Execution of AUVprocess_main version 1.86 at 2018-05-25T16:53:25Z on elvis Matlab command executed: AUVprocess_main('AUVCTD', 2014, ['289.04'], '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: 2014.289.04 Data path is http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014289/2014.289.04/ Calibration path is http://ssds.shore.mbari.org/auvctd/missionlogs/2014/2014289/2014.289.04/ 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/2014/2014289/2014.289.04/navigation.nc') Creating vector time with 134335 elements. Creating vector mPos_x with 134335 elements. Creating vector time with 134335 elements. Creating vector mPos_y with 134335 elements. Creating vector time with 134335 elements. Creating vector mDepth with 134335 elements. Creating vector time with 134335 elements. Creating vector mGpsNorth with 134335 elements. Creating vector time with 134335 elements. Creating vector mGpsEast with 134335 elements. Creating vector time with 134335 elements. Creating vector mGpsValid with 134335 elements. Creating vector time with 134335 elements. Creating vector mPhi with 134335 elements. Creating vector time with 134335 elements. Creating vector mTheta with 134335 elements. Creating vector time with 134335 elements. Creating vector mPsi with 134335 elements. Creating vector time with 134335 elements. Creating vector mOmega_x with 134335 elements. Creating vector time with 134335 elements. Creating vector mOmega_y with 134335 elements. Creating vector time with 134335 elements. Creating vector mOmega_z with 134335 elements. Creating vector time with 134335 elements. Creating vector mPsaRange with 134335 elements. Creating vector time with 134335 elements. Creating vector mAltitude with 134335 elements. Creating vector time with 134335 elements. Creating vector multibeamAltitude with 134335 elements. Creating vector time with 134335 elements. Creating vector mDvlAltitude with 134335 elements. Creating vector time with 134335 elements. Creating vector mEchoAltitude with 134335 elements. Creating vector time with 134335 elements. Creating vector mEchoHorizRange with 134335 elements. Creating vector time with 134335 elements. Creating vector mEchoAltitudeLast with 134335 elements. Creating vector time with 134335 elements. Creating vector mEchoHorizRangeLast with 134335 elements. Creating vector time with 134335 elements. Creating vector mEchoNumOfPings with 134335 elements. Creating vector time with 134335 elements. Creating vector nadirCnts with 134335 elements. Creating vector time with 134335 elements. Creating vector obstacleCnts with 134335 elements. Creating vector time with 134335 elements. Creating vector mWaterSpeed with 134335 elements. Creating vector time with 134335 elements. Creating vector mDvlValid with 134335 elements. Creating vector time with 134335 elements. Creating vector mDvlNewData with 134335 elements. Creating vector time with 134335 elements. Creating vector mDeltaT with 134335 elements. Creating vector time with 134335 elements. Creating vector nfix with 134335 elements. Creating vector time with 134335 elements. Creating vector efix with 134335 elements. Creating vector time with 134335 elements. Creating vector filter_north with 134335 elements. Creating vector time with 134335 elements. Creating vector filter_east with 134335 elements. Creating vector time with 134335 elements. Creating vector filter_depth with 134335 elements. Creating vector time with 134335 elements. Creating vector north_current with 134335 elements. Creating vector time with 134335 elements. Creating vector east_current with 134335 elements. Creating vector time with 134335 elements. Creating vector speed_bias with 134335 elements. Creating vector time with 134335 elements. Creating vector heading_bias with 134335 elements. Creating vector time with 134335 elements. Creating vector latitude with 134335 elements. Creating vector time with 134335 elements. Creating vector longitude with 134335 elements. Creating vector time with 134335 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014289/2014.289.04/navigation.nc'); processNav(): median of positive valued depths = 15.1054 processNav(): Finding depths less than 105.7379 and times > 0 processNav(): length(Nav.depth) = 134335 processNav(): length(gindx) = 134335 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/2014/2014289/2014.289.04/gps.nc') Creating vector time with 1428 elements. Creating vector hours with 1428 elements. Creating vector time with 1428 elements. Creating vector minutes with 1428 elements. Creating vector time with 1428 elements. Creating vector seconds with 1428 elements. Creating vector time with 1428 elements. Creating vector centiSeconds with 1428 elements. Creating vector time with 1428 elements. Creating vector latitude with 1428 elements. Creating vector time with 1428 elements. Creating vector longitude with 1428 elements. Creating vector time with 1428 elements. Creating vector quality with 1428 elements. Creating vector time with 1428 elements. Creating vector numberOfSatellites with 1428 elements. Creating vector time with 1428 elements. Creating vector hdop with 1428 elements. Creating vector time with 1428 elements. Creating vector antennaHeight with 1428 elements. Creating vector time with 1428 elements. Creating vector geoHeight with 1428 elements. Creating vector time with 1428 elements. Creating vector dgpsDataAge with 1428 elements. Creating vector time with 1428 elements. Creating vector dgpsRSID with 1428 elements. Creating vector time with 1428 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014289/2014.289.04/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/2014/2014289/2014.289.04/parosci.nc') Creating vector time with 264543 elements. Creating vector depth with 264543 elements. Creating vector time with 264543 elements. Creating vector temp with 264543 elements. Creating vector time with 264543 elements. Creating vector pressure with 264543 elements. Creating vector time with 264543 elements. Creating vector temp_period with 264543 elements. Creating vector time with 264543 elements. Creating vector pres_period with 264543 elements. Creating vector time with 264543 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014289/2014.289.04/parosci.nc'); in processDepth.m Before: min(Depth.data) = -0.22473 max(Depth.data) = 82.1261 Found 0 bad (> 300 | < -1.0) depth values in Depth.data. Replacing with NaNs After: min(Depth.data) = -0.22473 max(Depth.data) = 82.1261 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/2014/2014289/2014.289.04/hydroscatlog.nc') Creating vector time with 107585 elements. Creating vector Seconds with 107585 elements. Creating vector time with 107585 elements. Creating vector HundrethsOfSeconds with 107585 elements. Creating vector time with 107585 elements. Creating vector Snorm1 with 107585 elements. Creating vector time with 107585 elements. Creating vector Snorm2 with 107585 elements. Creating vector time with 107585 elements. Creating vector Snorm3 with 107585 elements. Creating vector time with 107585 elements. Creating vector Gain_Status_1 with 107585 elements. Creating vector time with 107585 elements. Creating vector Gain_Status_2 with 107585 elements. Creating vector time with 107585 elements. Creating vector Gain_Status_3 with 107585 elements. Creating vector time with 107585 elements. Creating vector RawDepthValue with 107585 elements. Creating vector time with 107585 elements. Creating vector RawTempValue with 107585 elements. Creating vector time with 107585 elements. Creating vector Temperature with 107585 elements. Creating vector time with 107585 elements. Creating vector ErrorValue with 107585 elements. Creating vector time with 107585 elements. Creating vector bb470 with 107585 elements. Creating vector time with 107585 elements. Creating vector bb676 with 107585 elements. Creating vector time with 107585 elements. Creating vector fl676u with 107585 elements. Creating vector time with 107585 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014289/2014.289.04/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/2014/2014289/2014.289.04/ctdDriver.nc') Creating vector time with 107520 elements. Creating vector conductivity with 107520 elements. Creating vector time with 107520 elements. Creating vector temperature with 107520 elements. Creating vector time with 107520 elements. Creating vector cond_frequency with 107520 elements. Creating vector time with 107520 elements. Creating vector temp_frequency with 107520 elements. Creating vector time with 107520 elements. Creating vector spare with 107520 elements. Creating vector time with 107520 elements. Creating vector humidity with 107520 elements. Creating vector time with 107520 elements. Creating vector flow1 with 107520 elements. Creating vector time with 107520 elements. Creating vector CDOM with 107520 elements. Creating vector time with 107520 elements. Creating vector dissolvedO2 with 107520 elements. Creating vector time with 107520 elements. Creating vector salinity with 107520 elements. Creating vector time with 107520 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014289/2014.289.04/ctdDriver.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2014/2014289/2014.289.04/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/2014/2014289/2014.289.04/ctdDriver2.nc') Creating vector time with 107389 elements. Creating vector conductivity with 107389 elements. Creating vector time with 107389 elements. Creating vector temperature with 107389 elements. Creating vector time with 107389 elements. Creating vector cond_frequency with 107389 elements. Creating vector time with 107389 elements. Creating vector temp_frequency with 107389 elements. Creating vector time with 107389 elements. Creating vector flow2 with 107389 elements. Creating vector time with 107389 elements. Creating vector spare with 107389 elements. Creating vector time with 107389 elements. Creating vector salinity with 107389 elements. Creating vector time with 107389 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014289/2014.289.04/ctdDriver2.nc'); Obtaining calibration from http://ssds.shore.mbari.org/auvctd/missionlogs/2014/2014289/2014.289.04/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/2014/2014289/2014.289.04/isuslog.nc') Creating vector time with 20873 elements. Creating vector isusNitrate with 20873 elements. Creating vector time with 20873 elements. Creating vector isusTemp with 20873 elements. Creating vector time with 20873 elements. Creating vector isusQuality with 20873 elements. Creating vector time with 20873 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014289/2014.289.04/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/2014/2014289/2014.289.04/biolume.nc') Creating vector time with 26465 elements. Creating vector rrr with 26465 elements. Creating vector time with 26465 elements. Creating vector cal_striing with 26465 elements. Creating vector time with 26465 elements. Creating vector avg_biolume with 26465 elements. Creating vector time with 26465 elements. Creating vector pump with 26465 elements. Creating vector time with 26465 elements. Creating vector system_voltage with 26465 elements. Creating vector time with 26465 elements. Creating vector flow with 26465 elements. Creating vector time with 26465 elements. Creating vector HV with 26465 elements. Creating vector time with 26465 elements. Creating vector reserved with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_0 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_1 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_2 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_3 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_4 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_5 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_6 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_7 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_8 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_9 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_10 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_11 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_12 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_13 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_14 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_15 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_16 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_17 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_18 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_19 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_20 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_21 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_22 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_23 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_24 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_25 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_26 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_27 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_28 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_29 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_30 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_31 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_32 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_33 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_34 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_35 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_36 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_37 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_38 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_39 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_40 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_41 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_42 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_43 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_44 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_45 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_46 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_47 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_48 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_49 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_50 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_51 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_52 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_53 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_54 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_55 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_56 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_57 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_58 with 26465 elements. Creating vector time with 26465 elements. Creating vector raw_59 with 26465 elements. Creating vector time with 26465 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014289/2014.289.04/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/2014/2014289/2014.289.04/lopc.nc') Creating vector bin with 994 elements. Creating matrix sepCountList (2563 x 994) with 2547622 elements. Creating vector time with 2563 elements. Creating vector bin with 994 elements. Creating matrix mepCountList (2563 x 994) with 2547622 elements. Creating vector time with 2563 elements. Creating vector bin with 994 elements. Creating matrix countList (2563 x 994) with 2547622 elements. Creating vector time with 2563 elements. Creating vector bin with 994 elements. Creating vector LCcount with 2563 elements. Creating vector time with 2563 elements. Creating vector transCount with 2563 elements. Creating vector time with 2563 elements. Creating vector nonTransCount with 2563 elements. Creating vector time with 2563 elements. Creating vector ai_mean with 2563 elements. Creating vector time with 2563 elements. Creating vector ai_min with 2563 elements. Creating vector time with 2563 elements. Creating vector ai_max with 2563 elements. Creating vector time with 2563 elements. Creating vector ai_std with 2563 elements. Creating vector time with 2563 elements. Creating vector esd_mean with 2563 elements. Creating vector time with 2563 elements. Creating vector esd_min with 2563 elements. Creating vector time with 2563 elements. Creating vector esd_max with 2563 elements. Creating vector time with 2563 elements. Creating vector esd_std with 2563 elements. Creating vector time with 2563 elements. Creating vector countSum with 2563 elements. Creating vector time with 2563 elements. Creating vector snapshot with 2563 elements. Creating vector time with 2563 elements. Creating vector threshold with 2563 elements. Creating vector time with 2563 elements. Creating vector sampleCount with 2563 elements. Creating vector time with 2563 elements. Creating vector flowCount with 2563 elements. Creating vector time with 2563 elements. Creating vector flowTime with 2563 elements. Creating vector time with 2563 elements. Creating vector bufferStatus with 2563 elements. Creating vector time with 2563 elements. Creating vector laserLevel with 2563 elements. Creating vector time with 2563 elements. Creating vector counter with 2563 elements. Creating vector time with 2563 elements. Creating vector counterPeriod with 2563 elements. Creating vector time with 2563 elements. Creating vector laserControl with 2563 elements. Creating vector time with 2563 elements. Creating vector countUnknownFrameCharacter with 2563 elements. Creating vector time with 2563 elements. Creating vector countBeginLFrameWithoutEndOfPreviousFrame with 2563 elements. Creating vector time with 2563 elements. Creating vector countBeginMFrameWithoutEndOfPreviousFrame with 2563 elements. Creating vector time with 2563 elements. Creating vector flowSpeed with 2563 elements. Creating vector time with 2563 elements. Creating vector countShortLFrameError with 2563 elements. Creating vector time with 2563 elements. Creating vector countGarbledLFrame with 2563 elements. Creating vector time with 2563 elements. Creating vector cFrameEsecs with 2563 elements. Creating vector time with 2563 elements. Creating vector correctedSampleCountList with 2563 elements. Creating vector time with 2563 elements. Creating vector time with 2563 elements. att = loaddap('-A', 'http://dods.mbari.org/cgi-bin/nph-nc/data/ssdsdata/ssds/generated/netcdf/files/ssds.shore.mbari.org/auvctd/missionlogs/2014/2014289/2014.289.04/lopc.nc'); save /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014.289.04.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_2014.289.04.mat Calling matchDVLtoGPS to adjust dvl data in the underwater segments... setting up UTM transformation using M_Map calls... Looping over 14 segments. Current plot held Printing navigation adjust plot to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_289_04_289_04_nav_adjust.png Saving survey data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_289_04_289_04.mat Done saving to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_289_04_289_04.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 = 248 Gridding with nix = 744, iZ = 161 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 133727 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 133727 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 118918 elements. ds = cfdataset with properties: netcdf: [1x1 ucar.nc2.dataset.NetcdfDataset] variables: {16x1 cell} SWR data read from OPeNDAP has time range: 10/16/2014 06:30 to 10/16/2014 16:29 swr = 0.5458 24.8216 180.2865 357.5011 555.0710 589.5615 696.0938 706.4772 526.6161 332.1501 298.1144 Contouringf SWR to file: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_289_04_289_04_swr.png [Warning: Contour not rendered for constant ZData] [> In contourf (line 60) In plot_sections (line 564) In create_data_products (line 119) In build_auv_survey (line 522) In AUVprocess_main (line 255)] Done plotting SWR. Executing: /bin/rm -f ../results/2014289_GulperTimes.txt && touch ../results/2014289_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/2014/2014289/2014.289.04/navigation.nc.ascii?time[0:1:0] Executing: perl parseGulper.pl -syslogFile /mbari/AUVCTD/missionlogs/2014/2014289/2014.289.04/syslog -startEsecs 1413474474.8778 -surveyName Dorado389_2014_289_04_289_04 >> ../results/2014289_GulperTimes.txt Executing: removeGulpDups.py ../results/2014289_GulperTimes.txt Bottle: 0 Time: 1413475459.83 Depth: 2.7825 Dist: 0.93021 Bottle: 1 Time: 1413476045.83 Depth: 3.6066 Dist: 1.506 Bottle: 2 Time: 1413476728.42 Depth: 2.7488 Dist: 2.1823 Bottle: 3 Time: 1413477343.42 Depth: 2.7766 Dist: 2.7845 Bottle: 4 Time: 1413479372.42 Depth: 2.0776 Dist: 4.9409 Bottle: 5 Time: 1413480065.22 Depth: 4.8398 Dist: 5.7019 Bottle: 6 Time: 1413480929.43 Depth: 3.3644 Dist: 6.6057 Bottle: 7 Time: 1413481557.82 Depth: 2.1918 Dist: 7.2935 Bottle: 8 Time: 1413483370.83 Depth: 23.5199 Dist: 9.2151 Bottle: 9 Time: 1413484075.23 Depth: 30.5397 Dist: 9.7668 Bottle: 10 Time: 1413484654.43 Depth: 5.2697 Dist: 10.2402 Bottle: 11 Time: 1413485196.62 Depth: 27.1157 Dist: 10.6704 Bottle: 12 Time: 1413493655.22 Depth: 9.2025 Dist: 18.7667 Bottle: 13 Time: 1413494639.83 Depth: 13.2324 Dist: 19.7615 Bottle: 14 Time: 1413495541.82 Depth: 8.157 Dist: 20.6343 Bottle: 15 Time: 1413496533.03 Depth: 8.7269 Dist: 21.5861 Bottle: 16 Time: 1413496949.63 Depth: 5.93 Dist: 21.9634 Bottle: 17 Time: 1413497517.03 Depth: 5.0781 Dist: 22.4829 Bottle: 18 Time: 1413498045.62 Depth: 4.8338 Dist: 22.9595 Bottle: 19 Time: 1413498851.43 Depth: 2.4152 Dist: 23.6853 Saving gridded, filtered data to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_289_04_289_04_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_2014_289_04_289_04_2column.png Elapsed time to save image: 11 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_2014_289_04_289_04_biolume.png Elapsed time to save image: 36 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_2014_289_04_289_04_lopc.png Elapsed time to save image: 10 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_2014_289_04_289_04_hist_stats.png Printing section summary to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_289_04_289_04_prof_stats.png Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_289_04_289_04_2column.png... Copied to /mbari/AUVCTD/surveys/2014/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_289_04_289_04_biolume.png... Copied to /mbari/AUVCTD/surveys/2014/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_289_04_289_04_lopc.png... Copied to /mbari/AUVCTD/surveys/2014/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_289_04_289_04_nav_adjust.png... Copied to /mbari/AUVCTD/surveys/2014/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_289_04_289_04_hist_stats.png... Copied to /mbari/AUVCTD/surveys/2014/images/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_289_04_289_04_prof_stats.png... Copied to /mbari/AUVCTD/surveys/2014/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_289_04_289_04_Temperature.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_289_04_289_04_Temperature.kmz... Copied to /mbari/AUVCTD/surveys/2014/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_289_04_289_04_Salinity.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_289_04_289_04_Salinity.kmz... Copied to /mbari/AUVCTD/surveys/2014/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_289_04_289_04_Nitrate.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_289_04_289_04_Nitrate.kmz... Copied to /mbari/AUVCTD/surveys/2014/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_289_04_289_04_Oxygen.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_289_04_289_04_Oxygen.kmz... Copied to /mbari/AUVCTD/surveys/2014/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_289_04_289_04_Optical_Backscatter_420_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_289_04_289_04_Optical_Backscatter_420_nm.kmz... Copied to /mbari/AUVCTD/surveys/2014/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_289_04_289_04_Optical_Backscatter_700_nm.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_289_04_289_04_Optical_Backscatter_700_nm.kmz... Copied to /mbari/AUVCTD/surveys/2014/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_289_04_289_04_Chlorophyll_Fluorescence.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_289_04_289_04_Chlorophyll_Fluorescence.kmz... Copied to /mbari/AUVCTD/surveys/2014/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_289_04_289_04_Bioluminescence.kml (deflated 93%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_289_04_289_04_Bioluminescence.kmz... Copied to /mbari/AUVCTD/surveys/2014/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); adding: u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_289_04_289_04_LOPC_Total_Count.kml (deflated 92%) Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_289_04_289_04_LOPC_Total_Count.kmz... Copied to /mbari/AUVCTD/surveys/2014/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Creating Dorado389_2014_289_04_289_04.kml file to hold all the variable .kmz files... Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_289_04_289_04.kml... Copied to /mbari/AUVCTD/surveys/2014/kml/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ [Warning: File '/u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results//Dorado389_2014_289_04_289_04_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_2014_289_04_289_04.mat ... Iterpolating to isus time values... Interpolating ctd1 temperature... Interpolating ctd1 salinity... Encountered 95 NaN values in array of lon that is 20873 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 20778 points from grid Monterey25.grd (2876 x 2447) Number of depths returned from grdtrack = 20778 are not equal to number of Lat lon points = 20873 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_2014_289_04_289_04.txt Writing to /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_289_04_289_04_Gulper.txt Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_289_04_289_04.txt... Copied to /mbari/AUVCTD/surveys/2014/odv/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_289_04_289_04_Gulper.txt... Copied to /mbari/AUVCTD/surveys/2014/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... Saving Global Attributes Saving Variables and attributes Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_289_04_289_04_decim.nc... Copied to /mbari/AUVCTD/surveys/2014/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_2014_289_04_289_04.nc... Copied to /mbari/AUVCTD/surveys/2014/netcdf/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_289_04_289_04_gridded.mat... Copied to /mbari/AUVCTD/surveys/2014/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Copying /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014_289_04_289_04.mat... Copied to /mbari/AUVCTD/surveys/2014/mat/. Removing from /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/ ************************************************************************* Composing email to send to mccann@mbari.org ... !mail -s "Survey Dorado389_2014_289_04_289_04 processed" mccann@mbari.org < mail_Dorado389_2014_289_04_289_04.txt Removing mission .mat files: /u/ssdsadmin/dev/auv_ctd/src/matlab/doradosdp/results/Dorado389_2014.289.04.mat Processing time: 178 seconds