Execution of AUVprocess_main version 1.88 at 2021-07-29T17:29:53Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2018, ['220.00'], '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: 2018.220.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018220/2018.220.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2018/2018220/2018.220.00/ 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/2018/2018220/2018.220.00/navigation.nc') Creating vector time with 377525 elements. Creating vector mPos_x with 377525 elements. Creating vector time with 377525 elements. Creating vector mPos_y with 377525 elements. Creating vector time with 377525 elements. Creating vector mDepth with 377525 elements. Creating vector time with 377525 elements. Creating vector mGpsNorth with 377525 elements. Creating vector time with 377525 elements. Creating vector mGpsEast with 377525 elements. Creating vector time with 377525 elements. Creating vector mGpsValid with 377525 elements. Creating vector time with 377525 elements. Creating vector mPhi with 377525 elements. Creating vector time with 377525 elements. Creating vector mTheta with 377525 elements. Creating vector time with 377525 elements. Creating vector mPsi with 377525 elements. Creating vector time with 377525 elements. Creating vector mOmega_x with 377525 elements. Creating vector time with 377525 elements. Creating vector mOmega_y with 377525 elements. Creating vector time with 377525 elements. Creating vector mOmega_z with 377525 elements. Creating vector time with 377525 elements. Creating vector mPsaRange with 377525 elements. Creating vector time with 377525 elements. Creating vector mAltitude with 377525 elements. Creating vector time with 377525 elements. Creating vector multibeamAltitude with 377525 elements. Creating vector time with 377525 elements. Creating vector mDvlAltitude with 377525 elements. Creating vector time with 377525 elements. Creating vector mEchoAltitude with 377525 elements. Creating vector time with 377525 elements. Creating vector mEchoHorizRange with 377525 elements. Creating vector time with 377525 elements. Creating vector mEchoAltitudeLast with 377525 elements. Creating vector time with 377525 elements. Creating vector mEchoHorizRangeLast with 377525 elements. Creating vector time with 377525 elements. Creating vector mEchoNumOfPings with 377525 elements. Creating vector time with 377525 elements. Creating vector nadirCnts with 377525 elements. Creating vector time with 377525 elements. Creating vector obstacleCnts with 377525 elements. Creating vector time with 377525 elements. Creating vector nGoodNadirBeams with 377525 elements. Creating vector time with 377525 elements. Creating vector medianNadirBeamNo with 377525 elements. Creating vector time with 377525 elements. Creating vector mWaterSpeed with 377525 elements. Creating vector time with 377525 elements. Creating vector mDvlValid with 377525 elements. Creating vector time with 377525 elements. Creating vector mDvlNewData with 377525 elements. Creating vector time with 377525 elements. Creating vector mDeltaT with 377525 elements. Creating vector time with 377525 elements. Creating vector nfix with 377525 elements. Creating vector time with 377525 elements. Creating vector efix with 377525 elements. Creating vector time with 377525 elements. Creating vector filter_north with 377525 elements. Creating vector time with 377525 elements. Creating vector filter_east with 377525 elements. Creating vector time with 377525 elements. Creating vector filter_depth with 377525 elements. Creating vector time with 377525 elements. Creating vector north_current with 377525 elements. Creating vector time with 377525 elements. Creating vector east_current with 377525 elements. Creating vector time with 377525 elements. Creating vector speed_bias with 377525 elements. Creating vector time with 377525 elements. Creating vector heading_bias with 377525 elements. Creating vector time with 377525 elements. Creating vector latitude with 377525 elements. Creating vector time with 377525 elements. Creating vector longitude with 377525 elements. Creating vector time with 377525 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018220/2018.220.00/navigation.nc'); processNav(): median of positive valued depths = 31.7234 processNav(): Finding depths less than 222.0639 and times > 0 processNav(): length(Nav.depth) = 377525 processNav(): length(gindx) = 377525 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/2018/2018220/2018.220.00/gps.nc') Creating vector time with 15743 elements. Creating vector hours with 15743 elements. Creating vector time with 15743 elements. Creating vector minutes with 15743 elements. Creating vector time with 15743 elements. Creating vector seconds with 15743 elements. Creating vector time with 15743 elements. Creating vector centiSeconds with 15743 elements. Creating vector time with 15743 elements. Creating vector latitude with 15743 elements. Creating vector time with 15743 elements. Creating vector longitude with 15743 elements. Creating vector time with 15743 elements. Creating vector quality with 15743 elements. Creating vector time with 15743 elements. Creating vector numberOfSatellites with 15743 elements. Creating vector time with 15743 elements. Creating vector hdop with 15743 elements. Creating vector time with 15743 elements. Creating vector antennaHeight with 15743 elements. Creating vector time with 15743 elements. Creating vector geoHeight with 15743 elements. Creating vector time with 15743 elements. Creating vector dgpsDataAge with 15743 elements. Creating vector time with 15743 elements. Creating vector dgpsRSID with 15743 elements. Creating vector time with 15743 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018220/2018.220.00/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/2018/2018220/2018.220.00/parosci.nc') Creating vector time with 751805 elements. Creating vector depth with 751805 elements. Creating vector time with 751805 elements. Creating vector temp with 751805 elements. Creating vector time with 751805 elements. Creating vector pressure with 751805 elements. Creating vector time with 751805 elements. Creating vector temp_period with 751805 elements. Creating vector time with 751805 elements. Creating vector pres_period with 751805 elements. Creating vector time with 751805 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018220/2018.220.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.32813 max(Depth.data) = 103.5763 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.32813 max(Depth.data) = 103.5763 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/2018/2018220/2018.220.00/hydroscatlog.nc') Creating vector time with 296129 elements. Creating vector Seconds with 296129 elements. Creating vector time with 296129 elements. Creating vector HundrethsOfSeconds with 296129 elements. Creating vector time with 296129 elements. Creating vector Snorm1 with 296129 elements. Creating vector time with 296129 elements. Creating vector Snorm2 with 296129 elements. Creating vector time with 296129 elements. Creating vector Snorm3 with 296129 elements. Creating vector time with 296129 elements. Creating vector Gain_Status_1 with 296129 elements. Creating vector time with 296129 elements. Creating vector Gain_Status_2 with 296129 elements. Creating vector time with 296129 elements. Creating vector Gain_Status_3 with 296129 elements. Creating vector time with 296129 elements. Creating vector RawDepthValue with 296129 elements. Creating vector time with 296129 elements. Creating vector RawTempValue with 296129 elements. Creating vector time with 296129 elements. Creating vector Temperature with 296129 elements. Creating vector time with 296129 elements. Creating vector ErrorValue with 296129 elements. Creating vector time with 296129 elements. Creating vector bb470 with 296129 elements. Creating vector time with 296129 elements. Creating vector bb676 with 296129 elements. Creating vector time with 296129 elements. Creating vector fl676u with 296129 elements. Creating vector time with 296129 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018220/2018.220.00/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/2018/2018220/2018.220.00/ctdDriver.nc') Creating vector time with 297318 elements. Creating vector conductivity with 297318 elements. Creating vector time with 297318 elements. Creating vector temperature with 297318 elements. Creating vector time with 297318 elements. Creating vector cond_frequency with 297318 elements. Creating vector time with 297318 elements. Creating vector temp_frequency with 297318 elements. Creating vector time with 297318 elements. Creating vector spare with 297318 elements. Creating vector time with 297318 elements. Creating vector humidity with 297318 elements. Creating vector time with 297318 elements. Creating vector flow1 with 297318 elements. Creating vector time with 297318 elements. Creating vector CDOM with 297318 elements. Creating vector time with 297318 elements. Creating vector dissolvedO2 with 297318 elements. Creating vector time with 297318 elements. Creating vector salinity with 297318 elements. Creating vector time with 297318 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018220/2018.220.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2018/2018220/2018.220.00/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/2018/2018220/2018.220.00/ctdDriver2.nc') Creating vector time with 297204 elements. Creating vector conductivity with 297204 elements. Creating vector time with 297204 elements. Creating vector temperature with 297204 elements. Creating vector time with 297204 elements. Creating vector cond_frequency with 297204 elements. Creating vector time with 297204 elements. Creating vector temp_frequency with 297204 elements. Creating vector time with 297204 elements. Creating vector flow2 with 297204 elements. Creating vector time with 297204 elements. Creating vector spare with 297204 elements. Creating vector time with 297204 elements. Creating vector salinity with 297204 elements. Creating vector time with 297204 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018220/2018.220.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2018/2018220/2018.220.00/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/2018/2018220/2018.220.00/isuslog.nc') Creating vector time with 58864 elements. Creating vector isusNitrate with 58864 elements. Creating vector time with 58864 elements. Creating vector isusTemp with 58864 elements. Creating vector time with 58864 elements. Creating vector isusQuality with 58864 elements. Creating vector time with 58864 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018220/2018.220.00/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/2018/2018220/2018.220.00/biolume.nc') Creating vector time with 73455 elements. Creating vector rrr with 73455 elements. Creating vector time with 73455 elements. Creating vector cal_striing with 73455 elements. Creating vector time with 73455 elements. Creating vector avg_biolume with 73455 elements. Creating vector time with 73455 elements. Creating vector pump with 73455 elements. Creating vector time with 73455 elements. Creating vector system_voltage with 73455 elements. Creating vector time with 73455 elements. Creating vector flow with 73455 elements. Creating vector time with 73455 elements. Creating vector HV with 73455 elements. Creating vector time with 73455 elements. Creating vector reserved with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_0 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_1 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_2 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_3 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_4 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_5 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_6 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_7 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_8 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_9 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_10 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_11 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_12 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_13 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_14 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_15 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_16 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_17 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_18 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_19 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_20 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_21 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_22 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_23 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_24 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_25 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_26 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_27 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_28 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_29 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_30 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_31 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_32 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_33 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_34 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_35 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_36 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_37 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_38 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_39 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_40 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_41 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_42 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_43 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_44 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_45 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_46 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_47 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_48 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_49 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_50 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_51 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_52 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_53 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_54 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_55 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_56 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_57 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_58 with 73455 elements. Creating vector time with 73455 elements. Creating vector raw_59 with 73455 elements. Creating vector time with 73455 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018220/2018.220.00/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/2018/2018220/2018.220.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (6926 x 994) with 6884444 elements. Creating vector time with 6926 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (6926 x 994) with 6884444 elements. Creating vector time with 6926 elements. Creating vector bin with 994 elements. Creating matrix countList (6926 x 994) with 6884444 elements. Creating vector time with 6926 elements. Creating vector bin with 994 elements. Creating vector LCcount with 6926 elements. Creating vector time with 6926 elements. Creating vector transCount with 6926 elements. Creating vector time with 6926 elements. Creating vector nonTransCount with 6926 elements. Creating vector time with 6926 elements. Creating vector ai_mean with 6926 elements. Creating vector time with 6926 elements. Creating vector ai_min with 6926 elements. Creating vector time with 6926 elements. Creating vector ai_max with 6926 elements. Creating vector time with 6926 elements. Creating vector ai_std with 6926 elements. Creating vector time with 6926 elements. Creating vector esd_mean with 6926 elements. Creating vector time with 6926 elements. Creating vector esd_min with 6926 elements. Creating vector time with 6926 elements. Creating vector esd_max with 6926 elements. Creating vector time with 6926 elements. Creating vector esd_std with 6926 elements. Creating vector time with 6926 elements. Creating vector countSum with 6926 elements. Creating vector time with 6926 elements. Creating vector snapshot with 6926 elements. Creating vector time with 6926 elements. Creating vector threshold with 6926 elements. Creating vector time with 6926 elements. Creating vector sampleCount with 6926 elements. Creating vector time with 6926 elements. Creating vector flowCount with 6926 elements. Creating vector time with 6926 elements. Creating vector flowTime with 6926 elements. Creating vector time with 6926 elements. Creating vector bufferStatus with 6926 elements. Creating vector time with 6926 elements. Creating vector laserLevel with 6926 elements. Creating vector time with 6926 elements. Creating vector counter with 6926 elements. Creating vector time with 6926 elements. Creating vector counterPeriod with 6926 elements. Creating vector time with 6926 elements. Creating vector laserControl with 6926 elements. Creating vector time with 6926 elements. Creating vector countUnknownFrameCharacter with 6926 elements. Creating vector time with 6926 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 6926 elements. Creating vector time with 6926 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 6926 elements. Creating vector time with 6926 elements. Creating vector flowSpeed with 6926 elements. Creating vector time with 6926 elements. Creating vector countShortLFrameError with 6926 elements. Creating vector time with 6926 elements. Creating vector countGarbledLFrame with 6926 elements. Creating vector time with 6926 elements. Creating vector cFrameEsecs with 6926 elements. Creating vector time with 6926 elements. Creating vector correctedSampleCountList with 6926 elements. Creating vector time with 6926 elements. Creating vector time with 6926 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2018/2018220/2018.220.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018.220.00.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_2018.220.00.mat has_par2 = 0 Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 28 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_220_00_220_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_220_00_220_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_220_00_220_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 = 422 Gridding with nix = 1266, 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 334591 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 334591 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: 08/08/2018 07:29 to 08/09/2018 06:30 swr = 54.2811 108.2948 231.1718 391.5500 499.5027 708.4391 853.4931 893.4334 762.9192 432.2710 237.7269 108.7188 27.2966 2.3402 1.5527 1.2093 1.4294 0.9093 0.9100 1.0280 1.0093 1.1047 1.2426 9.5030 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_220_00_220_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2018220_GulperTimes.txt && touch ../results/2018220_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/2018/2018220/2018.220.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2018/2018220/2018.220.00/syslog -startEsecs 1533747521.2949 -surveyName Dorado389_2018_220_00_220_00 >> ../results/2018220_GulperTimes.txt Executing: removeGulpDups.py ../results/2018220_GulperTimes.txt Bottle: 0 Time: 1533752365.32 Depth: 6.4688 Dist: 6.1667 Bottle: 1 Time: 1533754740.12 Depth: 4.1526 Dist: 9.3512 Bottle: 2 Time: 1533756967.72 Depth: 5.4234 Dist: 12.2629 Bottle: 3 Time: 1533764636.12 Depth: 3.2093 Dist: 20.746 Bottle: 4 Time: 1533767249.72 Depth: 6.8048 Dist: 23.5327 Bottle: 5 Time: 1533771110.52 Depth: 7.0189 Dist: 27.5551 Bottle: 6 Time: 1533782191.92 Depth: 4.0873 Dist: 39.4683 Bottle: 7 Time: 1533783562.13 Depth: 3.4016 Dist: 41.2829 Bottle: 8 Time: 1533784805.12 Depth: 6.4235 Dist: 42.6305 Bottle: 9 Time: 1533786603.93 Depth: 6.8651 Dist: 45.0271 Bottle: 10 Time: 1533788136.52 Depth: 7.9201 Dist: 46.8454 Bottle: 11 Time: 1533789763.72 Depth: 2.7113 Dist: 48.7867 Bottle: 12 Time: 1533791758.32 Depth: 1.9614 Dist: 51.1745 Bottle: 13 Time: 1533797225.92 Depth: 3.3104 Dist: 57.347 Bottle: 14 Time: 1533799313.33 Depth: 3.1929 Dist: 59.5454 Bottle: 15 Time: 1533801896.12 Depth: 1.5502 Dist: 62.2967 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_220_00_220_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_220_00_220_00_2column.png Elapsed time to save image: 13 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_220_00_220_00_biolume.png Elapsed time to save image: 48 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_220_00_220_00_lopc.png Elapsed time to save image: 13 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_220_00_220_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_220_00_220_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_220_00_220_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_220_00_220_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_220_00_220_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_220_00_220_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_220_00_220_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_220_00_220_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... 3 NaNs found in bbpBlue. Interpolating anyway. 17 NaNs found in bbpRed. Interpolating anyway. 1 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_2018_220_00_220_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_220_00_220_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2018_220_00_220_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_220_00_220_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2018_220_00_220_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_220_00_220_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2018_220_00_220_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_220_00_220_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2018_220_00_220_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_220_00_220_00_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2018_220_00_220_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_220_00_220_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2018_220_00_220_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_220_00_220_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2018_220_00_220_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_220_00_220_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2018_220_00_220_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_220_00_220_00_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2018_220_00_220_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_220_00_220_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_220_00_220_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_220_00_220_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_220_00_220_00.mat ... Iterpolating to isus time values... Interpolating ctd2 temperature... Interpolating ctd2 salinity... 3 NaNs found in bbpBlue. Interpolating anyway. 17 NaNs found in bbpRed. Interpolating anyway. 1 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 6617 NaN values in array of lon that is 58662 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 52045 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 52045 are not equal to number of Lat lon points = 58662 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_220_00_220_00.txt Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_220_00_220_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018_220_00_220_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_220_00_220_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_220_00_220_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_220_00_220_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_220_00_220_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_220_00_220_00.nc ************************************************************************* Composing email to send to auvctd@listserver.mbari.org ... !mail -s "Survey Dorado389_2018_220_00_220_00 processed" auvctd@listserver.mbari.org < mail_Dorado389_2018_220_00_220_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2018.220.00.mat Processing time: 279 seconds