Execution of AUVprocess_main version 1.88 at 2020-11-24T21:04:48Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2020, ['233.14'], '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: 2020.233.14 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020233/2020.233.14/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2020/2020233/2020.233.14/ 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/2020/2020233/2020.233.14/navigation.nc') Creating vector time with 350695 elements. Creating vector mPos_x with 350695 elements. Creating vector time with 350695 elements. Creating vector mPos_y with 350695 elements. Creating vector time with 350695 elements. Creating vector mDepth with 350695 elements. Creating vector time with 350695 elements. Creating vector mGpsNorth with 350695 elements. Creating vector time with 350695 elements. Creating vector mGpsEast with 350695 elements. Creating vector time with 350695 elements. Creating vector mGpsValid with 350695 elements. Creating vector time with 350695 elements. Creating vector mPhi with 350695 elements. Creating vector time with 350695 elements. Creating vector mTheta with 350695 elements. Creating vector time with 350695 elements. Creating vector mPsi with 350695 elements. Creating vector time with 350695 elements. Creating vector mOmega_x with 350695 elements. Creating vector time with 350695 elements. Creating vector mOmega_y with 350695 elements. Creating vector time with 350695 elements. Creating vector mOmega_z with 350695 elements. Creating vector time with 350695 elements. Creating vector mPsaRange with 350695 elements. Creating vector time with 350695 elements. Creating vector mAltitude with 350695 elements. Creating vector time with 350695 elements. Creating vector multibeamAltitude with 350695 elements. Creating vector time with 350695 elements. Creating vector mDvlAltitude with 350695 elements. Creating vector time with 350695 elements. Creating vector mEchoAltitude with 350695 elements. Creating vector time with 350695 elements. Creating vector mEchoHorizRange with 350695 elements. Creating vector time with 350695 elements. Creating vector mEchoAltitudeLast with 350695 elements. Creating vector time with 350695 elements. Creating vector mEchoHorizRangeLast with 350695 elements. Creating vector time with 350695 elements. Creating vector mEchoNumOfPings with 350695 elements. Creating vector time with 350695 elements. Creating vector nadirCnts with 350695 elements. Creating vector time with 350695 elements. Creating vector obstacleCnts with 350695 elements. Creating vector time with 350695 elements. Creating vector nGoodNadirBeams with 350695 elements. Creating vector time with 350695 elements. Creating vector medianNadirBeamNo with 350695 elements. Creating vector time with 350695 elements. Creating vector mWaterSpeed with 350695 elements. Creating vector time with 350695 elements. Creating vector mDvlValid with 350695 elements. Creating vector time with 350695 elements. Creating vector mDvlNewData with 350695 elements. Creating vector time with 350695 elements. Creating vector mDeltaT with 350695 elements. Creating vector time with 350695 elements. Creating vector nfix with 350695 elements. Creating vector time with 350695 elements. Creating vector efix with 350695 elements. Creating vector time with 350695 elements. Creating vector filter_north with 350695 elements. Creating vector time with 350695 elements. Creating vector filter_east with 350695 elements. Creating vector time with 350695 elements. Creating vector filter_depth with 350695 elements. Creating vector time with 350695 elements. Creating vector north_current with 350695 elements. Creating vector time with 350695 elements. Creating vector east_current with 350695 elements. Creating vector time with 350695 elements. Creating vector speed_bias with 350695 elements. Creating vector time with 350695 elements. Creating vector heading_bias with 350695 elements. Creating vector time with 350695 elements. Creating vector latitude with 350695 elements. Creating vector time with 350695 elements. Creating vector longitude with 350695 elements. Creating vector time with 350695 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020233/2020.233.14/navigation.nc'); processNav(): median of positive valued depths = 49.7497 processNav(): Finding depths less than 348.2479 and times > 0 processNav(): length(Nav.depth) = 350695 processNav(): length(gindx) = 350695 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/2020/2020233/2020.233.14/gps.nc') Creating vector time with 14825 elements. Creating vector hours with 14825 elements. Creating vector time with 14825 elements. Creating vector minutes with 14825 elements. Creating vector time with 14825 elements. Creating vector seconds with 14825 elements. Creating vector time with 14825 elements. Creating vector centiSeconds with 14825 elements. Creating vector time with 14825 elements. Creating vector latitude with 14825 elements. Creating vector time with 14825 elements. Creating vector longitude with 14825 elements. Creating vector time with 14825 elements. Creating vector quality with 14825 elements. Creating vector time with 14825 elements. Creating vector numberOfSatellites with 14825 elements. Creating vector time with 14825 elements. Creating vector hdop with 14825 elements. Creating vector time with 14825 elements. Creating vector antennaHeight with 14825 elements. Creating vector time with 14825 elements. Creating vector geoHeight with 14825 elements. Creating vector time with 14825 elements. Creating vector dgpsDataAge with 14825 elements. Creating vector time with 14825 elements. Creating vector dgpsRSID with 14825 elements. Creating vector time with 14825 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020233/2020.233.14/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/2020/2020233/2020.233.14/parosci.nc') Creating vector time with 698403 elements. Creating vector depth with 698403 elements. Creating vector time with 698403 elements. Creating vector temp with 698403 elements. Creating vector time with 698403 elements. Creating vector pressure with 698403 elements. Creating vector time with 698403 elements. Creating vector temp_period with 698403 elements. Creating vector time with 698403 elements. Creating vector pres_period with 698403 elements. Creating vector time with 698403 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020233/2020.233.14/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.2734 max(Depth.data) = 91.8489 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.2734 max(Depth.data) = 91.8489 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/2020/2020233/2020.233.14/hydroscatlog.nc') Creating vector time with 280536 elements. Creating vector Seconds with 280536 elements. Creating vector time with 280536 elements. Creating vector HundrethsOfSeconds with 280536 elements. Creating vector time with 280536 elements. Creating vector Snorm1 with 280536 elements. Creating vector time with 280536 elements. Creating vector Snorm2 with 280536 elements. Creating vector time with 280536 elements. Creating vector Snorm3 with 280536 elements. Creating vector time with 280536 elements. Creating vector Gain_Status_1 with 280536 elements. Creating vector time with 280536 elements. Creating vector Gain_Status_2 with 280536 elements. Creating vector time with 280536 elements. Creating vector Gain_Status_3 with 280536 elements. Creating vector time with 280536 elements. Creating vector RawDepthValue with 280536 elements. Creating vector time with 280536 elements. Creating vector RawTempValue with 280536 elements. Creating vector time with 280536 elements. Creating vector Temperature with 280536 elements. Creating vector time with 280536 elements. Creating vector ErrorValue with 280536 elements. Creating vector time with 280536 elements. Creating vector bb470 with 280536 elements. Creating vector time with 280536 elements. Creating vector bb676 with 280536 elements. Creating vector time with 280536 elements. Creating vector fl676u with 280536 elements. Creating vector time with 280536 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020233/2020.233.14/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/2020/2020233/2020.233.14/ctdDriver.nc') Creating vector time with 280629 elements. Creating vector conductivity with 280629 elements. Creating vector time with 280629 elements. Creating vector temperature with 280629 elements. Creating vector time with 280629 elements. Creating vector cond_frequency with 280629 elements. Creating vector time with 280629 elements. Creating vector temp_frequency with 280629 elements. Creating vector time with 280629 elements. Creating vector spare with 280629 elements. Creating vector time with 280629 elements. Creating vector humidity with 280629 elements. Creating vector time with 280629 elements. Creating vector flow1 with 280629 elements. Creating vector time with 280629 elements. Creating vector CDOM with 280629 elements. Creating vector time with 280629 elements. Creating vector dissolvedO2 with 280629 elements. Creating vector time with 280629 elements. Creating vector salinity with 280629 elements. Creating vector time with 280629 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020233/2020.233.14/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2020/2020233/2020.233.14/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/2020/2020233/2020.233.14/ctdDriver2.nc') Creating vector time with 280631 elements. Creating vector conductivity with 280631 elements. Creating vector time with 280631 elements. Creating vector temperature with 280631 elements. Creating vector time with 280631 elements. Creating vector cond_frequency with 280631 elements. Creating vector time with 280631 elements. Creating vector temp_frequency with 280631 elements. Creating vector time with 280631 elements. Creating vector flow2 with 280631 elements. Creating vector time with 280631 elements. Creating vector par with 280631 elements. Creating vector time with 280631 elements. Creating vector spare with 280631 elements. Creating vector time with 280631 elements. Creating vector salinity with 280631 elements. Creating vector time with 280631 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020233/2020.233.14/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2020/2020233/2020.233.14/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/2020/2020233/2020.233.14/isuslog.nc') Creating vector time with 54745 elements. Creating vector isusNitrate with 54745 elements. Creating vector time with 54745 elements. Creating vector isusTemp with 54745 elements. Creating vector time with 54745 elements. Creating vector isusQuality with 54745 elements. Creating vector time with 54745 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020233/2020.233.14/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/2020/2020233/2020.233.14/biolume.nc') Creating vector time with 68994 elements. Creating vector rrr with 68994 elements. Creating vector time with 68994 elements. Creating vector cal_striing with 68994 elements. Creating vector time with 68994 elements. Creating vector avg_biolume with 68994 elements. Creating vector time with 68994 elements. Creating vector pump with 68994 elements. Creating vector time with 68994 elements. Creating vector system_voltage with 68994 elements. Creating vector time with 68994 elements. Creating vector flow with 68994 elements. Creating vector time with 68994 elements. Creating vector HV with 68994 elements. Creating vector time with 68994 elements. Creating vector reserved with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_0 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_1 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_2 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_3 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_4 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_5 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_6 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_7 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_8 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_9 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_10 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_11 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_12 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_13 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_14 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_15 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_16 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_17 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_18 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_19 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_20 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_21 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_22 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_23 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_24 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_25 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_26 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_27 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_28 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_29 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_30 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_31 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_32 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_33 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_34 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_35 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_36 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_37 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_38 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_39 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_40 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_41 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_42 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_43 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_44 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_45 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_46 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_47 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_48 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_49 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_50 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_51 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_52 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_53 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_54 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_55 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_56 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_57 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_58 with 68994 elements. Creating vector time with 68994 elements. Creating vector raw_59 with 68994 elements. Creating vector time with 68994 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020233/2020.233.14/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/2020/2020233/2020.233.14/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (6683 x 994) with 6642902 elements. Creating vector time with 6683 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (6683 x 994) with 6642902 elements. Creating vector time with 6683 elements. Creating vector bin with 994 elements. Creating matrix countList (6683 x 994) with 6642902 elements. Creating vector time with 6683 elements. Creating vector bin with 994 elements. Creating vector LCcount with 6683 elements. Creating vector time with 6683 elements. Creating vector transCount with 6683 elements. Creating vector time with 6683 elements. Creating vector nonTransCount with 6683 elements. Creating vector time with 6683 elements. Creating vector ai_mean with 6683 elements. Creating vector time with 6683 elements. Creating vector ai_min with 6683 elements. Creating vector time with 6683 elements. Creating vector ai_max with 6683 elements. Creating vector time with 6683 elements. Creating vector ai_std with 6683 elements. Creating vector time with 6683 elements. Creating vector esd_mean with 6683 elements. Creating vector time with 6683 elements. Creating vector esd_min with 6683 elements. Creating vector time with 6683 elements. Creating vector esd_max with 6683 elements. Creating vector time with 6683 elements. Creating vector esd_std with 6683 elements. Creating vector time with 6683 elements. Creating vector countSum with 6683 elements. Creating vector time with 6683 elements. Creating vector snapshot with 6683 elements. Creating vector time with 6683 elements. Creating vector threshold with 6683 elements. Creating vector time with 6683 elements. Creating vector sampleCount with 6683 elements. Creating vector time with 6683 elements. Creating vector flowCount with 6683 elements. Creating vector time with 6683 elements. Creating vector flowTime with 6683 elements. Creating vector time with 6683 elements. Creating vector bufferStatus with 6683 elements. Creating vector time with 6683 elements. Creating vector laserLevel with 6683 elements. Creating vector time with 6683 elements. Creating vector counter with 6683 elements. Creating vector time with 6683 elements. Creating vector counterPeriod with 6683 elements. Creating vector time with 6683 elements. Creating vector laserControl with 6683 elements. Creating vector time with 6683 elements. Creating vector countUnknownFrameCharacter with 6683 elements. Creating vector time with 6683 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 6683 elements. Creating vector time with 6683 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 6683 elements. Creating vector time with 6683 elements. Creating vector flowSpeed with 6683 elements. Creating vector time with 6683 elements. Creating vector countShortLFrameError with 6683 elements. Creating vector time with 6683 elements. Creating vector countGarbledLFrame with 6683 elements. Creating vector time with 6683 elements. Creating vector cFrameEsecs with 6683 elements. Creating vector time with 6683 elements. Creating vector correctedSampleCountList with 6683 elements. Creating vector time with 6683 elements. Creating vector time with 6683 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2020/2020233/2020.233.14/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020.233.14.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_2020.233.14.mat has_par2 = 0 Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 6 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_233_14_233_14_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_233_14_233_14.mat Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_233_14_233_14.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 = 170 Gridding with nix = 510, iZ = 181 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 298721 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 298721 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 140703 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 08/20/2020 11:30 to 08/21/2020 09:30 swr = 297.6297 481.1269 501.9397 434.0330 306.7124 181.4893 98.9909 55.9048 25.5759 2.2252 2.2545 1.9748 2.3000 2.1333 2.0163 2.4088 2.3538 1.9129 2.1081 5.2663 57.9623 154.9035 217.7554 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_233_14_233_14_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2020233_GulperTimes.txt && touch ../results/2020233_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/2020/2020233/2020.233.14/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2020/2020233/2020.233.14/syslog -startEsecs 1597955751.0501 -surveyName Dorado389_2020_233_14_233_14 >> ../results/2020233_GulperTimes.txt Executing: removeGulpDups.py ../results/2020233_GulperTimes.txt Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_233_14_233_14_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_233_14_233_14_2column.png Elapsed time to save image: 19 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_233_14_233_14_biolume.png Elapsed time to save image: 32 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_233_14_233_14_lopc.png Elapsed time to save image: 9 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_233_14_233_14_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_233_14_233_14_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_233_14_233_14_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_233_14_233_14_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_233_14_233_14_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_233_14_233_14_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_233_14_233_14_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_233_14_233_14_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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_233_14_233_14_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_233_14_233_14_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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_233_14_233_14_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_233_14_233_14_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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_233_14_233_14_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_233_14_233_14_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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_233_14_233_14_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_233_14_233_14_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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_233_14_233_14_Optical_Backscatter_420_nm.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_233_14_233_14_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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_233_14_233_14_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_233_14_233_14_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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_233_14_233_14_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_233_14_233_14_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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_233_14_233_14_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_233_14_233_14_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); adding: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_233_14_233_14_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2020_233_14_233_14_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_233_14_233_14.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_233_14_233_14.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_233_14_233_14_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_233_14_233_14.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 6 NaNs found in bbpRed. Interpolating anyway. Encountered 8107 NaN values in array of lon that is 54745 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 46638 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 46638 are not equal to number of Lat lon points = 54745 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_233_14_233_14.txt Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020_233_14_233_14.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_233_14_233_14_Gulper.txt... Tried, but failed to copy to /mbari/AUVCTD/surveys/2020/odv/ Unknown error occurred. ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 6 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_2020_233_14_233_14_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_233_14_233_14.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_233_14_233_14_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_233_14_233_14.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_233_14_233_14.nc ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2020_233_14_233_14 processed" mccann@mbari.org < mail_Dorado389_2020_233_14_233_14.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2020.233.14.mat Processing time: 368 seconds