Execution of AUVprocess_main version 1.86 at 2018-05-29T15:58:27Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2017, ['347.00'], '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: 2017.347.00 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017347/2017.347.00/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017347/2017.347.00/ 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/2017/2017347/2017.347.00/navigation.nc') Creating vector time with 247908 elements. Creating vector mPos_x with 247908 elements. Creating vector time with 247908 elements. Creating vector mPos_y with 247908 elements. Creating vector time with 247908 elements. Creating vector mDepth with 247908 elements. Creating vector time with 247908 elements. Creating vector mGpsNorth with 247908 elements. Creating vector time with 247908 elements. Creating vector mGpsEast with 247908 elements. Creating vector time with 247908 elements. Creating vector mGpsValid with 247908 elements. Creating vector time with 247908 elements. Creating vector mPhi with 247908 elements. Creating vector time with 247908 elements. Creating vector mTheta with 247908 elements. Creating vector time with 247908 elements. Creating vector mPsi with 247908 elements. Creating vector time with 247908 elements. Creating vector mOmega_x with 247908 elements. Creating vector time with 247908 elements. Creating vector mOmega_y with 247908 elements. Creating vector time with 247908 elements. Creating vector mOmega_z with 247908 elements. Creating vector time with 247908 elements. Creating vector mPsaRange with 247908 elements. Creating vector time with 247908 elements. Creating vector mAltitude with 247908 elements. Creating vector time with 247908 elements. Creating vector multibeamAltitude with 247908 elements. Creating vector time with 247908 elements. Creating vector mDvlAltitude with 247908 elements. Creating vector time with 247908 elements. Creating vector mEchoAltitude with 247908 elements. Creating vector time with 247908 elements. Creating vector mEchoHorizRange with 247908 elements. Creating vector time with 247908 elements. Creating vector mEchoAltitudeLast with 247908 elements. Creating vector time with 247908 elements. Creating vector mEchoHorizRangeLast with 247908 elements. Creating vector time with 247908 elements. Creating vector mEchoNumOfPings with 247908 elements. Creating vector time with 247908 elements. Creating vector nadirCnts with 247908 elements. Creating vector time with 247908 elements. Creating vector obstacleCnts with 247908 elements. Creating vector time with 247908 elements. Creating vector nGoodNadirBeams with 247908 elements. Creating vector time with 247908 elements. Creating vector medianNadirBeamNo with 247908 elements. Creating vector time with 247908 elements. Creating vector mWaterSpeed with 247908 elements. Creating vector time with 247908 elements. Creating vector mDvlValid with 247908 elements. Creating vector time with 247908 elements. Creating vector mDvlNewData with 247908 elements. Creating vector time with 247908 elements. Creating vector mDeltaT with 247908 elements. Creating vector time with 247908 elements. Creating vector nfix with 247908 elements. Creating vector time with 247908 elements. Creating vector efix with 247908 elements. Creating vector time with 247908 elements. Creating vector filter_north with 247908 elements. Creating vector time with 247908 elements. Creating vector filter_east with 247908 elements. Creating vector time with 247908 elements. Creating vector filter_depth with 247908 elements. Creating vector time with 247908 elements. Creating vector north_current with 247908 elements. Creating vector time with 247908 elements. Creating vector east_current with 247908 elements. Creating vector time with 247908 elements. Creating vector speed_bias with 247908 elements. Creating vector time with 247908 elements. Creating vector heading_bias with 247908 elements. Creating vector time with 247908 elements. Creating vector latitude with 247908 elements. Creating vector time with 247908 elements. Creating vector longitude with 247908 elements. Creating vector time with 247908 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017347/2017.347.00/navigation.nc'); processNav(): median of positive valued depths = 40.58 processNav(): Finding depths less than 284.06 and times > 0 processNav(): length(Nav.depth) = 247908 processNav(): length(gindx) = 247908 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/2017/2017347/2017.347.00/gps.nc') Creating vector time with 4857 elements. Creating vector hours with 4857 elements. Creating vector time with 4857 elements. Creating vector minutes with 4857 elements. Creating vector time with 4857 elements. Creating vector seconds with 4857 elements. Creating vector time with 4857 elements. Creating vector centiSeconds with 4857 elements. Creating vector time with 4857 elements. Creating vector latitude with 4857 elements. Creating vector time with 4857 elements. Creating vector longitude with 4857 elements. Creating vector time with 4857 elements. Creating vector quality with 4857 elements. Creating vector time with 4857 elements. Creating vector numberOfSatellites with 4857 elements. Creating vector time with 4857 elements. Creating vector hdop with 4857 elements. Creating vector time with 4857 elements. Creating vector antennaHeight with 4857 elements. Creating vector time with 4857 elements. Creating vector geoHeight with 4857 elements. Creating vector time with 4857 elements. Creating vector dgpsDataAge with 4857 elements. Creating vector time with 4857 elements. Creating vector dgpsRSID with 4857 elements. Creating vector time with 4857 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017347/2017.347.00/gps.nc'); processGPS(): *** skipping bad position (lat,lon) = 55.7435, -128.9765 Processing depth data... loaddap('http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017347/2017.347.00/parosci.nc') Creating vector time with 486613 elements. Creating vector depth with 486613 elements. Creating vector time with 486613 elements. Creating vector temp with 486613 elements. Creating vector time with 486613 elements. Creating vector pressure with 486613 elements. Creating vector time with 486613 elements. Creating vector temp_period with 486613 elements. Creating vector time with 486613 elements. Creating vector pres_period with 486613 elements. Creating vector time with 486613 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017347/2017.347.00/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.30836 max(Depth.data) = 203.656 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.30836 max(Depth.data) = 203.656 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/2017/2017347/2017.347.00/hydroscatlog.nc') Creating vector time with 197932 elements. Creating vector Seconds with 197932 elements. Creating vector time with 197932 elements. Creating vector HundrethsOfSeconds with 197932 elements. Creating vector time with 197932 elements. Creating vector Snorm1 with 197932 elements. Creating vector time with 197932 elements. Creating vector Snorm2 with 197932 elements. Creating vector time with 197932 elements. Creating vector Snorm3 with 197932 elements. Creating vector time with 197932 elements. Creating vector Gain_Status_1 with 197932 elements. Creating vector time with 197932 elements. Creating vector Gain_Status_2 with 197932 elements. Creating vector time with 197932 elements. Creating vector Gain_Status_3 with 197932 elements. Creating vector time with 197932 elements. Creating vector RawDepthValue with 197932 elements. Creating vector time with 197932 elements. Creating vector RawTempValue with 197932 elements. Creating vector time with 197932 elements. Creating vector Temperature with 197932 elements. Creating vector time with 197932 elements. Creating vector ErrorValue with 197932 elements. Creating vector time with 197932 elements. Creating vector bb470 with 197932 elements. Creating vector time with 197932 elements. Creating vector bb676 with 197932 elements. Creating vector time with 197932 elements. Creating vector fl676u with 197932 elements. Creating vector time with 197932 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017347/2017.347.00/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/2017/2017347/2017.347.00/ctdDriver.nc') Creating vector time with 197925 elements. Creating vector conductivity with 197925 elements. Creating vector time with 197925 elements. Creating vector temperature with 197925 elements. Creating vector time with 197925 elements. Creating vector cond_frequency with 197925 elements. Creating vector time with 197925 elements. Creating vector temp_frequency with 197925 elements. Creating vector time with 197925 elements. Creating vector spare with 197925 elements. Creating vector time with 197925 elements. Creating vector humidity with 197925 elements. Creating vector time with 197925 elements. Creating vector flow1 with 197925 elements. Creating vector time with 197925 elements. Creating vector CDOM with 197925 elements. Creating vector time with 197925 elements. Creating vector dissolvedO2 with 197925 elements. Creating vector time with 197925 elements. Creating vector salinity with 197925 elements. Creating vector time with 197925 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017347/2017.347.00/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017347/2017.347.00/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/2017/2017347/2017.347.00/ctdDriver2.nc') Creating vector time with 198028 elements. Creating vector conductivity with 198028 elements. Creating vector time with 198028 elements. Creating vector temperature with 198028 elements. Creating vector time with 198028 elements. Creating vector cond_frequency with 198028 elements. Creating vector time with 198028 elements. Creating vector temp_frequency with 198028 elements. Creating vector time with 198028 elements. Creating vector flow2 with 198028 elements. Creating vector time with 198028 elements. Creating vector spare with 198028 elements. Creating vector time with 198028 elements. Creating vector salinity with 198028 elements. Creating vector time with 198028 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017347/2017.347.00/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2017/2017347/2017.347.00/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/2017/2017347/2017.347.00/isuslog.nc') Creating vector time with 38594 elements. Creating vector isusNitrate with 38594 elements. Creating vector time with 38594 elements. Creating vector isusTemp with 38594 elements. Creating vector time with 38594 elements. Creating vector isusQuality with 38594 elements. Creating vector time with 38594 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017347/2017.347.00/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/2017/2017347/2017.347.00/biolume.nc') Creating vector time with 48776 elements. Creating vector rrr with 48776 elements. Creating vector time with 48776 elements. Creating vector cal_striing with 48776 elements. Creating vector time with 48776 elements. Creating vector avg_biolume with 48776 elements. Creating vector time with 48776 elements. Creating vector pump with 48776 elements. Creating vector time with 48776 elements. Creating vector system_voltage with 48776 elements. Creating vector time with 48776 elements. Creating vector flow with 48776 elements. Creating vector time with 48776 elements. Creating vector HV with 48776 elements. Creating vector time with 48776 elements. Creating vector reserved with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_0 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_1 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_2 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_3 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_4 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_5 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_6 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_7 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_8 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_9 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_10 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_11 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_12 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_13 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_14 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_15 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_16 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_17 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_18 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_19 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_20 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_21 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_22 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_23 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_24 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_25 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_26 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_27 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_28 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_29 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_30 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_31 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_32 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_33 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_34 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_35 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_36 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_37 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_38 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_39 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_40 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_41 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_42 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_43 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_44 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_45 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_46 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_47 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_48 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_49 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_50 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_51 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_52 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_53 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_54 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_55 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_56 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_57 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_58 with 48776 elements. Creating vector time with 48776 elements. Creating vector raw_59 with 48776 elements. Creating vector time with 48776 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017347/2017.347.00/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/2017/2017347/2017.347.00/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (4724 x 994) with 4695656 elements. Creating vector time with 4724 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (4724 x 994) with 4695656 elements. Creating vector time with 4724 elements. Creating vector bin with 994 elements. Creating matrix countList (4724 x 994) with 4695656 elements. Creating vector time with 4724 elements. Creating vector bin with 994 elements. Creating vector LCcount with 4724 elements. Creating vector time with 4724 elements. Creating vector transCount with 4724 elements. Creating vector time with 4724 elements. Creating vector nonTransCount with 4724 elements. Creating vector time with 4724 elements. Creating vector ai_mean with 4724 elements. Creating vector time with 4724 elements. Creating vector ai_min with 4724 elements. Creating vector time with 4724 elements. Creating vector ai_max with 4724 elements. Creating vector time with 4724 elements. Creating vector ai_std with 4724 elements. Creating vector time with 4724 elements. Creating vector esd_mean with 4724 elements. Creating vector time with 4724 elements. Creating vector esd_min with 4724 elements. Creating vector time with 4724 elements. Creating vector esd_max with 4724 elements. Creating vector time with 4724 elements. Creating vector esd_std with 4724 elements. Creating vector time with 4724 elements. Creating vector countSum with 4724 elements. Creating vector time with 4724 elements. Creating vector snapshot with 4724 elements. Creating vector time with 4724 elements. Creating vector threshold with 4724 elements. Creating vector time with 4724 elements. Creating vector sampleCount with 4724 elements. Creating vector time with 4724 elements. Creating vector flowCount with 4724 elements. Creating vector time with 4724 elements. Creating vector flowTime with 4724 elements. Creating vector time with 4724 elements. Creating vector bufferStatus with 4724 elements. Creating vector time with 4724 elements. Creating vector laserLevel with 4724 elements. Creating vector time with 4724 elements. Creating vector counter with 4724 elements. Creating vector time with 4724 elements. Creating vector counterPeriod with 4724 elements. Creating vector time with 4724 elements. Creating vector laserControl with 4724 elements. Creating vector time with 4724 elements. Creating vector countUnknownFrameCharacter with 4724 elements. Creating vector time with 4724 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 4724 elements. Creating vector time with 4724 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 4724 elements. Creating vector time with 4724 elements. Creating vector flowSpeed with 4724 elements. Creating vector time with 4724 elements. Creating vector countShortLFrameError with 4724 elements. Creating vector time with 4724 elements. Creating vector countGarbledLFrame with 4724 elements. Creating vector time with 4724 elements. Creating vector cFrameEsecs with 4724 elements. Creating vector time with 4724 elements. Creating vector correctedSampleCountList with 4724 elements. Creating vector time with 4724 elements. Creating vector time with 4724 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2017/2017347/2017.347.00/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017.347.00.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_2017.347.00.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 20 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_347_00_347_00_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_347_00_347_00.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_347_00_347_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 = 278 Gridding with nix = 834, iZ = 404 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 247724 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 247724 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 119013 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 12/13/2017 12:29 to 12/14/2017 04:30 swr = 543.9123 473.1854 352.1705 210.4449 36.6074 1.3430 1.2491 1.2631 1.2035 1.0702 0.7474 0.7140 0.1211 0.8708 0.6159 0.9315 1.3490 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_347_00_347_00_swr.png Done plotting SWR. Executing: /bin/rm -f ../results/2017347_GulperTimes.txt && touch ../results/2017347_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/2017/2017347/2017.347.00/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2017/2017347/2017.347.00/syslog -startEsecs 1513205196.105 -surveyName Dorado389_2017_347_00_347_00 >> ../results/2017347_GulperTimes.txt Executing: removeGulpDups.py ../results/2017347_GulperTimes.txt Bottle: 0 Time: 1513206531.1035 Depth: 200.0183 Dist: 1.5048 Bottle: 1 Time: 1513206661.9046 Depth: 149.9106 Dist: 1.665 Bottle: 2 Time: 1513206795.3054 Depth: 99.992 Dist: 1.842 Bottle: 3 Time: 1513206857.4712 Depth: 79.9223 Dist: 1.9063 Bottle: 4 Time: 1513206920.1069 Depth: 59.9449 Dist: 1.9851 Bottle: 5 Time: 1513206987.9023 Depth: 39.8477 Dist: 2.0727 Bottle: 6 Time: 1513207026.4996 Depth: 29.9681 Dist: 2.1146 Bottle: 7 Time: 1513207062.6971 Depth: 19.9954 Dist: 2.1534 Bottle: 8 Time: 1513207099.9046 Depth: 9.9852 Dist: 2.1962 Bottle: 9 Time: 1513207184.6988 Depth: 0.36373 Dist: 2.2645 Bottle: 10 Time: 1513237922.9031 Depth: 200.0546 Dist: 36.0045 Bottle: 11 Time: 1513238059.1037 Depth: 149.9431 Dist: 36.1628 Bottle: 12 Time: 1513238190.9047 Depth: 99.9377 Dist: 36.3276 Bottle: 13 Time: 1513238252.5005 Depth: 79.9695 Dist: 36.3948 Bottle: 14 Time: 1513238313.7063 Depth: 59.9139 Dist: 36.4663 Bottle: 15 Time: 1513238380.3017 Depth: 39.918 Dist: 36.5467 Bottle: 16 Time: 1513238417.6992 Depth: 29.9506 Dist: 36.5874 Bottle: 17 Time: 1513238454.7066 Depth: 19.9619 Dist: 36.6271 Bottle: 18 Time: 1513238489.9042 Depth: 9.9711 Dist: 36.6689 Bottle: 19 Time: 1513238727.8979 Depth: -0.074556 Dist: 36.7644 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_347_00_347_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_347_00_347_00_2column.png Elapsed time to save image: 14 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_347_00_347_00_biolume.png Elapsed time to save image: 56 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_347_00_347_00_lopc.png Elapsed time to save image: 17 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_347_00_347_00_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_347_00_347_00_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_347_00_347_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_347_00_347_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_347_00_347_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_347_00_347_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_347_00_347_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_347_00_347_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_347_00_347_00_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_347_00_347_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_347_00_347_00_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_347_00_347_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_347_00_347_00_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_347_00_347_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_347_00_347_00_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_347_00_347_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_347_00_347_00_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_347_00_347_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_347_00_347_00_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_347_00_347_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_347_00_347_00_Chlorophyll_Fluorescence.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_347_00_347_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_347_00_347_00_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_347_00_347_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_347_00_347_00_LOPC_Total_Count.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2017_347_00_347_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_347_00_347_00.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_347_00_347_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_347_00_347_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_347_00_347_00.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... 80 NaNs found in bbpBlue. Interpolating anyway. 261 NaNs found in bbpRed. Interpolating anyway. 4 NaNs found in flRed_uncorr. Interpolating anyway. Encountered 30 NaN values in array of lon that is 38579 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 38549 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 38549 are not equal to number of Lat lon points = 38579 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_347_00_347_00.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_347_00_347_00_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_347_00_347_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_347_00_347_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... 80 NaNs found in bbpBlue. Interpolating anyway. 261 NaNs found in bbpRed. Interpolating anyway. 4 NaNs found in flRed_uncorr. Interpolating anyway. Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017_347_00_347_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_347_00_347_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_347_00_347_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_347_00_347_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_347_00_347_00 processed" mccann@mbari.org < mail_Dorado389_2017_347_00_347_00.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2017.347.00.mat Processing time: 372 seconds