Execution of AUVprocess_main version 1.88 at 2021-07-29T16:36:54Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2017, ['044.00'], '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: 2017.044.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017044/2017.044.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017044/2017.044.00/ 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/2017/2017044/2017.044.00/navigation.nc') Creating vector time with 399460 elements. Creating vector mPos_x with 399460 elements. Creating vector time with 399460 elements. Creating vector mPos_y with 399460 elements. Creating vector time with 399460 elements. Creating vector mDepth with 399460 elements. Creating vector time with 399460 elements. Creating vector mGpsNorth with 399460 elements. Creating vector time with 399460 elements. Creating vector mGpsEast with 399460 elements. Creating vector time with 399460 elements. Creating vector mGpsValid with 399460 elements. Creating vector time with 399460 elements. Creating vector mPhi with 399460 elements. Creating vector time with 399460 elements. Creating vector mTheta with 399460 elements. Creating vector time with 399460 elements. Creating vector mPsi with 399460 elements. Creating vector time with 399460 elements. Creating vector mOmega_x with 399460 elements. Creating vector time with 399460 elements. Creating vector mOmega_y with 399460 elements. Creating vector time with 399460 elements. Creating vector mOmega_z with 399460 elements. Creating vector time with 399460 elements. Creating vector mPsaRange with 399460 elements. Creating vector time with 399460 elements. Creating vector mAltitude with 399460 elements. Creating vector time with 399460 elements. Creating vector multibeamAltitude with 399460 elements. Creating vector time with 399460 elements. Creating vector mDvlAltitude with 399460 elements. Creating vector time with 399460 elements. Creating vector mEchoAltitude with 399460 elements. Creating vector time with 399460 elements. Creating vector mEchoHorizRange with 399460 elements. Creating vector time with 399460 elements. Creating vector mEchoAltitudeLast with 399460 elements. Creating vector time with 399460 elements. Creating vector mEchoHorizRangeLast with 399460 elements. Creating vector time with 399460 elements. Creating vector mEchoNumOfPings with 399460 elements. Creating vector time with 399460 elements. Creating vector nadirCnts with 399460 elements. Creating vector time with 399460 elements. Creating vector obstacleCnts with 399460 elements. Creating vector time with 399460 elements. Creating vector nGoodNadirBeams with 399460 elements. Creating vector time with 399460 elements. Creating vector medianNadirBeamNo with 399460 elements. Creating vector time with 399460 elements. Creating vector mWaterSpeed with 399460 elements. Creating vector time with 399460 elements. Creating vector mDvlValid with 399460 elements. Creating vector time with 399460 elements. Creating vector mDvlNewData with 399460 elements. Creating vector time with 399460 elements. Creating vector mDeltaT with 399460 elements. Creating vector time with 399460 elements. Creating vector nfix with 399460 elements. Creating vector time with 399460 elements. Creating vector efix with 399460 elements. Creating vector time with 399460 elements. Creating vector filter_north with 399460 elements. Creating vector time with 399460 elements. Creating vector filter_east with 399460 elements. Creating vector time with 399460 elements. Creating vector filter_depth with 399460 elements. Creating vector time with 399460 elements. Creating vector north_current with 399460 elements. Creating vector time with 399460 elements. Creating vector east_current with 399460 elements. Creating vector time with 399460 elements. Creating vector speed_bias with 399460 elements. Creating vector time with 399460 elements. Creating vector heading_bias with 399460 elements. Creating vector time with 399460 elements. Creating vector latitude with 399460 elements. Creating vector time with 399460 elements. Creating vector longitude with 399460 elements. Creating vector time with 399460 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017044/2017.044.00/navigation.nc'); processNav(): median of positive valued depths = 33.978 processNav(): Finding depths less than 237.8458 and times > 0 processNav(): length(Nav.depth) = 399460 processNav(): length(gindx) = 399460 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/2017/2017044/2017.044.00/gps.nc') Creating vector time with 12250 elements. Creating vector hours with 12250 elements. Creating vector time with 12250 elements. Creating vector minutes with 12250 elements. Creating vector time with 12250 elements. Creating vector seconds with 12250 elements. Creating vector time with 12250 elements. Creating vector centiSeconds with 12250 elements. Creating vector time with 12250 elements. Creating vector latitude with 12250 elements. Creating vector time with 12250 elements. Creating vector longitude with 12250 elements. Creating vector time with 12250 elements. Creating vector quality with 12250 elements. Creating vector time with 12250 elements. Creating vector numberOfSatellites with 12250 elements. Creating vector time with 12250 elements. Creating vector hdop with 12250 elements. Creating vector time with 12250 elements. Creating vector antennaHeight with 12250 elements. Creating vector time with 12250 elements. Creating vector geoHeight with 12250 elements. Creating vector time with 12250 elements. Creating vector dgpsDataAge with 12250 elements. Creating vector time with 12250 elements. Creating vector dgpsRSID with 12250 elements. Creating vector time with 12250 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017044/2017.044.00/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/2017/2017044/2017.044.00/parosci.nc') Creating vector time with 784155 elements. Creating vector depth with 784155 elements. Creating vector time with 784155 elements. Creating vector temp with 784155 elements. Creating vector time with 784155 elements. Creating vector pressure with 784155 elements. Creating vector time with 784155 elements. Creating vector temp_period with 784155 elements. Creating vector time with 784155 elements. Creating vector pres_period with 784155 elements. Creating vector time with 784155 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017044/2017.044.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.30405 max(Depth.data) = 102.4867 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.30405 max(Depth.data) = 102.4867 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/2017/2017044/2017.044.00/hydroscatlog.nc') Creating vector time with 319548 elements. Creating vector Seconds with 319548 elements. Creating vector time with 319548 elements. Creating vector HundrethsOfSeconds with 319548 elements. Creating vector time with 319548 elements. Creating vector Snorm1 with 319548 elements. Creating vector time with 319548 elements. Creating vector Snorm2 with 319548 elements. Creating vector time with 319548 elements. Creating vector Snorm3 with 319548 elements. Creating vector time with 319548 elements. Creating vector Gain_Status_1 with 319548 elements. Creating vector time with 319548 elements. Creating vector Gain_Status_2 with 319548 elements. Creating vector time with 319548 elements. Creating vector Gain_Status_3 with 319548 elements. Creating vector time with 319548 elements. Creating vector RawDepthValue with 319548 elements. Creating vector time with 319548 elements. Creating vector RawTempValue with 319548 elements. Creating vector time with 319548 elements. Creating vector Temperature with 319548 elements. Creating vector time with 319548 elements. Creating vector ErrorValue with 319548 elements. Creating vector time with 319548 elements. Creating vector bb470 with 319548 elements. Creating vector time with 319548 elements. Creating vector bb676 with 319548 elements. Creating vector time with 319548 elements. Creating vector fl676u with 319548 elements. Creating vector time with 319548 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017044/2017.044.00/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/2017/2017044/2017.044.00/ctdDriver.nc') Creating vector time with 319626 elements. Creating vector conductivity with 319626 elements. Creating vector time with 319626 elements. Creating vector temperature with 319626 elements. Creating vector time with 319626 elements. Creating vector cond_frequency with 319626 elements. Creating vector time with 319626 elements. Creating vector temp_frequency with 319626 elements. Creating vector time with 319626 elements. Creating vector spare with 319626 elements. Creating vector time with 319626 elements. Creating vector humidity with 319626 elements. Creating vector time with 319626 elements. Creating vector flow1 with 319626 elements. Creating vector time with 319626 elements. Creating vector CDOM with 319626 elements. Creating vector time with 319626 elements. Creating vector dissolvedO2 with 319626 elements. Creating vector time with 319626 elements. Creating vector salinity with 319626 elements. Creating vector time with 319626 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017044/2017.044.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017044/2017.044.00/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/2017/2017044/2017.044.00/ctdDriver2.nc') Creating vector time with 319624 elements. Creating vector conductivity with 319624 elements. Creating vector time with 319624 elements. Creating vector temperature with 319624 elements. Creating vector time with 319624 elements. Creating vector cond_frequency with 319624 elements. Creating vector time with 319624 elements. Creating vector temp_frequency with 319624 elements. Creating vector time with 319624 elements. Creating vector flow2 with 319624 elements. Creating vector time with 319624 elements. Creating vector spare with 319624 elements. Creating vector time with 319624 elements. Creating vector salinity with 319624 elements. Creating vector time with 319624 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017044/2017.044.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017044/2017.044.00/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/2017/2017044/2017.044.00/isuslog.nc') Creating vector time with 61982 elements. Creating vector isusNitrate with 61982 elements. Creating vector time with 61982 elements. Creating vector isusTemp with 61982 elements. Creating vector time with 61982 elements. Creating vector isusQuality with 61982 elements. Creating vector time with 61982 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017044/2017.044.00/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) In reprocess_surveys (line 1344)] [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) In reprocess_surveys (line 1344)] loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017044/2017.044.00/biolume.nc') Creating vector time with 77995 elements. Creating vector rrr with 77995 elements. Creating vector time with 77995 elements. Creating vector cal_striing with 77995 elements. Creating vector time with 77995 elements. Creating vector avg_biolume with 77995 elements. Creating vector time with 77995 elements. Creating vector pump with 77995 elements. Creating vector time with 77995 elements. Creating vector system_voltage with 77995 elements. Creating vector time with 77995 elements. Creating vector flow with 77995 elements. Creating vector time with 77995 elements. Creating vector HV with 77995 elements. Creating vector time with 77995 elements. Creating vector reserved with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_0 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_1 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_2 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_3 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_4 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_5 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_6 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_7 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_8 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_9 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_10 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_11 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_12 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_13 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_14 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_15 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_16 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_17 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_18 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_19 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_20 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_21 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_22 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_23 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_24 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_25 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_26 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_27 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_28 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_29 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_30 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_31 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_32 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_33 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_34 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_35 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_36 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_37 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_38 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_39 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_40 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_41 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_42 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_43 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_44 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_45 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_46 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_47 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_48 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_49 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_50 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_51 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_52 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_53 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_54 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_55 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_56 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_57 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_58 with 77995 elements. Creating vector time with 77995 elements. Creating vector raw_59 with 77995 elements. Creating vector time with 77995 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017044/2017.044.00/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/2017/2017044/2017.044.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (3758 x 994) with 3735452 elements. Creating matrix mepCountList (3758 x 994) with 3735452 elements. Creating matrix countList (3758 x 994) with 3735452 elements. Creating vector LCcount with 3758 elements. Creating vector transCount with 3758 elements. Creating vector nonTransCount with 3758 elements. Creating vector ai_mean with 3758 elements. Creating vector ai_min with 3758 elements. Creating vector ai_max with 3758 elements. Creating vector ai_std with 3758 elements. Creating vector esd_mean with 3758 elements. Creating vector esd_min with 3758 elements. Creating vector esd_max with 3758 elements. Creating vector esd_std with 3758 elements. Creating vector countSum with 3758 elements. Creating vector snapshot with 3758 elements. Creating vector threshold with 3758 elements. Creating vector sampleCount with 3758 elements. Creating vector flowCount with 3758 elements. Creating vector flowTime with 3758 elements. Creating vector bufferStatus with 3758 elements. Creating vector laserLevel with 3758 elements. Creating vector counter with 3758 elements. Creating vector counterPeriod with 3758 elements. Creating vector laserControl with 3758 elements. Creating vector countUnknownFrameCharacter with 3758 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 3758 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 3758 elements. Creating vector flowSpeed with 3758 elements. Creating vector countShortLFrameError with 3758 elements. Creating vector countGarbledLFrame with 3758 elements. Creating vector cFrameEsecs with 3758 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017044/2017.044.00/lopc.nc'); *** Setting lopc structure to NaNs. *** save /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017.044.00.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_2017.044.00.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_2017_044_00_044_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_044_00_044_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_044_00_044_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 = 390 Gridding with nix = 1170, iZ = 202 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 Only one good point or fewer - NaNing the gLOPCcount array. - NaNing the gLOPCtransCount array. - NaNing the gLOPCnonTransCount array. - NaNing the gLOPCLCcount array. 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 No valid data for gLOPCcount cvarname = gLOPCtransCount No valid data for gLOPCtransCount cvarname = gLOPCnonTransCount No valid data for gLOPCnonTransCount cvarname = gLOPCLCcount No valid data for gLOPCLCcount Encountered 0 NaN values in array of lon that is 387509 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 387509 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: 02/13/2017 09:29 to 02/14/2017 09:29 swr = 354.7183 371.7550 475.8131 455.2208 490.3759 393.4802 148.0009 81.9672 25.4134 2.9913 2.9383 2.7250 2.2666 2.1434 2.0283 2.3149 2.2850 2.1717 1.9866 2.0283 1.9651 2.8617 77.8249 212.2367 399.3214 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_044_00_044_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2017044_GulperTimes.txt && touch ../results/2017044_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/2017/2017044/2017.044.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2017/2017044/2017.044.00/syslog -startEsecs 1487014274.3235 -surveyName Dorado389_2017_044_00_044_00 >> ../results/2017044_GulperTimes.txt Executing: removeGulpDups.py ../results/2017044_GulperTimes.txt Bottle: 0 Time: 1487021383.07 Depth: 2.7174 Dist: 8.1891 Bottle: 1 Time: 1487024013.87 Depth: 6.9347 Dist: 11.2482 Bottle: 2 Time: 1487026142.27 Depth: 6.26 Dist: 13.6704 Bottle: 3 Time: 1487034908.47 Depth: 7.0467 Dist: 22.836 Bottle: 4 Time: 1487037171.07 Depth: 2.7231 Dist: 25.2037 Bottle: 5 Time: 1487040183.07 Depth: 3.7577 Dist: 27.9555 Bottle: 6 Time: 1487050777.5229 Depth: -0.033744 Dist: 37.0801 Bottle: 7 Time: 1487050865.1169 Depth: 20.0946 Dist: 37.1631 Bottle: 8 Time: 1487050927.5226 Depth: 40.0079 Dist: 37.2318 Bottle: 9 Time: 1487050993.3181 Depth: 60.0371 Dist: 37.3091 Bottle: 10 Time: 1487053770.87 Depth: 11.4463 Dist: 39.7853 Bottle: 11 Time: 1487055859.27 Depth: 2.8427 Dist: 41.6117 Bottle: 12 Time: 1487060700.27 Depth: 6.4092 Dist: 46.4223 Bottle: 13 Time: 1487075981.87 Depth: 3.314 Dist: 60.2741 Bottle: 14 Time: 1487080990.87 Depth: 3.0753 Dist: 65.6126 Bottle: 15 Time: 1487083191.47 Depth: 3.0409 Dist: 67.6867 Bottle: 16 Time: 1487089852.716 Depth: 0.30873 Dist: 74.0441 Bottle: 17 Time: 1487089942.5199 Depth: 20.037 Dist: 74.1216 Bottle: 18 Time: 1487090003.3157 Depth: 40.0329 Dist: 74.1829 Bottle: 19 Time: 1487090067.1213 Depth: 60.0898 Dist: 74.2545 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_044_00_044_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_2017_044_00_044_00_2column.png Elapsed time to save image: 30 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_2017_044_00_044_00_biolume.png Elapsed time to save image: 88 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_2017_044_00_044_00_lopc.png Elapsed time to save image: 30 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_2017_044_00_044_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_044_00_044_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_044_00_044_00_2column.png... Copied to /mbari/AUVCTD/surveys/2017/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_2017_044_00_044_00_biolume.png... Copied to /mbari/AUVCTD/surveys/2017/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_2017_044_00_044_00_lopc.png... Copied to /mbari/AUVCTD/surveys/2017/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_2017_044_00_044_00_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2017/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_2017_044_00_044_00_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2017/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_2017_044_00_044_00_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2017/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... 601 NaNs found in bbpBlue. Interpolating anyway. 6015 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_2017_044_00_044_00_decim.nc... Copied to /mbari/AUVCTD/surveys/2017/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); updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_044_00_044_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_044_00_044_00_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Salinity', jetplus, varlimits(2,:), ctd1.S, time.ctd1, auvnav, depth.ctd1, resultspath); updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_044_00_044_00_Salinity.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_044_00_044_00_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Nitrate', jetplus, varlimits(3,:), isus.nitrate, time.isus, auvnav, depth.isus, resultspath); updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_044_00_044_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_044_00_044_00_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Oxygen', jetplus, varlimits(4,:), ctd1.O2, time.ctd1, auvnav, depth.ctd1, resultspath); updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_044_00_044_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_044_00_044_00_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @420 nm', jetplus, varlimits(5,:), hs2.bbp420, time.hs2, auvnav, depth.hs2, resultspath); updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_044_00_044_00_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_044_00_044_00_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Optical Backscatter @700 nm', jetplus, varlimits(6,:), hs2.bbp700, time.hs2, auvnav, depth.hs2, resultspath); updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_044_00_044_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_044_00_044_00_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Chlorophyll Fluorescence', jetplus, varlimits(7,:), hs2.fl700_uncorr, time.hs2, auvnav, depth.hs2, resultspath); updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_044_00_044_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_044_00_044_00_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'Bioluminescence', jetplus, varlimits(8,:), biolume.biolume, time.biolume, auvnav, depth.biolume, resultspath); updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_044_00_044_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_044_00_044_00_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2017/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); length(v_esecs(gindx)) = which is less than 2. Not processing. updating: u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_044_00_044_00_LOPC_Total_Count.kml (deflated 94%) Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results//Dorado389_2017_044_00_044_00_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/ Creating Dorado389_2017_044_00_044_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_044_00_044_00.kml... Copied to /mbari/AUVCTD/surveys/2017/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_2017_044_00_044_00_LOPC_Total_Count.kml' not found.] [> In create_data_products (line 445) In build_auv_survey (line 530) In AUVprocess_main (line 257) In reprocess_surveys (line 1344)] ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_044_00_044_00.mat ... Iterpolating to isus time values... Interpolating ctd2 temperature... Interpolating ctd2 salinity... 601 NaNs found in bbpBlue. Interpolating anyway. 6015 NaNs found in bbpRed. Interpolating anyway. 1 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 1856 NaN values in array of lon that is 61982 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 60126 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 60126 are not equal to number of Lat lon points = 61982 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_2017_044_00_044_00.txt Writing to /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_044_00_044_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017_044_00_044_00.txt... Copied to /mbari/AUVCTD/surveys/2017/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_2017_044_00_044_00_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2017/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_2017_044_00_044_00.nc... Copied to /mbari/AUVCTD/surveys/2017/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_2017_044_00_044_00_gridded.mat... Copied to /mbari/AUVCTD/surveys/2017/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_2017_044_00_044_00.mat... Copied to /mbari/AUVCTD/surveys/2017/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/2017/netcdf/Dorado389_2017_044_00_044_00.nc ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2017_044_00_044_00 processed" mccann@mbari.org < mail_Dorado389_2017_044_00_044_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd.cvs/src/matlab/doradosdp/results/Dorado389_2017.044.00.mat Processing time: 309 seconds