbari/AUVCTD/surveys/2020/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_2020_286_00_286_00_lopc.png... Copied to /mbari/AUVCTD/surveys/2020/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_2020_286_00_286_00_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2020/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_2020_286_00_286_00_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2020/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_2020_286_00_286_00_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2020/images/. 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); updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_286_00_286_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_286_00_286_00_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2020/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); updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_286_00_286_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_286_00_286_00_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2020/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); updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_286_00_286_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_286_00_286_00_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2020/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); updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_286_00_286_00_Oxygen.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_286_00_286_00_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2020/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); updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_286_00_286_00_Optical_Backscatter_420_nm.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_286_00_286_00_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2020/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); updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_286_00_286_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_286_00_286_00_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2020/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); updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_286_00_286_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_286_00_286_00_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2020/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); updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_286_00_286_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_286_00_286_00_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2020/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); updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_286_00_286_00_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_286_00_286_00_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2020/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Creating Dorado389_2020_286_00_286_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_286_00_286_00.kml... Copied to /mbari/AUVCTD/surveys/2020/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_2020_286_00_286_00_LOPC_Total_Count.kml' not found.] [> In create_data_products (line 419) 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_2020_286_00_286_00.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 26 NaNs found in bbpBlue. Interpolating anyway. 183 NaNs found in bbpRed. Interpolating anyway. 7 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 13 NaN values in array of lon that is 60049 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 60036 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 60036 are not equal to number of Lat lon points = 60049 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_2020_286_00_286_00.txt Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_286_00_286_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_286_00_286_00.txt... Copied to /mbari/AUVCTD/surveys/2020/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_2020_286_00_286_00_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2020/odv/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 26 NaNs found in bbpBlue. Interpolating anyway. 183 NaNs found in bbpRed. Interpolating anyway. 7 NaNs found in flRed_uncorr. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_286_00_286_00_decim.nc... Copied to /mbari/AUVCTD/surveys/2020/netcdf/. 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_2020_286_00_286_00.nc... Copied to /mbari/AUVCTD/surveys/2020/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_2020_286_00_286_00_gridded.mat... Copied to /mbari/AUVCTD/surveys/2020/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_2020_286_00_286_00.mat... Copied to /mbari/AUVCTD/surveys/2020/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/2020/netcdf/Dorado389_2020_286_00_286_00.nc ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2020_286_00_286_00 processed" mccann@mbari.org < mail_Dorado389_2020_286_00_286_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020.286.00.mat Processing time: 367 seconds