Execution of AUVprocess_main version 1.88 at 2021-07-29T17:44:21Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2019, ['042.00'], '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: 2019.042.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/ 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/2019/2019042/2019.042.00/navigation.nc') Creating vector time with 351435 elements. Creating vector mPos_x with 351435 elements. Creating vector time with 351435 elements. Creating vector mPos_y with 351435 elements. Creating vector time with 351435 elements. Creating vector mDepth with 351435 elements. Creating vector time with 351435 elements. Creating vector mGpsNorth with 351435 elements. Creating vector time with 351435 elements. Creating vector mGpsEast with 351435 elements. Creating vector time with 351435 elements. Creating vector mGpsValid with 351435 elements. Creating vector time with 351435 elements. Creating vector mPhi with 351435 elements. Creating vector time with 351435 elements. Creating vector mTheta with 351435 elements. Creating vector time with 351435 elements. Creating vector mPsi with 351435 elements. Creating vector time with 351435 elements. Creating vector mOmega_x with 351435 elements. Creating vector time with 351435 elements. Creating vector mOmega_y with 351435 elements. Creating vector time with 351435 elements. Creating vector mOmega_z with 351435 elements. Creating vector time with 351435 elements. Creating vector mPsaRange with 351435 elements. Creating vector time with 351435 elements. Creating vector mAltitude with 351435 elements. Creating vector time with 351435 elements. Creating vector multibeamAltitude with 351435 elements. Creating vector time with 351435 elements. Creating vector mDvlAltitude with 351435 elements. Creating vector time with 351435 elements. Creating vector mEchoAltitude with 351435 elements. Creating vector time with 351435 elements. Creating vector mEchoHorizRange with 351435 elements. Creating vector time with 351435 elements. Creating vector mEchoAltitudeLast with 351435 elements. Creating vector time with 351435 elements. Creating vector mEchoHorizRangeLast with 351435 elements. Creating vector time with 351435 elements. Creating vector mEchoNumOfPings with 351435 elements. Creating vector time with 351435 elements. Creating vector nadirCnts with 351435 elements. Creating vector time with 351435 elements. Creating vector obstacleCnts with 351435 elements. Creating vector time with 351435 elements. Creating vector nGoodNadirBeams with 351435 elements. Creating vector time with 351435 elements. Creating vector medianNadirBeamNo with 351435 elements. Creating vector time with 351435 elements. Creating vector mWaterSpeed with 351435 elements. Creating vector time with 351435 elements. Creating vector mDvlValid with 351435 elements. Creating vector time with 351435 elements. Creating vector mDvlNewData with 351435 elements. Creating vector time with 351435 elements. Creating vector mDeltaT with 351435 elements. Creating vector time with 351435 elements. Creating vector nfix with 351435 elements. Creating vector time with 351435 elements. Creating vector efix with 351435 elements. Creating vector time with 351435 elements. Creating vector filter_north with 351435 elements. Creating vector time with 351435 elements. Creating vector filter_east with 351435 elements. Creating vector time with 351435 elements. Creating vector filter_depth with 351435 elements. Creating vector time with 351435 elements. Creating vector north_current with 351435 elements. Creating vector time with 351435 elements. Creating vector east_current with 351435 elements. Creating vector time with 351435 elements. Creating vector speed_bias with 351435 elements. Creating vector time with 351435 elements. Creating vector heading_bias with 351435 elements. Creating vector time with 351435 elements. Creating vector latitude with 351435 elements. Creating vector time with 351435 elements. Creating vector longitude with 351435 elements. Creating vector time with 351435 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/navigation.nc'); processNav(): median of positive valued depths = 31.2166 processNav(): Finding depths less than 218.5164 and times > 0 processNav(): length(Nav.depth) = 351435 processNav(): length(gindx) = 351435 Processing GPS navigation data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/gps.nc') Creating vector time with 6975 elements. Creating vector hours with 6975 elements. Creating vector time with 6975 elements. Creating vector minutes with 6975 elements. Creating vector time with 6975 elements. Creating vector seconds with 6975 elements. Creating vector time with 6975 elements. Creating vector centiSeconds with 6975 elements. Creating vector time with 6975 elements. Creating vector latitude with 6975 elements. Creating vector time with 6975 elements. Creating vector longitude with 6975 elements. Creating vector time with 6975 elements. Creating vector quality with 6975 elements. Creating vector time with 6975 elements. Creating vector numberOfSatellites with 6975 elements. Creating vector time with 6975 elements. Creating vector hdop with 6975 elements. Creating vector time with 6975 elements. Creating vector antennaHeight with 6975 elements. Creating vector time with 6975 elements. Creating vector geoHeight with 6975 elements. Creating vector time with 6975 elements. Creating vector dgpsDataAge with 6975 elements. Creating vector time with 6975 elements. Creating vector dgpsRSID with 6975 elements. Creating vector time with 6975 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/gps.nc'); Processing depth data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/parosci.nc') Creating vector time with 699866 elements. Creating vector depth with 699866 elements. Creating vector time with 699866 elements. Creating vector temp with 699866 elements. Creating vector time with 699866 elements. Creating vector pressure with 699866 elements. Creating vector time with 699866 elements. Creating vector temp_period with 699866 elements. Creating vector time with 699866 elements. Creating vector pres_period with 699866 elements. Creating vector time with 699866 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.22951 max(Depth.data) = 103.4225 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.22951 max(Depth.data) = 103.4225 Processing hs2 backscattering and chlorophyll fluorescence data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/hydroscatlog.nc') Creating vector time with 281058 elements. Creating vector Seconds with 281058 elements. Creating vector time with 281058 elements. Creating vector HundrethsOfSeconds with 281058 elements. Creating vector time with 281058 elements. Creating vector Snorm1 with 281058 elements. Creating vector time with 281058 elements. Creating vector Snorm2 with 281058 elements. Creating vector time with 281058 elements. Creating vector Snorm3 with 281058 elements. Creating vector time with 281058 elements. Creating vector Gain_Status_1 with 281058 elements. Creating vector time with 281058 elements. Creating vector Gain_Status_2 with 281058 elements. Creating vector time with 281058 elements. Creating vector Gain_Status_3 with 281058 elements. Creating vector time with 281058 elements. Creating vector RawDepthValue with 281058 elements. Creating vector time with 281058 elements. Creating vector RawTempValue with 281058 elements. Creating vector time with 281058 elements. Creating vector Temperature with 281058 elements. Creating vector time with 281058 elements. Creating vector ErrorValue with 281058 elements. Creating vector time with 281058 elements. Creating vector bb470 with 281058 elements. Creating vector time with 281058 elements. Creating vector bb676 with 281058 elements. Creating vector time with 281058 elements. Creating vector fl676u with 281058 elements. Creating vector time with 281058 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/hydroscatlog.nc'); Processing CTD #1 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/ctdDriver.nc') Creating vector time with 281060 elements. Creating vector conductivity with 281060 elements. Creating vector time with 281060 elements. Creating vector temperature with 281060 elements. Creating vector time with 281060 elements. Creating vector cond_frequency with 281060 elements. Creating vector time with 281060 elements. Creating vector temp_frequency with 281060 elements. Creating vector time with 281060 elements. Creating vector spare with 281060 elements. Creating vector time with 281060 elements. Creating vector humidity with 281060 elements. Creating vector time with 281060 elements. Creating vector flow1 with 281060 elements. Creating vector time with 281060 elements. Creating vector CDOM with 281060 elements. Creating vector time with 281060 elements. Creating vector dissolvedO2 with 281060 elements. Creating vector time with 281060 elements. Creating vector salinity with 281060 elements. Creating vector time with 281060 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/ctdDriver.cfg Oxygen calibration loaded from CTD config file (current method) Using constant flow rate offset for oxygen... Processing CTD #2 data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/ctdDriver2.nc') Creating vector time with 281113 elements. Creating vector conductivity with 281113 elements. Creating vector time with 281113 elements. Creating vector temperature with 281113 elements. Creating vector time with 281113 elements. Creating vector cond_frequency with 281113 elements. Creating vector time with 281113 elements. Creating vector temp_frequency with 281113 elements. Creating vector time with 281113 elements. Creating vector flow2 with 281113 elements. Creating vector time with 281113 elements. Creating vector spare with 281113 elements. Creating vector time with 281113 elements. Creating vector salinity with 281113 elements. Creating vector time with 281113 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/ctdDriver2.cfg Processing ISUS data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/isuslog.nc') Creating vector time with 54865 elements. Creating vector isusNitrate with 54865 elements. Creating vector time with 54865 elements. Creating vector isusTemp with 54865 elements. Creating vector time with 54865 elements. Creating vector isusQuality with 54865 elements. Creating vector time with 54865 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/isuslog.nc'); Total lag applied to nitrate = 6 seconds Processing Biolume data... [Warning: "/mbari/matlab/toolbox/matlab/demos" not found in path.] [> In rmpath (line 71) In processBiolume (line 21) In processAUVmission (line 220) In AUVprocess_main (line 227)] [Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] [> In rmpath (line 71) In processBiolume (line 22) In processAUVmission (line 220) In AUVprocess_main (line 227)] loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/biolume.nc') Creating vector time with 69136 elements. Creating vector rrr with 69136 elements. Creating vector time with 69136 elements. Creating vector cal_striing with 69136 elements. Creating vector time with 69136 elements. Creating vector avg_biolume with 69136 elements. Creating vector time with 69136 elements. Creating vector pump with 69136 elements. Creating vector time with 69136 elements. Creating vector system_voltage with 69136 elements. Creating vector time with 69136 elements. Creating vector flow with 69136 elements. Creating vector time with 69136 elements. Creating vector HV with 69136 elements. Creating vector time with 69136 elements. Creating vector reserved with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_0 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_1 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_2 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_3 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_4 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_5 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_6 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_7 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_8 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_9 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_10 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_11 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_12 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_13 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_14 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_15 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_16 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_17 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_18 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_19 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_20 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_21 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_22 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_23 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_24 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_25 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_26 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_27 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_28 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_29 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_30 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_31 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_32 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_33 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_34 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_35 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_36 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_37 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_38 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_39 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_40 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_41 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_42 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_43 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_44 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_45 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_46 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_47 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_48 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_49 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_50 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_51 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_52 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_53 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_54 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_55 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_56 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_57 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_58 with 69136 elements. Creating vector time with 69136 elements. Creating vector raw_59 with 69136 elements. Creating vector time with 69136 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/biolume.nc'); Processing LOPC plankton data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (6695 x 994) with 6654830 elements. Creating vector time with 6695 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (6695 x 994) with 6654830 elements. Creating vector time with 6695 elements. Creating vector bin with 994 elements. Creating matrix countList (6695 x 994) with 6654830 elements. Creating vector time with 6695 elements. Creating vector bin with 994 elements. Creating vector LCcount with 6695 elements. Creating vector time with 6695 elements. Creating vector transCount with 6695 elements. Creating vector time with 6695 elements. Creating vector nonTransCount with 6695 elements. Creating vector time with 6695 elements. Creating vector ai_mean with 6695 elements. Creating vector time with 6695 elements. Creating vector ai_min with 6695 elements. Creating vector time with 6695 elements. Creating vector ai_max with 6695 elements. Creating vector time with 6695 elements. Creating vector ai_std with 6695 elements. Creating vector time with 6695 elements. Creating vector esd_mean with 6695 elements. Creating vector time with 6695 elements. Creating vector esd_min with 6695 elements. Creating vector time with 6695 elements. Creating vector esd_max with 6695 elements. Creating vector time with 6695 elements. Creating vector esd_std with 6695 elements. Creating vector time with 6695 elements. Creating vector countSum with 6695 elements. Creating vector time with 6695 elements. Creating vector snapshot with 6695 elements. Creating vector time with 6695 elements. Creating vector threshold with 6695 elements. Creating vector time with 6695 elements. Creating vector sampleCount with 6695 elements. Creating vector time with 6695 elements. Creating vector flowCount with 6695 elements. Creating vector time with 6695 elements. Creating vector flowTime with 6695 elements. Creating vector time with 6695 elements. Creating vector bufferStatus with 6695 elements. Creating vector time with 6695 elements. Creating vector laserLevel with 6695 elements. Creating vector time with 6695 elements. Creating vector counter with 6695 elements. Creating vector time with 6695 elements. Creating vector counterPeriod with 6695 elements. Creating vector time with 6695 elements. Creating vector laserControl with 6695 elements. Creating vector time with 6695 elements. Creating vector countUnknownFrameCharacter with 6695 elements. Creating vector time with 6695 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 6695 elements. Creating vector time with 6695 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 6695 elements. Creating vector time with 6695 elements. Creating vector flowSpeed with 6695 elements. Creating vector time with 6695 elements. Creating vector countShortLFrameError with 6695 elements. Creating vector time with 6695 elements. Creating vector countGarbledLFrame with 6695 elements. Creating vector time with 6695 elements. Creating vector cFrameEsecs with 6695 elements. Creating vector time with 6695 elements. Creating vector correctedSampleCountList with 6695 elements. Creating vector time with 6695 elements. Creating vector time with 6695 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019.042.00.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_2019.042.00.mat has_par2 = 0 Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 29 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_042_00_042_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_042_00_042_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_042_00_042_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 = 466 Gridding with nix = 1398, 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 349444 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 349444 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: 02/11/2019 13:30 to 02/12/2019 10:30 swr = 634.7098 519.2502 358.1518 128.3618 15.3619 1.2454 1.1213 0.6302 0.6820 0.5000 0.2375 0.4365 0.7696 0.5122 0.6849 0.6000 0.8501 1.1430 25.9758 81.4116 152.8542 211.9999 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_042_00_042_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2019042_GulperTimes.txt && touch ../results/2019042_GulperTimes.txt Getting mission start epoch seconds from: http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2019/2019042/2019.042.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2019/2019042/2019.042.00/syslog -startEsecs 1549927002.1713 -surveyName Dorado389_2019_042_00_042_00 >> ../results/2019042_GulperTimes.txt Executing: removeGulpDups.py ../results/2019042_GulperTimes.txt Bottle: 0 Time: 1549928412.5647 Depth: 100.0676 Dist: 1.484 Bottle: 1 Time: 1549928485.3697 Depth: 79.9422 Dist: 1.5473 Bottle: 2 Time: 1549928557.7647 Depth: 59.9092 Dist: 1.6298 Bottle: 3 Time: 1549928624.7701 Depth: 39.9789 Dist: 1.6784 Bottle: 4 Time: 1549928672.9668 Depth: 29.9516 Dist: 1.7215 Bottle: 5 Time: 1549928716.5639 Depth: 19.971 Dist: 1.7587 Bottle: 6 Time: 1549928757.571 Depth: 9.9564 Dist: 1.7967 Bottle: 7 Time: 1549928806.3677 Depth: -0.07522 Dist: 1.8421 Bottle: 8 Time: 1549960328.6574 Depth: 100.0085 Dist: 34.9545 Bottle: 9 Time: 1549960399.6625 Depth: 79.9098 Dist: 35.0229 Bottle: 10 Time: 1549960467.2579 Depth: 59.9449 Dist: 35.0672 Bottle: 11 Time: 1549960537.8531 Depth: 39.9343 Dist: 35.1336 Bottle: 12 Time: 1549960580.4602 Depth: 29.9959 Dist: 35.1747 Bottle: 13 Time: 1549960625.857 Depth: 19.9838 Dist: 35.2203 Bottle: 14 Time: 1549960673.2538 Depth: 9.9796 Dist: 35.2736 Bottle: 15 Time: 1549960721.6605 Depth: -0.012464 Dist: 35.3191 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_042_00_042_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_2019_042_00_042_00_2column.png Elapsed time to save image: 20 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_2019_042_00_042_00_biolume.png Elapsed time to save image: 57 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_2019_042_00_042_00_lopc.png Elapsed time to save image: 14 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_2019_042_00_042_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_042_00_042_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_042_00_042_00_2column.png... Copied to /mbari/AUVCTD/surveys/2019/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_2019_042_00_042_00_biolume.png... Copied to /mbari/AUVCTD/surveys/2019/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_2019_042_00_042_00_lopc.png... Copied to /mbari/AUVCTD/surveys/2019/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_2019_042_00_042_00_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2019/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_2019_042_00_042_00_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2019/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_2019_042_00_042_00_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2019/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... 2 NaNs found in bbpBlue. Interpolating anyway. 11 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_2019_042_00_042_00_decim.nc... Copied to /mbari/AUVCTD/surveys/2019/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_2019_042_00_042_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_042_00_042_00_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2019/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_2019_042_00_042_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_042_00_042_00_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2019/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_2019_042_00_042_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_042_00_042_00_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2019/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_2019_042_00_042_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_042_00_042_00_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2019/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_2019_042_00_042_00_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_042_00_042_00_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2019/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_2019_042_00_042_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_042_00_042_00_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2019/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_2019_042_00_042_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_042_00_042_00_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2019/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_2019_042_00_042_00_Bioluminescence.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_042_00_042_00_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2019/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_2019_042_00_042_00_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2019_042_00_042_00_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2019/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Creating Dorado389_2019_042_00_042_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_042_00_042_00.kml... Copied to /mbari/AUVCTD/surveys/2019/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_2019_042_00_042_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_2019_042_00_042_00.mat ... Iterpolating to isus time values... Interpolating ctd2 temperature... Interpolating ctd2 salinity... 2 NaNs found in bbpBlue. Interpolating anyway. 11 NaNs found in bbpRed. Interpolating anyway. Encountered 311 NaN values in array of lon that is 54823 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 54512 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 54512 are not equal to number of Lat lon points = 54823 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_2019_042_00_042_00.txt Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_042_00_042_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019_042_00_042_00.txt... Copied to /mbari/AUVCTD/surveys/2019/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_2019_042_00_042_00_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2019/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_2019_042_00_042_00.nc... Copied to /mbari/AUVCTD/surveys/2019/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_2019_042_00_042_00_gridded.mat... Copied to /mbari/AUVCTD/surveys/2019/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_2019_042_00_042_00.mat... Copied to /mbari/AUVCTD/surveys/2019/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/2019/netcdf/Dorado389_2019_042_00_042_00.nc ************************************************************************* Composing email to send to auvctd@listserver.mbari.org ... !mail -s "Survey Dorado389_2019_042_00_042_00 processed" auvctd@listserver.mbari.org < mail_Dorado389_2019_042_00_042_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2019.042.00.mat Processing time: 300 seconds