Execution of AUVprocess_main version 1.86 at 2018-05-25T23:41:18Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2017, ['068.00'], 'ssds.shore.mbari.org', 0, 'ssdsLoads-new-ssds.jar', 0, '/mbari/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/', [], 'ctd1') ************************************************************************* Processing data from SSDS via DODS server ************************************************************************* ************************************************************************* Processing AUV mission: 2017.068.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017068/2017.068.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017068/2017.068.00/ Processing results path (data and metadata) is /u/ssdsadmin/dev/auv_ctd/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/2017/2017068/2017.068.00/navigation.nc') Creating vector time with 408576 elements. Creating vector mPos_x with 408576 elements. Creating vector time with 408576 elements. Creating vector mPos_y with 408576 elements. Creating vector time with 408576 elements. Creating vector mDepth with 408576 elements. Creating vector time with 408576 elements. Creating vector mGpsNorth with 408576 elements. Creating vector time with 408576 elements. Creating vector mGpsEast with 408576 elements. Creating vector time with 408576 elements. Creating vector mGpsValid with 408576 elements. Creating vector time with 408576 elements. Creating vector mPhi with 408576 elements. Creating vector time with 408576 elements. Creating vector mTheta with 408576 elements. Creating vector time with 408576 elements. Creating vector mPsi with 408576 elements. Creating vector time with 408576 elements. Creating vector mOmega_x with 408576 elements. Creating vector time with 408576 elements. Creating vector mOmega_y with 408576 elements. Creating vector time with 408576 elements. Creating vector mOmega_z with 408576 elements. Creating vector time with 408576 elements. Creating vector mPsaRange with 408576 elements. Creating vector time with 408576 elements. Creating vector mAltitude with 408576 elements. Creating vector time with 408576 elements. Creating vector multibeamAltitude with 408576 elements. Creating vector time with 408576 elements. Creating vector mDvlAltitude with 408576 elements. Creating vector time with 408576 elements. Creating vector mEchoAltitude with 408576 elements. Creating vector time with 408576 elements. Creating vector mEchoHorizRange with 408576 elements. Creating vector time with 408576 elements. Creating vector mEchoAltitudeLast with 408576 elements. Creating vector time with 408576 elements. Creating vector mEchoHorizRangeLast with 408576 elements. Creating vector time with 408576 elements. Creating vector mEchoNumOfPings with 408576 elements. Creating vector time with 408576 elements. Creating vector nadirCnts with 408576 elements. Creating vector time with 408576 elements. Creating vector obstacleCnts with 408576 elements. Creating vector time with 408576 elements. Creating vector nGoodNadirBeams with 408576 elements. Creating vector time with 408576 elements. Creating vector medianNadirBeamNo with 408576 elements. Creating vector time with 408576 elements. Creating vector mWaterSpeed with 408576 elements. Creating vector time with 408576 elements. Creating vector mDvlValid with 408576 elements. Creating vector time with 408576 elements. Creating vector mDvlNewData with 408576 elements. Creating vector time with 408576 elements. Creating vector mDeltaT with 408576 elements. Creating vector time with 408576 elements. Creating vector nfix with 408576 elements. Creating vector time with 408576 elements. Creating vector efix with 408576 elements. Creating vector time with 408576 elements. Creating vector filter_north with 408576 elements. Creating vector time with 408576 elements. Creating vector filter_east with 408576 elements. Creating vector time with 408576 elements. Creating vector filter_depth with 408576 elements. Creating vector time with 408576 elements. Creating vector north_current with 408576 elements. Creating vector time with 408576 elements. Creating vector east_current with 408576 elements. Creating vector time with 408576 elements. Creating vector speed_bias with 408576 elements. Creating vector time with 408576 elements. Creating vector heading_bias with 408576 elements. Creating vector time with 408576 elements. Creating vector latitude with 408576 elements. Creating vector time with 408576 elements. Creating vector longitude with 408576 elements. Creating vector time with 408576 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017068/2017.068.00/navigation.nc'); processNav(): median of positive valued depths = 31.2405 processNav(): Finding depths less than 218.6836 and times > 0 processNav(): length(Nav.depth) = 408576 processNav(): length(gindx) = 408576 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/2017/2017068/2017.068.00/gps.nc') Creating vector time with 11063 elements. Creating vector hours with 11063 elements. Creating vector time with 11063 elements. Creating vector minutes with 11063 elements. Creating vector time with 11063 elements. Creating vector seconds with 11063 elements. Creating vector time with 11063 elements. Creating vector centiSeconds with 11063 elements. Creating vector time with 11063 elements. Creating vector latitude with 11063 elements. Creating vector time with 11063 elements. Creating vector longitude with 11063 elements. Creating vector time with 11063 elements. Creating vector quality with 11063 elements. Creating vector time with 11063 elements. Creating vector numberOfSatellites with 11063 elements. Creating vector time with 11063 elements. Creating vector hdop with 11063 elements. Creating vector time with 11063 elements. Creating vector antennaHeight with 11063 elements. Creating vector time with 11063 elements. Creating vector geoHeight with 11063 elements. Creating vector time with 11063 elements. Creating vector dgpsDataAge with 11063 elements. Creating vector time with 11063 elements. Creating vector dgpsRSID with 11063 elements. Creating vector time with 11063 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017068/2017.068.00/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/2017/2017068/2017.068.00/parosci.nc') Creating vector time with 802047 elements. Creating vector depth with 802047 elements. Creating vector time with 802047 elements. Creating vector temp with 802047 elements. Creating vector time with 802047 elements. Creating vector pressure with 802047 elements. Creating vector time with 802047 elements. Creating vector temp_period with 802047 elements. Creating vector time with 802047 elements. Creating vector pres_period with 802047 elements. Creating vector time with 802047 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017068/2017.068.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.33953 max(Depth.data) = 101.6945 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.33953 max(Depth.data) = 101.6945 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/2017/2017068/2017.068.00/hydroscatlog.nc') Creating vector time with 326828 elements. Creating vector Seconds with 326828 elements. Creating vector time with 326828 elements. Creating vector HundrethsOfSeconds with 326828 elements. Creating vector time with 326828 elements. Creating vector Snorm1 with 326828 elements. Creating vector time with 326828 elements. Creating vector Snorm2 with 326828 elements. Creating vector time with 326828 elements. Creating vector Snorm3 with 326828 elements. Creating vector time with 326828 elements. Creating vector Gain_Status_1 with 326828 elements. Creating vector time with 326828 elements. Creating vector Gain_Status_2 with 326828 elements. Creating vector time with 326828 elements. Creating vector Gain_Status_3 with 326828 elements. Creating vector time with 326828 elements. Creating vector RawDepthValue with 326828 elements. Creating vector time with 326828 elements. Creating vector RawTempValue with 326828 elements. Creating vector time with 326828 elements. Creating vector Temperature with 326828 elements. Creating vector time with 326828 elements. Creating vector ErrorValue with 326828 elements. Creating vector time with 326828 elements. Creating vector bb470 with 326828 elements. Creating vector time with 326828 elements. Creating vector bb676 with 326828 elements. Creating vector time with 326828 elements. Creating vector fl676u with 326828 elements. Creating vector time with 326828 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017068/2017.068.00/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/2017/2017068/2017.068.00/ctdDriver.nc') Creating vector time with 326862 elements. Creating vector conductivity with 326862 elements. Creating vector time with 326862 elements. Creating vector temperature with 326862 elements. Creating vector time with 326862 elements. Creating vector cond_frequency with 326862 elements. Creating vector time with 326862 elements. Creating vector temp_frequency with 326862 elements. Creating vector time with 326862 elements. Creating vector spare with 326862 elements. Creating vector time with 326862 elements. Creating vector humidity with 326862 elements. Creating vector time with 326862 elements. Creating vector flow1 with 326862 elements. Creating vector time with 326862 elements. Creating vector CDOM with 326862 elements. Creating vector time with 326862 elements. Creating vector dissolvedO2 with 326862 elements. Creating vector time with 326862 elements. Creating vector salinity with 326862 elements. Creating vector time with 326862 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017068/2017.068.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017068/2017.068.00/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/2017/2017068/2017.068.00/ctdDriver2.nc') Creating vector time with 326863 elements. Creating vector conductivity with 326863 elements. Creating vector time with 326863 elements. Creating vector temperature with 326863 elements. Creating vector time with 326863 elements. Creating vector cond_frequency with 326863 elements. Creating vector time with 326863 elements. Creating vector temp_frequency with 326863 elements. Creating vector time with 326863 elements. Creating vector flow2 with 326863 elements. Creating vector time with 326863 elements. Creating vector spare with 326863 elements. Creating vector time with 326863 elements. Creating vector salinity with 326863 elements. Creating vector time with 326863 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017068/2017.068.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017068/2017.068.00/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/2017/2017068/2017.068.00/isuslog.nc') Creating vector time with 63454 elements. Creating vector isusNitrate with 63454 elements. Creating vector time with 63454 elements. Creating vector isusTemp with 63454 elements. Creating vector time with 63454 elements. Creating vector isusQuality with 63454 elements. Creating vector time with 63454 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017068/2017.068.00/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 75) In processBiolume (line 21) In processAUVmission (line 220) In AUVprocess_main (line 225)] [Warning: "/mbari/matlabR2012a/toolbox/matlab/demos" not found in path.] [> In rmpath (line 75) In processBiolume (line 22) In processAUVmission (line 220) In AUVprocess_main (line 225)] loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017068/2017.068.00/biolume.nc') Creating vector time with 80369 elements. Creating vector rrr with 80369 elements. Creating vector time with 80369 elements. Creating vector cal_striing with 80369 elements. Creating vector time with 80369 elements. Creating vector avg_biolume with 80369 elements. Creating vector time with 80369 elements. Creating vector pump with 80369 elements. Creating vector time with 80369 elements. Creating vector system_voltage with 80369 elements. Creating vector time with 80369 elements. Creating vector flow with 80369 elements. Creating vector time with 80369 elements. Creating vector HV with 80369 elements. Creating vector time with 80369 elements. Creating vector reserved with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_0 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_1 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_2 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_3 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_4 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_5 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_6 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_7 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_8 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_9 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_10 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_11 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_12 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_13 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_14 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_15 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_16 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_17 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_18 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_19 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_20 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_21 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_22 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_23 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_24 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_25 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_26 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_27 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_28 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_29 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_30 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_31 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_32 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_33 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_34 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_35 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_36 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_37 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_38 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_39 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_40 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_41 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_42 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_43 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_44 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_45 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_46 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_47 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_48 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_49 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_50 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_51 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_52 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_53 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_54 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_55 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_56 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_57 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_58 with 80369 elements. Creating vector time with 80369 elements. Creating vector raw_59 with 80369 elements. Creating vector time with 80369 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017068/2017.068.00/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/2017/2017068/2017.068.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (7697 x 994) with 7650818 elements. Creating vector time with 7697 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (7697 x 994) with 7650818 elements. Creating vector time with 7697 elements. Creating vector bin with 994 elements. Creating matrix countList (7697 x 994) with 7650818 elements. Creating vector time with 7697 elements. Creating vector bin with 994 elements. Creating vector LCcount with 7697 elements. Creating vector time with 7697 elements. Creating vector transCount with 7697 elements. Creating vector time with 7697 elements. Creating vector nonTransCount with 7697 elements. Creating vector time with 7697 elements. Creating vector ai_mean with 7697 elements. Creating vector time with 7697 elements. Creating vector ai_min with 7697 elements. Creating vector time with 7697 elements. Creating vector ai_max with 7697 elements. Creating vector time with 7697 elements. Creating vector ai_std with 7697 elements. Creating vector time with 7697 elements. Creating vector esd_mean with 7697 elements. Creating vector time with 7697 elements. Creating vector esd_min with 7697 elements. Creating vector time with 7697 elements. Creating vector esd_max with 7697 elements. Creating vector time with 7697 elements. Creating vector esd_std with 7697 elements. Creating vector time with 7697 elements. Creating vector countSum with 7697 elements. Creating vector time with 7697 elements. Creating vector snapshot with 7697 elements. Creating vector time with 7697 elements. Creating vector threshold with 7697 elements. Creating vector time with 7697 elements. Creating vector sampleCount with 7697 elements. Creating vector time with 7697 elements. Creating vector flowCount with 7697 elements. Creating vector time with 7697 elements. Creating vector flowTime with 7697 elements. Creating vector time with 7697 elements. Creating vector bufferStatus with 7697 elements. Creating vector time with 7697 elements. Creating vector laserLevel with 7697 elements. Creating vector time with 7697 elements. Creating vector counter with 7697 elements. Creating vector time with 7697 elements. Creating vector counterPeriod with 7697 elements. Creating vector time with 7697 elements. Creating vector laserControl with 7697 elements. Creating vector time with 7697 elements. Creating vector countUnknownFrameCharacter with 7697 elements. Creating vector time with 7697 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 7697 elements. Creating vector time with 7697 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 7697 elements. Creating vector time with 7697 elements. Creating vector flowSpeed with 7697 elements. Creating vector time with 7697 elements. Creating vector countShortLFrameError with 7697 elements. Creating vector time with 7697 elements. Creating vector countGarbledLFrame with 7697 elements. Creating vector time with 7697 elements. Creating vector cFrameEsecs with 7697 elements. Creating vector time with 7697 elements. Creating vector correctedSampleCountList with 7697 elements. Creating vector time with 7697 elements. Creating vector time with 7697 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017068/2017.068.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017.068.00.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/src/matlab/doradosdp/results/Dorado389_2017.068.00.mat 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/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_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 = 430 Gridding with nix = 1290, iZ = 201 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 407292 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 407292 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 118925 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 03/09/2017 09:29 to 03/10/2017 10:30 swr = 582.4980 737.0613 716.2689 711.7816 497.7568 524.4138 386.3972 207.9683 50.7904 3.8580 2.6720 2.6333 2.3371 2.5348 2.4771 2.3774 2.5735 2.3212 2.4122 2.2599 2.0613 12.0825 84.6966 193.9729 339.4767 391.6707 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2017068_GulperTimes.txt && touch ../results/2017068_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/2017/2017068/2017.068.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2017/2017068/2017.068.00/syslog -startEsecs 1489089442.4212 -surveyName Dorado389_2017_068_00_068_00 >> ../results/2017068_GulperTimes.txt Executing: removeGulpDups.py ../results/2017068_GulperTimes.txt Bottle: 0 Time: 1489097742.9 Depth: 16.6533 Dist: 9.4591 Bottle: 1 Time: 1489101015.1 Depth: 2.4793 Dist: 12.9508 Bottle: 2 Time: 1489103982.9 Depth: 4.1677 Dist: 16.1892 Bottle: 3 Time: 1489112619.89 Depth: 8.3225 Dist: 24.8466 Bottle: 4 Time: 1489116549.29 Depth: 16.5293 Dist: 28.5388 Bottle: 5 Time: 1489118730.29 Depth: 19.8635 Dist: 30.3538 Bottle: 6 Time: 1489126556.4187 Depth: 0.63676 Dist: 37.1996 Bottle: 7 Time: 1489126668.2311 Depth: 20.0413 Dist: 37.3274 Bottle: 8 Time: 1489126751.6154 Depth: 40.0671 Dist: 37.4212 Bottle: 9 Time: 1489126832.6198 Depth: 60.0403 Dist: 37.5009 Bottle: 10 Time: 1489129032.5 Depth: 2.943 Dist: 39.4983 Bottle: 11 Time: 1489131752.3 Depth: 3.9195 Dist: 41.9949 Bottle: 12 Time: 1489135504.5 Depth: 2.2089 Dist: 45.7113 Bottle: 13 Time: 1489152186.1 Depth: 3.3055 Dist: 60.9074 Bottle: 14 Time: 1489154634.7 Depth: 3.9478 Dist: 63.1181 Bottle: 15 Time: 1489157196.9 Depth: 5.3506 Dist: 65.3404 Bottle: 16 Time: 1489167737.6176 Depth: 0.046458 Dist: 73.6425 Bottle: 17 Time: 1489167845.0203 Depth: 20.0687 Dist: 73.7553 Bottle: 18 Time: 1489167923.4149 Depth: 40.0486 Dist: 73.8426 Bottle: 19 Time: 1489168007.0192 Depth: 60.021 Dist: 73.9225 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_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/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00_2column.png Elapsed time to save image: 15 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/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00_biolume.png Elapsed time to save image: 58 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/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_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/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00_2column.png... Copied to /mbari/AUVCTD/surveys/2017/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00_biolume.png... Copied to /mbari/AUVCTD/surveys/2017/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00_lopc.png... Copied to /mbari/AUVCTD/surveys/2017/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2017/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2017/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2017/images/. Removing from /u/ssdsadmin/dev/auv_ctd/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/src/matlab/doradosdp/results//Dorado389_2017_068_00_068_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_068_00_068_00_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/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/src/matlab/doradosdp/results//Dorado389_2017_068_00_068_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_068_00_068_00_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/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/src/matlab/doradosdp/results//Dorado389_2017_068_00_068_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_068_00_068_00_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/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/src/matlab/doradosdp/results//Dorado389_2017_068_00_068_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_068_00_068_00_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/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/src/matlab/doradosdp/results//Dorado389_2017_068_00_068_00_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_068_00_068_00_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/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/src/matlab/doradosdp/results//Dorado389_2017_068_00_068_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_068_00_068_00_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/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/src/matlab/doradosdp/results//Dorado389_2017_068_00_068_00_Chlorophyll_Fluorescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_068_00_068_00_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/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/src/matlab/doradosdp/results//Dorado389_2017_068_00_068_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_068_00_068_00_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ KML = write_kml(survey_shrt_filename_base, 'LOPC Total Count', jetplus, varlimits(9,:), lopc.countSum, time.lopc, auvnav, depth.lopc, resultspath); updating: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_068_00_068_00_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_068_00_068_00_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2017_068_00_068_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00.kml... Copied to /mbari/AUVCTD/surveys/2017/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_068_00_068_00_LOPC_Total_Count.kml' not found.] [> In create_data_products (line 414) In build_auv_survey (line 522) In AUVprocess_main (line 255)] ************************************************************************* Writing ODV file ... Loading survey file /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 18 NaNs found in bbpBlue. Interpolating anyway. 13 NaNs found in bbpRed. Interpolating anyway. Encountered 202 NaN values in array of lon that is 63453 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 63251 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 63251 are not equal to number of Lat lon points = 63453 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/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00.txt... Copied to /mbari/AUVCTD/surveys/2017/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2017/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing decimated netCDF file ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 18 NaNs found in bbpBlue. Interpolating anyway. 13 NaNs found in bbpRed. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00_decim.nc... Copied to /mbari/AUVCTD/surveys/2017/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Writing netCDF file ... Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00.nc... Copied to /mbari/AUVCTD/surveys/2017/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00_gridded.mat... Copied to /mbari/AUVCTD/surveys/2017/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_068_00_068_00.mat... Copied to /mbari/AUVCTD/surveys/2017/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2017_068_00_068_00 processed" mccann@mbari.org < mail_Dorado389_2017_068_00_068_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017.068.00.mat Processing time: 492 seconds